@article {pmid41138002,
year = {2025},
author = {Yarahmadi, A and Emrahoglu, S and Afkhami, H and Mehdipour, A and Aghaali, M},
title = {Integrative insights into the oral microbiome's role in systemic diseases: novel therapeutic strategies and future directions.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {12},
pages = {178},
pmid = {41138002},
issn = {1572-9699},
mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; Periodontal Diseases/microbiology/therapy ; Dental Caries/microbiology/therapy ; Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The oral microbiome, which is known as the diverse and abundant microbial community within the human oral cavity, is an integral part of the human body. The investigation of its composition and functions in both wellness and illness has received notable attention from researchers in recent times. The presence of oral bacteria directly impacts the disease condition of dental caries and periodontal diseases. The oral microbiota interacts dynamically with the host to influence immune regulation and metabolic processes. Advances in sequencing technologies, including whole-metagenome shotgun sequencing, the examination of 16S ribosomal RNA, and meta-transcriptomes, we now possess the capability to comprehensively explore the diversity and functionalities of oral microorganisms, encompassing those that are not amenable to cultivation. As research advances, there is a growing body of evidence suggesting the notable contribution of the oral microbiome to various health conditions, extending beyond ailments solely associated with the oral cavity. This review advances current understanding by presenting a systemic, integrative perspective on the oral microbiome's role in chronic diseases, offering novel hypotheses and therapeutic directions beyond those explored in prior literature.},
}

Humans
*Microbiota
*Mouth/microbiology
Periodontal Diseases/microbiology/therapy
Dental Caries/microbiology/therapy
Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics

@article {pmid41137989,
year = {2025},
author = {Vílchez, B and Caneiro, L and Lima, C and Virto, L and Marín, MJ and Bravo, E and Chamorro, C and Sanz-Sánchez, I and Montero, E and Figuero, E and Blanco, J and Sanz, M},
title = {Early Microbiological and Immunological Parameters in Sandblasted, Large-Grit Acid-Etched Implant Surfaces: A Split Mouth Randomized Clinical Trial.},
journal = {Clinical oral implants research},
volume = {},
number = {},
pages = {},
doi = {10.1111/clr.70058},
pmid = {41137989},
issn = {1600-0501},
support = {//Institut Straumann AG (Basel, Switzerland)/ ; },
abstract = {AIM: To compare microbiological and immunological parameters of two sandblasted, large-grit, acid-etched implant surfaces during the first 8 weeks of healing following implant placement.

MATERIALS AND METHODS: A dual-center, split-mouth, randomized controlled clinical trial was conducted on patients receiving one test (modified hydrophilic surface) and one control (conventional surface) implant in different quadrants. Peri-implant crevicular fluid samples were collected at implant placement and at 1, 2, 4, and 8 weeks to assess biomarkers of inflammation (Interleukin [IL]-1β, IL-6, Tumor Necrosis Factor-α, IL-2), biomarkers of anti-inflammation (IL-4, IL-10), and biomarkers of bone metabolism (osteocalcin, osteopontin [OPN], and vascular endothelial growth factor-α [VEGF-α]). Additionally, submucosal samples were obtained at implant placement and at 1, 2, and 4 weeks and analyzed using quantitative polymerase chain reaction (qPCR) and 16S rRNA sequencing. Biomarkers and qPCR data were analyzed with a general linear model using log10-transformed values. Microbiome data were analyzed via Wilcoxon tests and PERMANOVA.

RESULTS: Sixty patients were included in the 8-week analysis. VEGF-α levels were significantly higher at 1 week for the conventional surface (p = 0.018). OPN and IL-10 significantly increased from baseline to 4 weeks in both groups. Porphyromonas gingivalis and Fusobacterium species were the most prevalent bacteria; however, no significant differences were found between the surfaces in bacterial load analysis by qPCR. Additionally, no significant differences were observed between groups for microbiome diversity.

CONCLUSION: No differences were detected between the conventional and the modified hydrophilic surfaces in the immunological and microbiological parameters assessed during early implant healing.},
}

@article {pmid41137867,
year = {2025},
author = {Niknejad, A and Hosseini, Y and Nazari Manesh, MA and Navabakhsh, M and Peyrovinasab, A and Mavaddat, H and Miri, MS and Hosseini, M and Büsselberg, D and Abdolghaffari, AH},
title = {Therapeutic impacts of oral anti-diabetic drugs on Inflammatory Bowel Disease (IBD), a comprehensive review of clinical and preclinical studies.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {41137867},
issn = {1432-1912},
abstract = {Inflammatory bowel disease (IBD) is a chronic condition with a rising incidence linked to inflammation and oxidative stress. This disorder includes two main subtypes: ulcerative colitis (UC) and Crohn's disease (CD). Current treatment plans lack effectiveness; as a result, finding novel approaches is encouraged. Various groups of oral anti-diabetic medications are employed in clinical practice, and they have shown beneficial effects against conditions beyond diabetes mellitus (DM). This review is aimed at evaluating the hypothesis that oral anti-diabetic medications may serve as potential therapeutic agents for IBD due to their anti-inflammatory and antioxidant effects. The current study investigated the protective effects of these agents against IBD. In this review, we gathered evidence from cellular, animal, and clinical studies within the scientific databases Medline, Scopus, and Web of Science regarding the favorable impacts of anti-diabetic drugs on IBD. We explored these databases from their inception to May 2024. Studies focusing on the therapeutic impacts of these medications on diverse models of IBD were included and reviewed. Biguanides, sulfonylureas, thiazolidinediones (TZD), dipeptidyl peptidase 4 inhibitors (DPP4I), and sodium-glucose cotransporter inhibitors (SGLT2I) exhibited protective effects against IBD. These medications promoted gut microbiome balance and the function of tight junction proteins, such as zonula occludens-1 (ZO-1), occludin, and claudin. Moreover, they affected key cytokines (tumor necrosis factor (TNF), malonaldehyde (MDA)), enzymes (superoxide dismutase (SOD), glutathione peroxidase (GPX), myeloperoxidase (MPO)), and signaling pathways (nuclear factor erythroid 2-related factor (Nrf2) transcription factor/hemoxygenase 1 (HO-1), high mobility group box 1 (HMGB1)/receptor for advanced glycation end-products (RAGE)/nuclear factor kappa B (NF-κB)). Anti-diabetic medications demonstrated positive effects against IBD. However, further comprehensive clinical assessments are necessary to confirm their efficacy and safety as an adjunctive therapy for IBD.},
}

@article {pmid41137523,
year = {2025},
author = {Tegegne, HA and Savidge, TC},
title = {Gut microbiome metagenomics in clinical practice: bridging the gap between research and precision medicine.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2569739},
doi = {10.1080/19490976.2025.2569739},
pmid = {41137523},
issn = {1949-0984},
mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Precision Medicine/methods ; },
abstract = {Gut microbiome metagenomics is emerging as a cornerstone of precision medicine, offering exceptional opportunities for improved diagnostics, risk stratification, and therapeutic development. Advances in high-throughput sequencing have uncovered robust microbial signatures linked to infectious, inflammatory, metabolic, and neoplastic diseases. Clinical applications now include pathogen detection, antimicrobial resistance profiling, microbiota-based therapies, and enterotype-guided patient stratification. However, translation into routine care is hindered by significant barriers including methodological variability, limited functional annotation, lack of bioinformatics standardization, and underrepresentation of global populations. This review synthesizes current translational strategies, emphasizing the need for hypothesis-driven designs, multi-omic integration, longitudinal and multi-center cohorts, and mechanistic validation. We also examine critical ethical, regulatory, and equity considerations shaping the clinical landscape. Realizing the full potential of microbiome-informed care will require globally harmonized standards, cross-sector collaboration, and inclusive frameworks that ensure scientific rigor and equitable benefit.},
}

Humans
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
*Precision Medicine/methods

@article {pmid41137522,
year = {2025},
author = {Rana, A and Smriti, },
title = {Probiotics: mechanism of action and gastrointestinal health: gut guardians: unlocking the power of probiotics.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70275},
pmid = {41137522},
issn = {1097-0010},
abstract = {The gut microbiota is fundamental to human health, contributing to nutrient metabolism, immune regulation and protection against pathogens. Disturbances in this microbial community, often caused by antibiotic use, poor diet or infections, can disrupt intestinal homeostasis and predispose individuals to gastrointestinal disorders. Restoring this balance has become a major therapeutic goal, with probiotics emerging as one of the most widely studied interventions. Probiotics exert their beneficial effects through multiple mechanisms, including strengthening the intestinal barrier, adhering to mucosal surfaces to prevent pathogen colonization, competing for nutrients and receptor sites, producing antimicrobial substances, and modulating host immune responses. By acting at the interface of the host and its microbiota, probiotics can influence both local gut function and systemic health outcomes. Clinical studies have demonstrated the potential of probiotics in managing gastrointestinal conditions such as antibiotic-associated diarrhea, Helicobacter pylori infection, acute gastroenteritis, necrotizing enterocolitis, irritable bowel syndrome and AIDS-associated diarrhea. Evidence suggests that therapeutic benefits are strain specific, underscoring the importance of precise strain selection for targeted outcomes. However, variability in host microbiota composition contributes to inconsistent clinical results and safety concerns remain for vulnerable populations such as immunocompromised patients. Future research must address these challenges through large scale, well controlled trials that clarify strain dependent mechanisms and establish standardized recommendations. Advances in microbiome science also highlight the potential of next generation probiotics such as Faecalibacterium prausnitzii and Akkermansia muciniphila, which may extend benefits beyond conventional strains. In conclusion, probiotics represent a promising adjunct to conventional therapies for gastrointestinal disorders. With further progress in standardization and safety validation, they may become reliable and personalized tools for promoting gut and overall health. © 2025 Society of Chemical Industry.},
}

@article {pmid41137451,
year = {2025},
author = {Liu, Y and Wu, X and Wegner, CE and Ma, K and Xu, G and Cui, Z and Zhang, F and Liesack, W and Peng, J},
title = {Temperature Increase in Paddy Soils Remodels the Relationship Between the Anaerobic Food Web and the Q10 of CH4 Production.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70156},
doi = {10.1111/mec.70156},
pmid = {41137451},
issn = {1365-294X},
support = {2021YFD1900100//National Key Research and Development Program of China/ ; 42277307 and 41977038//National Natural Science Foundation of China/ ; },
abstract = {Rice paddies are a major source of anthropogenic CH4 emissions globally, with the temperature sensitivity (Q10) of CH4 production playing a key role in forecasting emissions under future climate scenarios. However, the mechanistic links among Q10, the soil microbiome and mean annual temperature (MAT) in paddy soils remain poorly understood. To address this gap, we employed quantitative PCR, amplicon sequencing, genome-resolved metagenomics and metatranscriptomics to investigate CH4 production dynamics and the response of the methanogenic food web to warming in low MAT (LMAT, 4°C-9°C) and high MAT (HMAT, 14°C-16°C) soils. Our results indicate that CH4 production exhibits a higher Q10 in LMAT soils, while warming exerts a more pronounced impact on the methanogenic food web in HMAT soils. Notably, we identified negative correlations between the Q10 and the metagenomic abundance of genes encoding glycoside hydrolases, carbohydrate-binding modules, polysaccharide lyases-related carbohydrate-active enzymes (CAZymes), hydrogenotrophic methanogenesis, and the average genome size (AGS) of the microbiome. Conversely, genes encoding auxiliary activity CAZymes and those associated with acetate metabolism and fermentation were positively correlated with Q10. Genes linked to acetoclastic and hydrogenotrophic methanogenesis exhibited lower responsiveness to warming in LMAT soils compared to HMAT soils. Additionally, warming led to a significant reduction in both gene and transcript abundances associated with methylotrophic methanogenesis across both MAT regimes. These findings provide novel insights into the temperature-dependent restructuring of methanogenic pathways and resource utilisation strategies in paddy soils, with important implications for predicting CH4 emissions under climate change.},
}

@article {pmid41137189,
year = {2025},
author = {McGowen, K and Lee, J and Pedicord, VA},
title = {The Role of the Microbiome in the Resolution of Infection-Induced Inflammation.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.5c00668},
pmid = {41137189},
issn = {2373-8227},
abstract = {The host microbiome plays a crucial protective role against pathogenic infections, not only through direct competition with invading pathogens but also by coordinating host antimicrobial and barrier functions and educating immune cells. While essential for pathogen clearance, unchecked, prolonged, or excessive inflammation from host immune responses can paradoxically lead to serious consequences for the host including the development of chronic inflammatory and autoimmune diseases. Recent research highlights how microbiome disruptions can exacerbate infection-associated inflammation and pathology. Even with established links among microbes, inflammation, and infection susceptibility, a comprehensive understanding of the cellular and molecular mechanisms connecting the microbiome's role in resolving infection-associated inflammation remains largely undefined. This review discusses our current understanding of the microbiome's contribution to resolving inflammation and tissue damage postinfection and its potential impact on therapeutic approaches for alleviating infection-induced inflammatory diseases.},
}

@article {pmid41137143,
year = {2025},
author = {Meng, K and Hu, M and Chen, Y and Lin, X and Jiang, C and Song, J and Bai, Y and Zhao, Y and Liu, F and Luo, D},
title = {Natural sex reversal imparts permanent compositional changes to the swamp eel gonadal microbiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {217},
pmid = {41137143},
issn = {2049-2618},
support = {32425055//National Natural Science Foundation of China/ ; 2023BBB172//Natural Science Foundation of Hubei Province/ ; 2022hszd022//Foundation of Hubei Hongshan Laboratory/ ; },
mesh = {Animals ; Female ; Male ; *Ovary/microbiology ; *Testis/microbiology ; *Microbiota ; *Smegmamorpha/microbiology ; *Bacteria/classification/isolation & purification/genetics ; *Sex Differentiation ; *Gonads/microbiology ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: Microbial communities are increasingly recognized for their essential roles in the reproductive system. However, the microbial communities in healthy gonads-neither in the ovary nor the testis-have not been extensively explored, particularly with respect to sex differentiation. Sex reversal is a unique mode of sex differentiation that is a well-documented phenomenon in various animal species, with the swamp eel (Monopterus albus) being a notable example of a hermaphroditic species that undergoes natural female-to-male sex reversal. Thus, swamp eel offers a robust system for exploring gonad microbial communities and their biological and functional significance.

RESULTS: Our study revealed a living microbial community in the gonads of healthy swamp eel, with microbial loads comparable to those found in three distinct niches: gut, skin, and blood. The gonad microbial communities shared > 55% of their diversity with those in the gut and blood. We focused on the niche-specific differences in microbial communities, particularly between the ovary and testis. After isolating and injecting the ovarian-dominant bacteria Bacillus, we observed significant microbial dysbiosis and metabolic responses in the ovary. These changes were primarily reflected in the altered abundance of the ovarian microbiota involved in amino acid and lipid metabolism, which may contribute to ovarian function in swamp eel. Additionally, Bacillus inhibited sperm motility, reduced sperm count, and induced inflammatory responses in the testes of male swamp eel. These findings highlight the crucial role of bacteria in the sexual transition from the ovary to the testis and in gametogenesis.

CONCLUSIONS: Characterizing the microbial composition and distribution in the gonads is crucial for understanding the role of the reproductive microbiome in hermaphroditic species and during sex reversal. Our findings first indicate that ovarian-dominant bacterial communities contribute to maintaining ovarian function while inhibiting testicular function in swamp eel, further suggesting that microbial communities are involved in the process of sex reversal. Video Abstract.},
}

Animals
Female
Male
*Ovary/microbiology
*Testis/microbiology
*Microbiota
*Smegmamorpha/microbiology
*Bacteria/classification/isolation & purification/genetics
*Sex Differentiation
*Gonads/microbiology
Dysbiosis/microbiology

@article {pmid41137085,
year = {2025},
author = {Zhang, W and Song, J and Zhong, F and Yu, W and Qin, Z and Yang, Z and Liu, J and Wang, X and Chen, L and Lü, W and Xing, D and Liu, J and Huang, C and Wu, J and Liu, X and Yu, W and Lü, Y},
title = {Computerized cognitive training enhances cognitive function in Alzheimer's disease by downregulating Ruminococcus-TMAO pathway.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1173},
pmid = {41137085},
issn = {1479-5876},
support = {2022YSZX-JSX0002CSTB//grants from Innovation Programs Led by the Academicians in Chongqing under Project/ ; cstc2022ycjh-bgzxm0184//Chongqing Talent Plan/ ; CSTC2021jscx-gksb-N0020//Jiangsu Provincial Agricultural Science and Technology Independent Innovation Fund/ ; 2021ZD0201802//STI2030-Major Projects/ ; 2018YFC2001700//National Key R&D Program of China/ ; 0201[2023]160 202412//Chongqing Medical Key Discipline and Regional Medical Key Discipline Development Project/ ; },
mesh = {Humans ; Male ; *Alzheimer Disease/microbiology/physiopathology/therapy/blood ; Female ; *Cognition/physiology ; Aged ; *Methylamines/blood/metabolism ; *Down-Regulation ; Gastrointestinal Microbiome ; Cognitive Dysfunction/physiopathology ; Cognitive Training ; },
abstract = {BACKGROUND: The microbiota-gut-brain (MGB) axis is implicated in Alzheimer's disease (AD), but evidence for interventional strategies targeting this axis remains limited.

METHODS: In a 24-week, single-blind, randomized controlled trial, 84 individuals with mild cognitive impairment (MCI) or mild AD received either computerized cognitive training (CCT) or treatment as usual (TAU). Alzheimer's Disease Assessment Scale-cognitive subscale (ADAS-cog) was the primary outcome. We also assessed functional connectivity (fNIRS), plasma trimethylamine N-oxide (TMAO) levels, and gut microbiota at baseline and 24 weeks.

RESULTS: Seventy-four participants completed the study. The CCT group showed significant improvement in ADAS-cog scores compared to controls (Cohen's d = 1.57 by week 24). Notably, CCT also induced a distinct reorganization of prefrontal functional connectivity and significantly reduced plasma TMAO levels. Microbiome analysis revealed that CCT mitigated the expansion of Ruminococcus torques group (R.torques), which was observed in the control group. Crucially, R.torques was the only genus significantly correlated with improvements in cognition (ADAS-cog, r = 0.407), neuropsychiatric symptoms (NPI, r = 0.395), TMAO reduction (r = 0.443), and functional connectivity changes (r = 0.449).

CONCLUSION: A 24-week CCT program improves cognitive function in MCI and mild AD, potentially through downregulating the R.torques-TMAO pathway within the MGB axis. This pathway represents a promising novel target for multi-domain intervention in AD.},
}

Humans
Male
*Alzheimer Disease/microbiology/physiopathology/therapy/blood
Female
*Cognition/physiology
Aged
*Methylamines/blood/metabolism
*Down-Regulation
Gastrointestinal Microbiome
Cognitive Dysfunction/physiopathology
Cognitive Training

@article {pmid41136906,
year = {2025},
author = {Ji, X and Qiao, Y and Wu, J and Kong, W and Yu, R and Yang, X and Deng, X and Yu, H and Zhao, H},
title = {Oral microbiome dynamics in head and neck cancer patients undergoing oral healthcare: implications for prognosis and early diagnosis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {685},
pmid = {41136906},
issn = {1471-2180},
support = {2021YFS0156//The Science and Technology Department of Sichuan Province/ ; },
}

@article {pmid41136898,
year = {2025},
author = {Junier, T and Palmieri, F and Ubags, ND and Trompette, A and Koutsokera, A and Junier, P and Pagni, M and Neuenschwander, S},
title = {Prevalence of oxalotrophy in the human microbiome.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {954},
pmid = {41136898},
issn = {1471-2164},
support = {40B2-0_194701//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; GRS-064/18//Gebert Rüf Stiftung/ ; },
mesh = {Humans ; *Oxalates/metabolism ; *Microbiota/genetics ; Metagenome ; Gene Transfer, Horizontal ; *Bacteria/genetics/metabolism ; },
abstract = {BACKGROUND: Incomplete degradation of oxalate, a compound commonly found in the diet, can lead to disease in humans, particularly affecting the kidneys. The concentration of oxalate in the body depends on several factors, one of which is intestinal absorption-an aspect influenced by oxalotrophy among enteric bacteria. Despite its potential significance, oxalotrophy in the human microbiome remains poorly understood.

RESULTS: In this study, we conducted a systematic search for the co-occurrence of three key oxalotrophy genes-frc, oxc, and oxlT. We developed and validated specific conservation models for each gene and applied them to genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. Our analysis revealed that oxalotrophy, defined as the capacity to use oxalate as an energy source, is a rare metabolic trait predominantly confined to the gut. We also found evidence that this capacity can be acquired via horizontal gene transfer.

CONCLUSIONS: While oxalotrophy is relatively uncommon, the broader capacity for oxalate degradation is more widespread. Notably, the genes frc and oxc are frequently found in close proximity within genomes, suggesting a selective advantage for organisms possessing this capability. Incomplete degradation of oxalate, a compound commonly found in the diet, can cause disease in humans, particularly affecting the kidney. Its concentration in the body depends on several factors, one of which is intestinal absorption, which is itself affected by oxalotrophy among enteric bacteria. Oxalotrophy in the human microbiome is poorly known. In this study, we perform a systematic search for the simultaneous presence of the three oxalotrophy genes, namely frc, oxc and oxlT. Thanks to the construction and validation of specific conservation models for all three genes, we were able to search for oxalotrophy in genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. We report that oxalotrophy-the capacity to use oxalate as an energy source-is a rare metabolic trait, mostly confined to the gut, and also find evidence that it can be acquired by horizontal gene transfer. By contrast, the capacity for oxalate degradation is more widespread, and two genes responsible for it (frc and oxc) are almost always close together in the genome, suggesting selection pressure.},
}

Humans
*Oxalates/metabolism
*Microbiota/genetics
Metagenome
Gene Transfer, Horizontal
*Bacteria/genetics/metabolism

@article {pmid41136749,
year = {2025},
author = {Nagaraj, SK and Joy, CM and Shiraz, R and Narayan, R and Kaur, S and Khatun, O and Dubey, S and Ng, J and Mishra, N and Tripathi, S},
title = {Gut infection and dysbiosis are hallmarks of severe SARS-CoV-2 variants.},
journal = {Npj viruses},
volume = {3},
number = {1},
pages = {74},
pmid = {41136749},
issn = {2948-1767},
abstract = {SARS-CoV-2, the virus behind the COVID-19 pandemic, is primarily a respiratory pathogen, with host entry mediated by the ACE2 receptor that determines viral tropism. Notably, in humans, ACE2 is highly expressed in the gastrointestinal (GI) tract, particularly the small intestine (SI), prompting us to examine GI infectivity of SARS-CoV-2 variants of concern (VOCs). We found that ACE2 expression in Syrian hamsters closely resembles humans, supporting their use in studying GI tropism. Using this model, we compared infection and pathology of the ancestral Wuhan-like strain (Hong Kong), Delta, and Omicron variants. Despite high ACE2 expression, GI infection and pathology were generally low relative to the respiratory tract. However, the Delta variant showed markedly enhanced GI infectivity and pathology, especially in the SI, and caused the greatest disruption of the gut microbiome. These findings link SARS-CoV-2 virulence with GI infection and microbiome disturbance, establishing Syrian hamsters as a relevant model.},
}

@article {pmid41136740,
year = {2025},
author = {Talsma, TMW and de Winkel, KN},
title = {The gut feeling in motion sickness.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1497},
pmid = {41136740},
issn = {2399-3642},
mesh = {*Motion Sickness/physiopathology/microbiology/etiology/psychology ; Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; Enteric Nervous System/physiopathology ; *Gastrointestinal Tract/physiopathology ; },
abstract = {Motion sickness is a nearly universal response to the unnatural motions that are experienced when traveling by means other than the body's own faculties; in artificial realities; and in micro- and partial gravity environments. Despite being a known malady since ancient times, its underlying mechanisms, as well as the marked interpersonal variability in susceptibility, remain incompletely understood. While efferent brain-to-body signaling pathways involved in motion sickness have been previously described, recent findings on the functional role of the gut's (neuro)epithelial cells and microbiome point to a more intricate biological control system than previously appreciated. We examine (afferent) anatomical, hormonal, immune, and extracellular brain-body pathways, and their potential role in motion sickness etiology. This perspective proposes that an additional route may contribute to the pathophysiology of motion sickness, potentially under regulatory influence of the enteric nervous system. Candidate initiators, acting on these pathways, include humoral agents, enteroendocrine cells, and the gut microbiome.},
}

*Motion Sickness/physiopathology/microbiology/etiology/psychology
Humans
*Gastrointestinal Microbiome/physiology
Animals
Enteric Nervous System/physiopathology
*Gastrointestinal Tract/physiopathology

@article {pmid41136386,
year = {2025},
author = {Rodríguez-Daza, MC and Boeren, S and Tytgat, HLP and Desjardins, Y and de Vos, WM},
title = {Akkermansia muciniphila Muc[T] harnesses dietary polyphenols as xenosiderophores for enhanced iron uptake.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9428},
pmid = {41136386},
issn = {2041-1723},
support = {Grant 024.002.002//Stiftelsen Siamon/ ; },
mesh = {*Iron/metabolism ; *Polyphenols/metabolism/pharmacology ; *Siderophores/metabolism ; *Akkermansia/metabolism/genetics ; Gastrointestinal Microbiome/drug effects ; *Verrucomicrobia/metabolism/genetics ; Proteomics ; Zinc/metabolism ; ATP-Binding Cassette Transporters/metabolism ; },
abstract = {Dietary proanthocyanidins (PACs) are polyphenols that promote a healthy gut microbiome. PACs are notable for their rich catechol moieties with high affinity for iron, enabling them to interfere with pathogens' iron uptake. PACs selectively increase the abundance of Akkermansia muciniphila, a symbiont known for supporting metabolic and immune health. We discovered that A. muciniphila Muc[T] utilizes distinct iron-acquisition systems to take up iron sequestered by PACs, supporting its metabolic activity. Integrative proteomics and transcriptomics revealed that A. muciniphila has an active catechol-type siderophore-mediated iron uptake (Fe[3+]) system, involving membrane ATP-binding cassette transporters and lipocalins. Simultaneously, the expression of ferrous iron (Fe[2+]) transporters, zinc uptake, and iron storage proteins was upregulated. Administering iron-laden PACs in an iron-depleted medium restored the A. muciniphila growth to levels comparable to those in iron-amended conditions. This was associated with an increased expression of the A. muciniphila siderophore operon and lipocalin genes, indicating that iron-laden PACs are recognized as xenosiderophores to cope with iron depletion. Hence, we identified novel signaling mechanisms for iron acquisition and siderophore uptake regulation in A. muciniphila Muc[T] upon exposure to PACs, enhancing our understanding of the role of dietary PACs in selectively promoting this gut symbiont and potentially outcompeting pathogenic bacteria.},
}

*Iron/metabolism
*Polyphenols/metabolism/pharmacology
*Siderophores/metabolism
*Akkermansia/metabolism/genetics
Gastrointestinal Microbiome/drug effects
*Verrucomicrobia/metabolism/genetics
Proteomics
Zinc/metabolism
ATP-Binding Cassette Transporters/metabolism

@article {pmid41136092,
year = {2025},
author = {Chan-Ng, PPL and Leung, ASY and Goleva, E and Tham, EH},
title = {Treatment Strategies for Prevention of Atopic Dermatitis.},
journal = {Immunology and allergy clinics of North America},
volume = {45},
number = {4},
pages = {515-534},
doi = {10.1016/j.iac.2025.06.004},
pmid = {41136092},
issn = {1557-8607},
mesh = {Humans ; *Dermatitis, Atopic/prevention & control/etiology/therapy/immunology ; Probiotics/therapeutic use ; Breast Feeding ; Female ; Pregnancy ; Dietary Supplements ; Infant ; Vitamin D ; Fatty Acids, Omega-3 ; Immune Tolerance ; },
abstract = {Key strategies for atopic dermatitis prevention have been reviewed, which include maternal dietary modifications, breastfeeding, and early allergen introduction to promote immune tolerance. Maintaining skin barrier integrity is critical, with early emollient use in high-risk infants showing promise, but clarity on optimal emollient type, duration, and window of intervention is needed. Probiotic supplementation in pregnancy, lactation, and in early life, as well as infant dietary diversity from an early age may be beneficial. Evidence for omega-3 and vitamin D supplementation is inconclusive. Microbiome-targeted therapies are emerging areas for future research but have yet to reach clinical practice.},
}

Humans
*Dermatitis, Atopic/prevention & control/etiology/therapy/immunology
Probiotics/therapeutic use
Breast Feeding
Female
Pregnancy
Dietary Supplements
Infant
Vitamin D
Fatty Acids, Omega-3
Immune Tolerance

@article {pmid41136091,
year = {2025},
author = {Gao, JL and Hata, TR},
title = {Microbiome as a Potential Target for Treatment and Prevention of Atopic Dermatitis.},
journal = {Immunology and allergy clinics of North America},
volume = {45},
number = {4},
pages = {501-513},
doi = {10.1016/j.iac.2025.06.003},
pmid = {41136091},
issn = {1557-8607},
mesh = {Humans ; *Dermatitis, Atopic/therapy/microbiology/prevention & control/etiology ; *Microbiota/immunology/drug effects ; *Skin/microbiology/immunology ; Dysbiosis ; Animals ; Staphylococcus aureus ; },
abstract = {The skin microbiome in patients with atopic dermatitis (AD) is dysregulated with disproportionate dominance of Staphylococcus aureus, decreased microbial diversity, and decline in populations of commensal organisms with beneficial antimicrobial properties, such as coagulase-negative Staphylococci (CoNS). Emerging therapeutics target dysbiosis, S aureus elimination, CoNS growth, and microbial diversity improvement in the treatment and prevention of AD.},
}

Humans
*Dermatitis, Atopic/therapy/microbiology/prevention & control/etiology
*Microbiota/immunology/drug effects
*Skin/microbiology/immunology
Dysbiosis
Animals
Staphylococcus aureus

@article {pmid41136089,
year = {2025},
author = {Sung, M and Kim, BE and Leung, DYM},
title = {Early Predictors of Atopic Dermatitis and Food Allergy.},
journal = {Immunology and allergy clinics of North America},
volume = {45},
number = {4},
pages = {473-489},
doi = {10.1016/j.iac.2025.06.001},
pmid = {41136089},
issn = {1557-8607},
mesh = {Humans ; *Dermatitis, Atopic/diagnosis/etiology/metabolism ; *Food Hypersensitivity/diagnosis/etiology ; Biomarkers ; Infant ; Skin/immunology/metabolism/pathology ; Prognosis ; },
abstract = {Researchers have shown significant interest in the early prediction of atopic dermatitis (AD) and food allergy (FA) by analyzing factors such as genetics, skin barrier function, skin lipid profiles, epidermal cytokine profiles, cutaneous microbiome, and environmental influences, including air pollution and temperature. Early intervention is critical for preventing and mitigating the severity and progression of AD and FA. This article explored the pathogenesis of both AD and FA and highlighted the potential of skin tape stripping as a promising noninvasive tool for identifying predictive and follow-up biomarkers in infants predisposed to these conditions.},
}

Humans
*Dermatitis, Atopic/diagnosis/etiology/metabolism
*Food Hypersensitivity/diagnosis/etiology
Biomarkers
Infant
Skin/immunology/metabolism/pathology
Prognosis

@article {pmid41135734,
year = {2025},
author = {Li, X and Chen, K and Wang, S and Ma, J and Mao, X and Fang, M and Liu, X and Jiang, J and Jin, W},
title = {Hypericin Alleviates Depression via the Microbiota-Gut-Brain Axis: Role of Akkermansia muciniphila and Glycerophospholipid Metabolism.},
journal = {European journal of pharmacology},
volume = {},
number = {},
pages = {178283},
doi = {10.1016/j.ejphar.2025.178283},
pmid = {41135734},
issn = {1879-0712},
abstract = {BACKGROUND: Depression is one of the most severe mental disorders, affecting approximately 3.8% of the global population. Chronic stress represents a major contributing factor, with the microbiota-gut-brain (MGB) axis playing a critical role in its pathophysiology.

PURPOSE OF THE STUDY: This study aimed to evaluate whether hypericin can ameliorate depression through MGB axis and its underlying mechanism.

MATERIALS AND METHODS: To evaluate the antidepressant potential of hypericin, a chronic restraint stress mouse model was established. Behavioral tests were conducted. Fecal 16S rRNA sequencing and serum untargeted metabolomics were performed to investigate alterations in gut microbiota and metabolic profiles, followed by integrative analysis. The glycerophospholipid signaling pathway was further examined in both colon and hippocampus. Finally, microbiota depletion experiments were carried out to validate the essential role of gut microbiota in mediating the antidepressant effects of hypericin.

RESULTS: Hypericin ameliorated anxiety- and depression-like behaviors, accompanied by reduced histological damage, inflammation, and dysregulated serotonin metabolism in both the colon and hippocampus. Furthermore, significant alterations in Akkermansia muciniphila (A. muciniphila) abundance and glycerophospholipid metabolites were observed after hypericin treatment, with strong correlations identified among A. muciniphila, differential glycerophospholipid metabolites, and behavioral scores. The sPLA2/LPCATs/LYPLA1 axis was further demonstrated to mediate hypericin's regulatory effects on glycerophospholipid metabolism in both tissues. Finally, microbiota depletion abolished the behavioral improvements induced by hypericin.

CONCLUSIONS: Together, our findings offer novel insights into the role of the MGB axis in mediating the antidepressant effects of hypericin, potentially through mechanisms involving the modulation of A. muciniphila and glycerophospholipid metabolism.},
}

@article {pmid41135513,
year = {2025},
author = {Zhang, F and Zhou, G and Schewe, M and Kulling, SE and Ding, Y and Mozaffarian, D and Zuo, T},
title = {Dietary urbanization destabilizes host-gut microbiome homeostasis and informs precision nutrition for human health.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2025.09.013},
pmid = {41135513},
issn = {1932-7420},
abstract = {Since the industrial revolution, human dietary habits have invariably trended toward dietary urbanization, during which the human gut microbiota has rapidly changed. However, the human genome cannot change substantially over one generation, leaving it potentially ill-equipped to adapt to evolving microbial functions associated with rising non-communicable diseases (NCDs). In this review, we map the chronological alterations in dietary patterns and incidences of NCDs during global urbanization while emphasizing the gut microbiome as the centerpiece. We then illustrate losses and acquisitions of gut microbes during worldwide urbanization and delineate the mechanisms by which urbanized diets may disrupt host-microbiome interactions, linking to the onset of NCDs. Building on this, we further propose a microbiome-directed precision-nutrition framework that integrates both inter-population and intra-population variations to promote diet-fueled host-microbiome synergism and hence to counteract urbanization-associated diseases. These insights will instruct future microbiome-targeted diets to thwart NCDs.},
}

@article {pmid41135464,
year = {2025},
author = {Tang, Y and Han, X and Wang, Y and Xu, L and Qin, Q and Xu, Y},
title = {Magnetic fields facilitate microbial reductive dechlorination of Aroclor 1254: Insights into the shifts of dechlorination pathways, functional genes, and the effects of carbon source.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140167},
doi = {10.1016/j.jhazmat.2025.140167},
pmid = {41135464},
issn = {1873-3336},
abstract = {Microbial reductive dechlorination of the most toxic commercial PCB mixture Aroclor 1254 is challenging due to its high proportion of highly chlorinated congeners. This study demonstrates, for the first time, that a 5 mT static magnetic field (MF) significantly enhanced Aroclor 1254 dechlorination. Compared to non-MF-exposed controls (T-W), MF exposure (T-M, initial concentration: 39.85 ± 0.31 mg·kg[-1] slurry) greatly reduced the dechlorination lag period by approximately 6 weeks and significantly accelerated the dechlorination rate (Week 0-18: 0.526 ± 0.082 vs. 0.349 ± 0.035 mg·kg[-1] slurry·week[-1] for T-M vs. T-W). Although both groups reached a similar dechlorination plateau after Week 30, MF exposure enhanced ortho-dechlorination. Furthermore, the detailed PCB congener classification, based on redundancy analysis and temporal changes in PCB congener molar concentration, revealed more comprehensive dechlorination pathways. MF exposure enhanced dechlorination of PCB149 (236-245) and PCB71 (26-34) considered recalcitrant to be dechlorinated in Taihu Lake sediments. Microbiome analysis showed that MF exposure enriched the phylum Chloroflexi and promoted specific Dehalogenimonas-related amplicon sequence variants (ASVs) as keystone taxa in T-M. Notably, MF initially stimulated enrichment of the reductive dehalogenase gene pcbA1, potentially via enhanced carbon source utilization, which likely accelerated dechlorination occurrence and altered pathways. Weak intensity MF showed a potential for accelerating in situ PCB microbial reductive dechlorination.},
}

@article {pmid41135426,
year = {2025},
author = {Montalván, MIG and Guzmán Sánchez, M and Gutierrez, V and Tunçil, YE and Lindemann, SR},
title = {Designed dietary fibers: engineering carbohydrate structure for precision modulation of the human gut microbiome.},
journal = {Current opinion in biotechnology},
volume = {96},
number = {},
pages = {103371},
doi = {10.1016/j.copbio.2025.103371},
pmid = {41135426},
issn = {1879-0429},
abstract = {The human colonic microbiota exerts a profound influence on health, mediated by highly specific relationships among dietary fiber structures and microbial degraders. Systematic control of fiber structure offers opportunities to engineer microbiota-targeted interventions with increasing precision. Here, we examine the evolution of designed dietary fibers - biotechnologically produced oligosaccharides or polysaccharides synthesized de novo or naturally occurring polysaccharides intentionally modified post-extraction for their fine physical or chemical structures to influence gut microbiome. We propose a hierarchical framework to classify these fibers based on the degree of fine structure control, highlight current strategies for carbohydrate modification approaches, and discuss emerging directions for the field. Despite recent advances, much potential remains unrealized for the rational, reproducible design of microbiome-targeted fibers.},
}

@article {pmid41135275,
year = {2025},
author = {Ren, S and Gao, Y and Wang, J and Feng, J and Li, J and Xiang, T and Xuan, R and Zhou, Y},
title = {Yinchenhao decoction and its active compound rhein ameliorate intrahepatic cholestasis of pregnancy in mice via modulation of intestinal flora.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {148},
number = {},
pages = {157397},
doi = {10.1016/j.phymed.2025.157397},
pmid = {41135275},
issn = {1618-095X},
abstract = {BACKGROUND: Intrahepatic cholestasis of pregnancy (ICP), a medical condition, increases the risk of adverse pregnancy outcomes. Since the causes and mechanisms behind ICP remain unclear, the available treatment options are presently restricted.

PURPOSE: This research sought to explore the therapeutic efficacy of Yinchenhao decoction (YCHD), a traditional Chinese medicine formula, using two different ICP mouse models, as well as to clarify its fundamental mechanisms of action.

METHODS: Through HPLC-MS and network pharmacology, the active ingredients of YCHD for treating the two mouse models of ICP were studied. The therapeutic mechanisms of YCHD and its active ingredient rhein in the two mouse models of ICP were studied using 16S rRNA technology.

RESULTS: The findings of this research indicated that the gut microbiota in individuals with ICP undergoes specific changes. Furthermore, mice that are given the intestinal microbiome from these patients can exhibit characteristics of the ICP phenotype. Notably, YCHD led to significant enhancements in the clinical features of mice modeled for ICP and partially restored the balance of their gut flora. Further experiments revealed that rhein is the key active ingredient of YCHD in ICP treatment. Rhein can significantly improve the clinical phenotypes of mice in two different ICP models and correct their imbalanced intestinal flora. In addition, interventions involving YCHD and rhein led to a decrease in g_Fimenecus abundance, while simultaneously increasing g_Intestimonas abundance, which may be the key mechanism by which YCHD and rhein affect ICP.

CONCLUSION: YCHD and rhein could have beneficial impacts on ICP mouse models through the modulation of gut microbiota, offering a novel approach to clinical ICP management.},
}

@article {pmid41135049,
year = {2025},
author = {Zhang, X and Guo, Y and Shi, J and Zang, Q and Li, Y},
title = {Exclusive Effects of Moxibustion on Gut Microbiota: Protocol for a Focused Systematic Review and Meta-Analysis.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e73317},
doi = {10.2196/73317},
pmid = {41135049},
issn = {1929-0748},
mesh = {*Moxibustion/methods ; *Gastrointestinal Microbiome/physiology ; Humans ; Meta-Analysis as Topic ; Systematic Reviews as Topic ; Animals ; Research Design ; },
abstract = {BACKGROUND: The gut microbiota (GM) plays a critical role in systemic health, influencing immune, metabolic, and neurological functions. There is emerging evidence suggesting that moxibustion, a traditional thermal therapy, may modulate the GM to restore microbial homeostasis, yet its exclusive effects remain undifferentiated from those of combined therapies such as acupuncture. Previous meta-analyses lack mechanistic specificity, necessitating a focused evaluation of moxibustion's impact on microbial ecology.

OBJECTIVE: This systematic review and meta-analysis aims to quantify moxibustion-induced changes in GM diversity, taxonomic composition, and functional metabolites (eg, short-chain fatty acids).

METHODS: We will systematically search the PubMed, Web of Science, Cochrane Library, China National Knowledge Infrastructure, Wanfang, and VIP databases from inception to December 31, 2024, using keywords such as "moxibustion," "gut microbiota," and "intestinal flora." Eligible preclinical (animal) and clinical (human) studies evaluating stand-alone moxibustion interventions on the GM will be included. Primary outcomes include microbial α diversity indexes (Shannon and Simpson) and relative abundance of key taxa (eg, Firmicutes and Bacteroidetes). Risk of bias will be assessed using the Systematic Review Center for Laboratory Animal Experimentation risk-of-bias tool for animal studies and the modified Collaborative Approach to Meta-Analysis and Review of Animal Data from Experimental Studies criteria for human trials. Pooled effect estimates for continuous outcomes (eg, diversity indexes and taxa ratios) will be calculated using the ratio of means with 95% CIs. Statistical analyses will be conducted in RevMan (version 5.4) and R (metafor package), with data archived on Figshare for reproducibility.

RESULTS: As of March 2025, the literature search and screening have been completed, and 31 studies meeting the inclusion criteria have been identified. The comprehensive analysis is scheduled to be completed by October 2025, with results anticipated to be published in late 2025. On the basis of previous work, an anticipated result is that moxibustion may reduce pathogenic genera such as Ruminococcus while enhancing beneficial genera, effects that are expected to be associated with improved intestinal barrier integrity and anti-inflammatory responses.

CONCLUSIONS: This protocol provides a rigorous framework to evaluate moxibustion's unique role in GM modulation, bridging traditional medicine with microbiome science. The results will inform optimized, nonpharmacological strategies for managing microbiome-associated chronic diseases and guide future research priorities.},
}

*Moxibustion/methods
*Gastrointestinal Microbiome/physiology
Humans
Meta-Analysis as Topic
Systematic Reviews as Topic
Animals
Research Design

@article {pmid41134872,
year = {2025},
author = {Zhou, H and Chen, J and Zhang, X},
title = {BMDD: A probabilistic framework for accurate imputation of zero-inflated microbiome sequencing data.},
journal = {PLoS computational biology},
volume = {21},
number = {10},
pages = {e1013124},
doi = {10.1371/journal.pcbi.1013124},
pmid = {41134872},
issn = {1553-7358},
abstract = {Microbiome sequencing data are inherently sparse and compositional, with excessive zeros arising from biological absence or insufficient sampling. These zeros pose significant challenges for downstream analyses, particularly those that require log-transformation. We introduce BMDD (BiModal Dirichlet Distribution), a novel probabilistic modeling framework for accurate imputation of microbiome sequencing data. Unlike existing imputation approaches that assume unimodal abundance, BMDD captures the bimodal abundance distribution of the taxa via a mixture of Dirichlet priors. It uses variational inference and a scalable expectation-maximization algorithm for efficient imputation. Through simulations and real microbiome datasets, we demonstrate that BMDD outperforms competing methods in reconstructing true abundances and improves the performance of differential abundance analysis. Through multiple posterior samples, BMDD enables robust inference by accounting for uncertainty in zero imputation. Our method offers a principled and computationally efficient solution for analyzing high-dimensional, zero-inflated microbiome sequencing data and is broadly applicable in microbial biomarker discovery and host-microbiome interaction studies.},
}

@article {pmid41134799,
year = {2025},
author = {Orwa, P and Kuhl-Nagel, T and Meinhold-Ernst, R and Seyer, A and Jehle, JA and Mwirichia, R and Linkies, A},
title = {Chaetomium, Chlonostachys, and Pseudogymnoascus isolates from tomato tissues significantly suppress Phytophthora infestans in tomato.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0335007},
doi = {10.1371/journal.pone.0335007},
pmid = {41134799},
issn = {1932-6203},
mesh = {*Solanum lycopersicum/microbiology/parasitology ; *Phytophthora infestans/pathogenicity/physiology ; *Plant Diseases/microbiology/prevention & control/parasitology ; *Chaetomium/isolation & purification/physiology ; Soil Microbiology ; Antibiosis ; *Ascomycota/isolation & purification/physiology ; },
abstract = {Late blight is a disease whose causative agent is the oomycete Phytophthora infestans. It is one of the most destructive pathogenic oomycetes and a major challenge to global tomato production. The pathogen is difficult to manage because of its ability to evolve thereby evading host resistance. The aim of this study was to screen for potential antagonists of P. infestans using a combination of culture and microbiome-based approaches. Samples were collected from healthy and P. infestans-infected tomato plants grown in soil collected from two organic tomato growers in the Rhine-Main area in Germany. A total of 246 fungal isolates were screened for their antagonistic activity against P. infestans. Most of the isolates that exhibited in vitro antagonistic activity were from the genera Penicillium, Trichoderma, Chlonostachys, Mortierella, and Pseudogymnoascus. Following a stepwise in vitro screening strategy that accounted for growth features, ecological aspects, taxonomic data, potential health risks, commercial properties, and antagonistic efficacy, five fungal isolates were eventually selected for plant trials. Chaetomium subaffine showed the highest inhibitory effect against P. infestans across three trials whereby the percentage of diseased leaf area reduced by 90% compared to the control. Chlonostachys and Pseudogymnoascus spp. were effective in two trials, while Trichoderma and Ctenomyces spp. showed weak disease suppressive effects. In parallel, we characterized the fungal microbiome of the rhizosphere, phyllosphere, and endosphere from healthy and diseased tomato plants using ITS-rRNA sequencing. The fungal community differed significantly between the two soil origins, but P. infestans did not significantly influence fungal microbiota composition. Notably, 70% of our antagonistic fungi from the culture collection were detected in the tomato microbiome. This work identified isolates of Chaetomium subaffine, Clonostachys sp., and Pseudogymnoascus sp. as potential biocontrol candidates promoting plant health. The findings highlight the importance of combined functional screening and microbiome profiling for identifying fungal antagonists.},
}

*Solanum lycopersicum/microbiology/parasitology
*Phytophthora infestans/pathogenicity/physiology
*Plant Diseases/microbiology/prevention & control/parasitology
*Chaetomium/isolation & purification/physiology
Soil Microbiology
Antibiosis
*Ascomycota/isolation & purification/physiology

@article {pmid41134684,
year = {2025},
author = {Wang, C and Hao, Y and Liu, Y and He, L and Xu, S and Zhang, M and Wang, X and Wang, H},
title = {Baseline Fusobacterium Abundance Predicts Ustekinumab Response in Crohn's Disease: A Prospective Microbiome Cohort Study.},
journal = {Microbial biotechnology},
volume = {18},
number = {10},
pages = {e70250},
doi = {10.1111/1751-7915.70250},
pmid = {41134684},
issn = {1751-7915},
support = {JSDW202233//Jiangsu Provincial Medical Key Discipline Cultivation Unit/ ; YCT202305//The Affiliated Huai'an First People's Hospital of Nanjing Medical University Research and Innovation Team Project/ ; LKM2023044//Jiangsu Provincial Geriatric Health Research Project/ ; },
mesh = {Humans ; *Ustekinumab/therapeutic use ; Prospective Studies ; Male ; *Crohn Disease/drug therapy/microbiology ; Female ; Adult ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; Treatment Outcome ; *Fusobacterium/isolation & purification/genetics ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Young Adult ; DNA, Ribosomal/chemistry/genetics ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; },
abstract = {The gut microbiota composition in Crohn's disease (CD) patients may influence their response to ustekinumab (UST) therapy. A total of 51 patients with active CD undergoing UST therapy were prospectively enrolled. Clinical activity was evaluated using the Crohn's Disease Activity Index (CDAI), and faecal microbiota were characterised by 16S rRNA sequencing at baseline and week 24. Microbial compositional and functional alterations were assessed, and their correlations with clinical outcomes were examined. At week 24, 46.7% of patients achieved clinical remission and 82.2% achieved clinical response. At baseline, Megamonas (p = 0.009) and Erysipelatoclostridium (p = 0.030) were enriched in the remission group, whereas Fusobacterium (p = 0.016) was more abundant in the non-remission group and correlated positively with C-reactive protein (CRP) but negatively with body mass index (BMI) and serum albumin (ALB). Longitudinal analysis showed that CR patients exhibited increased Clostridium sensu stricto 1 (p = 0.028) and decreased Granulicatella (p = 0.043) after 24 weeks. This study provides real-world evidence supporting the clinical efficacy of UST in Asian patients with active CD. The observed association between elevated baseline Fusobacterium abundance and poorer treatment response suggests a potential microbial influence on therapeutic outcomes. These findings highlight the potential of Fusobacterium as a predictive biomarker for UST response and could provide a rationale for integrating microbiota-modulating strategies to enhance the efficacy of biologics in the future.},
}

Humans
*Ustekinumab/therapeutic use
Prospective Studies
Male
*Crohn Disease/drug therapy/microbiology
Female
Adult
*Gastrointestinal Microbiome/drug effects
Feces/microbiology
Treatment Outcome
*Fusobacterium/isolation & purification/genetics
RNA, Ribosomal, 16S/genetics
Middle Aged
Young Adult
DNA, Ribosomal/chemistry/genetics
DNA, Bacterial/genetics/chemistry
Sequence Analysis, DNA

@article {pmid41134679,
year = {2025},
author = {Jin, N and Hoyd, R and Yilmaz, AS and Zhu, J and Liu, Y and Jagjit Singh, MS and Grencewicz, DJ and Mo, X and Kalady, MF and Rosenberg, DW and Dravillas, CE and Singer, EA and Carpten, JD and Chan, CHF and Churchman, ML and Denko, N and Di Clemente, F and Dodd, RD and Eljilany, I and Fei, N and Hardikar, S and Ikeguchi, AP and Ma, A and Ma, Q and McCarter, MD and Osman, AEG and Riedlinger, G and Robinson, LA and Schneider, BP and Tarhini, AA and Tinoco, G and Figueiredo, JC and Zakharia, Y and Ulrich, CM and Tan, A and Spakowicz, D},
title = {Epigenetic Modulation, Intra-tumoral Microbiome and Immunity in Early Onset Colorectal Cancer.},
journal = {Cancer research communications},
volume = {},
number = {},
pages = {},
doi = {10.1158/2767-9764.CRC-25-0177},
pmid = {41134679},
issn = {2767-9764},
abstract = {The incidence of colorectal cancer (CRC) in young adults (age of diagnosis < 50 years old) has been rapidly increasing. Although ~20% of early-onset (EO) CRC cases are due to germline mutations, the etiology of the majority of EOCRC cases remains poorly understood. Non-genetic factors such as environmental exposure and lifestyle changes are likely to have a direct link to the increased incidence of sporadic EOCRC. We hypothesize that such factors may be observable as alterations in the epigenome, microbiome and immunome. We characterized DNA methylation signature and measured DNA methylation (DNAm) age in EOCRC by using The Cancer Genome Atlas (TCGA). Further, we carefully identified intra-tumoral microbes from TCGA and the Oncology Research Information Exchange Network (ORIEN) datasets and then related the microbes with deconvolved immune cell abundances in EOCRC. We observed DNAm age in EOCRC cohort were 12 years older when compared with average-onset CRC (AOCRC) cohort, by using three different epigenetic clocks. Differential methylated sites associated with gene expressions include CREB signaling in neurons, G protein coupled receptor signaling, phagosome formation and S100 family signaling. These differences were validated in the gene expression from TCGA and ORIEN. When compared the intra-tumoral microbes between EOCRC and AOCRC, no consistent differences were observed. Interestingly, the most abundant microbes interacted with the immune systems differently between the EOCRC and AOCRC tumors, characterized by more, larger, positive correlations in EOCRC. These data suggest epigenetic modulation and accelerated aging may play a key role in the development of EOCRC.},
}

@article {pmid41134670,
year = {2025},
author = {Xu, W and Zhou, Y and Ding, H and Ye, M and Li, S and Xu, L and Jin, X and Zhan, Z and Song, L and Zhang, Y and Wang, C and Zhu, Z and Ma, L and Pan, L and Fang, L},
title = {PreTA-mediated metabolism of 5-fluorouracil by intratumoral Citrobacter freundii drives chemoresistance in pancreatic cancer.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116473},
doi = {10.1016/j.celrep.2025.116473},
pmid = {41134670},
issn = {2211-1247},
abstract = {Pancreatic cancer is highly malignant, and while fluoropyrimidines (5-fluorouracil [5-FU] and capecitabine) are critical first-line treatments for metastatic cases, drug resistance remains a major challenge. In this study, we identified an association between Citrobacter enrichment in pancreatic tumors and poor overall survival in patients with pancreatic cancer, particularly in patients receiving fluoropyrimidine-based treatment. Co-culture of 5-FU with the Citrobacter freundii strain isolated from pancreatic cancer and intratumoral injection of this strain in xenograft models significantly reduce the antitumor efficacy of 5-FU. Subsequent analyses using mass spectrometry, bioinformatics, and gene knockout experiments revealed that C. freundii strain inactivates 5-FU via the PreTA, which is homologous to human dihydropyrimidine dehydrogenase (DPD). Gimeracil, a DPD inhibitor, preserves the efficacy of 5-FU by blocking PreTA activity. Other preTA-harboring bacteria also metabolized 5-FU, indicating broader bacteria-mediated 5-FU resistance. These findings reveal a potential microbiome-driven mechanism of chemotherapy failure and identify PreTA as a druggable target.},
}

@article {pmid41134485,
year = {2025},
author = {Tang, C and Qian, Y and Jia, S and Zhang, J and Zhang, Y and Ren, Y and Yong, H and Xu, J and Kan, J and Liu, J},
title = {The Potential Anticancer Mechanisms of Probiotics: A Comprehensive Review.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41134485},
issn = {1867-1314},
support = {137012822 and 137012843//High-level Talent Research Startup Fund of Yangzhou University/ ; BK20230587//Natural Science Foundation of Jiangsu Province/ ; 137013072//"Green Yangzhou Golden Phoenix" funding of Yangzhou/ ; 32402268//National Outstanding Youth Science Fund Project of National Natural Science Foundation of China/ ; },
abstract = {Cancer is a leading cause of mortality. With the changes in people's daily lifestyle and environmental pollution, the incidence of cancer has been increasing all over the world. Cancer not only increases patients' physical and mental burdens, but also brings a huge economic burden to the society. Thus, it is urgent to develop anti-cancer therapies with low side effects and high efficiency. Nowadays, probiotics have been considered as an effective strategy owing to their anti-tumor efficacy. In this review, we comprehensively summarize anti-cancer mechanisms of probiotics. Mechanistically, cell and animal experiments have revealed that probiotics prevent and/or alleviate cancer by blocking carcinogenesis-associated signaling pathways, initiating cancer cell apoptosis, detoxifying or reducing pro-carcinogenic compounds, regulating intestinal microbiota and their metabolites, increasing the efficacy of anti-cancer therapies, inhibiting inflammation, enhancing anti-tumor immunity, and reprogramming metabolism. Clinical evidence of probiotics in cancer treatment is also summarized. Finally, it discusses the future perspectives in the safety concerns, limitation use, and strain-specific effects of probiotics.},
}

@article {pmid41134211,
year = {2025},
author = {Tegegne, BA and Abebaw, D and Teffera, ZH and Fenta, A and Belew, H and Belayneh, M and Jemal, M and Getinet, M and Baylie, T and Tamene, FB and Belay, WY and Wondim, SA and Zeleke, TK},
title = {Microbial Therapeutics in Cancer: Translating Probiotics, Prebiotics, Synbiotics, and Postbiotics From Mechanistic Insights to Clinical Applications: A Topical Review.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {20},
pages = {e71146},
doi = {10.1096/fj.202502118R},
pmid = {41134211},
issn = {1530-6860},
mesh = {Humans ; *Probiotics/therapeutic use ; *Prebiotics/administration & dosage ; *Synbiotics/administration & dosage ; *Neoplasms/therapy/microbiology/immunology ; *Gastrointestinal Microbiome ; Animals ; },
abstract = {The gut microbiome plays a pivotal role in cancer development, progression, and treatment response, driving interest in microbiome-based interventions. This review examines probiotics, prebiotics, synbiotics, and postbiotics (PPSPs) as precision tools in oncology, highlighting their mechanisms, clinical applications, and challenges. Gut microbiota influence cancer through immune modulation, metabolic regulation, and inflammatory control, while also shaping chemotherapy pharmacokinetics and immunotherapy efficacy. PPSPs demonstrate antitumor effects via: (1) immune activation, (2) intestinal barrier reinforcement, (3) pathogen suppression, and (4) carcinogen neutralization. Clinically, probiotics/postbiotics reduce chemotherapy-induced mucositis and enhance checkpoint inhibitor responses, while synbiotics/prebiotics selectively nourish beneficial microbes. Despite promise, hurdles like strain-specific variability, dosing optimization, and individual microbiome differences hinder translation. By integrating preclinical and clinical data, this review underscores PPSPs' potential to bridge gut ecology with antitumor immunity, advancing precision oncology. Future priorities include large-scale trials, standardized protocols, and mechanistic insights into host-microbiome-cancer crosstalk. Personalized microbiota therapies, engineered consortia, and combination regimens represent promising frontiers. With robust evidence, PPSPs may emerge as essential adjuvants, improving outcomes while minimizing toxicity in cancer care.},
}

Humans
*Probiotics/therapeutic use
*Prebiotics/administration & dosage
*Synbiotics/administration & dosage
*Neoplasms/therapy/microbiology/immunology
*Gastrointestinal Microbiome
Animals

@article {pmid41134210,
year = {2025},
author = {Zhang, Y and Mo, W and Chen, K and Ding, Y and Mao, K and Wan, H and Zhou, J and Ju, F},
title = {Cooperative Microbial Metabolism Enhances Tryptophan-Mediated Insecticide Detoxification in the Fall Armyworm.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf237},
pmid = {41134210},
issn = {1751-7370},
abstract = {The fall armyworm, Spodoptera frugiperda, is a major global agricultural pest, known for its rapid evolution of insecticide resistance. Although host genetic adaptation contributes to this trait, the role of gut symbiont-mediated metabolic pathways in promoting resistance remains poorly understood. Here, we show that besides direct biodegradation, a generalist symbiont Enterococcus casseliflavus EMBL-3 indirectly promotes chlorantraniliprole resistance by compensating for tryptophan deficiency in a maize-based diet. Metabolomics and isotope tracing identify EMBL-3 as the primary producer of tryptophan, which is subsequently converted by co-resident microbes to indoleacetic acid. Indoleacetic acid activates the aryl hydrocarbon receptor, leading to upregulation of UDP-glucuronosyltransferase, a detoxification enzyme essential for chlorantraniliprole resistance, as confirmed by CRISPR/Cas9 knockout. This tripartite EMBL-3-indoleacetic acid-UDP-glucuronosyltransferase axis defines a hierarchical symbiont-host metabolic network driving chlorantraniliprole resistance. Our findings provide a framework and targets for disrupting pest adaptability by targeting critical symbiont metabolic nodes, positioning microbiome-mediated detoxification as a universal vulnerability in resistant pests.},
}

@article {pmid41134169,
year = {2025},
author = {Roy, YJ and Mirani, Y and Raju, J and Ali, AHM and Gigi, AA and Fawunmi, A and Kombara, JS},
title = {The Role of Colonic Microbiota in Constipation Predominant Irritable Bowel Syndrome: A Literature Review.},
journal = {British journal of hospital medicine (London, England : 2005)},
volume = {86},
number = {10},
pages = {1-11},
doi = {10.12968/hmed.2025.0184},
pmid = {41134169},
issn = {1750-8460},
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology/physiopathology/complications ; *Constipation/microbiology/physiopathology ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/physiopathology/microbiology ; Gastrointestinal Motility/physiology ; *Colon/microbiology/physiopathology ; },
abstract = {Irritable Bowel Syndrome with Constipation (IBS-C) is a functional gastrointestinal disorder characterised by abdominal pain, bloating, and altered bowel habits. Emerging research highlights the role of colonic microbiota in its pathophysiology, with IBS-C patients often exhibiting dysbiosis marked by reduced beneficial bacteria (Bifidobacterium, Lactobacillus) and increased inflammatory microbes (Enterobacteriaceae, Escherichia coli). Dysbiosis in IBS-C leads to reduced short-chain fatty acid production, impaired gut motility, and altered serotonin signalling, affecting peristalsis and sensitivity. It also increases intestinal permeability, inflammation, and gut-brain axis interactions, worsening pain and gastrointestinal dysfunction. These alterations impact gut motility, serotonin metabolism, and gut-brain axis signalling, contributing to IBS-C symptoms. Despite growing evidence, inconsistencies in study findings highlight the need for standardised research methods. Future studies should focus on long-term microbiota dynamics, targeted therapies, and personalised treatment strategies to improve symptom management and clinical outcomes. This review systematically summarises the changes in gut microbiota connected to IBS-C and provides a reference for future personalised treatment strategies.},
}

Humans
*Irritable Bowel Syndrome/microbiology/physiopathology/complications
*Constipation/microbiology/physiopathology
*Gastrointestinal Microbiome/physiology
Dysbiosis/physiopathology/microbiology
Gastrointestinal Motility/physiology
*Colon/microbiology/physiopathology

@article {pmid41134061,
year = {2025},
author = {Ikegami, S and Ito, T and Okamoto, H and Fujikura, C and Itatani, H and Yagi, M and Ohkuma, A and Okumura, N and Yamaki, A and Shigematsu, N and Kunimoto, K and Jinnin, M},
title = {Effect of Protease-Treated Royal Jelly Extract on Facial Wrinkles: A Placebo-Controlled, Double-Blind, Parallel-Group Study.},
journal = {Journal of cosmetic dermatology},
volume = {24},
number = {10},
pages = {e70503},
doi = {10.1111/jocd.70503},
pmid = {41134061},
issn = {1473-2165},
support = {//Yamada Bee Company Inc./ ; },
mesh = {Humans ; *Skin Aging/drug effects ; Female ; Double-Blind Method ; *Fatty Acids/administration & dosage/pharmacology/chemistry ; Middle Aged ; Adult ; *Skin Cream/administration & dosage/pharmacology ; *Peptide Hydrolases ; Face ; Treatment Outcome ; Microbiota/drug effects ; Administration, Cutaneous ; Stem Cells/drug effects ; },
abstract = {BACKGROUND: No clinical trials have reported on the wrinkle-improving effects of cosmetics which activate stem cells in vitro.

AIMS: To evaluate the anti-wrinkle effects of protease-treated royal jelly (pRJ)-containing cream application to the skin.

MATERIALS & METHODS: Seventy healthy Japanese women concerned about skin aging were treated with pRJ-containing cream or placebo for 12 weeks using the split-face method in a placebo-controlled, double-blind, parallel-group study.

RESULTS: The pRJ-containing cream group showed an improvement in the maximum depth and average depth of the biggest wrinkle in the crow's feet wrinkle, along with increased water content of the stratum corneum and dermal thickness, compared to the placebo group. Significant decreases in the relative amount of bacterial microbiome of the cheeks were observed only in the pRJ-containing cream group. In the ex vivo study, expression of COL17A1, epidermal stem cell function marker, was significantly up-regulated with the use of the pRJ-containing cream compared with the placebo cream.

CONCLUSION: This is the first study to demonstrate the wrinkle-improving effects of pRJ. Our results suggest that pRJ not only controls stratum corneum water content, dermal thickness, and bacterial microbiome, but also affects stem cell competition and mesenchymal stem cell activation. pRJ can reduce or eliminate certain skin concerns of women by improving age-related wrinkles.},
}

Humans
*Skin Aging/drug effects
Female
Double-Blind Method
*Fatty Acids/administration & dosage/pharmacology/chemistry
Middle Aged
Adult
*Skin Cream/administration & dosage/pharmacology
*Peptide Hydrolases
Face
Treatment Outcome
Microbiota/drug effects
Administration, Cutaneous
Stem Cells/drug effects

@article {pmid41133998,
year = {2025},
author = {Bağci, C and Negri, T and Atienza, EB and Gross, C and Ossowski, S and Ziemert, N},
title = {Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes.},
journal = {GigaScience},
volume = {},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf135},
pmid = {41133998},
issn = {2047-217X},
abstract = {BACKGROUND: Soil ecosystems have long been recognised as hotspots of microbial diversity, but most estimates of their microbial and functional complexity remain speculative despite decades of study, in part because conventional sequencing campaigns lack the depth and contiguity required to recover low-abundance and repetitive genomes. Here, we revisit this question using one of the deepest metagenomic sequencing efforts to date, applying 148 billion base pairs of Nanopore long-read and 122 billion base pairs of Illumina short-read data to a single forest soil sample.

RESULTS: Our hybrid assembly reconstructed 837 metagenome-assembled genomes, including 466 that meet high- and medium-quality standards, nearly all lacking close relatives among cultivated taxa. Rarefaction and k-mer analyses reveal that, even at this depth, we capture only a fraction of the extant diversity: non-parametric models project that more than ten trillion base pairs of sequencing data would be required to approach saturation. These findings offer a quantitative, technology-enabled update to long-standing diversity estimates and demonstrate that conventional metagenomic sequencing efforts likely miss the majority of microbial and biosynthetic potential in soil. We further identify more than 11 000 biosynthetic gene clusters, over 99% of which have no match in current databases, underscoring the breadth of unexplored metabolic capacity.

CONCLUSIONS: Taken together, our results emphasise both the power and the present limitations of metagenomics in resolving natural microbial complexity, and they provide a new baseline for evaluating future advances in microbial genome recovery, taxonomic classification, and natural product discovery.},
}

@article {pmid41133990,
year = {2025},
author = {Rohani, P and Ansari, A and Shaygantabar, M and Hekmatdoost, A and Sohouli, MH},
title = {The Effects of the Crohn's Disease Exclusion Diet (CDED) Alone Versus CDED Plus Partial Enteral Nutrition (PEN) on Gut Microbiome Composition in Pediatric CD Patients.},
journal = {MicrobiologyOpen},
volume = {14},
number = {5},
pages = {e70099},
doi = {10.1002/mbo3.70099},
pmid = {41133990},
issn = {2045-8827},
support = {//The authors received no specific funding for this work./ ; },
mesh = {Humans ; *Crohn Disease/diet therapy/microbiology/therapy ; *Enteral Nutrition/methods ; *Gastrointestinal Microbiome ; Child ; Male ; Female ; Adolescent ; Feces/microbiology ; Treatment Outcome ; Bacteria/classification/isolation & purification/genetics ; },
abstract = {Crohn's disease (CD) is a chronic inflammatory bowel condition characterized by relapsing inflammation and microbial dysbiosis. Diet-based therapies have emerged as promising adjuncts in pediatric CD management. To our knowledge, this is the first randomized trial to directly compare Crohn's Disease Exclusion Diet (CDED) with and without Partial Enteral Nutrition (PEN) in pediatric Crohn's patients from a microbiome perspective, highlighting the potential clinical relevance of dietary strategies that are more feasible than exclusive enteral nutrition. In this randomized controlled trial, 60 children with mild-to-moderate CD were assigned to either a CDED-only group or a CDED + PEN group. Gut microbiota composition was assessed using quantitative PCR before and after the 8-week intervention. After 8 weeks, both groups exhibited significant increases in Faecalibacterium prausnitzii, with the CDED + PEN group demonstrating a significantly greater increase compared to the CDED group alone (+8.94 vs. +5.00 log CFU, p < 0.001). In the CDED + PEN group, levels of Bifidobacterium and Lactobacillus also rose significantly, whereas in the CDED-only group, Bifidobacterium slightly decreased and Lactobacillus showed only a modest increase. Moreover, a significant reductions in Escherichia coli and Fusobacterium were observed in the CDED + PEN group compared to CDED alone (E. coli, -1.44 log CFU, p < 0.001; Fusobacterium, -1.08 log CFU, p < 0.001). Changes in Clostridium leptum and Ruminococcus were minimal and not statistically significant between or within groups. These findings suggest a synergistic effect of CDED when combined with PEN in modulating the gut microbiome toward a more anti-inflammatory profile. These findings suggest that CDED + PEN may enhance microbiome modulation compared to CDED alone; however, given the modest sample size and 8-week follow-up, these results should be interpreted cautiously.},
}

Humans
*Crohn Disease/diet therapy/microbiology/therapy
*Enteral Nutrition/methods
*Gastrointestinal Microbiome
Child
Male
Female
Adolescent
Feces/microbiology
Treatment Outcome
Bacteria/classification/isolation & purification/genetics

@article {pmid41133741,
year = {2025},
author = {Quezada, R and Kirchmayr, M and Arellano-Plaza, M and Morales, JA and Morrissey, JP and Gschaedler, A},
title = {Dominance of non-Saccharomyces yeasts in artisanal mezcal fermentations.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {10},
pages = {},
doi = {10.1099/mic.0.001584},
pmid = {41133741},
issn = {1465-2080},
mesh = {Fermentation ; *Agave/microbiology ; *Yeasts/classification/genetics/isolation & purification/metabolism ; *Alcoholic Beverages/microbiology/analysis ; Mexico ; Bacteria/classification/genetics/isolation & purification/metabolism ; Microbiota ; Food Microbiology ; Biodiversity ; },
abstract = {Mezcal is a spirit obtained from the fermentation and distillation of juices obtained from different agave species. It is one of the distilled beverages with great sociocultural value in different regions of Mexico, and in recent years, it has also gained great economic importance. It is known to present differences in its flavour, thanks to the richness of compounds incorporated within the spirit, which vary according to the agave species used, the microbial population present and the processes involved in its manufacture. This variety reflects the richness of local traditions and the craftsmanship behind its production. The main objective of the present work was to explore parameters that could impact fungal and bacterial diversity. The microbiome of bacteria and yeasts present in fermentations in the same distillery, in two different years and with three different agave species was investigated by metataxonomic analysis obtained from the sequencing of regions V3-V4 for bacteria and ITS1 for yeasts. The results showed that the dominant fungal genera in the fermentations correspond to non-Saccharomyces yeasts (Hanseniaspora, Pichia and Zygosaccharomyces). A major finding was that Saccharomyces was not the dominant yeast in any of the 15 fermentations characterized. The dominant bacteria belong to the groups of lactic acid bacteria and acetic acid bacteria. The statistical analysis of the alpha and beta diversities shows that the main statistical differences are seen in the year of fermentation rather than in the species of agave used. Finally, the microbial consortium was composed of the same genera during the different fermentations studied; the fundamental difference was the dominant genus in each fermentation.},
}

Fermentation
*Agave/microbiology
*Yeasts/classification/genetics/isolation & purification/metabolism
*Alcoholic Beverages/microbiology/analysis
Mexico
Bacteria/classification/genetics/isolation & purification/metabolism
Microbiota
Food Microbiology
Biodiversity

@article {pmid41133518,
year = {2025},
author = {Abdullah, IA and Khan, S and Hassan, FE},
title = {Gut-Brain Axis and Perioperative Gut Microbiome in Postoperative Cognitive Dysfunction: Implications for Neurosurgical Patients.},
journal = {Medical sciences (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/medsci13040236},
pmid = {41133518},
issn = {2076-3271},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Postoperative Cognitive Complications/microbiology/etiology/prevention & control ; *Brain ; *Neurosurgical Procedures/adverse effects ; Dysbiosis ; Animals ; Probiotics/therapeutic use ; },
abstract = {Background: Postoperative cognitive dysfunction (POCD) is a common postoperative condition after neurosurgery, and in patients of advancing age, with far-reaching implications for recovery and quality of life. Current evidence points to the gut-brain axis as the main mechanism for the regulation of perioperative neuroinflammation and cognition. Objective: The aim of this review is to consolidate the existing evidence for perioperative gut microbiome dysbiosis in POCD, specifically in neurosurgical patients. Methods: A review of preclinical and clinical evidence on the gut microbiome, surgical stress, and cognitive recovery was conducted. Both mechanistic and therapeutic evidence were examined. Results: Surgery and anesthesia enhance gut microbial diversity, intestinal permeability, and systemic inflammation, thereby compromising neuroplasticity and the integrity of blood-brain barriers. Preclinical models show that interventions to reestablish microbial homeostasis with probiotics, prebiotics, or fecal microbiota transplantation decrease postoperative cognition. Clinical studies offer evidence supporting the associations between decreased short-chain fatty acid-producing bacteria and POCD risk. Randomized controlled trials have demonstrated that perioperative probiotics lower the incidence and markers of POCD. Multi-omic approaches to integrating microbiome, metabolome, and neuroimaging signatures are being engineered to discern recovery phenotypes prior to surgery. Conclusions: Perioperative gut microbiota are a modifiable target for the optimization of cognitive recovery from neurosurgery. The inclusion of microbiome treatments and diagnostics into standard surgical care pathways is one potential pathway to POCD minimization, but large randomized trials will be necessary to establish this.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Postoperative Cognitive Complications/microbiology/etiology/prevention & control
*Brain
*Neurosurgical Procedures/adverse effects
Dysbiosis
Animals
Probiotics/therapeutic use

@article {pmid41133412,
year = {2025},
author = {Zheng, J and Liu, X and Jia, C},
title = {Comment on "Gut microbiome changes associated with chronic pancreatitis and pancreatic cancer: a systematic review and meta-analysis".},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000003707},
pmid = {41133412},
issn = {1743-9159},
}

@article {pmid41133096,
year = {2025},
author = {Lee, DH and Seong, H and Kim, SA and Han, NS},
title = {Synbiotic modulation of adult gut microbiome by 2'-fucosyllactose and Bifidobacterium longum subsp. infantis EFEL8008.},
journal = {Microbiome research reports},
volume = {4},
number = {3},
pages = {26},
pmid = {41133096},
issn = {2771-5965},
abstract = {Aim: This study aimed to evaluate the combination of 2'-fucosyllactose (2'-FL) and Bifidobacterium longum subsp. infantis (B. infantis) EFEL8008 as a synbiotic pair for adult gut health, using an in vitro digestion and fecal fermentation model. Methods: The resistance of 2'-FL to digestion was evaluated through simulated digestion encompassing oral, gastric, intestinal, and brush border membrane phases. Fecal fermentation was conducted using adult microbiota to investigate taxonomic and metabolic alterations following treatment with 2'-FL, EFEL8008, or their combination. Microbial composition was profiled using 16S rRNA gene sequencing and quantitative PCR targeting B. infantis. Short-chain fatty acids (SCFAs) and trimethylamine (TMA) levels were quantified by [1]H-NMR. Results: A total of 86.67% of 2'-FL remained intact after digestion, demonstrating its resistance to digestion throughout the upper gastrointestinal tract. The synbiotic combination significantly increased Bifidobacterium abundance and improved alpha diversity compared to single treatments. Heat tree and correlation analyses indicated selective enrichment of commensal taxa including Bifidobacterium and Lactobacillus, accompanied by a reduction in the abundance of potentially pathogenic genera such as Escherichia-Shigella. In addition, co-treatment markedly elevated the concentrations of acetate, propionate, lactate, and butyrate, and suppressed the microbial conversion of betaine to TMA, suggesting a favorable metabolic outcome. Conclusion: These results demonstrate that the synbiotic combination of 2'-FL and EFEL8008 promotes beneficial microbial modulation, enhances metabolite production, and supports gut health, highlighting its potential as a next-generation synbiotic strategy.},
}

@article {pmid41133094,
year = {2025},
author = {Lin, F and Sun, M and Yuan, X and Cai, Y and Chen, W and Liu, S and He, Z},
title = {Postoperative insulin resistance and the intestinal microbiota: mechanisms and research advances.},
journal = {Microbiome research reports},
volume = {4},
number = {3},
pages = {36},
pmid = {41133094},
issn = {2771-5965},
abstract = {Postoperative insulin resistance (PIR) is a common metabolic complication that significantly affects patient recovery and long-term outcomes. Recent studies have revealed a robust association between the gut microbiota and PIR, underscoring the potential role of microbial communities in modulating insulin sensitivity. In this comprehensive review, we synthesize current literature on the interplay between PIR and the gut microbiota, delve into the underlying mechanisms linking the two, and provide an overview of recent research progress in this field. Evidence suggests that the gut microbiota may influence PIR through mechanisms involving metabolic endotoxins, short-chain fatty acids, branched-chain amino acids, and other metabolites. Overall, the gut microbiota plays a crucial role in the onset and progression of PIR. This review aims to provide a theoretical basis for developing PIR intervention strategies based on microbiome regulation.},
}

@article {pmid41133047,
year = {2025},
author = {Al-Juhani, A and Desoky, MS and Almuhaimid, AA and Zaheer, M and Alhaqbani, HF and Abalkhail, EA and Alanazi, SA and Alzahrani, RS and Alrefaai, M and Desoky, R},
title = {Efficacy of Gut Microbiome-Targeted Therapies in Modulating Systemic Inflammation and Low-Grade Chronic Inflammatory States in Adults With Metabolic Disorders: A Systematic Review.},
journal = {Cureus},
volume = {17},
number = {9},
pages = {e92881},
pmid = {41133047},
issn = {2168-8184},
abstract = {Gut microbiome-targeted therapies have shown promise in promoting the outcomes of metabolic inflammation-related disease management. This review aims to assess the effectiveness of microbiome-targeted interventions and pinpoint the most promising therapies for clinical implementation. Following the PRISMA 2020 standards, we searched four main databases: PubMed, EMBASE, Scopus, and the Cochrane Library. We integrated medical subject headings (MeSH) and free-text keywords search pertinent to gut microbiome-targeted interventions, along with related outcomes such as inflammation and insulin resistance. English studies were conducted on primary adults with a metabolic disease diagnosis or deemed a high risk, and were mandated to report at least one outcome pertinent to metabolic health or systemic inflammation. To assess the risk bias, data were extracted, and the Cochrane Risk of Bias (RoB) 2.0 tool was employed. Fifteen studies fulfilled the inclusion criteria. A narrative synthesis was conducted. We found that probiotics significantly enhanced insulin resistance (HOMA-IR), reduced circulating endotoxin levels, decreased visceral fat, BMI, and fat mass, and increased beneficial taxa with obesity-associated bacteria reduction. However, inconsistent outcomes were shown for lipid parameters. Prebiotic therapies showed significant decreases in fasting glucose in overweight people, and insulin levels and HOMA-IR in patients with metabolic syndrome, enhanced anti-inflammatory effects (31% C-reactive protein (CRP) reduction, decreased interleukin (IL)-6, tumor necrosis factor-alpha (TNF)-α, and lipopolysaccharide (LPS) levels), and promoted butyrate-producing bacteria. Synbiotic interventions showed complementary benefits for glucose metabolism and body composition. Fecal microbiota transplantation (FMT) studies indicated improved insulin sensitivity and donor microbiota engraftment in responders. Fiber-rich diet trials markedly improved HbA1c levels in diabetic and prediabetic individuals. In conclusion, prebiotics demonstrated the most consistent metabolic and anti-inflammatory benefits across multiple parameters. Probiotics showed targeted effects on insulin resistance and body composition but inconsistent lipid outcomes. FMT and synbiotics require further investigation to establish clinical efficacy. This evidence supports prebiotics as a priority intervention for metabolic disease management through microbiome modulation.},
}

@article {pmid41132869,
year = {2025},
author = {Cardoso, LM and Wainford, RD},
title = {The immune-microbiome axis in salt-sensitive hypertension: a focus on renal and neural mechanisms.},
journal = {Frontiers in physiology},
volume = {16},
number = {},
pages = {1653387},
pmid = {41132869},
issn = {1664-042X},
abstract = {Systemic arterial hypertension (SAH) is a prevalent condition affecting humans and other mammals, with high salt intake recognized as a major risk factor for its development and progression. This review examines the intricate interplay between dietary salt, immune signaling, neural regulation and renal mechanisms in the pathophysiology of salt-sensitive hypertension (SSH). High salt consumption not only directly influences blood pressure but also induces low-grade inflammation by activating both innate and adaptive immune responses, particularly promoting pro-inflammatory T cell (TH17/IL-17) and macrophage phenotypes. These immune alterations impact key organs involved in blood pressure regulation, including the kidneys and central nervous system (CNS). In the CNS, salt-induced immune activation, especially microglial activation and cytokine production in regions such as the paraventricular nucleus, enhances sympathetic outflow and contributes to neurogenic hypertension. Disruption of the blood-brain barrier further facilitates immune cell infiltration and perpetuates neuroinflammation. Additionally, recent evidence shows that high salt intake alters the gut microbiome, reducing its diversity and favoring pro-inflammatory bacterial populations, which further amplify immune dysregulation via the gut-grain axis. The role of the kidneys in sodium handling is modulated by immune cell infiltration and cytokine-drive changes in sodium channel expression, reinforcing salt sensitivity. Aging and sex differences further modulate these pathways, increasing SSH risk in older individuals and postmenopausal women. Emerging therapeutic strategies targeting the gut microbiota, immune signaling, and neural pathways offer promise improvement for SAH management. However, further research is needed to clarify causal mechanisms and optimize interventions that address the neural-immune-microbiome axis in hypertension.},
}

@article {pmid41132660,
year = {2025},
author = {Xie, Y and Lv, G and Su, D and Li, M and Xu, Q and Chen, H and Cheng, F and Dai, D},
title = {Lactobacillus plantarum-derived cytoplasmic membrane vesicles as novel anti-inflammatory nanotherapeutics for psoriasis management.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1647466},
pmid = {41132660},
issn = {1664-3224},
mesh = {*Lactobacillus plantarum/immunology/metabolism ; *Psoriasis/therapy/immunology/microbiology/metabolism ; Animals ; Mice ; Humans ; *Probiotics ; *Anti-Inflammatory Agents/pharmacology ; Keratinocytes/metabolism/immunology ; Disease Models, Animal ; Macrophages/immunology/metabolism ; Skin ; Male ; },
abstract = {INTRODUCTION: Current research underscores the critical role of the gut-skin axis in inflammatory skin disorders such as psoriasis, with growing interest in the therapeutic application of probiotics. Despite this promise, the specific mechanisms and bioactive compounds through which probiotics exert their effects remain poorly characterized. In this study, we aimed to systematically evaluate the therapeutic potential of Lactobacillus plantarum (Lp)-derived bioactive fractions in psoriasis, with a particular focus on identifying key anti-inflammatory and immunomodulatory metabolites.

METHODS: The microbiome characteristics of psoriasis were analyzed through open microflora data mining and bibliometrics, and the probiotics with potential therapeutic effects were identified. Four bioactive fractions from L. plantarum were extracted and characterized. CCK-8, qPCR, and flow cytometry were used to evaluate the effects of four bioactive components on oxidative stress in keratinocytes and inflammatory responses in macrophages. Metabolomics was used to analyze the metabolic profiles of bioactive components with anti-inflammatory and antioxidant properties, and to screen and identify the main metabolite that play a role. To evaluate the efficacy and safety of bioactive components in the treatment of IMQ-induced psoriasis in mice.

RESULTS: A common feature of downregulation of Lactobacillus abundance was shown in patients with four inflammatory skin diseases including psoriasis. Four bioactive fractions, namely cytoplastic membrane vesicles (CMVs), bacterial lysate supernatant (BL-S), bacterial lysate precipitate (BL-P) and cell-free fermentation supernatant (CFS), were extracted from L. plantarum ATCC BAA-793, and CMVs were identified as having typical extracellular vesicles. In efficacy evaluation, CMVs and BL-S significantly reduced the mRNA levels of inflammatory factors in macrophages and the ROS levels of inflamed keratinocytes, among which CMVs had a more significant anti-inflammatory effect and had a unique inhibitory effect on M1 polarization of macrophages. Metabolomics revealed significant differences in metabolite profiles between CMVs and BL-S, and AEA enriched in both played anti-inflammatory, antioxidant and inhibitory roles in macrophage M1 polarization. In IMQ-induced psoriasis mouse models, CMVs demonstrated superior effects over BL-S in anti-hyperkeratosis, inhibiting inflammatory factor production, and down-regulating the proportion of M1 macrophages in skin and spleen. Both showed good biosafety in vivo.

DISCUSSION: This study demonstrates that L. plantarum-derived CMVs, enriched with AEA, ameliorate psoriasis through multi-faceted mechanisms including anti-inflammation, antioxidative stress reduction, and reprogramming of macrophage polarization. These findings not only position bacterial nanovesicles as a novel cell-free therapeutic strategy for inflammatory skin diseases but also establish a functional screening platform for precision microbiome-based interventions.},
}

*Lactobacillus plantarum/immunology/metabolism
*Psoriasis/therapy/immunology/microbiology/metabolism
Animals
Mice
Humans
*Probiotics
*Anti-Inflammatory Agents/pharmacology
Keratinocytes/metabolism/immunology
Disease Models, Animal
Macrophages/immunology/metabolism
Skin
Male

@article {pmid41132642,
year = {2025},
author = {Chen, Y and Shan, Y and Wang, T and Liu, Z and Zhao, Z and He, Y},
title = {The Effect of Semaglutide on Gut Microbiota in Chinese Patients with Type 2 Diabetes Poorly Controlled by Metformin.},
journal = {Diabetes, metabolic syndrome and obesity : targets and therapy},
volume = {18},
number = {},
pages = {3865-3881},
pmid = {41132642},
issn = {1178-7007},
abstract = {BACKGROUND: Type 2 diabetes mellitus (T2DM) is a highly prevalent metabolic disorder with increasing global incidence, linked to gut microbiota dysbiosis. This study investigated the effects of semaglutide, a long-acting GLP-1 receptor agonist, on gut microbiota composition and metabolic profiles in 15 Chinese patients with T2DM poorly controlled by metformin.

METHODS: Participants received semaglutide for 12 weeks, with fecal and blood samples collected before and after treatment. 16S rRNA gene sequencing revealed significant changes in gut microbiota diversity and composition after semaglutide treatment.

RESULTS: Alpha diversity indices increased, though not significantly, while beta diversity analysis showed structural shifts. At the phylum level, Firmicutes decreased, while Bacteroidota, Actinobacteriota and Proteobacteria increased. At the genus level, beneficial bacteria like Bifidobacterium increased, while potentially harmful genera like Klebsiella decreased. Metabolomic analysis identified 362 differentially expressed metabolites, with key pathways affected including Fc epsilon RI signaling, vascular smooth muscle contraction, and linoleic acid metabolism. Clinically, semaglutide improved glycemic control, reduced body weight, BMI and lipid. Significant correlations were observed between gut microbiota species, metabolites, and clinical indices such as BMI, HbA1c and lipid profiles.

CONCLUSION: Taken together, this study suggested that semaglutide's therapeutic benefits may be mediated through modulation of the gut microbiota and associated metabolic pathways, highlighting the potential for targeting the gut microbiome in diabetes management.},
}

@article {pmid41132492,
year = {2025},
author = {Zhang, L and Xu, T and Chen, W and Chai, Y and Wu, Y and Du, X},
title = {The potential of the microbiome as a target for prevention and treatment of carbapenem-resistant Enterobacteriaceae infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1674534},
pmid = {41132492},
issn = {2235-2988},
mesh = {Humans ; *Carbapenem-Resistant Enterobacteriaceae/drug effects/physiology ; *Enterobacteriaceae Infections/prevention & control/microbiology/therapy ; *Gastrointestinal Microbiome/drug effects ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use/administration & dosage ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Animals ; Dysbiosis ; Carbapenems/pharmacology ; Fatty Acids, Volatile ; },
abstract = {Carbapenem-resistant Enterobacteriaceae (CRE) present an escalating threat to global health due to their high transmissibility, limited treatment options, and high mortality rates. The gastrointestinal tract serves as both a major reservoir and a transmission hub for CRE, especially under conditions of antibiotic-induced dysbiosis. This review highlights the growing interest in the gut microbiome as a potential target for preventing and managing CRE infections. Building upon the understanding of CRE pathogenesis, we examine how commensal microbiota contribute to colonization resistance through mechanisms such as nutrient competition, spatial niche exclusion, immune modulation, and the production of antimicrobial metabolites. We further discuss microbiome-based therapeutic strategies, including probiotic administration, fecal microbiota transplantation (FMT), and supplementation with short-chain fatty acids (SCFAs), that have shown encouraging results in reducing intestinal CRE colonization. In addition, we explore emerging microbiome engineering approaches, particularly CRISPR-Cas9-mediated systems, which enable the selective elimination of resistant strains while maintaining microbial homeostasis. Current microbiome-based approaches have shown promise in the treatment and prevention of CRE infections, but further research is still needed to clarify their mechanisms, evaluate long-term safety, and determine their effectiveness in different clinical settings. With continued studies and thoughtful integration into existing infection control and antibiotic stewardship practices, these strategies may gradually contribute to a more practical and sustainable way to manage CRE.},
}

Humans
*Carbapenem-Resistant Enterobacteriaceae/drug effects/physiology
*Enterobacteriaceae Infections/prevention & control/microbiology/therapy
*Gastrointestinal Microbiome/drug effects
Fecal Microbiota Transplantation
Probiotics/therapeutic use/administration & dosage
Anti-Bacterial Agents/pharmacology/therapeutic use
Animals
Dysbiosis
Carbapenems/pharmacology
Fatty Acids, Volatile

@article {pmid41132413,
year = {2025},
author = {Mokhashi, O and Chakladar, J and Li, WT and Karin, M and Uzelac, M and Ongkeko, WM},
title = {Obesity-related microbial dysbiosis as a potential modulator of tumour progression.},
journal = {Access microbiology},
volume = {7},
number = {10},
pages = {},
pmid = {41132413},
issn = {2516-8290},
abstract = {Although there is a well-established connection between the gut microbiome and obesity, the specific mechanisms by which microbes regulate cell signalling, inflammation and adipocyte growth to influence disease severity in obese patients remain largely unclear. Subsequently, while obesity itself is a well-established risk factor for various cancers, the exact mechanisms by which it drives disease progression are not yet definitively known. In this study, we explored the link between obesity-associated microbiome alterations and cancer progression by analysing microbial abundance in tissue samples from obese and cancer patients, and we identified specific microbes correlated with body mass index (BMI) that are associated with key cancer-related pathways. Notably, BMI-associated microbial species such as Pseudomonas fluorescens and Lactobacillus sakei were linked with both pro-tumour and anti-tumour progression in cancer patients. Additionally, microbes found to be abundant in cancer and obese tissue, such as Pseudomonas baetica, were significantly associated with the upregulation of certain oncogenic signalling pathways. BMI-associated microbes were also correlated with chemokine signalling and TFR2/NFkB-related genes. Both of these have well-established roles in inflammatory activity and inflammasome expression, a critical step in obesity-related cancer progression. Therefore, these microbes were found to be associated with variations in disease prognosis and patient survival. This study provides new insights into how obesity-related microbiome dysbiosis may be associated with cancer development and aims to introduce novel potential avenues for precision medicine approaches in cancer treatment.},
}

@article {pmid41132374,
year = {2025},
author = {Zhang, L and Jin, S and Ma, D and Liu, Z and Ye, J and Liu, Q},
title = {The global trends and clinical progress in influenza co-infection: a visualization and bibliometric analysis (2005-2025).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1658752},
pmid = {41132374},
issn = {1664-302X},
abstract = {OBJECTIVES: Influenza co-infection, characterized by concurrent or sequential infection with influenza and other pathogens, lacks comprehensive quantitative analysis. This study evaluates the status, key hotspots, and clinical advancements in influenza co-infection research from 2005 to 2025 to guide future investigations.

METHODS: We analyzed articles from 2005 to 2025 sourced from the Web of Science database using R, VOSviewer, and CiteSpace. Concurrently, we extracted clinical trials from PubMed within the same timeframe to assess advancements in the field.

RESULTS: The study analyzed 3,058 articles, noting a consistent rise in publications on influenza co-infection from 2005 to 2025, with a significant spike between 2020 and 2021. The United States led in publication numbers, followed by China, Germany, the United Kingdom, and France. Among these, the United Kingdom exhibited the highest international collaboration. Key collaborative centers included the Centers for Disease Control and Prevention, Emory University, and St. Jude Children's Research Hospital. "PLOS ONE" and "BMC Infectious Diseases" published the most articles, while "Journal of Virology" and "Journal of Infectious Diseases" were the most cited. Keywords such as "infection", "virus", "COVID-19", "children", and "respiratory syncytial virus" highlighted research hotspots and emerging trends in influenza co-infection. The study of pathogenic mechanisms and immune interactions in influenza-bacterial co-infection remains crucial. The COVID-19 pandemic has intensified research on the epidemiological shifts and clinical impacts of co-infection. Emphasis has also been placed on the significance of pediatric populations in influenza and respiratory viral co-infections. Clinical trials have mainly targeted preventive strategies for high-risk groups and the effects of influenza vaccination on the respiratory microbiome.

CONCLUSION: This study comprehensively analyzes the current research landscape and identifies key hotspots in influenza co-infection. The findings offer crucial guidance for future studies in this field.},
}

@article {pmid41132334,
year = {2025},
author = {Chen, M and Zhong, W and Yu, T and Cao, C and Huang, H and Yu, J},
title = {Effect of Preoperative Sleep Disorders on Postoperative Enteral Nutrition Intolerance in Patients with Digestive Tract Tumors: A Prospective Cohort Study.},
journal = {Nature and science of sleep},
volume = {17},
number = {},
pages = {2699-2713},
pmid = {41132334},
issn = {1179-1608},
abstract = {PURPOSE: To investigate the effect of preoperative sleep disorders (SD) on postoperative enteral nutrition intolerance (ENI) and intestinal barrier, and explore its potential mechanism.

PATIENTS AND METHODS: This study was a prospective cohort study that included 67 patients (26 in SD group and 41 in non-SD group) undergoing digestive tract tumor surgery. Preoperative sleep status was assessed using the Pittsburgh Sleep Quality Index. Postoperative ENI was evaluated using the Enteral Nutrition Tolerance Scale. Perioperative serum cortisol, intestinal barrier markers (D-lactate, diamine oxidase and human lipopolysaccharide binding protein), ferroptosis markers (ferrous ions, reduced glutathione and lipid peroxide malondialdehyde) and intestinal flora characteristics were measured.

RESULTS: The incidence of ENI in SD group was 53.8%, which was significantly higher than that in non-SD group (26.8%, P=0.038). Perioperative levels of serum intestinal barrier markers in SD group were higher than those in non-SD group (P<0.05). The preoperative cortisol level was positively correlated with the increase in the intestinal barrier marker human lipopolysaccharide binding protein (r=0.3621, P=0.0170) and ferroptosis marker malondialdehyde (r=0.3660, P=0.0171). In SD group, the relative abundance of opportunistic pathogens (Enterobacteriaceae, Burkholderiaceae, etc) increased, while the relative abundance of probiotics (Bifidobacteriaceae) decreased.

CONCLUSION: Preoperative sleep disturbances were significantly associated with the occurrence of postoperative enteral nutrition intolerance in patients with gastrointestinal tumors. The intestinal barrier damage of these patients may be related to hypothalamic-pituitary-adrenal axis activation, oxidative stress induction and intestinal flora imbalance.},
}

@article {pmid41132309,
year = {2025},
author = {Koopaie, M and Fatahzadeh, M and Kolahdooz, S},
title = {Oral microbiome as a diagnostic biomarker for pancreatic cancer: a systematic review and meta-analysis of diagnostic accuracy.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2571188},
pmid = {41132309},
issn = {2000-2297},
abstract = {BACKGROUND: This systematic review and meta-analysis aim to assess the diagnostic accuracy of the oral microbiome in detecting pancreatic cancer.

METHODS: A comprehensive search of relevant studies was conducted using key terms across multiple databases. The methodological quality of the included studies was assessed using the Quality Assessment Tool for Diagnostic Accuracy Studies-2 (QUADAS-2). Diagnostic accuracy metrics were calculated including specificity, sensitivity, likelihood ratios, and diagnostic odds ratio (DOR). Subgroup analyses were performed to explore the effects of oral sample collection methods, bacterial taxonomy, and oral microbiome classifications.

RESULTS: This systematic review included nine studies, comprising 188 study units with 6601 subjects The pooled specificity, sensitivity, and diagnostic odds ratio (DOR) for the use of a single oral microbiome were 0.70 (95% CI: 0.68-0.71), 0.65 (95% CI: 0.64-0.67), and 4.85 (95% CI: 4.11-5.74), respectively. Subgroup meta-analysis revealed that using multiple oral microbiome approaches could increase the DOR to 16.33. Subgroup analysis was performed based on bacterial phylum classification, multiple oral microbiomes, sampling methods, bacterial taxonomy, and subgenus-level taxonomy (g_Streptococcus and g_Prevotella).

CONCLUSIONS: Oral microbiome holds promise as a diagnostic biomarker for pancreatic cancer, supporting its potential as a noninvasive tool for the screening and early detection of this malignancy.},
}

@article {pmid41132114,
year = {2025},
author = {Omidian, H and Akhzarmehr, A and Bertol, CD},
title = {Natural-based antioxidants in cosmeceuticals: Extraction, bioavailability and skin ageing applications.},
journal = {International journal of cosmetic science},
volume = {},
number = {},
pages = {},
doi = {10.1111/ics.70039},
pmid = {41132114},
issn = {1468-2494},
abstract = {This review offers an in-depth exploration of the bioactivities, extraction techniques, formulation approaches and practical uses of naturally derived antioxidants in anti-ageing skincare. A critical analysis of the literature was performed. Extracts from leaves, aerial parts, seeds, peels, fruits and barks exhibit potent antioxidant, anti-inflammatory, photoprotective and anti-tyrosinase activities. Natural-based antioxidants exhibit a wide range of bioactivities as neutralizing free radicals through mechanisms such as metal chelation and activation of cellular antioxidant pathways (e.g. Nrf2/ARE) and anti-inflammatory effects by modulating cytokines like TNF-α and IL-6 and promoting wound healing by stimulating collagen synthesis and bioactive compound production. Extracts from Mucuna species, Magnolia officinalis and Arbutus unedo, for instance, demonstrate anti-ageing efficacy by inhibiting enzymes such as collagenase, elastase and MMPs. Certain fruit and seed extracts provide photoprotection with high SPF values, while others-such as mushroom extracts and essential oils-display potent antimicrobial activity. Their bioactivity is often enhanced through fermentation processes, innovative delivery systems like liposomes, niosomes and polymeric micelles, which improve stability, bioavailability and topical effectiveness. Extraction methods for natural antioxidants-including aqueous, hydroalcoholic, ultrasound-assisted (UAE), fermentation-assisted and alternative solvent (NaDES) techniques-are crucial for recovering and stabilizing bioactive compounds. Emerging green technologies such as supercritical CO2 extraction (SC-CO2), subcritical water extraction (SWE), supramolecular solvents (SUPRAS) and cloud point extraction (CPE) offer sustainable and selective recovery of bioactives with reduced environmental impact. These bioactives address oxidative stress, UV damage and dermal ageing, offering multifunctional applications in cosmeceuticals, pharmaceuticals and nutraceuticals. However, challenges such as photostability, inconsistent bioavailability and regulatory hurdles persist. Future research focusing on synergistic formulations, clinical validation and microbiome-friendly antioxidants will drive their advancement in next-generation sustainable skincare.},
}

@article {pmid41132061,
year = {2025},
author = {Chen, JW and Wang, SY and Yang, WY},
title = {Fecal microbiome associated with egg production efficiency in laying hens.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.25.0256},
pmid = {41132061},
issn = {2765-0189},
abstract = {OBJECTIVE: This study aimed to characterize the fecal microbiome of highly productive laying hens to identify microbial signatures linked with enhanced egg production performance.

METHODS: Six commercial layer farms were enrolled in the study. Farms with an average monthly egg production rate (amEPR) above 80% over six consecutive months were classified as the high-production group (D group; n=3), while those with amEPR below 60% were designated as the low-production group (P group; n=3). All hens were raised in open-type housing systems without a history of forced molting. From each farm, 36 fecal samples were randomly collected and subjected to full-length 16S ribosomal RNA gene sequencing to characterize the microbiome.

RESULTS: The D group showed significantly higher Firmicutes-to-Bacteroidetes ratios (p<0.0001) and lower species richness (Menhinick index, p<0.05) compared with the P group. Multivariate analyses (Adonis, ANOSIM, and MRPP; all p<0.001) revealed distinct microbial community structures between the groups. Taxonomic profiling indicated that the D group harbored higher relative abundances of Enterococcus cecorum and Lactobacillus kitasatonis (both p<0.05). In contrast, the P group had elevated levels of Bacteroides eggerthii and Bacteroides coprosuis (p<0.001 and p<0.05, respectively). Principal component analysis and Linear discriminant analysis effect size further identified Enterococcus cecorum and Lactobacillus kitasatonis as biomarkers associated with superior egg production. In Hy-Line hens, Lactobacillus gallinarum and Lactobacillus salivarius were also identified as biomarkers linked to high productivity.

CONCLUSION: The fecal microbiome of highly productive laying hens is characterized by an enrichment of Enterococcus cecorum and lactic acid bacteria, particularly Lactobacillus kitasatonis, Lactobacillus gallinarum, and Lactobacillus salivarius. Their targeted supplementation may represent a promising probiotic strategy to improve egg production efficiency in commercial laying hens.},
}

@article {pmid41132059,
year = {2025},
author = {Anggraeni, AS and Windarsih, A and Suratno, S and Jayanegara, A and Sofyan, A and Laconi, EB and Kumalasari, NR},
title = {Impact of chitosan supplementation on metabolomic profiles and microbial community dynamics in total mixed ration silage and rumen fluid.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.25.0178},
pmid = {41132059},
issn = {2765-0189},
abstract = {OBJECTIVE: This study aimed to investigate the effects of varying levels of chitosan supplementation in total mixed ration (TMR) silage on the abundance and dynamics of rumen microbial communities, as well as their associated metabolomic profiles.

METHODS: Next-generation sequencing (NGS) and LC/HRMS-based metabolomics were employed to assess alterations in rumen microbiota and metabolites composition in response to chitosan supplementation in TMR silage.

RESULTS: A total of 308 metabolites were identified in TMR silage, 144 of which had a variable importance in projection (VIP) scores greater than 1, marking them as distinguishing metabolites. Notably, chitosan supplementation increased L-valine levels, identifying it as a potential biomarker metabolite. In rumen fluid samples, 33 metabolites were identified, with 13 exhibiting VIP scores over 1, classifiying them as key metabolite indicators. Chitosan supplementation significantly elevated amine compounds, particularly Dibenzylamine and N,N-Bis(2-hydroxyethyl) dodecanamide, in rumen fluid. The primary phyla affected by chitosan in TMR silage were Proteobacteria, Bacteroidota, and Firmicutes. Additionally, the genera Succinivibrionaceae_UCG-002 and Prevotella decreased with chitosan supplementation, whereas Rikenellaceae_RC9_gut_group exhibited increased abundance. Predominantly negative correlations were observed between rumen fluid metabolites (particularly amines and indoles) and microbial populations belonging to Bacteroidota and Firmicutes.

CONCLUSION: These findings indicate that chitosan supplementation alters rumen metabolic activity and reduced microbial diversity within the rumen.},
}

@article {pmid41132038,
year = {2025},
author = {Tanca, A and Uzzau, S},
title = {Contribution of metaproteomics to unveiling the functional role of the gut microbiome in human physiology and metabolism.},
journal = {Expert review of proteomics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14789450.2025.2580644},
pmid = {41132038},
issn = {1744-8387},
abstract = {INTRODUCTION: The human gut microbiome (HGM) profoundly influences human physiology. In recent years, it has become clearer that a healthy HGM is much better defined by its functional profile than by its taxonomic composition. Metaproteomics is the optimal approach to assessing the functional profile of the HGM in a taxon-specific manner, offering a direct view of its biological activity.

AREAS COVERED: First, we summarized the main wet lab and data analysis approaches used in gut metaproteomics. Next, we reviewed metaproteomic studies that have characterized the HGM of healthy adults. Lastly, we examined the functional changes induced in the HGM by specific dietary interventions.

EXPERT OPINION: Current fecal metaproteomics provides an initial understanding of the roles of gut microbes in human health, revealing redundant and taxon-specific functions. Future research should prioritize standardization, large-scale studies, and integration with multi-omics to better understand HGM metabolism. Emerging technologies, advanced mass spectrometry platforms, and AI-driven analytics are expected to increase sensitivity and depth of gut metaproteomics, accelerating discovery and potential clinical applications.},
}

@article {pmid41132005,
year = {2025},
author = {Chakraborty, A and Mahajan, S and Prasoodanan P K, V and Khamkar, AS and Sharma, VK},
title = {Life inside a Bag: Multi-omics insights into the bagworm species Eumeta crameri.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {},
number = {},
pages = {},
doi = {10.1093/dnares/dsaf029},
pmid = {41132005},
issn = {1756-1663},
abstract = {Bagworms are commonly known for the well-organized case or bag surrounding them constructed using their silk and plant materials. To understand the genetic basis of these unique characteristics in bagworms, we performed multi-omics analyses of a bagworm species, Eumeta crameri. The genome and transcriptome sequencing of E. crameri were used to construct the nuclear genome with a size of 668.2 Mb, N50 value of 6.6 Mb, and 13,554 coding genes, which was further assembled into 31 pseudochromosomes. The mitochondrial genome had a size of 15.6 Kb. We established the phylogenetic position of E. crameri with respect to 54 other insect species. The comparative analyses of E. crameri with other Lepidopterans revealed the adaptive evolution of genes related to primary metabolic pathways, defense, molting and metamorphosis, and silk formation in the bagworm species. We also showed the ultrafine nature of the E. crameri silk fibers. Further, we performed the gut microbiome sequencing for E. crameri and constructed a gut microbial gene catalog, which revealed the unique composition of the gut microbiome and its significance for host metabolism and defense. Together, the results provide multi-faceted insights into the biological processes that support the well-organized holometabolous metamorphosis inside the bags of E. crameri.},
}

@article {pmid41131749,
year = {2025},
author = {Deng, X and Xu, M and DU, C},
title = {[Artificial intelligence in stomatology: Innovations in clinical practice, research, education, and healthcare management].},
journal = {Beijing da xue xue bao. Yi xue ban = Journal of Peking University. Health sciences},
volume = {57},
number = {5},
pages = {821-826},
pmid = {41131749},
issn = {1671-167X},
mesh = {*Artificial Intelligence ; Humans ; *Oral Medicine/education/trends ; China ; Delivery of Health Care ; Machine Learning ; },
abstract = {In recent years, China has continued to face a high prevalence of oral diseases, along with uneven access to high-quality dental care. Against this backdrop, artificial intelligence (AI), as a data-driven, algorithm-supported, and model-centered technology system, has rapidly expanded its role in transforming the landscape of stomatology. This review summarizes recent advances in the application of AI in stomatology across clinical care, biomedical and materials research, education, and hospital management. In clinical settings, AI has improved diagnostic accuracy, streamlined treatment planning, and enhanced surgical precision and efficiency. In research, machine learning has accelerated the identification of disease biomarkers, deepened insights into the oral microbiome, and supported the development of novel biomaterials. In education, AI has enabled the construction of knowledge graphs, facilitated personalized learning, and powered simulation-based training, driving innovation in teaching methodologies. Meanwhile, in hospital operations, intelligent agents based on large language models (LLMs) have been widely deployed for intelligent triage, structured pre-consultations, automated clinical documentation, and quality control, contributing to more standardized and efficient healthcare delivery. Building on these foundations, a multi-agent collaborative framework centered around an AI assistant for stomatology is gradually emerging, integrating task-specific agents for imaging, treatment planning, surgical navigation, follow-up prediction, patient communication, and administrative coordination. Through shared interfaces and unified knowledge systems, these agents support seamless human-AI collaboration across the full continuum of care. Despite these achievements, the broader deployment of AI still faces challenges including data privacy, model robustness, cross-institution generalization, and interpretability. Addressing these issues will require the development of federated learning frameworks, multi-center validation, causal reasoning approaches, and strong ethical governance. With these foundations in place, AI is poised to move from a supportive tool to a trusted partner in advancing accessible, efficient, and high-quality stomatology services in China.},
}

*Artificial Intelligence
Humans
*Oral Medicine/education/trends
China
Delivery of Health Care
Machine Learning

@article {pmid41131656,
year = {2025},
author = {Chen, X and Xu, J and Zhang, L and Xie, B and Ren, J and He, J and Liu, T and Liu, Q and Dong, Y and He, X and Yao, J and Wu, S},
title = {Altered ruminal microbiome tryptophan metabolism and their derived 3-indoleacetic acid inhibit ruminal inflammation in subacute ruminal acidosis goats.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {215},
pmid = {41131656},
issn = {2049-2618},
support = {2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; },
mesh = {Animals ; Goats/microbiology ; *Rumen/microbiology/metabolism ; *Acidosis/veterinary/microbiology/metabolism ; Animal Feed/analysis ; *Tryptophan/metabolism ; *Indoleacetic Acids/metabolism ; *Gastrointestinal Microbiome ; *Inflammation ; *Goat Diseases/microbiology/metabolism ; Diet ; Female ; Metagenomics ; Bacteria/classification/genetics/metabolism/isolation & purification ; Fermentation ; Metagenome ; },
abstract = {BACKGROUND: Subacute ruminal acidosis (SARA) is a digestive disorder that often severely jeopardizes the health and lactation performance of ruminants fed a high-energy diet. Different dairy ruminants exhibit varying degrees of inflammation accompanied by variations in the rumen microbiota when SARA occurs. Our understanding of the occurrence of SARA and varying degrees of rumen epithelial inflammation is lacking. Hence, we performed rumen metagenomic, metagenome-assembled genome and metabolomic analyses, with transcriptome and single-nucleus RNA sequence analyses, to explore the microbial mechanism of SARA occurrence and different degrees of inflammation.

RESULTS: A total of 36 goats fed two diets with gradually increasing levels of rumen-degradable starch (RDS) were included in this study, and SARA goats fed 70% concentrate diets supplemented with whole corn (HGW-SARA) and SARA goats fed 70% concentrate diets supplemented with crushed corn (HGC-SARA) were identified. Moreover, 11 goats fed a control basal diet, named LGW-CON, were also included. Compared with those in the LGW-CON group, the rumen fermentation capacity was enhanced, accompanied by ruminal epithelial and systemic inflammation, in goats from HGW-SARA and HGC-SARA. Between them, HGC-SARA goats presented less inflammation. Notably, the ruminal inflammation-related pathways were increased only in the HGW-SARA group but not in the HGC-SARA group. Metagenomic analysis revealed that the β diversity of SARA goats was significantly different from that of LGW-CON goats. Ruminococcus significantly increased in both SARA groups, whereas Prevotella and Bacteroidales significantly decreased, which was accompanied by a decrease in cellulose and hemicellulose enzymes and an increase in lysozymes and lipopolysaccharide synthesis enzymes. Multi-omics analysis of the ruminal contents and tissues suggested that epithelial inflammation was caused by disturbed ruminal microbiome-induced Th17 cell differentiation and IL-17 signalling pathway activation. Comparative analyses between the HGW-SARA and HGC-SARA groups highlighted the importance of Selenomonas and Bifidobacterium, as well as bacterial tryptophan metabolism, in the production of 3-indoleacetic acid, which mitigated ruminal epithelial inflammation by modulating Th17 cells and inhibiting IL-17 signalling. Ruminal microbiota transplantation from HGW-SARA goats to healthy dairy goats and mice revealed the role of microbes in epithelial inflammation. Additionally, 3-indoleacetic acid supplementation reduced rumen inflammation and the IL-17 concentration in the serum, improved VFAs absorption, and enhanced milk production.

CONCLUSIONS: This study unveiled that after SARA was induced by high-concentrate feeding, the rumen homeostasis was disrupted, and rumen fiber degradation capacity of dairy goats decreased, but the LPS synthesis capacity increased, and inflammation of the rumen epithelium was observed. However, the ruminal microbial species from the Bifidobacterium and Selenomonas genera and bacterial 3-indole acetic acid are pivotal in mitigating ruminal epithelial inflammation during SARA in dairy goats. This could potentially be attributed to the modulation of ruminal Th17 cell proportions and the inhibition of IL-17 signalling pathways. Video Abstract.},
}

Animals
Goats/microbiology
*Rumen/microbiology/metabolism
*Acidosis/veterinary/microbiology/metabolism
Animal Feed/analysis
*Tryptophan/metabolism
*Indoleacetic Acids/metabolism
*Gastrointestinal Microbiome
*Inflammation
*Goat Diseases/microbiology/metabolism
Diet
Female
Metagenomics
Bacteria/classification/genetics/metabolism/isolation & purification
Fermentation
Metagenome

@article {pmid41131628,
year = {2025},
author = {Venegas, L and Araya, C and Palomo, R and Galarce, N and Siel, D and Yáñez, JM and Correa-Fiz, F and Calderón-Amor, J and Cartes, D and Ceballos, MC and Piña, A and Guzmán-Pino, S and Luna, D},
title = {The role of human-pig interactions in modulating gut microbiota, stress, and performance.},
journal = {Porcine health management},
volume = {11},
number = {1},
pages = {51},
pmid = {41131628},
issn = {2055-5660},
support = {11220280//National Research and Development Agency (ANID), Programme FONDECYT Iniciación/ ; },
abstract = {BACKGROUND: The microbiota‒gut‒brain axis modulates pigs' stress response, behavior, and overall welfare. Stressful management practices can disrupt gut microbiota (GM), negatively impacting pigs' health and welfare. This study evaluated how the quality of human handling influences stress-related physiological responses, productive performance, and gut microbiota (GM) composition in pigs during the nursery phase.

RESULTS: Female pigs (n= 36, 21 days old) were randomly assigned to three experimental groups (12 pigs/group, four pens per treatment): positive human handling (PHH), negative human handling (NHH), and a control group (CG). The PHH group experienced gentle tactile interactions, whereas the NHH group was subjected to chronic intermittent stress through acute stressors, and the CG group received minimal handling for routine practices. Hair cortisol concentrations were measured as an indicator of chronic stress (days 15 and 64). Productive performance was assessed through body weight (BW), average daily gain (ADG), average daily feed intake (ADFI), and feed conversion (FC). Fecal samples were collected at baseline (T0, day 16), mid-study (T1, day 37), and end of the study (T2, day 65) and analyzed using 16S rRNA gene amplicon sequencing to assess GM changes over time. Pigs in the PHH group showed a significant reduction in cortisol levels from baseline to post-treatment (P < 0.0001), while no significant changes were observed in the NHH group (P = 0.26). A smaller but significant decrease was also detected in the CG group (P = 0.001). PHH pigs had higher BW (P = 0.0009) and ADG (P = 0.03) during the later growth phase compared to NHH pigs. At T2, PHH pigs exhibited greater diversity and richness compared to NHH pigs, indicating a restorative effect on GM composition. Differential abundance analyses identified four bacterial genera that distinguished treatment groups: Blautia, Megasphaera, and Subdoligranulum were enriched in PHH pigs, while Terrisporobacter was enriched in NHH pigs. Additionally, bacterial interaction networks exhibited the least complex network in the NHH group, with ecological associations primarily involving Clostridium and Terrisporobacter.

CONCLUSIONS: The quality of human handling influenced stress physiology, performance, and gut microbiota in pigs. Positive handling reduced cortisol levels, improved growth, and promoted microbial diversity, while negative handling was linked to decreased performance and reduced microbial network complexity. These results highlight the potential of positive interactions to enhance welfare and productivity, and identify specific bacterial genera as potential biomarkers differentiating negative and positive handling conditions.},
}

@article {pmid41131626,
year = {2025},
author = {La Rosa, GRM and Samaranayake, LP and Zaura, E and Fuochi, V and Furneri, PM and Kowalski, J and Chapple, I and Polosa, R},
title = {Impact of electronic cigarette use on the oral microbiome: a protocol for a systematic review of clinical studies.},
journal = {Systematic reviews},
volume = {14},
number = {1},
pages = {199},
pmid = {41131626},
issn = {2046-4053},
support = {UPB: 6C725202048/2024//Department of Clinical and Experimental Medicine, University of Catania/ ; },
mesh = {Humans ; Systematic Reviews as Topic ; *Microbiota ; *Electronic Nicotine Delivery Systems ; *Vaping/adverse effects ; *Mouth/microbiology ; Research Design ; },
abstract = {BACKGROUND: The oral microbiome plays a pivotal role in maintaining both oral and systemic health, yet it can be disrupted by lifestyle factors such as tobacco use. Electronic cigarette (e-cig) has emerged as a popular alternative to conventional smoking, often perceived as a harm reduction tool. While combustible tobacco smoking is known to promote pathogenic shifts in the oral microbiota, evidence on the impact of e-cig use remains limited and inconsistent. A systematic synthesis of current evidence is therefore warranted to assess the potential microbiological and clinical implications of e-cig use. This systematic review aims to critically evaluate clinical studies assessing the effects of e-cig use on the oral microbiome, with specific comparisons to current smokers and never smokers.

METHODS: PubMed, Scopus, and Web of Science have been searched from 2010 up to August 27, 2025, using MeSH terms and free-text keywords related to e-cigs, vaping, oral microbiome, and microbial diversity. Eligible studies will include randomized controlled trials, cross-sectional, and longitudinal observational designs comparing e-cig users with current smokers and/or never smokers, and using culture-independent, next-generation sequencing techniques for microbiome profiling. Two reviewers will independently perform study selection, data extraction, and quality assessment using the Joanna Briggs Institute critical appraisal tools. Given expected heterogeneity, findings will be synthesized narratively and tabulated; subgroup analyses will examine differences according to oral health status, e-cig use patterns, and sampling site.

RESULTS: Database searching was completed on Aug 27, 2025, and identified 39 records in PubMed, 46 in Scopus, and 83 in Web of Science. Secondary searches, including gray literature screening and snowballing, have not yet been conducted. Screening and selection of retrieved articles are in progress, with review completion expected by November 2025.

DISCUSSION: This review is expected to provide a comprehensive and critical appraisal of the current evidence on the relationship between e-cig use and oral microbiome composition. By summarizing key microbial diversity patterns, identifying taxa-level differences, and highlighting methodological strengths and limitations, it will clarify the extent to which e-cig use may influence oral microbial communities. The anticipated heterogeneity in study designs, outcome measures, and sampling methods underscores the need for cautious interpretation and for standardization in future research. The findings aim to inform clinical understanding of potential local and systemic implications of e-cig use and to guide the design of robust, longitudinal studies with careful control of residual confounding.

PROSPERO registration: CRD420251120281.},
}

Humans
Systematic Reviews as Topic
*Microbiota
*Electronic Nicotine Delivery Systems
*Vaping/adverse effects
*Mouth/microbiology
Research Design

@article {pmid41131583,
year = {2025},
author = {Lou, Y and Lv, Y and Wang, X and Luo, Y and Lou, J and Yu, Y and Gu, W and Yu, J and Fang, Y and Zhao, H and Peng, K and Chen, J and Ni, Y},
title = {Ruminococcus torques ameliorates the inflammation bowel disease and gut barrier dysfunction by modulating gut microbiota and bile acid metabolism.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1162},
pmid = {41131583},
issn = {1479-5876},
support = {No. CCCF-QF-2022B04-4//the China Crohn's & Colitis Foundation/ ; 2024KY1171//Medical Science and Technology Project of Zhejiang Province/ ; 82170583//National Natural Science Foundation of China/ ; U23A20167//National Natural Science Foundation of China/ ; 82400595//National Natural Science Foundation of China/ ; 2025C02085//the Key R&D Program of Zhejiang/ ; 2021YFC2701900//the National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Animals ; Male ; *Bile Acids and Salts/metabolism ; *Inflammatory Bowel Diseases/microbiology ; *Ruminococcus/physiology ; *Intestinal Mucosa/pathology/microbiology ; Child ; Colitis/pathology/microbiology ; Mice ; Female ; Mice, Inbred C57BL ; Crohn Disease/microbiology ; Adolescent ; },
abstract = {BACKGROUND: Recent advances in microbiome-targeted therapies have uncovered immunomodulatory bacterial taxa with strain-specific therapeutic potential; however, the microbial signatures driving exclusive enteral nutrition (EEN) efficacy, particularly protective microbiota, and their mechanistic links to therapeutic outcomes remain uncharacterized in pediatric inflammatory bowel disease (IBD). Elucidating these microbial determinants and their functional pathways is critical for advancing targeted probiotic strategies in children.

METHODS: A cohort of treatment-naïve pediatric Crohn's disease (CD) patients and age-matched healthy controls (HC) were enrolled. Fecal samples were collected from both HC and CD patients during active phase and remission following EEN therapy. Metagenomic sequencing, qPCR validation, and targeted bile acid (BA) analysis were conducted to identify candidate protective strains and potential impacts on BA homeostasis. Mechanistic investigations were conducted using dextran sulfate sodium (DSS)- and trinitrobenzene sulfonic acid (TNBS)-induced colitis model in male mice.

RESULTS: The relative abundance of Ruminococcus torques (R. torques) demonstrated significant depletion in active CD cases (p = 0.02) compared to HC, which was restored after EEN treatment at remission status (p < 0.001). Its level was negatively correlated with the disease severity index (PCDAI r=-0.64; CDEIS r=-0.70) and positively correlated with the secondary to primary BA ratio (r = 0.27). In murine models, R. torques supplementation attenuated colitis severity through enhancing epithelial integrity (claudin-3, 3.3-fold; occludin, 7.5-fold), suppressing pro-inflammatory mediators (TNF-α, -44%; IL-6, -71%), regulating BA metabolism (secondary/unconjugated BAs, 29%) and autophagy pathway (LC3-II/LC3-I ratio, -1.8-fold).

CONCLUSIONS: Our findings demonstrated R. torques as a novel microbial therapeutic candidate for IBD management. The anti-colitis mechanisms involve the modulation of BA metabolic homeostasis, epithelial barrier reinforcement, and inflammation resolution.},
}

Humans
*Gastrointestinal Microbiome
Animals
Male
*Bile Acids and Salts/metabolism
*Inflammatory Bowel Diseases/microbiology
*Ruminococcus/physiology
*Intestinal Mucosa/pathology/microbiology
Child
Colitis/pathology/microbiology
Mice
Female
Mice, Inbred C57BL
Crohn Disease/microbiology
Adolescent

@article {pmid41131553,
year = {2025},
author = {Pan, Z and Chen, Y and Zhou, M and McAllister, TA and McNeilly, TN and Guan, LL},
title = {Host miRNAs regulate Escherichia coli O157 mucosal colonization through host-mucosa-attached microbiota interactions in calves.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {213},
pmid = {41131553},
issn = {2049-2618},
support = {FOS.07.17//Beef Cattle Research Council/ ; FOS.07.17//Beef Cattle Research Council/ ; FOS.07.17//Beef Cattle Research Council/ ; FOS.07.17//Beef Cattle Research Council/ ; FOS.07.17//Beef Cattle Research Council/ ; ALLRP 561309-2020, AOO 561309-2020//Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery, and NSERC Alliance program/ ; ALLRP 561309-2020, AOO 561309-2020//Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery, and NSERC Alliance program/ ; ALLRP 561309-2020, AOO 561309-2020//Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery, and NSERC Alliance program/ ; ALLRP 561309-2020, AOO 561309-2020//Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery, and NSERC Alliance program/ ; ALLRP 561309-2020, AOO 561309-2020//Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery, and NSERC Alliance program/ ; FS101055//UK Food Standards Agency/Food Standards Scotland/ ; },
mesh = {Animals ; Cattle ; *Escherichia coli O157/growth & development/pathogenicity/genetics ; *MicroRNAs/genetics/metabolism ; *Escherichia coli Infections/microbiology/veterinary/genetics ; *Intestinal Mucosa/microbiology ; *Microbiota ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Host Microbial Interactions ; Shiga Toxin 2/metabolism ; },
abstract = {INTRODUCTION: Host responses to pathogen colonization are central to understanding host homeostasis dynamics. Here, we used Shiga toxin (Stx)-producing Escherichia coli (STEC) O157 as an example to illustrate how pathogen colonization alters host-microbiome interactions and stimulates host responses. The STEC O157 is a critical foodborne pathogen, and cattle are the major asymptotic carrier with rectal anal junction (RAJ) being the major colonization site, leading to the transmission of this organism through the production chain. Therefore, this study leverages the multi-omics to evaluate host mechanisms to STEC O157 and to illustrate how mucosa-attached microbiome together with host miRNAs respond to the colonization of STEC O157.

RESULTS: The calf model was orally challenged with E. coli O157 with and without Stx2a during the 30-day trial. Mucosa-attached microbiome analysis revealed that mucosal E. coli O157 colonization limited niche occupancy of mucosa-attached microbiota regardless of the presence or absence of Stx2a. The production of Stx2a did not induce proper local host mRNA responses but miRNA profiles were more responsive to this virulent factor during high fecal shedding. The shift of toll-like receptor (TLR) expressions together with Stx2a production possibly underlined varied miRNAome-mucosa-attached microbiota interactions. For instance, during the high fecal shedding, the increased expression of TLR2 promoted bta-miR-181b mediated host functionality, a response that was possibly blocked by Stx2a. Decreased fecal O157 shedding promoted activation of TLR4-stimulated host responses, which were coregulated by multiple miRNAs (i.e. bta-miR-146a and-184) and mucosa-attached microbes.

CONCLUSION: Host mechanisms regulating STEC O157 colonization are complex interplay among mucosa-attached microbiota and host miRNAs where virulence factors could modulate such crosstalk and cause differential host responses, highlighting the importance of host-microbiome-pathogen virulence factor interactions for pathogen colonization process. Video Abstract.},
}

Animals
Cattle
*Escherichia coli O157/growth & development/pathogenicity/genetics
*MicroRNAs/genetics/metabolism
*Escherichia coli Infections/microbiology/veterinary/genetics
*Intestinal Mucosa/microbiology
*Microbiota
Feces/microbiology
*Gastrointestinal Microbiome
*Host Microbial Interactions
Shiga Toxin 2/metabolism

@article {pmid41131551,
year = {2025},
author = {Muhummed, AM and Lanker, KC and Yersin, S and Zinsstag, J and Vonaesch, P},
title = {One Health, One Microbiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {216},
pmid = {41131551},
issn = {2049-2618},
support = {2021//Swiss Government Excellence Scholarship ESKAS/ ; 2021//Swiss Government Excellence Scholarship ESKAS/ ; 7F-09057.01.02//Direktion für Entwicklung und Zusammenarbeit/ ; 7F-09057.01.02//Direktion für Entwicklung und Zusammenarbeit/ ; TMSGI3_218455//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
mesh = {Humans ; *Microbiota ; *One Health ; Animals ; *Bacteria/genetics/classification/drug effects ; Climate Change ; },
abstract = {One Health is a concept and framework for addressing the interconnected nature of humans, animals and their environments to improve the health and wellbeing of all three, along with added social and financial benefits. On a microscopic level, the microbiota is a clear biological connector with strains shared across domains (One Health Microbiome). In this review, we introduce the concept of One Health and the One Health Microbiome and discuss strain-sharing across and within domains. We also highlight its impact on the spread of antimicrobial resistance (AMR) genes as well as overall microbiome diversity and resilience to climate change. Finally, we discuss critical areas for further research and conceptual development, encouraging future research integrating One Health and microbiota-AMR concepts.},
}

Humans
*Microbiota
*One Health
Animals
*Bacteria/genetics/classification/drug effects
Climate Change

@article {pmid41131465,
year = {2025},
author = {Hamdene, I and Bez, C and Bertani, I and López-Menchero, JR and Yahyaoui, A and Venturi, V and Sadfi-Zouaoui, N},
title = {Endophytic bacterial communities associated with halophytic plants in kebili and Gabes regions of Southern Tunisia.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {683},
pmid = {41131465},
issn = {1471-2180},
mesh = {Tunisia ; *Salt-Tolerant Plants/microbiology ; *Endophytes/classification/isolation & purification/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Soil Microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology ; DNA, Bacterial/genetics ; Soil/chemistry ; *Microbiota ; Salinity ; Biodiversity ; Sequence Analysis, DNA ; Amaranthaceae/microbiology ; },
abstract = {In the arid regions of southern Tunisia, soil and irrigation water salinity represent major challenges to agricultural sustainability. Despite the increasing interest in plant-associated microbes, the role of endophytic bacteria in conferring salt tolerance remains largely unexplored in this context. To address this gap, twenty-two halophytic plants and their associated soils were sampled from five distinct sites across the Kebili and Gabes governorates. Significant differences in soil physicochemical properties were observed between sampling sites. The soils are generally poorly developed, non-fertile (with very low organic matter and high CaCO3 levels), and highly saline, leading to limited cultivation potential. Molecular identification of plants revealed nine different families and 14 genera, with the Amaranthaceae family being the most prominent, including Atriplex spp. (2), Bassia spp. (2), Suaeda spp. (4), and Halocnemum spp. (1). Bacterial community studies were conducted of both culturable and non-culturable endophyte communities inhabiting the green and root compartments of different halotolerant plants. Endophytic microbiome compositions differed between above-ground and below-ground tissues within the same plant family. A higher prevalence of three phyla Proteobacteria (67.80%), Firmicutes (14.06%), and Actinobacteria (6.57%) was detected across all samples. At the genus level, Acinetobacter, Halomonas, Kushneria, Pseudomonas, Psychrobacter, Stenotrophomonas, and Streptomyces formed the common core microbiome. Functional predictions of endophytic bacteria in halophytes highlighted multiple KEGG functional pathways, indicating recruitment of beneficial bacterial taxa to adapt to extreme hypersaline conditions, including plant growth-promoting, biocontrol, and halophilic bacteria.},
}

Tunisia
*Salt-Tolerant Plants/microbiology
*Endophytes/classification/isolation & purification/genetics
*Bacteria/classification/genetics/isolation & purification
*Soil Microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics
Plant Roots/microbiology
DNA, Bacterial/genetics
Soil/chemistry
*Microbiota
Salinity
Biodiversity
Sequence Analysis, DNA
Amaranthaceae/microbiology

@article {pmid41131131,
year = {2025},
author = {Corduneanu, A and Bendjeddou, ML and Sándor, AD and Mihalca, AD and Hornok, S and Péter, Á and Khelfaoui, F and Aželytè, J and Obregon, D and Mateos-Hernández, L and Maitre, A and Abuin-Denis, L and Wu-Chuang, A and Kratou, M and Ben Said, M and Cabezas-Cruz, A},
title = {Microbial network assembly in bat flies with differing host specificity from North Africa.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41131131},
issn = {1618-1905},
support = {14/2022-2024//Ministerul Cercetării şi Inovării/ ; 1500107//Hungarian Research Network/ ; NTP-NFTÖ-20-B-0094//Hungarian Ministry of Human Resources, Hungary/ ; SGCE - RAPPORT No 0300//Collectivité de Corse/ ; ANR-10-LABX-62-IBEID//Agence Nationale de la Recherche/ ; },
abstract = {The study investigates the microbial composition of bat flies (Diptera: Nycteribiidae) collected from Myotis punicus in Algeria, focusing on the diversity and dynamics of their microbiota through network analysis. The analysis targets two genera, Nycteribia and Penicillidia, comparing oioxenous and stenoxenous species to understand host specificity's influence on microbial communities. Utilizing 16S rRNA sequencing, alpha and beta diversity metrics, and co-occurrence networks, the study assesses microbial diversity, community composition, and the impact of specific bacteria (endosymbionts, commensals, and pathogens) on network stability. Results reveal significant microbial community variations between genera and species, with N. latreillii exhibiting the most complex network. We showed that host specificity and feeding strategies significantly influence microbial diversity and interactions within bat flies. Robustness analysis through node removal simulations identifies the roles of key bacteria, such as Wolbachia, Arsenophonus, and Bartonella, in maintaining network stability. Findings highlight the complex interplay between these microorganisms and their hosts, offering insights into microbial ecology and vector-pathogen dynamics. The research underscores the importance of bat flies in shaping pathogen transmission networks, contributing valuable knowledge to wildlife ecology, disease control, and conservation strategies.},
}

@article {pmid41131104,
year = {2025},
author = {Park, MA and Kim, YS and Jang, HJ and Cho, ES and Park, M and Park, S and Kim, DH and Hong, JK and Kim, Y},
title = {Maternal microbial effects and the dynamic distribution, networks, and functions of pig gut microbiota across the entire life cycle.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37092},
pmid = {41131104},
issn = {2045-2322},
support = {1711177233//Ministry of Science and ICT, Republic of Korea/ ; 1711177233//Ministry of Science and ICT, Republic of Korea/ ; 1711177233//Ministry of Science and ICT, Republic of Korea/ ; 1711177233//Ministry of Science and ICT, Republic of Korea/ ; 1711177233//Ministry of Science and ICT, Republic of Korea/ ; PJ017026022022//Rural Development Administration, Republic of Korea/ ; PJ017026022022//Rural Development Administration, Republic of Korea/ ; PJ017026022022//Rural Development Administration, Republic of Korea/ ; RS-2023-00234143//Ministry of Agriculture, Food and Rural Affairs, Republic of Korea/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Female ; Swine/microbiology ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Pregnancy ; },
abstract = {This study investigated the impact of sow microbiota and developmental stages on the gut microbiome of pigs throughout their life cycle. Fecal samples using rectal swab from 30 sows and 179 piglets were collected on days 5, 35, 80, and 145. A dynamic shift in the gut microbiota was observed as the pigs progressed through different growth stages. Maternal fecal microbiota influenced the piglets' microbiota, with higher transfer rates of Escherichia-Shigella, Bacteroides, and Fusobacterium. Notably, our findings revealed that not only Bacteroides, a genus essential for breast milk digestion, but also Escherichia-Shigella and Fusobacterium, previously regarded as and assumed to be of environmental origin, in fact originated from the sow. Correlation analysis between bacterial genera and metabolic functional pathways revealed that heme biosynthesis, crucial for pregnancy maintenance, was predicted to increase in postpartum sows and was significantly associated with the presence of Acinetobacter and Campylobacter. Furthermore, potentially beneficial genera such as Butyricicoccus, Parabacteroides, Ruminiclostridium, Ruminococcus, Blautia, Prevotella, Alloprevotella, and Eubacterium were significantly correlated with energy metabolism pathways in pigs during the growing period. This study emphasizes the importance of analyzing microbial functions and networks beyond abundance alone, highlighting the potential of computational microbiome analysis to guide swine health and productivity strategies.},
}

Animals
*Gastrointestinal Microbiome
Female
Swine/microbiology
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
Pregnancy

@article {pmid41131087,
year = {2025},
author = {Chafino, S and Tarancon-Diez, L and Hurtado-Gallego, J and Flores-Piñas, M and Alcolea, S and Olveira, A and Navarro, ML and Fernández-Arroyo, S and Viladés, C and Montes, ML and Vidal, F and Peraire, J and Rull, A and Sainz, T},
title = {Metabolomics for searching non-invasive biomarkers of metabolic dysfunction-associated steatotic liver disease in youth with vertical HIV.},
journal = {Communications medicine},
volume = {5},
number = {1},
pages = {433},
pmid = {41131087},
issn = {2730-664X},
support = {CP19/00146, PI20/00326, PI23/0080//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; CP23/00009//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; FI24/00034//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; CB21/13/00077//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; PI19/01337//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; PI23/0080, CB21/13/00020//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; 2021SGR01404//Government of Catalonia | Agència de Gestió d'Ajuts Universitaris i de Recerca (Agency for Management of University and Research Grants)/ ; },
abstract = {BACKGROUND: In adults living with HIV, non-invasive biomarkers have been described for the early identification of metabolic dysfunction-associated steatotic liver diseases (MASLD). However, this issue remains unexplored in children and young people with vertical HIV (YWVH), among whom MASLD prevalence is around 30%.

METHODS: To identify biomarkers associated with MASLD in YWVH under sustained viral suppression with antiretroviral therapy, we analysed plasma lipid species, plasma bile acid profile, and gut microbiome composition in a cross-sectional cohort of 10 YWVH with MASLD and 19 YWVH without clinical evidence of MASLD (control).

RESULTS: Here we show that YWVH with MASLD have significantly increased circulating levels of eight specific lipid molecules and one bile acid, ursodeoxycholic acid (UDCA). UDCA and two triglycerides (TG54:5 and TG56:7) are identified as key biomolecules with strong discriminatory potential. The regression model incorporating these markers, along with hepatic steatosis index (HSI) and triglycerides-glucose index (TyG), demonstrates the highest predictive accuracy for MASLD (AUC of 0.932). UDCA correlates positively with Blautia and Collinsella genus (p = 0.040 and p = 0.021, respectively), and negatively with Faecalibacterium (p = 0.030). Notably, principal component analysis based on bile acid levels reveals two possible subpopulations within the control group, one potentially at higher risk for MASLD.

CONCLUSIONS: Combining UDCA, TG54:5 and TG56:7 with the validated HSI score provides a potential model with high specificity and sensitivity for predicting MASLD in YWVH. Moreover, early alterations in the bile acid profile may help identify YWVH at risk of developing MASLD.},
}

@article {pmid41131086,
year = {2025},
author = {Sharma, BM and Mohapatra, M and Kumar, R and Swain, PP and Das, II and Sahoo, L and Vasam, M and Bag, D and Debbarma, J and Jaiswal, S and Iquebal, MA and Angadi, UB and Rai, A and Kumar, D and Sundaray, JK},
title = {Comprehensive insight into gut microbiota and their interaction with fatty acid profiles in Channa striata during the spawning season.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37065},
pmid = {41131086},
issn = {2045-2322},
support = {Code: 1006449//Centre for Agricultural Bioinformatics (CABin) Project/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Female ; *Fatty Acids/metabolism ; Male ; RNA, Ribosomal, 16S/genetics ; Seasons ; *Perciformes/microbiology/physiology/metabolism ; Bacteria/genetics/classification ; Reproduction ; },
abstract = {Striped murrel (Channa striata) is renowned for its nutritional benefits, such as antimicrobial, antioxidant, anti-obesity, and anti-inflammatory properties, attributed to its rich content of short-chain and polyunsaturated fatty acids (SCFAs and PUFAs). Unlike many food fish, it successfully breeds in captivity, adding to its value. Despite its nutritional significance, specific composition of its gut microbiota and its influence on fatty acid (FA) profiles remain underexplored. This study investigated sex-specific differences in gut bacterial communities and their association with FA profiles across two rearing conditions: fish maintained in water tanks (T1) and those reared in pond-simulated habitats (T2). Gut tissue samples underwent high-throughput 16S rRNA gene amplicon sequencing (V3-V4 region) and muscle tissue samples were analyzed for FA profiling. Significant variations were observed across habitat and sex. Habitat influenced FA and microbiota composition, with females from T2 showed higher palmitic (44.32%) and linoleic acids (12.01%), while T1 females had greater oleic acid (32.32%). Pseudoalteromonadaceae (Pseudoalteromonas) and Salmonella enterica were enriched in T1 than in T2. Females exhibited distinct FA profiles dominated by palmitic, oleic, and linoleic acids and sequencing results showed greater species richness and shannon diversity in their gut microbiota, with a higher abundance of Alphaproteobacteria. Males, by contrast, had higher levels of Clostridia and Fusobacteriia. Functional predictions revealed that females exhibited higher enrichment in energy metabolism, lipid biosynthesis, and xenobiotic biodegradation, while males showed greater enrichment in nucleotide and amino acid metabolism. Key microbial taxa such as Methylobacterium organophilum, Pseudomonas stutzeri and Faecalibacterium prausnitzii contributed to PUFA synthesis and antioxidant production. Co-occurrence networks in female displayed stronger interactions and connectivity compared to male. Notably, Cetobacterium somerae, Clostridium perfringens, and M. organophilum were key taxa in females, while Propionibacterium acnes, M. organophilum, and Plesiomonas shigelloides were prominent in males. Overall, the findings highlight sex- and habitat-specific gut microbiome dynamics that shape the FA composition of C. striata, offering insights for aquaculture improvement and nutritional optimization.},
}

Animals
*Gastrointestinal Microbiome
Female
*Fatty Acids/metabolism
Male
RNA, Ribosomal, 16S/genetics
Seasons
*Perciformes/microbiology/physiology/metabolism
Bacteria/genetics/classification
Reproduction

@article {pmid41131078,
year = {2025},
author = {Chen, R and Guo, X and Wu, M and Zheng, T and Chen, S and He, B},
title = {Bacillus velezensis ES2-4 modulates root exudation and microbiome remodeling to enhance soybean resistance against gray mold.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37098},
pmid = {41131078},
issn = {2045-2322},
support = {32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; },
mesh = {*Bacillus/physiology ; *Glycine max/microbiology/metabolism/immunology ; *Plant Roots/microbiology/metabolism ; *Botrytis/pathogenicity ; *Microbiota ; *Plant Diseases/microbiology/prevention & control ; Rhizosphere ; *Disease Resistance ; Soil Microbiology ; },
abstract = {Gray mold, caused by Botrytis cinerea, represents a significant threat to soybean productivity, while conventional chemical control strategies raise concerns regarding long-term sustainability. Plant-associated beneficial microbes, such as Bacillus velezensis, have been proposed as environmentally sustainable alternatives; however, their specific roles in modulating root-microbe interactions remain insufficiently characterized. This study investigated the mechanisms by which B. velezensis ES2-4 enhances soybean resistance by modulating root exudate composition and restructuring rhizosphere microbial communities. Metabolomic and metagenomic analyses indicated that ES2-4 inoculation led to the upregulation of antifungal metabolites (e.g., oxalic acid, eicosane) in root exudates, which facilitated the recruitment of beneficial bacteria while inhibiting B. cinerea proliferation. Pathogen infection was associated with disruptions in rhizosphere microbial diversity; however, ES2-4 application restored bacterial richness, particularly within the Alphaproteobacteria and Streptomyces lineages, while reducing the relative abundance of fungal pathogens. Co-occurrence network analysis further demonstrated that ES2-4 inoculation promoted microbial interactions associated with stress-responsive pathways, including two-component signaling systems and fatty acid metabolism, while downregulating pathogen-associated metabolic functions. These findings elucidate a dual mechanism through which ES2-4 enhances plant immunity via metabolite-mediated microbiome modulation, highlighting its potential as a sustainable biocontrol agent against soybean gray mold.},
}

*Bacillus/physiology
*Glycine max/microbiology/metabolism/immunology
*Plant Roots/microbiology/metabolism
*Botrytis/pathogenicity
*Microbiota
*Plant Diseases/microbiology/prevention & control
Rhizosphere
*Disease Resistance
Soil Microbiology

@article {pmid41130938,
year = {2025},
author = {Li, L and Simopoulos, CMA and Mayne, J and Ning, Z and Zhang, X and Hamada, M and Butcher, J and Serrana, JM and Wang, L and Cheng, K and Qin, H and Walker, K and Zhang, X and Stintzi, A and Figeys, D},
title = {Systematic metaproteomics mapping reveals functional and ecological landscapes of Ex vivo human gut microbiota responses to therapeutic drugs.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9383},
pmid = {41130938},
issn = {2041-1723},
support = {32370050//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Humans ; *Proteomics/methods ; Bacteria/drug effects/metabolism/genetics/classification ; *Proteome/metabolism/drug effects ; Bacterial Proteins/metabolism ; },
abstract = {Therapeutic compounds exert impacts on gut microbiota; however, how they affect the community functional ecology, especially as reflected at the protein level, remains largely unexplored. In this study, we systematically map metaproteomic responses of ex vivo human gut microbiota to 312 compounds, generating 4.6 million microbial protein responses, available as an interactive resource (https://shiny.imetalab.ca/MPR_Viz/). Protein-level analyses identify significant metaproteomic shifts induced by 47 compounds, with neuropharmaceuticals as the sole drug class significantly enriched among these hits. Further analyses on the community level reveal a tri-stability pattern in microbial composition and the emergence of three distinct functional states, based on a functional beta-diversity metric. Notably, neuropharmaceuticals cause particularly strong effects on the microbiomes, lowering the proteome-level functional redundancy and raising the level of antimicrobial resistance proteins, ultimately pushing the microbiome into an alternative functional state. Preliminary validation suggests that enhancing functional redundancy may contribute to maintaining microbiota resilience against neuropharmaceutical-induced antimicrobial resistance. Overall, this work establishes a comprehensive view of how drugs influence gut microbiome function and ecology at the protein level, proposes a landscape-based framework for interpreting community resilience, and highlights the need to consider protein-level and ecological responses in the evaluation of therapeutic interventions.},
}

*Gastrointestinal Microbiome/drug effects/genetics
Humans
*Proteomics/methods
Bacteria/drug effects/metabolism/genetics/classification
*Proteome/metabolism/drug effects
Bacterial Proteins/metabolism

@article {pmid41130921,
year = {2025},
author = {Obregon, D and Maitre, A and Piloto-Sardiñas, E and Wu-Chuang, A and Abuin-Denis, L and Cano-Argüelles, AL and Aželytė, J and Corona-Guerrero, I and Mateos-Hernández, L and Kratou, M and Skičková, Š and Svobodová, K and Cabezas-Cruz, A},
title = {Decoding Microbial Community Assembly: Insights on Vectors of Infectious Diseases.},
journal = {Annual review of microbiology},
volume = {79},
number = {1},
pages = {547-572},
doi = {10.1146/annurev-micro-082024-094943},
pmid = {41130921},
issn = {1545-3251},
mesh = {*Microbiota ; Animals ; Humans ; *Vector Borne Diseases/microbiology/transmission/prevention & control ; Bacteria/classification/genetics/isolation & purification ; *Disease Vectors ; *Communicable Diseases/transmission/microbiology ; Ticks/microbiology ; },
abstract = {Vector-borne diseases (VBDs), which are caused by pathogens transmitted by vectors such as mosquitoes and ticks, account for more than 17% of infectious diseases and more than 700,000 deaths annually. The complexity of VBDs arises from ecological interactions among hosts, vectors, pathogens, and the environment, with vector microbiota playing a pivotal role in the modulation of vector competence. Advances in sequencing and in microbiome analysis have deepened our understanding of microbial community assembly within vectors and revealed opportunities for novel control strategies. Network analysis has become essential for uncovering microbial interactions and identifying keystone species that affect community stability and pathogen transmission. Despite progress, key challenges remain in deciphering the drivers of vector microbiota assembly. This review highlights factors shaping microbiota assembly, the potential of network analysis, and promising interventions such as antimicrobiota vaccines and paratransgenesis to reduce pathogen transmission. Future research should focus on standardizing methodologies and leveraging emerging technologies for effective and sustainable VBD control.},
}

*Microbiota
Animals
Humans
*Vector Borne Diseases/microbiology/transmission/prevention & control
Bacteria/classification/genetics/isolation & purification
*Disease Vectors
*Communicable Diseases/transmission/microbiology
Ticks/microbiology

@article {pmid41130916,
year = {2025},
author = {Wadsworth, CB and Goytia, M and Shafer, WM},
title = {Commensal Neisseria and Antimicrobial-Resistant Gonorrhea.},
journal = {Annual review of microbiology},
volume = {79},
number = {1},
pages = {215-240},
doi = {10.1146/annurev-micro-022024-024306},
pmid = {41130916},
issn = {1545-3251},
mesh = {*Gonorrhea/microbiology/drug therapy ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Gene Transfer, Horizontal ; *Neisseria gonorrhoeae/genetics/drug effects/physiology ; *Drug Resistance, Bacterial ; *Neisseria/genetics/drug effects/physiology ; Symbiosis ; },
abstract = {Alongside the crisis of antimicrobial-resistant gonorrhea is the threat of bystander selection on commensal Neisseria. As Neisseria species are permissive to gene flow across lineages, their evolutionary fates are irrevocably intertwined. Horizontal gene transfer (HGT) within the genus occurs through transformation and exchange of plasmids through conjugation. Both mechanisms of HGT threaten the long-term efficacy of antimicrobial treatments, with resistance passed between commensals and pathogens multiple times (e.g., mosaic penA and mtr alleles). Here, we underscore the importance of commensal Neisseria as a bubbling cauldron of adaptive solutions for pathogenic Neisseria, review the mechanisms of resistance harbored by commensals and transferred to the gonococcus, and discuss the impact of contemporary selective pressures on the future evolutionary trajectory of the genus. Ultimately, we believe that predicting the future efficacy of antimicrobials for the treatment of gonorrhea will only be successful if the commensal Neisseria are also considered.},
}

*Gonorrhea/microbiology/drug therapy
Humans
*Anti-Bacterial Agents/pharmacology/therapeutic use
Gene Transfer, Horizontal
*Neisseria gonorrhoeae/genetics/drug effects/physiology
*Drug Resistance, Bacterial
*Neisseria/genetics/drug effects/physiology
Symbiosis

@article {pmid41130888,
year = {2025},
author = {Shan, S},
title = {Unraveling microbiome integration in soil transplant.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.10.005},
pmid = {41130888},
issn = {1878-4380},
abstract = {Little is known about the processes that drive microbial community merging and development in transplanted soils. A recent study by Causevic et al. disentangled the relative contribution of habitat filtering and microbiota taxa origin in shaping transplant outcomes, providing valuable insights for advancing microbial engineering.},
}

@article {pmid41130610,
year = {2025},
author = {Karim, DM and Papp, M and Fehérvári, P and Turan, C and Hegyi, P and Molnar, Z and Madách, K},
title = {No difference in microbial diversity between bronchoalveolar lavage and tracheal sampling: a systematic review and meta-analysis.},
journal = {BMJ open respiratory research},
volume = {12},
number = {1},
pages = {},
doi = {10.1136/bmjresp-2025-003456},
pmid = {41130610},
issn = {2052-4439},
mesh = {Humans ; *Trachea/microbiology ; *Microbiota ; *Bronchoalveolar Lavage Fluid/microbiology ; *Bronchoalveolar Lavage/methods ; *Specimen Handling/methods ; },
abstract = {INTRODUCTION: The respiratory microbiome has a vital role in maintaining respiratory health and preventing pathogen colonisation, but traditional diagnostic methods fail to capture a complete picture of it. Metagenomic sequencing has improved our understanding of microbial ecosystems in both acute and chronic pathologies. However, its results have not been systematically compared between different respiratory sampling techniques, as has been done with traditional methods. Our study aims to compare the microbial diversity in bronchoalveolar lavage (BAL) and tracheal samples using microbiome sequencing.

METHODS: A systematic search was conducted in Medline, Embase and CENTRAL databases to identify studies where lower respiratory tract microbiome specimens were collected simultaneously using BAL and tracheal sampling and diversity was analysed postsequencing. Risk of bias was assessed with our specifically tailored tool. A random-effects model was used for data synthesis, analysing pooled Shannon, Chao1 and Simpson indices.

RESULTS: We screened 1050 potentially relevant publications, 10 of which were included. No significant difference was found in microbial alpha diversity between BAL and tracheal samples. The subgroup analysis of tracheal sample types, including sputum and endotracheal aspirate, revealed no significant differences compared with BAL.

CONCLUSIONS: Tracheal sampling methods offer a viable and less invasive alternative to BAL for characterising microbiome alpha diversity in clinical or research settings where segmental sampling is not required. However, further high-quality comparative studies are needed to confirm these findings.

PROSPERO REGISTRATION NUMBER: CRD42023436934.},
}

Humans
*Trachea/microbiology
*Microbiota
*Bronchoalveolar Lavage Fluid/microbiology
*Bronchoalveolar Lavage/methods
*Specimen Handling/methods

@article {pmid41130540,
year = {2025},
author = {Li, J and Yue, Y and Pan, J and Liang, F},
title = {Research progress on gut microbiota in colorectal cancer immunotherapy.},
journal = {Biochimica et biophysica acta. Reviews on cancer},
volume = {},
number = {},
pages = {189476},
doi = {10.1016/j.bbcan.2025.189476},
pmid = {41130540},
issn = {1879-2561},
abstract = {Immune checkpoint inhibitors (ICIs) have demonstrated significant clinical benefits in treating various malignancies. However, their therapeutic efficacy exhibits considerable interindividual variability in patients with colorectal cancer (CRC). In recent years, growing attention has been focused on the regulatory role of the gut microbiota and its metabolic microenvironment in modulating ICIs responses. This article systematically reviews key advances in understanding how the gut microbiota and its metabolites influence ICIs efficacy. For example: Specific bacterial species (e.g., Lactobacillus paracasei and Fusobacterium nucleatum) may regulate ICIs efficacy by modulating antigen presentation or the tumor immune microenvironment. Microbial metabolites, such as short-chain fatty acids (SCFAs), can enhance immune function and thereby improve ICIs outcomes. Potential microbiome-targeted interventions-including probiotic/prebiotic combinations, optimized antibiotic administration timing, refined fecal microbiota transplantation (FMT) protocols, and engineered synthetic biology-based bacterial therapies-are also discussed. By synthesizing current evidence, this review provides a theoretical foundation for developing novel personalized immunotherapy strategies for CRC, with a focus on microbiome modulation to optimize ICIs treatment efficacy.},
}

@article {pmid41130404,
year = {2025},
author = {Li, Y and Lv, Y and Song, M and Zhang, Z and Ni, M and Gong, X and Luo, J and Li, C},
title = {Characterization of chilled spoilage in pasteurized goat milk using an integrated microbiome-metabolomics analysis.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27202},
pmid = {41130404},
issn = {1525-3198},
abstract = {Pasteurized goat milk is mainly spoiled through the activity of various microorganisms. Microorganisms with protein-hydrolyzing and lipid-degrading activities can act on proteins and lipids, ultimately resulting in the release of undesired metabolites. Characterizing the corresponding microbiota and metabolite profiles and clarifying their relationships will enhance our understanding of the mechanisms underlying the spoilage of pasteurized goat milk during chilled storage. In this study, 16S rRNA sequencing was employed for microbiome profiling, and ultra-performance liquid chromatography and tandem mass spectrometry was used for metabolome profiling. Weighted gene correlation network analysis and Spearman's correlation analysis were both used to investigate correlations between the microbiomes and metabolomes of pasteurized goat milk samples. The results showed significant changes in microbial diversity throughout the spoilage process. The Proteobacteria phylum and Pseudomonas genus were identified as dominant microorganisms involved in the spoilage process. Bacteria may contribute to spoilage through metabolic pathways such as glycerophospholipid metabolism and purine metabolism. In addition, significant correlations were observed between key bacteria taxa and important metabolites. Stenotrophomonas was identified as the primary spoilage bacterium, the relative abundance of which increased significantly (by 3.84%) during chilled storage, and it may serve as a biomarker for goat milk spoilage. Taking all this information into consideration, the present study proposes an integrated microbiome and metabolomics approach to investigate the spoilage mechanisms of pasteurized goat milk caused by microbial activity. These findings provide comprehensive insights into the microbial and metabolic profiles associated with spoilage during chilled storage. Our study can assist the dairy industry in understanding issues that may arise during the preservation of goat milk, thereby enhancing product quality and shelf life.},
}

@article {pmid41130390,
year = {2025},
author = {van Gastelen, S and Dijkstra, J and Alferink, SJJ and Binnendijk, G and Klop, A and Loren van Themaat, EV and Walker, N and Bannink, A},
title = {Investigating interactions between grass silage- or corn silage-based diets and 3-nitrooxypropanol on fermentation and methane emission dynamics and rumen microbiome in dairy cattle.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-26957},
pmid = {41130390},
issn = {1525-3198},
abstract = {The objective of this study was to investigate mechanisms underlying the relationship between basal diet (BD) composition (grass silage- vs. corn silage-based) and 3-nitrooxypropanol (3-NOP) supplementation, focusing on the rumen microbiome, and gaseous emission and ruminal fermentation dynamics. Eight rumen-fistulated, multiparous Holstein-Friesian dairy cows producing 29.3 ± 8.17 kg/d of milk at 159 ± 82.8 DIM (mean ± SD) at the beginning of the experiment were blocked according to parity, DIM, and milk production, and randomly assigned to a double 4 × 4 Latin square design with 4 treatments. The 4 dietary treatments were arranged according to a 2 × 2 factorial design, with 2 BD and 2 dosages of 3-NOP. The grass silage-based diet (GS) consisted of 33.5% concentrate and 66.5% grass silage, whereas the corn silage-based diet (CS) consisted of 33.1% concentrate, 12.7% grass silage, and 54.2% corn silage (all on DM basis). Both BD were supplemented with either 0 or 80 mg 3-NOP/kg DM. Treatment periods lasted 17 d and consisted of a 14-d adaptation period in a freestall barn followed by a 3-d measurement period in climate respiration chambers. No significant interaction between BD and 3-NOP on CH4 emission was observed, although numerically CH4 emissions were more strongly reduced, and H2 emissions more strongly increased, upon 3-NOP supplementation with the CS diet (-25.9% for CH4 yield [g/kg DMI], -26.9% for CH4 intensity [g/kg ECM], +9.2-fold for H2 yield [g/kg DMI], and + 8.9-fold for H2 intensity [g/kg ECM]) compared with the GS diet (-12.9% for CH4 yield [g/kg DMI], -14.8% for CH4 intensity [g/kg ECM], 6.9-fold for H2 yield [g/kg DMI], and 6.7-fold for H2 intensity [g/kg ECM]). An interaction between BD and 3-NOP was observed for the apparent total-tract digestibility (ATTD) of DM, OM, and gross energy (GE), which were lower for CS compared with GS, but only with 0 mg 3-NOP/kg DM. The ATTD of CP was greater for CS compared with GS, but only with 80 mg 3-NOP/kg DM. Replacing grass silage with corn silage increased DMI and milk protein content, whereas milk fat content decreased, and milk production remained unaffected, resulting in a lower feed efficiency. No effect of BD on ruminal pH, ruminal VFA (except for molar proportion of isobutyrate), or CH4 emissions was observed. Although DMI decreased, none of the lactation characteristics were affected by 3-NOP. Methane yield and intensity decreased by 18.4% and 19.4%, respectively, and H2 yield and intensity increased by 7.6-fold and 7.8-fold, respectively, with 3-NOP. A shift in ruminal VFA was observed from acetate to propionate and butyrate. In line with this shift, 3-NOP decreased methanogenesis and the relative abundance of methanogens, whereas the Wood-Ljungdahl pathway increased, suggesting enhanced acetogenesis.},
}

@article {pmid41130385,
year = {2025},
author = {Rajczewski, AT and Mehta, S and Wagner, R and Gabriel, W and Johnson, J and Do, K and Vintila, S and Wilhelm, M and Kleiner, M and Searle, BC and Griffin, TJ and Jagtap, PD},
title = {Comparative performance of scribe and database search engines in metaproteomic profiling of a ground-truth microbiome dataset.},
journal = {Journal of proteomics},
volume = {},
number = {},
pages = {105549},
doi = {10.1016/j.jprot.2025.105549},
pmid = {41130385},
issn = {1876-7737},
abstract = {Mass spectrometry-based metaproteomics, the identification and quantification of thousands of proteins expressed by complex microbial communities, has become pivotal for unraveling functional interactions within microbiomes. However, metaproteomics data analysis encounters many challenges, including the search of tandem mass spectra against a protein sequence database using proteomics database search algorithms. We used a ground-truth dataset to assess a spectral library searching method against established database searching approaches. Mass spectrometry data collected by data-dependent acquisition (DDA-MS) was analyzed using database searching approaches (MaxQuant and FragPipe), as well as using Scribe with Prosit predicted spectral libraries. We used FASTA databases that included protein sequences from microbial species present in the ground-truth dataset along with background protein sequences, to estimate error rates and assess the effects on detection, peptide-spectral match quality, and quantification. Using the Scribe search engine resulted in more proteins detected at a 1 % false discovery rate (FDR) compared to MaxQuant or FragPipe, while FragPipe detected more peptides verified by PepQuery. Scribe was able to detect more low-abundance proteins in the microbiome dataset and was more accurate in quantifying the microbial community composition. This research provides insights and guidance for metaproteomics researchers aiming to optimize results in their analysis of DDA-MS data. SIGNIFICANCE OF THE STUDY: Metaproteomics requires a balance between high numbers of peptide and protein identification and confidence in the accuracy of the identifications made. We demonstrate the utility of the Scribe search engine for metaproteomics applications, as it was found to detect low-abundance proteins with accurate quantitation than other DDA-MS search engines. This tool has great utility for both novel metaproteomics studies as well as hypothesis-generating experiments using previously acquired open source proteomics raw data.},
}

@article {pmid41130218,
year = {2025},
author = {Coulibaly, B and Yan, D and Sié, A and Dramane, K and Bountogo, M and Clarisse, D and Lucienne, O and Yago-Wienne, F and Touré, D and Dimithé, G and Khassanov, R and Sidibé, S and Somé, NP and Zhong, L and Chen, C and Yu, D and Liu, Y and Abraham, T and Peterson, B and Hinterwirth, A and Arnold, BF and O'Brien, K and Oldenburg, CE and Lebas, E and Lietman, TM and Doan, T},
title = {Effect of Biannual Azithromycin Distribution to Infants on Community Gut Resistome and Microbiome: A Cluster-Randomized, Controlled Trial.},
journal = {The American journal of tropical medicine and hygiene},
volume = {},
number = {},
pages = {},
doi = {10.4269/ajtmh.25-0238},
pmid = {41130218},
issn = {1476-1645},
abstract = {Biannual azithromycin administration to preschool children in sub-Saharan Africa improved childhood mortality but selected for antibiotic resistance (AMR). WHO guidelines recommended focusing treatment on infants ages 1-11 months old to reduce mortality while minimizing selection of AMR. The Infant Mortality Reduction by the Mass Administration of Azithromycin study was a double-masked, placebo-controlled, cluster-randomized trial that investigated these WHO guidelines. Health centers from three regions of Burkina Faso were randomized in a 2:1 ratio to receive either biannual azithromycin (67%) or placebo (33%) distribution to children 1-11 months old. A total of 3,524 rectal samples from children ages 1-59 months old from 60 randomly selected communities were included in the analysis. The prespecified primary outcome was the community-level fold change in macrolide resistance determinants between arms at the 24-month time point. Macrolide resistance determinants in the gut of children in communities whose infants received azithromycin did not increase compared with those in communities treated with placebo (1.05-fold change). Similarly, the fold changes for resistance determinants for beta-lactams, metronidazole, sulfonamides, tetracycline, and trimethoprim were 0.99-fold, 1.00-fold, 1.22-fold, 0.96-fold, and 0.96-fold, respectively. At 6 months after the fourth treatment, there were no detectable differences in the microbiome structure (Euclidean permutational multivariate analysis of variance) and Shannon diversity index between treatment arms. These results suggest that biannual azithromycin administration to children 1-11 months old did not lead to a significant long-lasting increase in gut AMR or alterations of the gut microbiomes of children 1-59 months old in the community.},
}

@article {pmid41130083,
year = {2025},
author = {Tripathy, B and Singh, S and Behera, ID and Mishra, S and Das, AP},
title = {Metagenomic profiling of diversified marine microbiome across microplastic-contaminated niches of Bay of Bengal, India.},
journal = {Marine pollution bulletin},
volume = {222},
number = {Pt 3},
pages = {118872},
doi = {10.1016/j.marpolbul.2025.118872},
pmid = {41130083},
issn = {1879-3363},
abstract = {Diverse microorganisms in the marine sediment share a significant section of the global marine ecosystem and play a dominant role in marine biogeochemistry. The present study is the first to report an evaluation of shotgun metagenomic sequencing of microplastic-contaminated marine water and sediment samples from the coastal shores of the Bay of Bengal, India, across a stretch of 25 km, which houses a plethora of ubiquitous and uncultured microbial biodiversity coexisting with multitudinous human interventions. Illumina Nova sequencing 6000 suggested the presence of 88,539 scaffolds of data containing 132,568 identified genes of marine microorganisms. Taxonomic identification with the assistance of curated global databases ensued in the presence of Proteobacteria (53.12 %), Bacteroidetes (7.13 %), Actinobacteria (5.87 %), and miscellaneous (33.86 %) in abundance. Azonexus hydrophillus, Mycobacteroides abscessus, and Acidaminobacter hydrogenoformans were identified in profusion from the sequenced samples of the study area. The adaptation, sustenance, and survivability in the presence of plastic pollutants confirm the presence of microplastic-degrading enzymes in the microorganisms. The functional annotations revealed 54.32 % and 58.34 % similarities in genes with KEGG and COG databases, revealing the heavy presence of inorganic and amino acid transport channels. Further metabolic profiling of the identified novel microorganisms will assist in engineering the enhancement of microbial enzymes, such as cutinases, lipases, and esterases, leading to microplastic degradation activity. The present research work signifies the analysis and documentation of native microbiota of the marine shores of the Bay of Bengal and their interactive potentialities with microplastic-contaminated anthropogenic environments.},
}

@article {pmid41130025,
year = {2025},
author = {Elliott, BB and Vazquez, X and Ross, SA and McNeill, EM},
title = {Diet, nutrition, and healthy aging: Are miRNAs the link? A narrative review.},
journal = {The journal of nutrition, health & aging},
volume = {29},
number = {12},
pages = {100712},
doi = {10.1016/j.jnha.2025.100712},
pmid = {41130025},
issn = {1760-4788},
abstract = {MicroRNAs are a class of small, single-stranded, noncoding RNA molecules that regulate gene expression at the post-transcriptional level. Cellular and circulating microRNA expression alterations have been observed in non-pathological aging and age-related diseases. microRNAs have been proposed to regulate aging signaling pathways, including cell death and senescence, oxidative stress, DNA damage, nutrient-sensing, and other metabolic processes. MicroRNAs may provide a molecular mechanism whereby diet can regulate gene expression, affecting aging phenotypes and lifespan. Herein, we review the recent evidence for diet in modulating the expression of microRNAs to influence the aging process. Current challenges and approaches to studying microRNAs and their function in the context of diet and aging research are highlighted in this review. Diet-mediated regulation of microRNA in aging is an emerging area of study, and future research incorporating functional analyses of dietary-responsive microRNAs will be necessary to clarify their actions in the aging process.},
}

@article {pmid41130000,
year = {2025},
author = {Jin, G and Wang, M and Wang, X and Yuan, S and Peng, A and Chen, Z},
title = {Effects of sub-inhibitory antibiotic exposure on elemental cycling genes in an aquatic microbial community.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140201},
doi = {10.1016/j.jhazmat.2025.140201},
pmid = {41130000},
issn = {1873-3336},
abstract = {Understanding how low concentrations of antibiotics influence biogeochemical cycling mediated by aquatic microbes is essential for assessing the ecological risks of antibiotic pollution. Here we examined the responses of carbon, nitrogen, and sulfur cycling genes in an aquatic microbial community to trimethoprim, lincomycin, and their combined exposure across seven sub-inhibitory concentrations spanning three orders of magnitude. We found that while the diversity of elemental cycling genes remained largely unchanged, the abundance of associated metabolic pathways declined significantly under high antibiotic levels,particularly after seven days of exposure to 10 mg/L lincomycin or ≥ 1 mg/L trimethoprim-lincomycin combinations. Some elemental cycling genes increased in abundance under elevated antibiotic exposure, accompanied by concentration-dependent enrichment of antibiotic resistance genes (ARGs). Metagenomic assembly further revealed that enriched ARGs and cycling genes co-localized on the same contigs. In addition, antibiotic exposure reshaped the topological structure of molecular ecological networks among cycling genes, indicating altered microbial interactions and ecological processes. Together, these findings show that antibiotics not only enrich resistance determinants but also modulate the abundance of carbon, nitrogen, and sulfur cycling genes, underscoring the complex impacts of anthropogenic antibiotic pollution on microbially mediated biogeochemical cycles.},
}

@article {pmid41129937,
year = {2025},
author = {Yusuf, SA and Fetarayani, D and Vidyani, A and Sutanto, H},
title = {Food-driven inflammation in inflammatory bowel disease: Dietary instigators and emerging nutritional strategies.},
journal = {Semergen},
volume = {51},
number = {9},
pages = {102599},
doi = {10.1016/j.semerg.2025.102599},
pmid = {41129937},
issn = {1578-8865},
abstract = {Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is influenced not only by genetics and immunity but also profoundly by dietary factors. Emerging research identifies specific food components - such as ultra-processed foods, high-fat diets, and red meats - as potent exacerbators of intestinal inflammation through mechanisms involving dysbiosis, immune activation, and gut barrier disruption. Conversely, fiber-rich, fermented, and certain dairy products may confer protective effects by enhancing microbiota diversity and mucosal integrity. Patient-specific factors like lactose or gluten sensitivity further modulate dietary responses. Personalized nutrition strategies, including elimination diets and microbiome-informed interventions, are gaining traction as adjunct therapies. Novel approaches such as ketogenic diets and intermittent fasting are under investigation, with mixed outcomes. Despite growing evidence, clinical dietary guidelines remain fragmented. This review synthesizes mechanistic and clinical data on diet-induced modulation of inflammation in IBD, highlighting the need for personalized, evidence-based nutritional strategies to improve disease outcomes and patient quality of life.},
}

@article {pmid41129320,
year = {2025},
author = {Thoms, D and Chen, MY and Liu, Y and Fulton, L and Luo, Y and Hiott, DE and Song, S and Morales Moreira, Z and Wang, NR and Zorio, D and Rejzek, M and Potter, R and Carella, P and Haney, CH},
title = {A bacterial exotoxin-triggered plant immune response restricts pathogen growth.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116457},
doi = {10.1016/j.celrep.2025.116457},
pmid = {41129320},
issn = {2211-1247},
abstract = {For optimal growth and development, hosts must promote healthy symbiotic interactions while restricting pathogens. To ask whether hosts can distinguish phylogenetically similar pathogens and beneficial bacteria, we used two closely related plant root-associated strains within the Pseudomonas fluorescens species complex. Despite having similar immunogenic microbe-associated molecular patterns, one strain is beneficial and the other exhibits exotoxin-dependent virulence. We show that the two strains co-exist in vitro, but the beneficial strain outcompetes the pathogen in the rhizosphere. We find that plants respond to the pathogen, but not the beneficial strain, predominantly via an exotoxin-triggered defense response in roots. The purified exotoxin is sufficient to induce immunity and restrict bacterial growth in a BAK1/BKK1/CERK1-dependent manner. We show that these immune components are also required for balancing the growth between the beneficial and pathogenic strains. We conclude that plant immunity can distinguish phylogenetically similar microbes with distinct lifestyles, in part, through perception of exotoxins.},
}

@article {pmid41129263,
year = {2025},
author = {Comba, IY and Louwies, T and Mars, RA and Xiao, Y and Sekhon, PK and Edwards, BS and Willits, A and Shields-Cutler, RR and Bellampalli, S and Mercado-Perez, A and Tienter, DR and Till, LM and Linden, DR and Farrugia, G and Beyder, A and Smith-Edwards, KM and Kashyap, PC},
title = {Distinct human small intestinal microbiome communities underlie visceral hypersensitivity in a humanized mouse model.},
journal = {The Journal of clinical investigation},
volume = {},
number = {},
pages = {},
doi = {10.1172/JCI190638},
pmid = {41129263},
issn = {1558-8238},
}

@article {pmid41129028,
year = {2025},
author = {Zhang, B and Wang, S and Li, X and Wang, J and Fang, C and Zhang, J and Su, J},
title = {The effects of the previous host on the adaptability of Tetranychus turkestani on soybean and its microbiome.},
journal = {Experimental & applied acarology},
volume = {95},
number = {4},
pages = {52},
pmid = {41129028},
issn = {1572-9702},
support = {2024B02003//Key Research and Development Project of the Xinjiang/ ; 2022B02043//Key Research and Development Project of Autonomous Region/ ; 2022ZD053//Guiding Science and Technology Plan Project of Xinjiang Production and Construction Corps/ ; },
mesh = {Animals ; *Glycine max ; *Tetranychidae/microbiology/physiology/growth & development ; *Microbiota ; Female ; Male ; Adaptation, Physiological ; Herbivory ; },
abstract = {Polyphagous pests often undergo the phenomenon of host-switching to expand their diet and enhance their environmental adaptability. The Tetranychus turkestani is the dominant mite pest in the northern Xinjiang region. To evaluate the influence of feeding experiences and its microbiome on the adaptation of T. turkestani to soybean hosts. we constructed age-stage two-sex life table and 16 S rDNA sequencing technology, the effects of the pre-host on the adaptability of T. turkestani to soybeans and the microbiome community were systematically evaluated, and the correlation between the two was further explored. The results show that: before host-switching, T. turkestani exhibited the highest intrinsic rate (0.277 d [-1]) and net reproductive rate (124.500) on the soybean host. The r (0.185 d[-1]) and R0 (37.488) of T. turkestani are lowest when reared on Amaranthus retroflexus. After the host was switched to soybean, both the r and R0 of T. turkestani increased. Similarly, the Chao1 index of T. turkestani exhibited a significant increase. When T. turkestani feeds on A. retroflexus, Wolbachia (97.01%), an insect endosymbiont, is the predominant microbiome. In contrast, when it feeds on Chenopodium album, Spiroplasma (54.59%) becomes the dominant microbiome. After the host was switched to soybean, the composition of microbiome in T. turkestani became similar to that of populations feeding on soybean. Correlation analysis revealed that Spiroplasma and Wolbachia were significantly positively correlated with both the oviposition period in host-switching of T. turkestani.},
}

Animals
*Glycine max
*Tetranychidae/microbiology/physiology/growth & development
*Microbiota
Female
Male
Adaptation, Physiological
Herbivory

@article {pmid41129014,
year = {2025},
author = {Mohanty, A and Bashir, B and Kolekar, KA and Acharya, A and Gulati, M and Chaitanya, M and Gupta, M and Patle, D and Gupta, G and Singh, SK},
title = {Therapeutic perspective of postbiotics in managing health of women with polycystic ovarian syndrome: a holistic approach.},
journal = {Inflammopharmacology},
volume = {},
number = {},
pages = {},
pmid = {41129014},
issn = {1568-5608},
abstract = {Polycystic Ovary Syndrome (PCOS) is an amalgamation of several factors such as complex combination of endocrine and metabolic disorder caused due to insulin resistance, hyperandrogenism and chronic inflammation. Research shows that postbiotics and their metabolic byproducts represent a new therapeutic opportunity for PCOS treatment. Postbiotics produce various therapeutic properties including anti-inflammatory, antioxidant and immunomodulatory effects that assist in balancing the metabolism. Postbiotics strengthen gut wall integrity and reduces inflammation while it affects the interaction between gut and ovaries to stabilize hormone regulation and insulin activity. Postbiotic compounds containing short-chain fatty acids (SCFAs) and microbial-derived enzymes possess the ability to enhance glucose metabolism and reduce androgen excess and support ovarian function. Malfunctioning of the gut leads to several abnormalities such as anorexia, weight gain and maintaining healthy gut homeostasis restores the same. Additionally, it restores menstrual irregularity and ovulation. Postbiotics have superior stability characteristics which provide safe operation during production and simplified formulation processes. The nature of postbiotics emerges as a promising therapy for managing PCOS since they address metabolic and reproductive disorders through microbiome-based operations.},
}

@article {pmid41129013,
year = {2025},
author = {Ribeiro, JL and Santos, TA and Anbinder, AL},
title = {Benefits that Death Does Not Part: the Promise of Postbiotics for Bone Health.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41129013},
issn = {1867-1314},
abstract = {Postmenopausal osteoporosis (PMO) is a widespread global health concern characterized by hormone deficiency. The existing therapies for PMO often have undesirable side effects, necessitating the development of safe and effective alternative treatments. Probiotics, which are live microorganisms that promote the host health, have been explored as a potential solution. However, concerns have been raised regarding their use, particularly the safety when administered to vulnerable populations (e.g., elderly and immunodeficient individuals). Additionally, the industrial processing and storage of probiotic products present technological challenges that can compromise their viability. To address these drawbacks, the focus has shifted towards non-viable probiotics known as postbiotics. Postbiotics are defined as inactivated (dead) microbial cells or their byproducts that provide health benefits to consumers. They exhibit immunomodulatory properties and demonstrate antagonistic effects against pathogens. Furthermore, postbiotics offer enhanced safety, technological advantages, and practical benefits. By leveraging these unique attributes, postbiotics present a promising opportunity to introduce novel therapies that are safer and more stable. This review provides an overview of key considerations surrounding postbiotics, summarizes recent literature on their application in PMO, and underscores the urgent need for further randomized clinical trials. These trials should evaluate the safety, efficacy, and mechanisms of action of postbiotic products to support regulatory decision-making processes.},
}

@article {pmid41128861,
year = {2025},
author = {Qi, W and Yan, X and Li, C and Jing, J and Zhang, Y and Xi, J and Liang, C},
title = {Linoelaidic acid alleviates COM-induced kidney injury and crystal deposition via the PPARγ/MAPK signaling pathway.},
journal = {Urolithiasis},
volume = {53},
number = {1},
pages = {205},
pmid = {41128861},
issn = {2194-7236},
support = {2024byzd392, 2024byzd379//Science and technology project of Bengbu Medical University/ ; 82000672//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Mice ; *Kidney Calculi/metabolism/drug therapy/pathology ; Humans ; *Calcium Oxalate/metabolism ; *PPAR gamma/metabolism ; *MAP Kinase Signaling System/drug effects ; Disease Models, Animal ; Male ; Apoptosis/drug effects ; Kidney/drug effects/pathology/metabolism ; Gastrointestinal Microbiome/drug effects ; Cell Line ; *Linolenic Acids/pharmacology/therapeutic use ; Female ; Glyoxylates ; },
abstract = {Renal injury and calcium oxalate crystal deposition are the core pathological processes of kidney stone formation, and their molecular mechanisms have not been fully elucidated while the clinical intervention methods are limited. Many studies have shown that the intestinal microbiota can produce various metabolites that affect renal function through the gut-kidney axis and participate in the formation of kidney stones. This study aims to identify the microbial metabolites related to kidney stone patients and explore their mechanism of action in kidney stones. Microbiome and metabolome analyses are used to search for microbial-related metabolites in the intestines of kidney stone patients. Using COM crystal-treated TCMK-1 cells as a model, the functions of metabolites are evaluated by detecting cell viability, apoptosis rate, cell-crystal adhesion, reactive oxygen species and MDA levels in vitro. In vivo, a glyoxylate-based kidney stone mouse model is established, and the effects of metabolites on renal function are assessed by HE staining, PAS staining, creatinine and urea nitrogen levels. The effects of metabolites on renal injury and crystal deposition are evaluated by Tunel, Von-Kossa staining, CD44 and OPN level detection. Transcriptional sequencing combined with western blot is used to search and verify the related signaling pathways affected by metabolites. It is found that linoelaidic acid is significantly decreased in kidney stone patients. Supplementing linoelaidic acid in vitro can significantly reduce COM crystal-induced cell apoptosis, crystal adhesion, ROS and MDA levels, and increase cell viability. In kidney stone mice, supplementing linoelaidic acid reduces renal tubular damage, crystal deposition, and improves renal function. Mechanistically, linoelaidic acid upregulates the expression of PPARγ in kidney stones to inhibit the activation of the MAPK signaling pathway. Linoelaidic acid can alleviate renal injury, oxidative stress and crystal deposition by regulating the PPARγ/MAPK signaling pathway, and may be a useful strategy for the treatment of kidney stones.},
}

Animals
Mice
*Kidney Calculi/metabolism/drug therapy/pathology
Humans
*Calcium Oxalate/metabolism
*PPAR gamma/metabolism
*MAP Kinase Signaling System/drug effects
Disease Models, Animal
Male
Apoptosis/drug effects
Kidney/drug effects/pathology/metabolism
Gastrointestinal Microbiome/drug effects
Cell Line
*Linolenic Acids/pharmacology/therapeutic use
Female
Glyoxylates

@article {pmid41128607,
year = {2025},
author = {Dang, Y and Huang, J and Peng, X and Wang, Y and Wang, J},
title = {Identification of intratumoral bacteria correlated with hepatitis B virus (HBV) levels: a prognostic indicator for patient outcomes in hepatocellular carcinoma patients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0118825},
doi = {10.1128/spectrum.01188-25},
pmid = {41128607},
issn = {2165-0497},
abstract = {Hepatocellular carcinoma (HCC) is a prevalent liver cancer associated with global health. The tumor microenvironment's (TME) microbial composition significantly influences HCC's development and prognosis. This study analyzed bacterial 16S rRNA genes from liver cancer patients' tumor, adjacent tumor, and normal tissues, revealing distinct microbiome profiles between tumor and normal tissues. HCC microbiota was more abundant, with Bacteroides, Ochrobactrum, Akkermansia, and Lactobacillus as the most prevalent genera. Hepatitis B virus (HBV)-positive (HBV+) and HBV-negative (HBV-) HCC tissues showed different microbial network patterns, with Bacteroides enrichment in HBV+ tissues being associated with HCC prognosis. HBV is associated with clinicopathological features and serves as an independent prognostic factor in HCC. The study underscores the microbiota's complexity in HCC and the potential of HBV as a prognostic biomarker post-surgery. This study provides critical insights into the relationship between the microbiota within the TME and HCC, a leading cause of cancer-related mortality. By identifying distinct microbiome profiles in HCC patients, particularly the enrichment of Bacteroides in HBV-positive tissues, our research not only uncovers the complexity of microbial interactions in liver cancer but also highlights the potential of using HBV status as a prognostic biomarker. This could significantly inform personalized treatment strategies and improve clinical outcomes for HCC patients, emphasizing the relevance of microbiome-based diagnostics and therapies in oncology.IMPORTANCEIn our study of the tumor microenvironment (TME) in hepatocellular carcinoma (HCC), we used DNA sequencing of bacterial 16S rRNA genes to analyze microbial compositions in tumor, adjacent tumor, and normal tissues from 213 liver cancer patients. Fluorescence in situ hybridization confirmed the presence of microbiota within tumors. Our results showed significant differences in microbiome profiles between tumor and normal tissues, with increased abundance of Bacteroides, Ochrobactrum, Akkermansia, and Lactobacillus in the HCC TME. Hepatitis B virus (HBV) status further stratified these differences, with Bacteroides significantly enriched in HBV-positive tissues and correlating with patient prognosis. Additionally, Bacteroides and Akkermansia showed interdependent population changes. Clinicopathological features, such as tumor size, were associated with HBV status, identifying HBV infection as an independent prognostic factor. These findings highlight the HCC microbiota's complexity and suggest HBV status as a potential prognostic biomarker, opening avenues for personalized therapeutic strategies.},
}

@article {pmid41128541,
year = {2025},
author = {Liu, C and He, Y and Zhang, H and Zhang, D and Ai, C and Tang, X and Yang, Q and Yu, Z and Tan, S and Friman, V-P and Liao, H and Zhou, S},
title = {Metabolic activity and survival strategies of thermophilic microbiomes during hyperthermophilic composting.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0095625},
doi = {10.1128/msystems.00956-25},
pmid = {41128541},
issn = {2379-5077},
abstract = {UNLABELLED: Hyperthermophilic composting (HTC) is a promising strategy for the treatment of organic solid waste, leveraging extreme thermophilic conditions (up to 90°C) driven by specialized microbial communities. While microbial community composition and succession have been previously described during HTC, the metabolic activity and adaptation of thermophilic microbiomes remain largely unexplored. In this study, we conducted time-series metagenomic and metatranscriptomic analyses on samples from a full-scale HTC system to characterize the composition, functional potential, and metabolic activity of thermophilic bacteria. A total of 227 non-redundant metagenome-assembled genomes (MAGs) were recovered, including 45 thermophilic MAGs (optimal growth temperatures > 45°C). Metatranscriptomic profiling revealed that thermophilic taxa-such as Thermus thermophilus, Planifilum fulgidum, and Thermaerobacter spp.-were highly transcriptionally active and played vital roles in heat generation through the upregulation of energy production and carbohydrate metabolism pathways. Additionally, these thermophiles exhibited survival and adaptation strategies involving physiological changes (e.g., spore formation, enhanced motility, and genome streamlining) and the induction of thermal resistance mechanisms (e.g., DNA repair systems, heat-shock proteins, and synthesis of compatible solutes). Overall, this study provides novel insights into the diverse survival strategies of thermophilic microbiomes in HTC and suggests potential avenues for optimizing thermophilic biotreatment processes for solid waste management.

IMPORTANCE: Despite increasing interest in hyperthermophilic composting as a sustainable waste treatment strategy, the mechanisms by which microbial communities both tolerate and drive extreme thermal conditions remain unclear. This study fills a critical knowledge gap by identifying a small group of highly active thermophilic bacteria that dominate during peak composting temperatures and orchestrate endogenous heat production. Using genome-resolved multi-omics, we demonstrate that these thermophiles couple high metabolic output with specialized survival strategies-such as genome streamlining, thermotolerance systems, and adaptive motility systems. These findings advance our understanding of microbial function under extreme conditions and provide a framework for optimizing thermophilic microbiome performance in engineered ecosystems.},
}

@article {pmid41128412,
year = {2025},
author = {Peng, L and Song, H and Shi, H and Wu, L and Ma, Y and Fan, X and Wu, M and Duan, L and Li, Z and Yuan, H},
title = {Oral Multi-Enzymatic Manganese-Carbon Dots Alleviate Sepsis-Associated Lung Injury via the Gut-Lung Axis.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.5c10625},
pmid = {41128412},
issn = {1936-086X},
abstract = {Sepsis-induced pulmonary injury represents a life-threatening global health challenge due to poorly defined pathological mechanisms. The gut-lung axis has been proven to be widely involved in sepsis-induced lung injury, yet effective interventions targeting gut microbiota homeostasis remain unknown. Single-cell sequencing revealed increased alveolar apoptosis and impaired macrophage efferocytosis during sepsis pathogenesis. Thus, we designed oral manganese-doped carbon dots (Mn-CDs) to alleviate septic lung injury by remodeling gut microbiota homeostasis and targeting the gut-lung axis. Biochemical characterization demonstrated Mn-CDs possess multienzyme mimetic activities (SOD-, CAT-, POD-, GPx-like) and potent ROS scavenging capacity. In murine sepsis models, Mn-CDs significantly improved systemic indices and were associated with macrophage anti-inflammatory states with enhanced efferocytosis, as evidenced by transcriptomic profiling. Integrated metagenomic/metabolomic analyses identified Mn-CDs-mediated enrichment of g_Clostridium and g_Bacteroides, concomitant with elevated indole-3-propionic acid (IPA) production. Subsequent in vitro studies demonstrate that IPA likely binds primarily to the aryl hydrocarbon receptor (AHR), promoting both efferocytosis and anti-inflammatory polarization in macrophages, thereby mitigating septic lung injury. Notably, the fecal microbiota transplantation (FMT) from Mn-CDs-treated mice not only alleviated systemic symptoms but also effectively promoted efferocytic polarization of pulmonary macrophages in septic mice. Depletion of the gut microbiota resulted in a significant loss of the protective efficacy of Mn-CDs in a murine model of septic lung injury. Collectively, the gut-lung axis mediated by microbiota-derived IPA and macrophage efferocytosis contributes to the remediation of septic lung injury, highlighting the potential of Mn-CDs in microbiome-directed critical care.},
}

@article {pmid41127671,
year = {2025},
author = {Bautista, J and Altamirano-Colina, A and López-Cortés, A},
title = {The vaginal microbiome in HPV persistence and cervical cancer progression.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1634251},
pmid = {41127671},
issn = {2235-2988},
mesh = {Female ; Humans ; *Vagina/microbiology/virology ; *Uterine Cervical Neoplasms/virology/microbiology/pathology/prevention & control ; *Microbiota ; *Papillomavirus Infections/complications/virology/microbiology ; Dysbiosis/microbiology ; Disease Progression ; *Papillomaviridae ; *Persistent Infection/microbiology/virology ; Probiotics ; },
abstract = {Persistent infection with high-risk human papillomaviruses (HR-HPV) is the primary cause of cervical cancer, but its progression depends on host and environmental factors beyond viral presence. The vaginal microbiome, particularly the transition from Lactobacillus crispatus-dominated communities to dysbiotic states enriched in Gardnerella, Fannyhessea, and Sneathia, has emerged as a key modulator of HPV persistence, local inflammation, and epithelial transformation. First, community state type IV (CST IV) microbiota strongly predict persistent HR-HPV infection and progression to high-grade lesions, highlighting their potential as non-invasive biomarkers for early risk stratification. Second, cervicovaginal dysbiosis alters mucosal immunity and promotes epigenetic reprogramming of both host and viral genomes, facilitating immune evasion and oncogenesis. Third, restoring Lactobacillus dominance through probiotics or microbial engineering holds translational promise for enhancing HPV vaccine efficacy and reducing cervical cancer burden. These findings position the vaginal microbiome not as a passive bystander, but as an active determinant of HPV-driven carcinogenesis and underscore its diagnostic and therapeutic potential in cervical cancer prevention.},
}

Female
Humans
*Vagina/microbiology/virology
*Uterine Cervical Neoplasms/virology/microbiology/pathology/prevention & control
*Microbiota
*Papillomavirus Infections/complications/virology/microbiology
Dysbiosis/microbiology
Disease Progression
*Papillomaviridae
*Persistent Infection/microbiology/virology
Probiotics

@article {pmid41127624,
year = {2025},
author = {Gao, F and Ma, L and Chen, X and Xue, X and Hou, J and Dong, J and Shen, W and Yang, C and Shi, Y},
title = {Distinct responses of wheat microbial communities in phyllosphere and rhizosphere to Puccinia striiformis infection.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1639152},
pmid = {41127624},
issn = {1664-302X},
abstract = {In the plant ecosystem, microbiomes are of great significance in sustaining plant health, participating in multiple physiological activities like nutrient metabolism, stress resistance, and hormone regulation. However, the invasion of pathogens like Puccinia striiformis can disrupt the balance of the plant microbiome, significantly affecting plant growth, development, and metabolism. This study delved into the responses of wheat microbial communities in different niches, namely the phyllosphere and rhizosphere, to P. striiformis infection. The structure of the phyllosphere fungal community was predominantly affected by the wheat variety. The α-diversity of phyllosphere fungi increased with the enhancement of wheat resistance. In the rhizosphere, although the inoculation did not cause a notable alteration to the overall architecture of the bacterial and fungal communities, remarkable variations were detected in the relative proportion of certain microbial taxa across various resistant wheat varieties. The co-occurrence network of the rhizosphere underwent significant structural and functional reorganization, and the network became substantially more complex after inoculation. The study also uncovered the interaction among the microbial communities in the phyllosphere and rhizosphere, with highly resistant varieties showing a stronger ability to coordinate this interaction to optimize microbial community functions and enhance disease resistance. This research deepens the understanding of the wheat-Puccinia striiformis-microbial community interaction system and paves the way for further research on wheat disease prevention and control strategies.},
}

@article {pmid41127619,
year = {2025},
author = {Wang, Y and Wu, Y and Qin, R and Chen, X and Liu, L and Wang, L and Wang, W and Liu, Y},
title = {Chinese herbal medicine promotes growth by improving nutrient utilization and rumen microbiota in suckling lambs.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1644331},
pmid = {41127619},
issn = {1664-302X},
abstract = {This study investigated the effects of compound Chinese herbal medicine (CCHM) on nutrient digestibility, rumen fermentation parameters, and microbial structure in suckling lambs. Sixty Lambs born as twins (from the same ewe), each 8 days old, were randomly assigned to two groups. The control and treatment groups received 0 and 0.2% CCHM in the basal diet, respectively. Digestion experiments were conducted during the trial. Rumen fluid samples were collected from slaughtered lambs in the final week for microbiome analysis. The results indicated that average daily gain and average daily feed intake were significantly improved by CCHM. The apparent digestibility of dry matter and acid detergent fiber also increased significantly. CCHM supplementation elevated Ammonia nitrogen (NH3-N), total volatile fatty acids (TVFAs), acetate, and propionate concentrations in the rumen. The relative abundance of Firmicutes, Actinobacteria, Patescibacteria, Succiniclasticum, Selenomonas, Olsenella, and Shuttleworthia increased in the treatment group. Linear discriminant analysis Effect Size (LEfSe) revealed ten bacterial groups significantly enriched in the treatment group. These included Patescibacteria (Phylum), Negativicutes and Saccharimonadia (Class), Saccharimonadia and Rhodobacterales (Order), Saccharimonadiahe and Rhodobacteraceae (Family), and Prevotell-9, Saccharimonadales, and Limosilicobacillus (Genus). Thirteen CAZyme families were detected. Two enzyme families, GH34-5 and CBM4, were enriched in the control group, while eleven families were enriched in the treatment group: GT14, GH89, GH84, GH63, GH5-36, CBM58, PL37, GH85, GH165, GH110, and GH50. Correlation analysis between rumen bacteria, carbohydrate enzymes, and fermentation parameters showed a positive correlation between Saccharimonadales and GH63. Limosilactobacillus showed a positive correlation with CBM58. Negative correlations were found between Romboutsia and both GT14 and PL37. GH84, GH165, GH85, and GH50 were positively correlated with NH3-N concentration. CBM58, GT14, GH89, GH110, GH50, and PL37 showed positive associations with TVFAs. This study demonstrates that dietary supplementation with CCHM during the suckling period improves growth performance, enhances nutrient digestibility, increases rumen fermentation capacity, modulates microbial abundance, and promotes lamb development in Hu sheep.},
}

@article {pmid41127618,
year = {2025},
author = {Singh, R and Sic-Hernandez, WR and Crane, CF and Shim, S and Telenko, DEP and Goodwin, SB},
title = {Tar spot susceptibility of corn influences phyllosphere-associated bacterial and fungal microbiomes.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1581312},
pmid = {41127618},
issn = {1664-302X},
abstract = {Tar spot, caused by the obligate fungal pathogen Phyllachora maydis, is a major economic concern for corn producers in the United States. To test the hypothesis that P. maydis can interact with other foliar microorganisms, we investigated phyllosphere microbiomes in relation to corn inbreds with differential tar spot symptoms under natural field infestation. Sixteen inbred lines were assessed for tar spot symptoms, and bacterial and fungal microbiomes were characterized using Illumina MiSeq Sequencing. Comparison of the phyllosphere microbiomes revealed distinct bacterial and fungal communities between resistant and susceptible lines in a sample-specific manner. Bacterial alpha diversity did not differ significantly between susceptible and resistant lines, while fungal diversity (richness, evenness, and phylogenetic diversity) was significantly higher in resistant lines. Beta diversity analysis revealed significant structural differences in both bacterial and fungal communities, with fungal differences more pronounced and driven by relative abundance. Resistant lines were associated with plant-beneficial bacterial genera such as Quadrisphaera, Klenkia and Nocardioides and fungal genera Cladosporium, Coniothyrium, Alternaria, Epicoccum, Bipolaris, Phyllozyma, and Papiliotrema, while susceptible lines were dominated by Erwiniaceae, Aureimonas, Pseudomonas, Microbacterium, and Deinococcus and fungal genera Hannaella, Paraphaeosphaeria, Sphaerellopsis and Phyllachora. Coniothyrium, a potential mycoparasite of P. maydis, was also detected but whether it is the same species that was identified in Central and South America is unknown. Our findings imply that P. maydis infection may result in a distinct, less diverse microbiome. Differential abundance analysis revealed enrichment of Erwiniaceae and Enterobacterales, particularly Amnibacterium in susceptible lines, and Microbacteriaceae in resistant lines. Correlation analysis between P. maydis reads and abundant taxa revealed a predominance of negative correlations, suggesting increased ecological niche differentiation driven by intense competition within the microbial community. These findings suggest that P. maydis infection is associated with a less diverse microbiome and that specific microbial taxa may play roles in P. maydis susceptibility and resistance. Further research on these correlated and distinct microbiotas could elucidate the role of foliar microbiomes in causing or resisting P. maydis infection.},
}

@article {pmid41127616,
year = {2025},
author = {Srivastava, AK and Kashyap, PL and Santoyo, G and Newcombe, G},
title = {Editorial: Plant microbiome: interactions, mechanisms of action, and applications, volume III.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1696341},
pmid = {41127616},
issn = {1664-302X},
}

@article {pmid41127559,
year = {2025},
author = {Thenappan, DP and Wicaksono, WA and Berg, G and Joshi, V},
title = {Niche-specific microbial diversity, interactions, and functional potential within the spinach microbiome.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100475},
pmid = {41127559},
issn = {2666-5174},
abstract = {Understanding the spatial organization and functional diversity of microbiomes across plant compartments is essential for unraveling the complex interactions between plants and their associated microbial consortia. This study examined the microbial communities associated with spinach (Spinacia oleracea L.) across five ecological niches, using 16S rRNA and ITS amplicon sequencing, in two commercial conventional cultivars: Hammerhead and Traverse. Microbial diversity, community composition, co-occurrence networks, and functional potential showed cultivar-specific effects, especially in the fungal community. The niche was a significant factor influencing all microbiome parameters, showing the same pattern in both cultivars: highest in bulk soil, followed by the rhizosphere, leaf episphere, and finally the root and leaf endosphere. We observed clear niche differentiation and enrichment of niche-specific genera. A core microbiome was identified, comprising 10 bacterial and 6 fungal taxa, with Streptomyces, Bacillus, and Rubrobacter being the key bacterial genera, and Alternaria and Cladosporium being the dominant fungi. SourceTracker2 analysis revealed a limited contribution of bulk soil to the rhizosphere (∼25 %), while the rhizosphere and leaf episphere were the primary sources for endosphere communities. Fungal communities showed higher transfer rates (75-96 %) between niches compared to bacterial communities (19-93 %). Co-occurrence network analysis revealed that Traverse had a denser microbial network than Hammerhead, with key hubs such as Streptomycetaceae and Chaetomiaceae. Inferred functional potential suggested metabolic capabilities in microbial communities across spinach niches, including those of potential plant pathogens. The microbial spatial distribution and identification of spinach from this study lays the foundation for designing targeted strategies to mitigate pathogen risks and introduce beneficial microbial functions into crops.},
}

@article {pmid41127419,
year = {2026},
author = {Dunn, N and Verma, N and Dunn, W},
title = {Artificial Intelligence for Predictive Diagnostics, Prognosis, and Decision Support in MASLD, Hepatocellular Carcinoma, and Digital Pathology.},
journal = {Journal of clinical and experimental hepatology},
volume = {16},
number = {1},
pages = {103184},
pmid = {41127419},
issn = {0973-6883},
abstract = {Artificial intelligence (AI) has fundamentally transformed the landscape of hepatology by enhancing disease diagnosis, risk stratification, and decision support. In metabolic dysfunction-associated steatotic liver disease (MASLD), AI has been integrated into large-scale consortia such as NIMBLE, LITMUS, TARGET-NASH, and SteatoSITE to improve diagnostic accuracy and patient management. These consortia utilize AI to derive and validate non-invasive biomarkers in fibrosis staging. AI-based models also enhance the detection of hepatocyte ballooning and metabolic dysfunction-associated steatohepatitis, minimizing interobserver variability and improving clinical trial enrollment criteria. Additionally, AI applications differentiate MASLD from alcohol-associated liver disease using gut microbiome and metabolic profiling. In hepatocellular carcinoma (HCC), AI has improved risk stratification, diagnosis, and prognostication. AI-driven models based on liver stiffness and clinical parameters can risk stratify patients for HCC development. Enhanced imaging techniques, radiomics, and histopathology powered by AI improve the accuracy of detecting indeterminate liver nodules and predicting microvascular invasion. AI also improves treatment response prediction for therapies such as transarterial chemoembolization (TACE) and immune checkpoint inhibitors and thereby individualizes therapeutic strategies and improves survival outcomes. In digital pathology, AI has redefined fibrosis staging, donor liver steatosis assessment, and disease diagnosis. FibroNest™ and qFibrosis are two exceptional AI platforms that utilize imaging techniques for the purposes of both standardizing histological assessments, as well as increasing diagnostic precision. The field of MASLD, HCC, and digital pathology is advancing towards precision medicine. FibroNest™ and qFibrosis are two exceptional AI platforms that utilize imaging techniques for the purposes of both standardizing histological assessments, as well as increasing diagnostic precision.},
}

@article {pmid41127208,
year = {2025},
author = {Magoutas, K and Holdcroft, A and Walls, M and Furfaro, L and Ireland, D and Payne, M},
title = {Investigating the Link Between Intimate Health, Hygiene and Sexual Practices and the Vaginal Microbiome-The INTIMATE Study.},
journal = {Reproductive medicine and biology},
volume = {24},
number = {1},
pages = {e12685},
pmid = {41127208},
issn = {1445-5781},
abstract = {PURPOSE: To explore how intimate hygiene practices and related products-such as feminine washes, wipes, and lubricants-affect the vaginal microbiome.

METHODS: Vaginal bacterial communities of 96 non-pregnant Western Australian women were characterised via full-length 16S rRNA gene sequencing. Participants completed an online questionnaire capturing demographics, intimate health, hygiene and sexual practices, to compare these with microbial composition.

RESULTS: Beta diversity varied significantly across multiple variables, particularly in relation to Lactobacillus spp. abundance. Compared to women with no partners or two or more sexual partners, monogamous women had lower L. crispatus (p = 0.002 and p = 0.04, respectively), higher L. iners (p = 0.017 and p = 0.044, respectively), and were least likely to cluster into CST I (p < 0.001). Postmenopausal women showed reduced L. crispatus (p = 0.009), increased levels of L. iners (p = 0.037), and were most likely to cluster into CST IV (p = 0.029) compared with women who did not report menopause. Regular perineal washing was associated with fewer reported infections (p = 0.029), whereas internal washing correlated with recurrent thrush (p = 0.017).

CONCLUSIONS: Sexual practices and menopause status are key factors influencing L. crispatus and L. iners colonisation. Most hygiene practices had minimal impact on Lactobacillus dominance, although behaviours associated with significant microbiome disruption were uncommon in this cohort.},
}

@article {pmid41127052,
year = {2025},
author = {Sheikh, A and Scano, C and Xu, J and Ojo, T and Conforti, JM and Haberman, KL and King, B and Martinez, AS and Pujol, M and Watkins, J and Lotter, J and Lin, EL and Zechmann, B and Sevcik, A and Sayes, C and Gallagher, ES and Lang, SP and Mell, J and Ehrlich, GD and Taube, JH and Greathouse, KL},
title = {Outer Membrane Vesicles From Bacteroides fragilis Contain Coding and Non-Coding Small RNA Species That Modulate Inflammatory Signalling in Intestinal Epithelial Cells.},
journal = {Journal of extracellular biology},
volume = {4},
number = {10},
pages = {e70086},
pmid = {41127052},
issn = {2768-2811},
abstract = {Alterations to the community structure and function of the microbiome are associated with changes to host physiology, including immune responses. However, the contribution of microbe-derived RNAs carried by outer membrane vesicles (OMVs) to host immune responses remains unclear. This study investigated the role of OMVs and OMV-associated small RNA (sRNA) species from pathogenic and commensal Bacteroides fragilis (ETBF and NTBF, respectively) in eliciting different immune responses from intestinal epithelial cells. To distinguish the differences in the sRNA profiles of the two strains and their OMVs, RNA-seq, qRT-PCR, and northern blotting were conducted to identify enrichment of discrete sRNA species in OMVs, which were also differentially expressed between the two strains. Specifically, coding and non-coding RNAs were enriched in OMVs from NTBF and ETBF, with BF9343_RS22680 and BF9343_RS17870 being significantly enriched in ETBF OMVs compared to NTBF. To understand the effects of OMVs on pattern recognition receptors, reporter cells of Toll-like receptor (TLR) activation were treated with OMVs, demonstrating activation of TLRs 2, 3, and 7. Treatment of Caco-2 and HT29-MTX cells with OMVs demonstrated increased expression of IL-8. Surprisingly, we discovered that degradation of RNase-accessible RNAs within ETBF OMVs, but not NTBF OMVs, resulted in vesicles with enhanced capacity to stimulate IL-8 expression, indicating that these extravesicular RNAs exert an immunosuppressive effect. This suggests a dual role for OMV-associated RNAs in modulating host immune responses, with implications for both bacterial pathogenesis and therapeutic applications.},
}

@article {pmid41127036,
year = {2025},
author = {Dubal, AS and Sarteau, AC and Azcarate-Peril, MA and Djukic, Z and Ercolino, G and Fruik, A and Ho, J and Lee, Z and Roach, J and Valancius, M and Young, LA and Carroll, IM and Kahkoska, AR},
title = {Exploring the Effects of Dietary Intake on Gut Microbiome Diversity and Composition of Older Adults with Type 1 Diabetes: A Pilot Study.},
journal = {Current developments in nutrition},
volume = {9},
number = {10},
pages = {107550},
pmid = {41127036},
issn = {2475-2991},
abstract = {BACKGROUND: Gut microbiome diversity and composition have been associated with type 1 diabetes (T1D) onset and progression. These features have not been explored among the growing number of older adults with T1D, including how they may differ by diet.

OBJECTIVES: In the present observational study, we investigated differences in gut microbiome diversity and composition across quantiles of high and low macronutrient, fiber, and simple sugar intake.

METHODS: We collected observational data on routine diabetes management, diet, and other health indicators from older adults with T1D over 7-9 d, including 2 24-h dietary recall interviews, diabetes technology, and medical record data. Stool samples were collected for gut microbiome characterization using high-throughput sequencing of the 16S ribosomal RNA gene. Gut microbiome characteristics were assessed by Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC2), Shannon index, and Bray-Curtis distances.

RESULTS: Among 17 older adults [mean (SD) age 73.5 (6.2) y; diabetes duration: 34.0 (16.0) y, and glycated hemoglobin: 7.0 (0.9) %], increased fat intake was associated with enriched genus Lactococcus, increased fiber intake was associated with enriched genus Hemophilus and unclassified Clostridium within family CAG:508, and increased fructose intake was associated with enrichment of unclassified genus SFMI01 within family Christensenellaceae. Greater carbohydrate intake was associated with depletion of the family Enterobacteriaceae. Microbial diversity differed significantly with greater fiber and fructose intake.

CONCLUSIONS: We found statistically significant evidence suggesting that the gut microbiome of older adults with T1D may be modulated by macronutrient, fiber, and fructose intake. Similar trends between fiber intake differences and significantly different microbial community structure have been found in younger populations. Together with the literature, our other findings suggest that macronutrient, fiber, and fructose intakes may impact the gut microbiome differently in older adults with T1D.},
}