@article {pmid40118220,
year = {2025},
author = {Rozera, T and Pasolli, E and Segata, N and Ianiro, G},
title = {Machine learning and artificial intelligence in the multi-omics approach to gut microbiota.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.02.035},
pmid = {40118220},
issn = {1528-0012},
abstract = {The gut microbiome is involved in human health and disease, and its comprehensive understanding is necessary to exploit it as a diagnostic or therapeutic tool. Multi-omics approaches, including metagenomics, metatranscriptomics, metabolomics, and metaproteomics, enable depicting the complexity of the gut microbial ecosystem. However, these tools generate a large data stream, which integration is needed to produce clinically useful readouts but, in turn, might be difficult to carry out with conventional statistical methods. Artificial intelligence and machine learning have been increasingly applied to multi-omics datasets in several conditions associated with microbiome disruption, from chronic disorders to cancer. Such tools show potential for clinical implementation, including the discovery of microbial biomarkers for disease classification or prediction, the prediction of response to specific treatments, the fine-tuning of microbiome-modulating therapies. Here we discuss the state of the art, potential, and limits, of artificial intelligence and machine learning in the multi-omics approach to gut microbiome.},
}

@article {pmid40118032,
year = {2025},
author = {Ge, AH and Wang, E},
title = {Exploring the plant microbiome: A pathway to climate-smart crops.},
journal = {Cell},
volume = {188},
number = {6},
pages = {1469-1485},
doi = {10.1016/j.cell.2025.01.035},
pmid = {40118032},
issn = {1097-4172},
mesh = {*Microbiota ; *Crops, Agricultural/microbiology ; *Rhizosphere ; Plant Roots/microbiology/metabolism ; Agriculture ; Soil Microbiology ; Climate ; },
abstract = {The advent of semi-dwarf crop varieties and fertilizers during the Green Revolution boosted yields and food security. However, unintended consequences such as environmental pollution and greenhouse gas emissions underscore the need for strategies to mitigate these impacts. Manipulating rhizosphere microbiomes, an aspect overlooked during crop domestication, offers a pathway for sustainable agriculture. We propose that modulating plant microbiomes can help establish "climate-smart crops" that improve yield and reduce negative impacts on the environment. Our proposed framework integrates plant genotype, root exudates, and microbes to optimize nutrient cycling, improve stress resilience, and expedite carbon sequestration. Integrating unselected ecological traits into crop breeding can promote agricultural sustainability, illuminating the nexus between plant genetics and ecosystem functioning.},
}

*Microbiota
*Crops, Agricultural/microbiology
*Rhizosphere
Plant Roots/microbiology/metabolism
Agriculture
Soil Microbiology
Climate

@article {pmid40118017,
year = {2025},
author = {Kehkashan, and Hussain, A and Murtaza, M and Lee, GJ and Mun, BG and Yun, BW},
title = {Low and high-density polyethylene and expanded polystyrene biodegradation by the greater wax moth Galleria mellonella L reveals a key role of the gut microbiome.},
journal = {Ecotoxicology and environmental safety},
volume = {294},
number = {},
pages = {118074},
doi = {10.1016/j.ecoenv.2025.118074},
pmid = {40118017},
issn = {1090-2414},
abstract = {Polyethylene (PE) is a ubiquitous pollutant that takes long time to degrade naturally. PE breaks down into persistent micro- or nano-plastics that are even more dangerous for the environment and human health. Here we investigated the ability of the wax worm Galleria mellonella (Lepidoptera, Pyralidae) to degrade two different types of PE and expanded polystyrene (EPS). Results showed a reduction of up to 69 %, 73 %, and 50 % in the weight of LDPE, HDPE, and EPS, respectively. Antibiotic treatments indicated that PE consumption is highly dependent upon an intact population of at least eight different bacteria from the Enterococcus, Pseudomonas, and Bacillus genera identified by 16S rRNA sequencing. Antibiotic treatment reduced the gut bacterial population, negatively affecting larval growth. The PE-only diet severely affected the growth and development of G. mellonella larvae, pupae, and male/female adults. SEM analysis of gut bacteria co-incubated LDPE discs revealed biofilm formation and PE biodegradation by all the bacteria in the culture, supporting the great potential of these bacteria for plastic biodegradation. FTIR analysis of frass after feeding on PE only revealed significantly strong PE biodegradation signals as results showed 33 peaks of strong (S) and medium (M) intensity corresponding to wave numbers with PE biodegradation signatures ranging between 1239.50 cm[-1] to 3077.69 cm[-1] coding for vinyl hydrocarbons, vinyl ether, vinylene, vinylene trisubst., ketones, ethers, aldehydes, acrylate, diazo ketones and epoxides which is a convincing evidence of PE metabolism. Further research is required to determine the practical implications of wax worm larvae for plastic degradation in the environment.},
}

@article {pmid40117915,
year = {2025},
author = {Ghemrawi, M and Ramírez Torres, A and Netherland, M and Wang, Y and Hasan, NA and El-Fahmawi, B and Duncan, G and McCord, B},
title = {Forensic insights from shotgun metagenomics: Tracing microbial exchange during sexual intercourse.},
journal = {Forensic science international. Genetics},
volume = {78},
number = {},
pages = {103266},
doi = {10.1016/j.fsigen.2025.103266},
pmid = {40117915},
issn = {1878-0326},
abstract = {The microbiome is becoming an emerging field of interest within forensic science with high potential for individualization; however, little is known about bacterial species specific to the genital area or their ability to transfer between individuals during sexual contact. In this proof-of-concept study, we investigated microbial transfer dynamics in seven monogamous, heterosexual couples by collecting pre- and post-sexual intercourse samples from their genital areas, including penile, vaginal, and labial locations. Utilizing Shotgun Metagenomic Sequencing, we sequenced the microbial profiles of these samples. Our findings reveal significant transfer from the vaginal microbiome onto the penile microbiome, predominantly originating from the labial genitalia. Moreover, strain analysis unveiled distinct differentiation between the same species of bacteria across individuals, underscoring the potential for microbial forensics to distinguish individuals. This study contributes to our understanding of microbial transfer during sexual contact and highlights the forensic implications of the genital microbiome.},
}

@article {pmid40117686,
year = {2025},
author = {Zhang, C and Cabreiro, F and Barron, LP and Stürzenbaum, SR},
title = {Carbamazepine-exposed earthworms are characterized by tissue-specific accumulation patterns and transcriptional profiles.},
journal = {Environment international},
volume = {198},
number = {},
pages = {109357},
doi = {10.1016/j.envint.2025.109357},
pmid = {40117686},
issn = {1873-6750},
abstract = {Pharmaceutically active compounds enter soils via wastewater reuse and biosolid application. A ubiquitous drug present in wastewater is carbamazepine, a frequently prescribed anti-convulsant. Its mode of action is not species-specific and affects the nervous system of non-target organisms, including most likely the soil dwelling earthworms, which in turn has the potential to negatively impact soil quality. In this project, soils were amended with carbamazepine to explore uptake dynamics and resultant changes in molecular and life cycle endpoints of earthworms (Dendrobaena veneta). Earthworms were maintained, under laboratory conditions, for 28 days in soil spiked with either a solvent control, 0.6 mg/kg carbamazepine (encountered in the terrestrial system) or 10 mg/kg carbamazepine (significantly above an environmental hotspot). Carbamazepine concentrations were quantified in soils and worms by liquid chromatography tandem mass spectrometry (LC-MS/MS) which revealed tissue, dose and time-dependent differences in accumulation. Carbamazepine also modulated the make-up of the microbiome in the soil as well as the earthworm's gut. De novo RNA sequencing identified novel transcripts and complex tissue-specific transcriptomic changes, where, for example, the expression of the tubulin polymerisation promoting protein (tppp) was inhibited (9-fold) in the gut but induced (11-fold) in the cerebral ganglion of exposed earthworms. However, the notable absence of a strong cytochrome P450 response across all conditions suggests that the terrestrial earthworm also relies on detoxification pathways that differ to those observed in well-studied aquatic models. The novel finding that carbamazepine exposure triggers tissue-specific impacts in non-target soil organisms highlights the value and need for a more comprehensive understanding of how contaminants of emerging concern behave within an ecotoxicological context. This, in turn, will lead to informed and reliable risk assessments defining the consequences of wastewater and biosolid amendment practices on soil ecology and ecosystem function.},
}

@article {pmid40117607,
year = {2025},
author = {Paz, M and Lio, P},
title = {Dermatological Manifestations and Sebum Composition in Parkinson's Disease.},
journal = {Dermatology practical & conceptual},
volume = {15},
number = {1},
pages = {},
pmid = {40117607},
issn = {2160-9381},
abstract = {INTRODUCTION: Parkinson disease (PD) is a multifaceted neurodegenerative disorder known for its hallmark motor symptoms. However, nonmotor manifestations, specifically dermatological changes, precede motor symptoms and may thus serve as vital early indicators of PD.

OBJECTIVES: This article explores the skin-related changes associated with PD, focusing on alterations in sebum composition, microbial dysbiosis, and the potential for leveraging dermatological assessments as early, noninvasive diagnostic markers for PD.

METHODS: A comprehensive literature review was conducted to investigate dermatological manifestations of PD, focusing on sebum changes in affected individuals. Research explored the clinical relevance of altered lipid profiles, volatile organic compound (VOC) contributions, and microbiome dysbiosis in those with PD.

RESULTS: Individuals with PD exhibit excess sebum production characterized by altered lipid profiles, including elevated short-chain fatty acids (SCFAs) and disruptions in sphingolipid metabolism. The lipid-rich environment also promotes overgrowth of Malessezia yeast, contributing to varied dermatological symptoms in those with PD. VOCs identified in sebum have been linked to unique odors and serve as biomarkers for diagnostic potential. These findings support the potential for early PD diagnosis through dermatologic assessment and sebum analysis.

CONCLUSION: Dermatological manifestations in PD offer promising noninvasive biomarkers for early diagnosis. Future research should aim to further elucidate the mechanisms underlying sebum dysregulation in PD and validate the clinical relevance of these biomarkers in larger populations.},
}

@article {pmid40117491,
year = {2025},
author = {Smith, SRM and Morgan, NV and Brill, A},
title = {Venous Thrombosis Unchained: Pandora's Box of Non-Inflammatory Mechanisms.},
journal = {Blood advances},
volume = {},
number = {},
pages = {},
doi = {10.1182/bloodadvances.2024014114},
pmid = {40117491},
issn = {2473-9537},
abstract = {Venous thromboembolism (VTE), which includes deep vein thrombosis (DVT) and pulmonary embolism (PE), represents a complex pathological process extending far beyond inflammatory mechanisms. This review comprehensively examines the multifaceted non-inflammatory mechanisms underlying thrombosis development, integrating insights from molecular, physiological, and systemic levels. Blood flow dynamics and endothelial function are known to be critical regulators of thrombus development. Platelets and microparticles play important roles beyond conventional inflammatory responses, actively contributing to thrombus formation through intricate molecular interactions. Metabolic syndrome and insulin resistance are associated with thrombotic risk, demonstrating the complex interplay between metabolic disorders and DVT. Certain genetic mutations also predispose individuals to venous thrombosis. Emerging research has discovered the essential role of previously underappreciated factors such as products of gut microbiota or endothelial glycocalyx modifications. Molecular regulators such as microRNAs and hormonal disbalance further illustrate the complex mechanisms of venous thrombosis. Interestingly, circadian rhythms exhibit certain influence on thrombotic potential, introducing chronobiology as emerging variable affecting the risk of thrombosis. Based on these insights, future therapeutic strategies may include various interventions targeting or at least considering metabolic, molecular, and systemic non-inflammatory factors. Potential approaches include personalized risk stratification, microbiome modulation, endothelial protection approaches, and chronotherapy-based therapeutic modalities, that would ensure promising more efficient and safe thrombosis management.},
}

@article {pmid40117176,
year = {2025},
author = {Zielińska, K and Udekwu, KI and Rudnicki, W and Frolova, A and Łabaj, PP},
title = {Healthy microbiome-moving towards functional interpretation.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf015},
pmid = {40117176},
issn = {2047-217X},
support = {2020/38/E/NZ2/00598//NCN/ ; PLG/2023/016234//Jagiellonian University in Krakow/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; *Metagenomics/methods ; Metagenome ; Phylogeny ; Dysbiosis/microbiology ; Principal Component Analysis ; COVID-19/virology ; },
abstract = {BACKGROUND: Microbiome-based disease prediction has significant potential as an early, noninvasive marker of multiple health conditions linked to dysbiosis of the human gut microbiota, thanks in part to decreasing sequencing and analysis costs. Microbiome health indices and other computational tools currently proposed in the field often are based on a microbiome's species richness and are completely reliant on taxonomic classification. A resurgent interest in a metabolism-centric, ecological approach has led to an increased understanding of microbiome metabolic and phenotypic complexity, revealing substantial restrictions of taxonomy-reliant approaches.

FINDINGS: In this study, we introduce a new metagenomic health index developed as an answer to recent developments in microbiome definitions, in an effort to distinguish between healthy and unhealthy microbiomes, here in focus, inflammatory bowel disease (IBD). The novelty of our approach is a shift from a traditional Linnean phylogenetic classification toward a more holistic consideration of the metabolic functional potential underlining ecological interactions between species. Based on well-explored data cohorts, we compare our method and its performance with the most comprehensive indices to date, the taxonomy-based Gut Microbiome Health Index (GMHI), and the high-dimensional principal component analysis (hiPCA) methods, as well as to the standard taxon- and function-based Shannon entropy scoring. After demonstrating better performance on the initially targeted IBD cohorts, in comparison with other methods, we retrain our index on an additional 27 datasets obtained from different clinical conditions and validate our index's ability to distinguish between healthy and disease states using a variety of complementary benchmarking approaches. Finally, we demonstrate its superiority over the GMHI and the hiPCA on a longitudinal COVID-19 cohort and highlight the distinct robustness of our method to sequencing depth.

CONCLUSIONS: Overall, we emphasize the potential of this metagenomic approach and advocate a shift toward functional approaches to better understand and assess microbiome health as well as provide directions for future index enhancements. Our method, q2-predict-dysbiosis (Q2PD), is freely available (https://github.com/Kizielins/q2-predict-dysbiosis).},
}

Humans
*Gastrointestinal Microbiome/genetics
*Inflammatory Bowel Diseases/microbiology
*Metagenomics/methods
Metagenome
Phylogeny
Dysbiosis/microbiology
Principal Component Analysis
COVID-19/virology

@article {pmid40116950,
year = {2025},
author = {Chan, YL and Liao, JC and Li, TL and Wu, CJ and Chiu, YH},
title = {Bifidobacterium lactis ameliorates AOM/DSS-induced inflammation, dysbiosis, and colonic precancerous lesions.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {69},
pmid = {40116950},
issn = {1432-0614},
support = {MOST 109-2320-B-031-001//Ministry of Science and Technology/ ; },
mesh = {Animals ; *Dysbiosis/microbiology ; *Probiotics/administration & dosage/pharmacology ; *Mice, Inbred C57BL ; Female ; Mice ; *Precancerous Conditions/prevention & control/microbiology/chemically induced/pathology ; *Dextran Sulfate/toxicity ; *Gastrointestinal Microbiome ; *Bifidobacterium animalis ; *Azoxymethane/toxicity ; *Inflammation/prevention & control ; *Disease Models, Animal ; Colonic Neoplasms/prevention & control/pathology ; Cytokines/metabolism ; NF-kappa B/metabolism ; },
abstract = {Bowel cancer is the third most common malignancy of tumors and one of the major causes of cancer-related death. Bowel precancerous conditions can develop without any symptoms, which either makes it difficult for early diagnosis or poses a poor prognosis/gloomy relapse. This study aimed to investigate the effects of Bifidobacterium animalis subsp. lactis TCI604 (B. lactis) on inflammatory responses, gut microbiome, and protectiveness against azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced colonic precancerous lesions. The AOM/DSS-induced colonic precancerous lesion murine model was studied with 24 female C57BL/6 J mice assigned to the control group, AOM/DSS-induced colonic precancerous lesion group (AOM/DSS), AOM/DSS treated with B. lactis probiotic group (B. lactis P), and AOM/DSS treated with B. lactis cell-free supernatant group (B. lactis S). The results showed that both B. lactis P and B. lactis S could attenuate AOM/DSS-induced body weight loss and intestine damage, reduce aberrant crypt foci (ACF) and the formation of colonic polyps, and significantly inhibit pro-inflammatory cytokines and the NF-κB signaling pathway, in which the B. lactis S group outperformed others. Further analysis using 16S rDNA sequencing suggested that both B. lactis P and B. lactis S optimize gut microbiota. Several bacteria, including Muribaculaceae, Prevotellaceae_UCG-001, Anaerostipes, Ruminococcaceae, Mucispirillum, Clostridia_UCG-014, and Clostridia_vadinBB60 that were known in close relation to colonic precancerous lesions, were sequenced at taxonomic level. Our results indicated that both B. lactis P and B. lactis S improved AOM/DSS-induced colonic precancerous lesions by regulating inflammation as well as optimizing gut microbiota, thereby establishing reciprocally cooperative net benefits between probiotics/postbiotics and mice with colonic precancerous lesions. KEY POINTS: • Prophylactic administration of probiotic and postbiotic of B. lactis is capable of alleviating the AOM/DSS-induced body weight loss and colon shortening, as well as diminishing the development of colonic precancerous lesions, such as the formation of ACF and colonic polyps, in an AOM/DSS mouse model • Either probiotic or postbiotic of B. lactis has a positive role in mediating immune imbalance and colonic inflammation via suppression of inflammatory immune cells, pro-inflammatory cytokines, and the NF-κB signaling pathway • AOM/DSS-induced dysbiosis can be reversed with the probiotic and postbiotic of B. lactis supplementation.},
}

Animals
*Dysbiosis/microbiology
*Probiotics/administration & dosage/pharmacology
*Mice, Inbred C57BL
Female
Mice
*Precancerous Conditions/prevention & control/microbiology/chemically induced/pathology
*Dextran Sulfate/toxicity
*Gastrointestinal Microbiome
*Bifidobacterium animalis
*Azoxymethane/toxicity
*Inflammation/prevention & control
*Disease Models, Animal
Colonic Neoplasms/prevention & control/pathology
Cytokines/metabolism
NF-kappa B/metabolism

@article {pmid40116510,
year = {2025},
author = {Lebovics, N and Heering, G and Frishman, WH and Lebovics, E},
title = {Lean MASLD and Cardiovascular Disease: A Review.},
journal = {Cardiology in review},
volume = {},
number = {},
pages = {},
doi = {10.1097/CRD.0000000000000893},
pmid = {40116510},
issn = {1538-4683},
abstract = {Metabolic-associated steatotic liver disease (MASLD), formerly known as nonalcoholic fatty liver disease, is prevalent worldwide and is highly associated with cardiovascular disease (CVD). Lean MASLD is defined by hepatic steatosis and cardiometabolic risk factors in individuals with a body mass index below 25 in Western populations or below 23 in Asian populations. Paradoxically, some studies indicate that lean MASLD is associated with an elevated risk of cardiovascular (CV) disease and CV mortality compared with nonlean MASLD. Lean MASLD patients exhibit distinctive metabolic, genetic, and microbiome profiles contributing to increased visceral adiposity, sarcopenia, hepatic fibrosis, systemic inflammation, and endothelial dysfunction. This review examines the epidemiology, pathophysiology, and CV outcomes associated with lean MASLD, addressing discrepancies in the literature. Furthermore, it highlights current clinical guidelines, emphasizes lifestyle modifications, and discusses emerging pharmacotherapies as potential treatment options.},
}

@article {pmid40116497,
year = {2025},
author = {Moreland, RB and Choi, BI and Fontes Noronha, M and Baker, J and Kaindl, J and Wolfe, AJ},
title = {Complete genome sequence of Trueperella bernardiae strain UMB8254, isolated from the bladder of a female with metabolic syndrome and nephrolithiasis.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0126524},
doi = {10.1128/mra.01265-24},
pmid = {40116497},
issn = {2576-098X},
abstract = {Trueperella bernardiae is infrequently isolated, usually in polymicrobial communities, from human hosts with a wide variety of symptoms and diseases. Here, we report a complete genome sequence of Trueperella bernardiae (UMB8254), isolated from the bladder of a human female with metabolic syndrome and nephrolithiasis.},
}

@article {pmid40116459,
year = {2025},
author = {Blakeley-Ruiz, JA and Bartlett, A and McMillan, AS and Awan, A and Walsh, MV and Meyerhoffer, AK and Vintila, S and Maier, JL and Richie, TG and Theriot, CM and Kleiner, M},
title = {Dietary protein source alters gut microbiota composition and function.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf048},
pmid = {40116459},
issn = {1751-7370},
support = {7002782//USDA National Institute of Food and Agriculture, Hatch/ ; P30 DK034987/NH/NIH HHS/United States ; },
abstract = {The source of protein in a person's diet affects their total life expectancy. However, the mechanisms by which dietary protein sources differentially impact human health and life expectancy are poorly understood. Dietary choices impact the composition and function of the intestinal microbiota that ultimately modulate host health. This raises the possibility that health outcomes based on dietary protein sources might be driven by interactions between dietary protein and the gut microbiota. In this study, we determined the effects of seven different sources of dietary protein on the gut microbiota of mice using an integrated metagenomics-metaproteomics approach. The protein abundances measured by metaproteomics can provide microbial species abundances, and evidence for the molecular phenotype of microbiota members because measured proteins indicate the metabolic and physiological processes used by a microbial community. We showed that dietary protein source significantly altered the species composition and overall function of the gut microbiota. Different dietary protein sources led to changes in the abundance of microbial proteins involved in the degradation of amino acids and the degradation of glycosylations conjugated to dietary protein. In particular, brown rice and egg white protein increased the abundance of amino acid degrading enzymes. Egg white protein increased the abundance of bacteria and proteins usually associated with the degradation of the intestinal mucus barrier. These results show that dietary protein sources can change the gut microbiota's metabolism, which could have major implications in the context of gut microbiota mediated diseases.},
}

@article {pmid40116078,
year = {2025},
author = {Whitlock, JW and Orwin, PM and Stahlschmidt, ZR},
title = {Multigenerational exposure to glyphosate has only modest effects on life history traits, stress tolerance, and microbiome in a field cricket.},
journal = {The Journal of experimental biology},
volume = {},
number = {},
pages = {},
doi = {10.1242/jeb.250210},
pmid = {40116078},
issn = {1477-9145},
support = {//University of the Pacific/ ; },
abstract = {Glyphosate (GLY) is the most used herbicide worldwide, and it can be toxic to off-target species, such as insects. While GLY-based herbicides (GBHs) can influence insect microbiomes, little is known about its cascading effects on fitness-related traits, such as life history or stress tolerance, especially in the context of long-term, multigenerational exposure. Thus, we exposed the variable field cricket, Gryllus lineaticeps, to GBH within- and across-generations to examine the potential role of GBH in developmental plasticity and evolution. Specifically, we measured its effects on life-history traits (e.g., developmental duration, adult body size and mass, and a life-history tradeoff between investment into reproduction and flight), stress (heat and desiccation) tolerance, and the gut microbiome. One generation of exposure to GBH reduced desiccation tolerance, which was also lower in flight-capable individuals. However, after 11 generations of exposure to GBH, this cost of GBH disappeared, and GBH exposure instead increased adult body size and mass in flight-incapable individuals. Flight capacity had a stronger effect on the gut bacterial community than GBH exposure where flight-capable individuals contained more than twice as many Family Oscillospiraceae and fewer than half as many Family Erysipelotrichaceae. The effects of both flight capacity and GBH on the microbiome were only evident in Generation 1. Together, our results indicate that GBH exposure may have quite modest long-term effects on stress tolerance and the gut microbiome. However, GBH may facilitate the evolution of flightlessness given its potential benefits to flight-incapable individuals, which exhibit greater reproductive potential and tolerance to climate stressors compared to flight-capable individuals.},
}

@article {pmid40115756,
year = {2025},
author = {Balaji, S and Jeyaraman, N and Jeyaraman, M and Ramasubramanian, S and Muthu, S and Santos, GS and da Fonseca, LF and Lana, JF},
title = {Impact of curcumin on gut microbiome.},
journal = {World journal of experimental medicine},
volume = {15},
number = {1},
pages = {100275},
pmid = {40115756},
issn = {2220-315X},
abstract = {The intricate interplay between natural compounds like curcumin and the gut microbiome has gained significant attention in recent years due to their potential therapeutic implications in various health conditions. Curcumin, a polyphenolic compound derived from turmeric, exhibits diverse pharmacological properties, including anti-inflammatory, antioxidant, and anticancer effects. Understanding how curcumin modulates gut microbiota composition and function is crucial for elucidating its therapeutic mechanisms. This review examines the current literature on the interactions between curcumin and the gut microbiome. A systematic search of relevant databases was conducted to identify studies investigating the effects of curcumin on gut microbial diversity and abundance. Key findings from studies exploring curcumin's efficacy in neurological disorders, gastrointestinal diseases, and metabolic dysfunction are synthesized and discussed. Studies have demonstrated that curcumin supplementation can modulate gut microbiota composition and function, leading to beneficial effects on gut health and homeostasis. Mechanisms underlying curcumin's therapeutic effects include immune modulation, neuroprotection, and inflammation regulation. However, challenges such as poor bioavailability and safety concerns remain significant hurdles to overcome. The interactions between curcumin and the gut microbiome hold promise for therapeutic interventions in a diverse range of health conditions. Further research is needed to optimize curcumin formulations, improve bioavailability, and address safety concerns.},
}

@article {pmid40115744,
year = {2025},
author = {Kimmel, M and Tong, B and Devall, AE and Björvang, RD and Schuppe-Koistinen, I and Engstrand, L and Fransson, E and Skalkidou, A and Hugerth, LW},
title = {Investigating the Microbiome in Relation to Mental Distress Across Two Points During Pregnancy: Data From U.S. and Swedish Cohorts.},
journal = {Biological psychiatry global open science},
volume = {5},
number = {3},
pages = {100453},
pmid = {40115744},
issn = {2667-1743},
abstract = {BACKGROUND: In this study, we aimed to characterize the gut microbiome and its potential functioning in 2 populations at 2 time points during pregnancy in relation to mental distress.

METHODS: During the second and third trimester, individuals from the United States and Sweden completed the Edinburgh Postnatal Depression Scale and provided fecal samples for whole-genome metagenomics. A total of 832 and 161 samples were sequenced and analyzed from the Swedish cohort and the U.S. cohort, respectively. Multiple characterizations of the microbial community were analyzed in relation to distress measured using the Edinburgh Postnatal Depression Scale. Principal coordinate analysis and distance-based redundancy analysis assessed variation in functional gut-brain modules. For the U.S. cohort, the Trier Social Stress Test was administered 8 weeks postpartum while collecting salivary cortisol.

RESULTS: Principal coordinate analysis identified 4 sample clusters based on the gut-brain modules distinguished by functions such as short-chain fatty acid synthesis and cortisol degradation. While with distance-based redundancy analysis, mental distress subtypes did not significantly contribute to variation in gut-brain modules (p = .085 for Sweden, p = .23 for the U.S.), a U.S. sample cluster distinguished by lower cortisol degradation from another cluster with higher gut microbial cortisol degradation abundance had significantly higher odds of being associated with depression (p = .024). The U.S. sample cluster with lower gut microbial cortisol degradation abundance also had significantly higher cortisol levels after a postpartum social stressor.

CONCLUSIONS: Further studies are warranted to investigate the potential for the gut microbiome to serve as biomarkers of gut-brain axis health during pregnancy across disparate populations.},
}

@article {pmid40115610,
year = {2025},
author = {Waterman, A and Doumas, SA and Fischer, M and Mattar, M and Charbel, S and Jennings, J and Doman, DB},
title = {Uncovering the Hidden Link Between the Aberrant Intestinal Microbiome and Fibromyalgia.},
journal = {Gastroenterology & hepatology},
volume = {21},
number = {2},
pages = {111-121},
pmid = {40115610},
issn = {1554-7914},
abstract = {Fibromyalgia is a multifaceted syndrome primarily characterized by chronic widespread pain and fatigue. Despite its significant prevalence and incidence, the mechanisms mediating the disease pathogenesis have remained poorly understood; however, increasing evidence suggests a potentially central role of intestinal dysbiosis. Researchers have been examining possible diagnostic biomarkers, such as Helicobacter pylori infection, urine metabolite profiles, and cytokine levels, which reflect these microbiome changes. Additionally, evaluation of therapeutic interventions targeting the gut microbiome, including probiotics, fecal microbiota transplantation, and antibiotics for specific infections, has highlighted their potential in alleviating fibromyalgia symptoms. This article delves into the emerging role of the gut microbiome in fibromyalgia pathogenesis, illustrating how alterations in gut bacterial composition and diversity are implicated in the pathophysiology of the disease through the gut-brain axis, and sets a direction for future research to enhance diagnostic accuracy and therapeutic efficacy of this complex condition.},
}

@article {pmid40115534,
year = {2025},
author = {Kushkevych, I and Dvořáková, M and Dordevic, D and Futoma-Kołoch, B and Gajdács, M and Al-Madboly, LA and Abd El-Salam, M},
title = {Advances in gut microbiota functions in inflammatory bowel disease: Dysbiosis, management, cytotoxicity assessment, and therapeutic perspectives.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {851-868},
pmid = {40115534},
issn = {2001-0370},
abstract = {Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, have become increasingly prevalent across all human generations. Despite advances in diagnosis, effective long-term therapeutic options remain limited, with many patients experiencing recurrent symptoms after treatment. The multifactorial origins of ulcerative colitis are widely recognized, but the intestinal microbiome, particularly bacteria from the Desulfovibrionaceae family, is thought to play a central role in the pathogenesis of the disease. These bacteria contribute significantly to gut microbial functions, yet their cytotoxic and viability characteristics under disease conditions remain poorly understood. Our review provides insights on recent advancements in methodologies for assessing the cytotoxicity and viability of anaerobic intestinal bacteria, with a specific focus on their relevance to gut health and disease. We introduce overview from current literature on modern techniques including flow cytometry, high-throughput screening, and molecular-based assays, highlighting their applications in understanding the role of Desulfovibrionaceae and other gut microbes in IBD pathogenesis. By bridging methodological advancements with functional implications, this review aims to enhance our understanding of gut microbiota-host interactions, which are crucial for maintaining health and preventing disease through immune modulation, where microbiota help regulate immune responses and prevent excessive inflammation; nutrient metabolism, including the breakdown of dietary fibers into short-chain fatty acids that support gut health; and colonization resistance, where beneficial microbes outcompete harmful pathogens to maintain microbial balance.},
}

@article {pmid40115500,
year = {2025},
author = {Liu, Q and Hao, N and Mi, L and Peng, S and Marie-Colette, AK and Zhao, X and Wang, J},
title = {From microbial communities to aroma profiles: A comparative study of spontaneous fermentation in merlot and cabernet sauvignon wines.},
journal = {Food chemistry: X},
volume = {26},
number = {},
pages = {102317},
pmid = {40115500},
issn = {2590-1575},
abstract = {This study aimed to compare the microbial community composition and aroma characteristics during the fermentation of different grape cultivars, Merlot and Cabernet Sauvignon. Principal Component Analysis (PCA), Partial Least Squares Discriminant Analysis (PLS-DA), and Odor Activity Value (OAV) screening identified 15 distinct active compounds. The sensory evaluation indicated that Merlot wine exhibited a more intense fruity aroma and received higher overall scores than Cabernet Sauvignon wine. High-throughput sequencing (HTS) results revealed that the microbial diversity in Merlot was higher than in Cabernet Sauvignon wine. Lachancea, Acremonium, Fructobacillus, and Lactiplantibacillus were unique to the Merlot wine, whereas Penicillium, Wickerhamomyces, Gluconobacter, and Klebsiella were exclusive to Cabernet Sauvignon wine. Saccharomyces and Tatumella were identified as the dominant microorganisms during the fermentation of both Merlot and Cabernet Sauvignon wines. Correlation analysis demonstrated a significant positive association among the dominant microbial communities, which played a crucial role in determining the formation of volatile compounds.},
}

@article {pmid40115072,
year = {2025},
author = {Li, J and Hu, X and Tao, X and Li, Y and Jiang, W and Zhao, M and Ma, Z and Chen, B and Sheng, S and Tong, J and Zhang, H and Shen, B and Gao, X},
title = {Deconstruct the link between gut microbiota and neurological diseases: application of Mendelian randomization analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1433131},
pmid = {40115072},
issn = {2235-2988},
mesh = {Humans ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics ; *Nervous System Diseases/genetics/microbiology ; Brain-Gut Axis ; Genome-Wide Association Study ; },
abstract = {BACKGROUND: Recent research on the gut-brain axis has deepened our understanding of the correlation between gut bacteria and the neurological system. The inflammatory response triggered by gut microbiota may be associated with neurodegenerative diseases. Additionally, the impact of gut microbiota on emotional state, known as the "Gut-mood" relationship, could play a role in depression and anxiety disorders.

RESULTS: This review summarizes recent data on the role of gut-brain axis in the pathophysiology of neuropsychiatric and neurological disorders including epilepsy, schizophrenia, Alzheimer's disease, brain cancer, Parkinson's disease, bipolar disorder and stroke. Also, we conducted a Mendelian randomization study on seven neurological disorders (Epilepsy, schizophrenia, Alzheimer's disease, brain cancer, Parkinson's disease, bipolar disorder and stroke). MR-Egger and MR-PRESSO tests confirmed the robustness of analysis against horizontal pleiotropy.

CONCLUSIONS: By comparing the protective and risk factors for neurological disorders found in our research and other researches, we can furtherly determine valuable indicators for disease evolution tracking and potential treatment targets. Future research should explore extensive microbiome genome-wide association study datasets using metagenomics sequencing techniques to deepen our understanding of connections and causality between neurological disorders.},
}

Humans
*Mendelian Randomization Analysis
*Gastrointestinal Microbiome/genetics
*Nervous System Diseases/genetics/microbiology
Brain-Gut Axis
Genome-Wide Association Study

@article {pmid40114846,
year = {2025},
author = {Changaris, DG},
title = {Rapid Reversal of Forearm Supinator Rigidity With Topical Isomerized Potassium Linoleate: A Novel Perspective on Microbiome-Induced Tetany.},
journal = {Cureus},
volume = {17},
number = {3},
pages = {e80896},
pmid = {40114846},
issn = {2168-8184},
abstract = {Microbes can alter host behavior, immunity, and neurological function at a distance without extension into the brain and spinal cord. Clostridia provides a predicate for such an infection in the periphery by causing "lock jaw" and generalized tetany. This case series presents five patients who showed rigidity or tetany of the forearm. All were diagnosed with vertigo of central origin by video nystagmography (VNG) and posturography. Each had an apparent slow-rolling tetany, most visible in the forearm. Each had a consistent focus of pain within the supinator, diminution of extended wrist rotation, and tender, taut bands. None had clinical evidence of injury to the ulnar, radial, or median nerves, ulnar epicondyles, or wrist. The author applied a commercial preparation of a cleanser containing isomerized potassium linoleate (KCLA) to the skin overlying the forearm's biceps, supinator, and pronator as an "alternative" medical approach to refractory rigidity and tenderness. The tenderness resolved within two to four minutes. After 3-10 minutes, follow-on extended wrist rotation improved toward the norm (p < 0.01). The improved range of motion lasted beyond discharge from the clinic visit. The rapid response in this series suggests the commensal skin biome may contribute to clinical tetany in the forearm supinator.},
}

@article {pmid40114632,
year = {2025},
author = {Zhao, X and Büdeyri Gökgöz, N and Xie, Z and Jakobsen, LMA and Nielsen, DS and Bertram, HC},
title = {Effects of calcium supplementation on the composition and activity of in vitro simulated gut microbiome during inulin fermentation.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo06365a},
pmid = {40114632},
issn = {2042-650X},
abstract = {The gut microbiome influences the availability of micronutrients in the gastrointestinal tract. However, our insights into how colonic fermentation of prebiotic fibers and lactose is modulated by the presence of micronutrients and local pH environment are limited. Here, we investigated the influence of different calcium salts (calcium phosphate (CaPi), calcium citrate (CaCi), and calcium carbonate (CaCa)) on gut microbiome composition and metabolism using inulin and lactose as carbohydrate sources under low, medium, and high in vitro colonic pH gradients. Our results showed that in vitro colonic pH gradient had a significant effect on gut microbiome diversity (observed ASVs and Shannon diversity index, p < 0.05). After 24 hours of fermentation, the calcium sources had a significant effect on beta diversity at all colonic pH gradients (adjusted p < 0.05). Although changes in GM composition were more pronounced after 24 hours, after 6 hours of fermentation, the CaPi group exhibited a higher abundance of Leuconostoc than other groups. After 24 hours of fermentation, the CaPi group exhibited a higher Blautia abundance at high colonic pH gradient and lower Bacteroides abundance at all colonic pH gradient levels. The CaCi and CaCa groups exhibited a pH-dependent decrease in the abundance of Bacteroides. In addition, Bifidobacterium abundance remained over 1% regardless of colonic pH gradient, calcium source, or fermentation time. In addition, short-chain fatty acid (SCFA) production was dependent on the calcium source. For instance, compared to the control group, the CaCi group exhibited higher acetate production at low and high colonic pH gradients, while the CaPi and CaCa groups showed enhanced lactate production at medium and low pH gradients. These findings can increase our understanding of the impacts of calcium-rich diets on the human gut microbiome and its metabolic activity.},
}

@article {pmid40114628,
year = {2025},
author = {Altun, M and Küçük, U and Yıldırım, N},
title = {Modulation of Gut Microbiota Using VSL#3 and Its Impact on Aortic Parameters in a Rat Model.},
journal = {Anatolian journal of cardiology},
volume = {},
number = {},
pages = {},
doi = {10.14744/AnatolJCardiol.2025.5048},
pmid = {40114628},
issn = {2149-2271},
abstract = {BACKGROUND: The increase in aortic stiffness is a significant parameter of cardiovascular diseases (CVDs), posing a substantial global health challenge and economic burden. The gut microbiota and its homeostasis, directly and indirectly, influence CVD. This study investigated the extent to which alterations in the gut microbiota can affect aortic parameters in a rat model through the administration of VSL#3.

METHODS: Twelve male Wistar rats were divided into VSL#3-treated and control groups. Cardiac function, aortic systolic, and diastolic values were assessed via echocardiography on day 0 and day 42, and fecal specimens were simultaneously collected from each rat. The formation and composition of the gut microbial flora were profiled using 16S rDNA gene sequencing.

RESULTS: Differences in bacterial density, as indicated by Chao analysis, exhibited statistical significance (P = .037) between the 2 groups. Additionally, in the VSL#3-treated group, significant improvements were observed in aortic systolic and diastolic diameters, as well as in aortic strain parameters, compared to the control group.

CONCLUSION: This research highlights the potential of gut microbiome modulation, specifically through VSL#3 administration, as a promising strategy to improve aortic parameters, suggesting a novel avenue for cardiovascular health interventions.},
}

@article {pmid40114538,
year = {2025},
author = {Salvatore, S and Dinleyici, EC and Szajewska, H and Canani, RB and Gutierrez-Castrellón, P and Hojsak, I and Indrio, F and Mihatsch, W and Orel, R and van Goudoever, JB and Vandenplas, Y and , },
title = {Technical review by the ESPGHAN Special Interest Group on Gut Microbiota and Modifications on the health outcomes of infant formula supplemented with synbiotic.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70031},
pmid = {40114538},
issn = {1536-4801},
support = {//None/ ; },
abstract = {This technical review-one of five developed by the European Society for Pediatric Gastroenterology, Hepatology, and Nutrition (ESPGHAN) Special Interest Group on Gut Microbiota and Modifications (SIG-GMM)-supports the preparation of a position paper on the use of biotic- and synbiotic-supplemented infant formulas. This paper also presents the statements made by the SIG-GMM after performing a technical review to evaluate the clinical effects of synbiotic-supplemented infant formulas in healthy full-term infants (0-12 months), as emerged from studies published before 2024. The review focused on the following clinical outcomes (if available): anthropometric measurements, safety, tolerability, stool frequency and consistency, infantile colic or crying, gastrointestinal symptoms, infections and antibiotic use, and allergic disorders. Following the review, all members of the SIG anonymously voted on each statement, scoring them between 0 and 9. A statement was accepted when ≥75% of the members scored >6. The technical review identified 16 randomized controlled trials that evaluated the clinical effects of synbiotic-supplemented infant formula in healthy full-term infants. The studies varied in terms of synbiotic composition, study design, intervention duration, and outcomes. Formulas supplemented with synbiotics studied so far were well tolerated and showed no significant difference compared to the non-supplemented formulas in growth parameters, gastrointestinal symptoms, stool characteristics, or safety. This technical review serves as the background for formulating recommendations on the use of synbiotic-supplemented infant formula in healthy infants studied so far.},
}

@article {pmid40114327,
year = {2025},
author = {Żychowska, M and Bakuła, Z and Decewicz, P and Hryncewicz-Gwóźdź, A and Dyląg, M and Jankowska-Konsur, A and Gawor, J and Gromadka, R and Żaczek, A and Jagielski, T},
title = {The Skin Mycobiome of Patients With Atopic Dermatitis and Healthy Volunteers: A Case-Control Study.},
journal = {Experimental dermatology},
volume = {34},
number = {3},
pages = {e70085},
doi = {10.1111/exd.70085},
pmid = {40114327},
issn = {1600-0625},
support = {0258/IP1/2016/74//Ministerstwo Edukacji i Nauki/ ; },
mesh = {Humans ; *Dermatitis, Atopic/microbiology ; *Mycobiome ; Case-Control Studies ; Adult ; Female ; Male ; *Skin/microbiology ; Middle Aged ; Young Adult ; Healthy Volunteers ; Malassezia/isolation & purification ; Adolescent ; },
abstract = {Atopic dermatitis (AD) is a common inflammatory skin disease, for which dysbiosis of the skin mycobiome is considered a triggering factor. The aim of this study was to explore the skin mycobiome of AD patients and healthy volunteers (HV). The study included 50 AD patients and as many HV. Culture-based species identification involved a battery of conventional phenotypic tests and PCR sequencing of the internal transcribed spacer (ITS) 1 and 2 regions within the rDNA cluster. Culture-independent, metataxonomic sequencing was performed with ITS1 as the target region. The overall culture-positive rate was higher in AD patients than in HV (74% vs 28%). Among the former, Rhodotorula spp. dominated, followed by Candida spp., Malassezia spp. and Naganishia albida. The congruence between PCR sequencing and phenotyping was 68.6%. Upon metataxonomy of AD samples, 33 (66%) demonstrated close clustering with HV samples ('control-like' AD), while 17 (34%) displayed a remarkably different mycobiome composition ('AD-specific'), with Cladosporium, Malassezia, Candida, Diplodia, Saccharomyces, Penicillium and Aspergillus genera showing increased abundance. Patients with 'AD-specific' mycobiomes were more commonly exposed to air-conditioning compared to 'control-like' AD patients (p = 0.030). A subset of patients with AD has a different cutaneous mycobiome make-up dominated by environmental moulds, and Malassezia and Candida yeasts. Anthropogenic factors may affect the cutaneous mycobiome composition in AD and should be taken into account in microbiome studies.},
}

Humans
*Dermatitis, Atopic/microbiology
*Mycobiome
Case-Control Studies
Adult
Female
Male
*Skin/microbiology
Middle Aged
Young Adult
Healthy Volunteers
Malassezia/isolation & purification
Adolescent

@article {pmid40114168,
year = {2025},
author = {Wu, Y and Qu, Z and Wu, Z and Zhuang, J and Wang, Y and Wang, Z and Chu, J and Qi, Q and Han, S},
title = {Multiple primary malignancies and gut microbiome.},
journal = {BMC cancer},
volume = {25},
number = {1},
pages = {516},
pmid = {40114168},
issn = {1471-2407},
support = {2022E50008, 2024ZY01056//Zhejiang Provincial Clinical Research Center for CANCER/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; Middle Aged ; *Metagenomics/methods ; *Neoplasms, Multiple Primary/microbiology/virology ; Colorectal Neoplasms/microbiology/virology ; Adult ; Aged ; Bacteria/classification/genetics/isolation & purification ; Enterovirus/isolation & purification/genetics ; Case-Control Studies ; Feces/microbiology/virology ; },
abstract = {BACKGROUND: Multiple primary malignancies (MPM) are two or more independent primary malignancies. Recently, the relationship between microbiome and various tumors has been gradually focused on.

OBJECTIVE: To describe the relationship between MPM patients (MPMs) and gut microbiome.

METHODS: A total of 27 MPMs, 30 colorectal cancer patients (CRCs), and 30 healthy individuals were included to obtain metagenomic sequencing data. The knowledge graphs of gut bacteria and enteroviruses were plotted based on metagenomics. Wilcoxon rank-sum test was used to screen the characteristic gut microbiome.

RESULTS: The knowledge graph of gut microbiome in MPM patients was plotted. A total of 26 different gut bacteria, including Dialister, Fecalibacterium and Mediterraneibacter, were found between MPMs and healthy individuals. Twenty gut bacteria, including Parvimonas, Dialister and Mediterraneibacter, were more abundant in MPM complicated by CRC compared with CRCs. Twenty-one different enterovirus, including Triavirus, Punavirus and Lilyvirus, were screened between MPMs and healthy individuals. Triavirus, Punavirus and Lilyvirus were less abundant in MPM than healthy individuals. The abundance of Triavirus, Punavirus and Lilyvirus in CRC patients were also lower than MPM complicated by CRC patients.

CONCLUSION: The knowledge graph of gut microbiome in MPM patients was plotted. It may provide basic data support for future research of MPM.},
}

Humans
*Gastrointestinal Microbiome
Female
Male
Middle Aged
*Metagenomics/methods
*Neoplasms, Multiple Primary/microbiology/virology
Colorectal Neoplasms/microbiology/virology
Adult
Aged
Bacteria/classification/genetics/isolation & purification
Enterovirus/isolation & purification/genetics
Case-Control Studies
Feces/microbiology/virology

@article {pmid40114065,
year = {2025},
author = {Pyakurel, S and Caddey, BJ and Dias, AP and De Buck, J and Morck, DW and Orsel, K},
title = {Profiling bacterial communities in feedlot cattle affected with bovine foot rot and bovine digital dermatitis lesions using 16S rRNA gene sequencing and quantitative real-time PCR.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {158},
pmid = {40114065},
issn = {1471-2180},
mesh = {Animals ; Cattle ; *RNA, Ribosomal, 16S/genetics ; *Real-Time Polymerase Chain Reaction/methods ; *Digital Dermatitis/microbiology ; *Cattle Diseases/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *DNA, Bacterial/genetics ; Microbiota ; Foot Diseases/microbiology/veterinary ; Skin/microbiology/pathology ; Treponema/genetics/classification/isolation & purification ; Fusobacterium necrophorum/genetics/isolation & purification ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: The primary infectious foot diseases in cattle, bovine foot rot (BFR) and bovine digital dermatitis (BDD), commonly associated with Fusobacterium necrophorum and Treponema spp., respectively, are considered polybacterial in etiology with several additional bacteria involved such as Porphyromonas levii, Bacteroides pyogenes, and Fusobacterium mortiferum. BDD is further classified into several M-stages (M2: active and ulcerative; M4: chronic proliferative). Using quantitative real-time PCR and 16S rRNA gene (V3-V4 region) sequencing, we quantified several specific bacteria and analyzed bacterial communities present in biopsies of visually diagnosed cases of BFR (n = 32), M2 (n = 17), and M4 (n = 12) stages of BDD in feedlot cattle in contrast to inconclusive (n = 14) clinical cases and healthy (n = 25) cattle.

RESULTS: Bacterial composition of healthy skin differed significantly from that of skin lesions, and between BFR and both lesion stages of BDD, which also differed from each other. All animal groups had generally the same bacterial species, albeit in distinct ratios. Differential abundance analysis relative to the healthy group identified a higher abundance of Fusobacterium spp. in BFR and Treponema spp. in both BDD-M2 and BDD-M4. P. levii had the highest absolute abundance in all animal groups. A significantly higher abundance of F. necrophorum was observed in BFR compared to BDD-M2, and F. mortiferum in both stages of BDD compared to the inconclusive group. Both BDD M-stages had a significantly higher abundance of Treponema phagedenis and Treponema pedis. Treponema medium was significantly more abundant in BDD-M4 compared to BDD-M2.

CONCLUSION: These results further the evidence of the involvement of Treponema spp., in BDD in feedlot cattle. However, it suggests further exploration of the role of Fusobacterium spp. in BFR and BDD. Importantly, a discriminating polybacterial involvement in these infections was evident demonstrated by changes in the population of multiple bacteria when compared to healthy animals.},
}

Animals
Cattle
*RNA, Ribosomal, 16S/genetics
*Real-Time Polymerase Chain Reaction/methods
*Digital Dermatitis/microbiology
*Cattle Diseases/microbiology
*Bacteria/classification/genetics/isolation & purification
*DNA, Bacterial/genetics
Microbiota
Foot Diseases/microbiology/veterinary
Skin/microbiology/pathology
Treponema/genetics/classification/isolation & purification
Fusobacterium necrophorum/genetics/isolation & purification
Sequence Analysis, DNA/methods

@article {pmid40113967,
year = {2025},
author = {Mannaa, M and Park, AR and Kim, JC and Seo, YS},
title = {Microbial allies recruited by Bacillus subtilis JCK-1398 to defend pine trees against pinewood nematode.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {9670},
pmid = {40113967},
issn = {2045-2322},
mesh = {Animals ; *Pinus/parasitology/microbiology ; *Plant Diseases/parasitology/microbiology/prevention & control ; *Bacillus subtilis/physiology ; Rhizosphere ; Microbiota ; Nematoda/microbiology/physiology ; Soil Microbiology ; Disease Resistance ; Pantoea/physiology/genetics ; },
abstract = {Pine wilt disease (PWD) is a devastating disease caused by the pinewood nematode (Bursaphelenchus xylophilus). Its substantial ecological disruption harms global forestry and poses serious economic challenges. Although previous research has demonstrated that Bacillus subtilis JCK-1398 has the potential to induce systemic resistance in pine trees, the ecological mechanisms underlying its biocontrol efficacy remain underexplored. This study investigated how JCK-1398 treatment influences rhizosphere- and nematode-associated microbial communities to mitigate PWD. Metabarcoding analyses revealed that JCK-1398 treatment increased the abundance of beneficial microbial taxa (e.g., Nocardioides and Mesorhizobium) in the rhizosphere microbiome. Concurrently, nematode-associated microbial communities became dominated by Pantoea, a genus with known nematicidal properties. Isolation and characterization of Pantoea dispersa BC11 confirmed that it significantly limits nematode viability. These findings highlight the multifaceted defense that JCK-1398 offers, not only inducing systemic resistance, but also orchestrating beneficial microbiome dynamics. This study emphasizes the potential of manipulating a microbial holobiont for eco-friendly and sustainable disease management. The ability of JCK-1398 to recruit and enhance microbial allies offers a novel framework for developing biocontrol agents, with implications for managing PWD and other plant-pathogen systems.},
}

Animals
*Pinus/parasitology/microbiology
*Plant Diseases/parasitology/microbiology/prevention & control
*Bacillus subtilis/physiology
Rhizosphere
Microbiota
Nematoda/microbiology/physiology
Soil Microbiology
Disease Resistance
Pantoea/physiology/genetics

@article {pmid40113862,
year = {2025},
author = {Groen-van Schooten, TS and Cabeza-Segura, M and Ferreira, RM and Martínez-Ciarpaglini, C and Barros, R and Santos-Antunes, J and Costa, A and Fernández-Figueroa, EA and Lino-Silva, L and Hernandez-Guerrero, AI and Ruiz-García, E and Caballero, C and Boggino, H and Gauna, C and Cantero, D and Freile, B and Esteso, F and O Connor, J and Riquelme, A and Owen, G and Riquelme, E and Roa, JC and Latorre, G and Garrido, M and Ruiz-Pace, F and Diez García, M and Alsina, M and Lordick, F and Farrés, J and Carbonell-Asins, JA and Villagrasa, R and Pereira, R and Pouw, RE and Jimenez-Martí, E and Miralles, A and Dientsmann, R and Figueiredo, C and Carneiro, F and Cervantes, A and Derks, S and Fleitas, T},
title = {Immune profiling of gastric adenocarcinomas in EU and LATAM countries identifies global differences in immune subgroups and microbiome influence.},
journal = {British journal of cancer},
volume = {},
number = {},
pages = {},
pmid = {40113862},
issn = {1532-1827},
abstract = {BACKGROUND: Gastric cancer (GC) patients from European (EU) and especially Latin American (LATAM) countries are underrepresented in previous large-scale multi-omic studies that have identified clinically relevant subgroups. The LEGACY study aimed to profile the molecular and immunological features of GCs from EU and LATAM countries.

METHODS: Tumor biopsies from 95 EU and 56 LATAM GCs were profiled with immunohistochemistry (CD3, CD8, FOXP3, PD-L1, MSI and HER2), Nanostring mRNA expression analyses, and microbiome sequencing.

RESULTS: Immune profiling identified four distinct immune clusters: a T cell dominant cluster with enriched activation pathways, a macrophage dominant cluster and an immune excluded microenvironment which were equally distributed among the countries. A fourth cluster of mostly Mexican patients consisted of excessive T cell numbers accompanied by enhanced cytokine signaling in absence of enhanced antigen presentation and cytotoxicity signatures and a strong association with H. pylori infection.

DISCUSSION: Both EU and LATAM countries have GCs with a T cell inflamed microenvironment that might benefit from checkpoint inhibition. We identified a highly inflamed GC subgroup that lacked antigen presentation and cytotoxicity associated with H. pylori CagA-positive strains, suggesting their contribution to tumor immune tolerance. Future studies are needed to unravel whether these cancers benefit from immunotherapy as well.},
}

@article {pmid40113782,
year = {2025},
author = {Park, G and Johnson, K and Miller, K and Kadyan, S and Singar, S and Patoine, C and Hao, F and Lee, Y and Patterson, AD and Arjmandi, B and Kris-Etherton, PM and Berryman, CE and Nagpal, R},
title = {Almond snacking modulates gut microbiome and metabolome in association with improved cardiometabolic and inflammatory markers.},
journal = {NPJ science of food},
volume = {9},
number = {1},
pages = {35},
pmid = {40113782},
issn = {2396-8370},
support = {ECP-Nagpal-NR-001//Almond Board of California/ ; 24A05//Florida Department of Health/ ; },
abstract = {Western-style dietary patterns have been linked with obesity and associated metabolic disorders and gut dysbiosis, whereas prudent dietary and snacking choices mitigate these predispositions. Using a multi-omics approach, we investigated how almond snacking counters gut imbalances linked to adiposity and an average American Diet (AAD). Fifteen adults with overweight or obesity underwent a randomized, crossover-controlled feeding trial comparing a 4-week AAD with a similar isocaloric diet supplemented with 42.5 g/day of almonds (ALD). Almond snacking increases functional gut microbes, including Faecalibacterium prausnitzii, while suppressing opportunistic pathogens, thereby favorably modulating gut microecological niches through symbiotic and microbe-metabolite interactions. Moreover, ALD elevates health-beneficial monosaccharides and fosters bacterial consumption of amino acids, owing to enhanced microbial homeostasis. Additionally, ALD enhances metabolic homeostasis through a ketosis-like effect, reduces inflammation, and improves satiety-regulating hormones. The findings suggest that prudent dietary choices, such as almond snacking, promote gut microbial homeostasis while modulating immune metabolic state.},
}

@article {pmid40113766,
year = {2025},
author = {Nodit, L and Kelley, JR and Panella, TJ and Bruckbauer, A and Nodit, PG and Shope, GA and Peyton, K and Klingeman, DM and Zaretzki, R and Carrell, A and Podar, M},
title = {Oral microbiome and mycobiome dynamics in cancer therapy-induced oral mucositis.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {463},
pmid = {40113766},
issn = {2052-4463},
mesh = {Humans ; *Stomatitis/microbiology/etiology ; *Microbiota ; *Mycobiome ; Longitudinal Studies ; Mouth/microbiology ; Carcinoma, Squamous Cell/therapy/microbiology ; Chemoradiotherapy/adverse effects ; Oropharyngeal Neoplasms/therapy/microbiology ; },
abstract = {Cancer therapy-induced oral mucositis is a frequent major oncological problem, secondary to cytotoxicity of chemo-radiation treatment. Oral mucositis commonly occurs 7-10 days after initiation of therapy; it is a dose-limiting side effect causing significant pain, eating difficulty, need for parenteral nutrition and a rise of infections. The pathobiology derives from complex interactions between the epithelial component, inflammation, and the oral microbiome. Our longitudinal study analysed the dynamics of the oral microbiome (bacteria and fungi) in nineteen patients undergoing chemo-radiation therapy for oral and oropharyngeal squamous cell carcinoma as compared to healthy volunteers. The microbiome was characterized in multiple oral sample types using rRNA and ITS sequence amplicons and followed the treatment regimens. Microbial taxonomic diversity and relative abundance may be correlated with disease state, type of treatment and responses. Identification of microbial-host interactions could lead to further therapeutic interventions of mucositis to re-establish normal flora and promote patients' health. Data presented here could enhance, complement and diversify other studies that link microbiomes to oral disease, prophylactics, treatments, and outcome.},
}

Humans
*Stomatitis/microbiology/etiology
*Microbiota
*Mycobiome
Longitudinal Studies
Mouth/microbiology
Carcinoma, Squamous Cell/therapy/microbiology
Chemoradiotherapy/adverse effects
Oropharyngeal Neoplasms/therapy/microbiology

@article {pmid40113321,
year = {2025},
author = {Yan, ZH and Cheng, X and Hu, TH and Zhong, QH},
title = {[Accumulation and Clearance of Polystyrene Microplastics in Brine Shrimp and the Responses of Microbiome and Metabolism].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {3},
pages = {1841-1849},
doi = {10.13227/j.hjkx.202403163},
pmid = {40113321},
issn = {0250-3301},
mesh = {Animals ; *Artemia ; *Microplastics/toxicity/metabolism ; *Polystyrenes/toxicity/metabolism ; *Water Pollutants, Chemical/metabolism ; *Microbiota ; Particle Size ; },
abstract = {To investigate the accumulation kinetics of microplastics （MPs） with different characteristics in zooplankton and the related biological effects, the accumulation and clearance of polystyrene microplastics （PS-MPs） with different concentrations and particle sizes in brine shrimp （Artemiasaline） were analyzed under different nutritional conditions. The responses of microbial communities and metabolic functions in brine shrimp were revealed using the combination methods of microbiome and metabolome. The results showed that the accumulation and clearance rate of PS-MPs in brine shrimp increased with the increase in exposure concentrations, showing a concentration-dependent manner. On the contrary, the accumulation and clearance of PS-MPs in brine shrimp were negatively correlated with their particle sizes. The nutritional condition did not alter the accumulation kinetics of PS-MPs in brine shrimp, indicating that short-term feeding may have had no effect on the uptake and clearance of PS-MPs in brine shrimp. Compared to that in the control, exposure to PS-MPs significantly enhanced the diversity of the microbial community in brine shrimp. The proportions of Proteobacteria and Acinetobacter were increased by 0.4 folds and 12.3 folds, respectively, whereas the proportions of Firmicutes and Bacillus were decreased by 43% and 86%, respectively. This finding indicates that PS-MPs may have caused an imbalance of the bacterial community in brine shrimp by inhibiting the beneficial bacteria and stimulating the harmful bacteria, thus disrupting the metabolic function in brine shrimp. In addition, exposure to PS-MPs resulted in a production of 2 311 different metabolites in brine shrimp and mainly disrupted the pyrimidine metabolism and the biosynthesis of dermal sulfate/chondroitin sulfate in brine shrimp, leading to toxicity in the shrimp. The accumulation and biological effects of MPs with different characteristics in zooplankton may further affect the stability of aquatic systems, leading to unpredictable ecological risks.},
}

Animals
*Artemia
*Microplastics/toxicity/metabolism
*Polystyrenes/toxicity/metabolism
*Water Pollutants, Chemical/metabolism
*Microbiota
Particle Size

@article {pmid40113228,
year = {2025},
author = {Cavon, J and Basso, M and Kadosh, KC and Gibbons, SM},
title = {The human gut microbiome and sleep across adulthood: associations and therapeutic potential.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf043},
pmid = {40113228},
issn = {1472-765X},
abstract = {Sleep is an essential homeostatic process that undergoes dynamic changes throughout the lifespan, with distinct life stages predisposed to specific sleep pathologies. Similarly, the gut microbiome also varies with age, with different signatures associated with health and disease in the latest decades of life. Emerging research has shown significant cross-talk between the gut microbiota and the brain through several pathways, suggesting the microbiota may influence sleep, though the specific mechanisms remain to be elucidated. Here, we critically examine the existing literature on the potential impacts of the gut microbiome on sleep and how this relationship varies across adulthood. We suggest that age-related shifts in gut microbiome composition and immune function may, in part, drive age-related changes in sleep. We conclude with an outlook on the therapeutic potential of microbiome-targeted interventions aimed at improving sleep across adulthood, particularly for individuals experiencing high stress or with sleep complaints.},
}

@article {pmid40113076,
year = {2025},
author = {Xu, HS and Chen, Y and Lin, YJ and Eldefrawy, F and Kramer, NE and Siracusa, JS and Kong, F and Guo, TL},
title = {Nanocellulose dysregulated glucose homeostasis in female mice on a Western diet: The role of gut microbiome.},
journal = {Life sciences},
volume = {},
number = {},
pages = {123567},
doi = {10.1016/j.lfs.2025.123567},
pmid = {40113076},
issn = {1879-0631},
abstract = {There is currently increased interest in nanocellulose as a food emulsifier and dietary supplement. It was hypothesized that nanocellulose could modulate behaviors and glucose homeostasis in female mice using mechanisms of altered gut microbiome and immune modulation. An initial experiment was conducted with the objective of examining whether three common types of nanocellulose affected the gut microbiome of female C57BL/6 mice on a Western diet. Cellulose nanofibrils (CNF), TEMPO-CNF and cellulose nanocrystals were administered at the physiologically relevant dose of 30 mg/kg/day for 30 days by gavage, with cellulose and water groups as the positive and negative controls, respectively. Findings suggested that CNF had the strongest effect on the gut microbiome. CNF was therefore selected for a chronic 6-month study on the gut microbiome, immune system and behaviors in female NOD mice, a model for type 1 diabetes. Gut microbiome analysis suggested that there might be some beneficial changes following subchronic exposure (e.g., at the two-month timepoint), however, this effect was no longer seen after chronic consumption (e.g., at the six-month timepoint). CNF treatment also altered the immune homeostasis, including decreases in the splenic Mac-3[+] population and serum level of proinflammatory chemokine LIX. Additionally, CNF consumption decreased diabetic incidences but had no effect on the depressive-like behavior and grip strength. However, further analysis, e.g., the insulin tolerance test, indicated that CNF-treated NOD mice might exhibit signs of insulin resistance. Taken together, nanocellulose dysregulated glucose homeostasis in female mice on a Western diet involving mechanisms related to alteration of the gut microbiome.},
}

@article {pmid40112923,
year = {2025},
author = {Majenka, P and Hoffmann, M and Strobel, S and Rötzer, I and Enk, A and Hassel, JC},
title = {Influence of high-fiber diet on ipilimumab-induced gastrointestinal toxicity in metastatic melanoma.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clnesp.2025.03.026},
pmid = {40112923},
issn = {2405-4577},
abstract = {BACKGROUND: The anti-cytotoxic T-lymphocyte-associated protein (CTLA)-4 antibody ipilimumab (ipi) and the anti-programmed death (PD)-1 antibody nivolumab (nivo) are routinely used to treat metastatic melanoma. One of the most frequent severe immune-related adverse events (irAEs) induced by ipi is diarrhea as a symptom of ir-colitis. Here, the composition of the gut microbiome was shown to correlate with the risk of developing colitis. Stimulated by a patient case and the knowledge that nutrition influences the gut microbiome, we performed a retrospective analysis to evaluate dietary habits and the frequency of colitis in patients with ipi +/- nivo therapy.

METHODS: Patients with metastasized stage III or IV melanoma who were treated with ipi +/- nivo and who were willing to take part in a nutritional survey and interview at least three months after the first ipi dose were included into the study. Dietary habits were investigated using the food frequency questionnaire (FFQ) and personal interviews. The calculated daily intake of calories, carbohydrates, fats, proteins, sugars, and dietary fiber was correlated with the development of ir-colitis.

RESULTS: 20 patients were included into this study, and all but one received ipi-nivo combination therapy. The median age was 59.5 years, and 60% were male. 4 of 20 patients (20%) developed ir-colitis grade 3 after two cycles in the median and were managed with at least high-dose corticosteroids. The FFQ and interview were conducted in a median of six months after treatment initiation. In general, the interviewed patients followed a typical western-pattern diet based on carbohydrates as the main, followed by fat as the second most important energy substrate. Comparing patients with and without colitis our investigation revealed that the achieved amount of recommended dietary fiber intake per total energy intake (TEI) was negatively associated with diarrhea and colitis (p = 0.061). No significant differences concerning daily intake of calories, carbohydrates, fats, proteins, and sugar were found. In addition, no significant differences were found among patients in terms of their age, gender, tobacco use, supplement intake, therapy regime, or body mass index (BMI).

CONCLUSIONS: This pilot study gives first hints that nutritional habits might influence treatment tolerability to ipi +/- nivo therapy. A high-fiber diet might protect against ir-colitis and diarrhea in ipi-treated patients. This observation should be validated by a prospective randomized interventional trial. However, if it is possible to prevent ir-colitis by a high-fiber diet that would be of great impact on routine patient treatment.},
}

@article {pmid40112626,
year = {2025},
author = {Sun, N and Xin, J and Zhao, Z and Chen, Y and Gan, B and Duan, L and Luo, J and Wang, D and Zeng, Y and Pan, K and Jing, B and Zeng, D and Ma, H and Wang, H and Ni, X},
title = {Improved effect of antibiotic treatments on the hippocampal spatial memory dysfunction of mice induced by high fluoride exposure: Insight from assembly processes and co-occurrence networks of gut microbial community.},
journal = {Ecotoxicology and environmental safety},
volume = {294},
number = {},
pages = {118048},
doi = {10.1016/j.ecoenv.2025.118048},
pmid = {40112626},
issn = {1090-2414},
abstract = {High fluoride exposure was widely demonstrated to be related with brain memory impairment. Since the absorption of F[-] enters the body mainly through the gastrointestinal tract, studying the effects of excessive intake of fluoride on brain memory function in various gut microbiome states might have profound implications for the prevention of fluorosis because growing evidence revealed the significance of the "microbiota-gut-brain" axis (MGBA). In the present study, we aimed to illustrate the potential mechanism of gut microbiota on high fluoride exposure-induced hippocampal lesions and spatial memory dysfunction in mice by the various intestinal microecological environments, which were constructed by antibiotic treatment. Mice fed with normal (CG1 and Exp1 groups) or sodium-fluoride (CG2 and Exp2 groups; 24 mg/kg sodium fluoride per mouse) by gavage administration with or without antibiotic treatments, a combination of metronidazole (1 g/L) and ciprofloxacin (0.2 g/L) in drinking water. Mice gavaged with excessive sodium fluoride alone exhibited reduced weight gain, hippocampal tissue damages, spatial memory levels dysfunction, impaired intestinal permeability, decreased inflammatory cytokines expression and antioxidant capability in the hippocampal and ileal tissues. In contrast, antibiotic intervention significantly reversed these high fluoride exposure-induced hippocampal and ileal changes.16S rRNA high throughput sequencing found that ileal microbiota were dominated by abundant taxa, which is conducive to constructing microbial interaction networks and module communities, and identifying keystone species targeted by high fluoride exposure compared with colonic microbiome. In addition, the microbial community composition and assembly mechanism of ileal microbiome under the effects of antibiotics were suitable for revealing the characteristics of high fluoride environment. In the later analysis, Lactobacillus, Staphylococcus, Muribaculaceae and Robinsoniella were considered as the keystone species targeted by high fluoride-exposed mice based on the analysis of network node properties and niche overlap of ileal microbes. Spearman rank correlation demonstrated that these keystone species had significant effects on hippocampal memory levels and intestinal health, as well as microbial communities functions. Compared to previous researches, this study further revealed intestinal microbial coummunity mediated the underlying mechanism through antibiotic treatment against high fluoride-induce hippocampal spatial memory impairment.},
}

@article {pmid40112608,
year = {2025},
author = {Chen, J and Wang, Z and Shen, X and Chen, R and Peng, Y and Cai, Y and Zeng, S and Liu, D and Yang, J and Zhuang, W and Wang, S and Xu, J and Ying, H},
title = {Solid-state fermentation through synthetic microbiome: An effective strategy for converting Chinese distillers' grains into functional protein feed.},
journal = {International journal of food microbiology},
volume = {435},
number = {},
pages = {111154},
doi = {10.1016/j.ijfoodmicro.2025.111154},
pmid = {40112608},
issn = {1879-3460},
abstract = {Chinese distillers' grains (CDGs), a byproduct of liquor production, have low protein, high fiber, and elevated alcohol/lactic acid levels, limiting their use as animal feed. This study utilised a synthetic microbiome composed of Candida utilis (protein enhancement), Trichoderma viride (fiber reduction), Bacillus subtilis (detoxification), and Lactobacillus casei (functional enhancement) for solid-state fermentation. The results showed that crude protein content increased to 23.61 %, and true protein content to 20.45 %. Crude fiber, ethanol, lactic acid, and acetic acid contents decreased by 22.31 %, 77.25 %, 85.08 %, and 73.89 %, respectively. Amino acid content increased by 23.80 %, and flavour compounds rose by 140.76 %. Mycotoxins like aflatoxin B1 (AFB1) and ochratoxin A (OTA) were undetectable, while vomitoxin (DON) remained below EU limits. In vitro digestibility of dry matter increased by 98.36 %. Pilot-scale trials showed a 1.42-fold increase in crude protein and a 1.34-fold increase in true protein, contributing to more efficient CDG utilisation and reduced agricultural costs.},
}

@article {pmid40111997,
year = {2025},
author = {Nikitashina, L and Chen, X and Radosa, L and Li, K and Straßburger, M and Seelbinder, B and Böhnke, W and Vielreicher, S and Nietzsche, S and Heinekamp, T and Jacobsen, ID and Panagiotou, G and Brakhage, AA},
title = {The murine lung microbiome is disbalanced by the human-pathogenic fungus Aspergillus fumigatus resulting in enrichment of anaerobic bacteria.},
journal = {Cell reports},
volume = {44},
number = {3},
pages = {115442},
doi = {10.1016/j.celrep.2025.115442},
pmid = {40111997},
issn = {2211-1247},
abstract = {Here, we report significant changes in the composition of the lung microbiome and metabolome of mice under immune suppression, infection of immunosuppressed mice with virulent and avirulent strains of the clinically important human-pathogenic fungus Aspergillus fumigatus, and treatment with the clinically used antifungal drug voriconazole. Our data also indicate the important role of the gut microbiome for lung homeostasis mediated by the plasma metabolome. In the lung microbiome, DNA sequencing indicates that infection by A. fumigatus leads to a significant increase of anaerobic bacteria, most prominently of Ligilactobacillus murinus; the latter has been confirmed by qPCR analyses. We also isolated live bacteria, including L. murinus, from the murine lower respiratory tract. Co-cultivation of L. murinus and A. fumigatus leads to a reduction in oxygen concentration accompanied by an increase of L. murinus cells, suggesting that A. fumigatus establishes a microaerophilic niche, thereby promoting growth of anaerobic bacteria.},
}

@article {pmid40111698,
year = {2025},
author = {Vernon, JJ},
title = {Modulation of the Human Microbiome: Probiotics, Prebiotics, and Microbial Transplants.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {277-294},
pmid = {40111698},
issn = {0065-2598},
mesh = {Humans ; *Prebiotics/administration & dosage ; *Probiotics/therapeutic use ; *Microbiota/physiology ; Mouth/microbiology ; Gastrointestinal Microbiome/physiology ; Fecal Microbiota Transplantation/methods ; },
abstract = {The balance between health and disease is intrinsically linked to the interactions between microbial communities and the host. This complex environment of antagonism and synergy involves both prokaryotic and eukaryotic cells, whose collaborative metabolic pathways and immunomodulatory elements influence system homeostasis. As with the gut and other niches, the oral microbiome has the capacity to affect distal host sites. The ability to manipulate this environment holds the potential to impact local and systemic disease.With the increasing threat of antimicrobial resistance, novel approaches to reduce the burden of disease are essential. The use of probiotics and prebiotics is one such strategy. Probiotics introduce non-pathogenic bacteria into the environment to compete with pathogens for nutrients and attachment sites, or to produce metabolites that counteract disease aetiologies. Prebiotic compounds enhance the growth of health-associated organisms, offering additional benefits, whilst a conjunctive approach with probiotics potentially holds even greater promise. Though widely studied in the gastrointestinal context, their potential for treating oral diseases, such as dental caries and periodontitis, is less understood. Additionally, the use of microbial transplantations has demonstrated efficacy in other areas, reducing systemic inflammation and recolonising with commensal bacteria. Here we evaluate their use in the oral context and their modulatory impact on overall health.In this chapter, we discuss how pro- and prebiotic strategies seek to modulate both the oral and gut environments to promote oral health and prevent disease. We assess novel approaches for utilising health-associated microorganisms to combat oral disorders, either administered locally in the mouth or imparting influence through immune modulation via the oral-gut axis. By examining available clinical trial data, we aim to further understand the intricacies involved in this discipline. Furthermore, we consider the challenges facing the research community, including optimal candidate organism/compound selection and colonisation retention, as well as considerations for future research.},
}

Humans
*Prebiotics/administration & dosage
*Probiotics/therapeutic use
*Microbiota/physiology
Mouth/microbiology
Gastrointestinal Microbiome/physiology
Fecal Microbiota Transplantation/methods

@article {pmid40111697,
year = {2025},
author = {Bartsch, S and Scholz, KJ and Al-Ahmad, A and Cieplik, F},
title = {Effects of Antimicrobial Agents Used for Dental Treatments: Impacts on the Human Oral Ecosystem and the Resistome.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {261-275},
pmid = {40111697},
issn = {0065-2598},
mesh = {Humans ; *Mouth/microbiology/drug effects ; *Drug Resistance, Bacterial/genetics/drug effects ; *Microbiota/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Anti-Infective Agents/pharmacology ; Bacteria/drug effects/genetics ; },
abstract = {Antimicrobial resistance (AMR) is a major public health concern, especially with regard to bacterial resistance to antibiotics. Dentists are responsible for approximately 10% of all antibiotic prescriptions. In addition, there seems to be a lack of awareness of potential resistance toward antiseptics and biocides such as chlorhexidine digluconate (CHX) or cetylpyridinium chloride (CPC), which are commonly used in dental practice but also included in over-the-counter products. In comparison to the gut microbiome, only a small number of studies have investigated the impact of antibiotics on the oral microbiome. Amoxicillin is a commonly prescribed antibiotic in dentistry, often used in combination with metronidazole. Several studies have addressed its impact on the oral microbiome. Similarly, the effects of ciprofloxacin, clindamycin, cephazolin, and benzylpenicillin have also been examined in various studies. However, due to variations in study designs, it is difficult to compare the effects of antibiotics on the oral microbiota, and conclusions can only be drawn at the phyla level. In contrast, studies on CPC and CHX have also focused on the genus level. The oral resistome mainly contains genes involved in resistance to macrolides, MLSB (macrolide, lincosamide, and streptogramin B), lincosamide and streptogramin A, fluoroquinolone, tetracycline, or penicillin. The oral cavity therefore serves as a reservoir for antibiotic resistance genes (ARGs), which are of crucial importance both for inflammations in the oral cavity and for the treatment of the entire human organism. Therefore, dentists must weigh up the benefits and risks of using antibiotics very carefully.},
}

Humans
*Mouth/microbiology/drug effects
*Drug Resistance, Bacterial/genetics/drug effects
*Microbiota/drug effects/genetics
Anti-Bacterial Agents/pharmacology
Anti-Infective Agents/pharmacology
Bacteria/drug effects/genetics

@article {pmid40115491,
year = {2024},
author = {Parizi, MK and Matsukawa, A and Alimohammadi, A and Klemm, J and Tsuboi, I and Fazekas, T and Laukhtina, E and Chiujdea, S and Karakiewicz, PI and Shariat, SF},
title = {Genitourinary microbiomes and prostate cancer: a systematic review and meta-analysis of tumorigeneses and cancer characteristics.},
journal = {Central European journal of urology},
volume = {77},
number = {3},
pages = {447-455},
pmid = {40115491},
issn = {2080-4806},
abstract = {INTRODUCTION: We assessed the association of genitourinary microbiomes with prostate cancer (PCa) tumorigeneses and cancer characteristics.

MATERIAL AND METHODS: A systematic search and meta-analysis was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement. The primary endpoints were the association between relative abundance of genitourinary microbiomes and PCa compared to non-cancerous men/prostate specimen, high grade disease, and disease progression. The odds ratio (OR) was used as the summary statistic, and results were reported with 95% confidence intervals (CI).

RESULTS: Seventeen studies, comprising 2,195 patients were eligible for review and meta-analysis. The specific microbiomes in urine, prostate tissue, and prostate (or seminal) secretions were significantly more abundant in patients with PCa compared to men in the control groups in individual studies. Certain bacterial phyla, genuses, and species were significantly associated with PCa aggressiveness and disease progression in individual studies. The relative abundance meta-analysis of five urine microbiomes revealed no statistically significant differences between PCa patients and control groups (pooled OR, 1.35; 95% CI: 0.70-2.59).

CONCLUSIONS: Our systematic review indicates that specific genitourinary microbiomes are more abundant in PCa and have a potential to predict/prognosticate disease aggressiveness and clinical outcomes. Nevertheless, these findings should be interpreted with caution owing to the significant heterogeneity among studies in terms of microbiome analysis method, assessed sample's characteristics, and individual biological behavior of microbiomes for analysis. Further studies are needed to validate these observations and shed more light on the role of the microbiome across the development and natural history of PCa.},
}

@article {pmid40114931,
year = {2024},
author = {Dockman, RL and Ottesen, EA},
title = {Purified fibers in chemically defined synthetic diets destabilize the gut microbiome of an omnivorous insect model.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {},
pmid = {40114931},
issn = {2813-4338},
abstract = {The macronutrient composition of a host's diet shapes its gut microbial community, with dietary fiber in particular escaping host digestion to serve as a potent carbon source for gut microbiota. Despite widespread recognition of fiber's importance to microbiome health, nutritional research often fails to differentiate hyper-processed fibers from cell-matrix-derived intrinsic fibers, limiting our understanding of how individual polysaccharides influence the gut community. We use the American cockroach (Periplaneta americana) as a model system to dissect the response of complex gut microbial communities to dietary modifications that are difficult to test in traditional host models. Here, we designed synthetic diets from lab-grade, purified ingredients to identify how the cockroach microbiome responds to six different carbohydrates (chitin, methylcellulose, microcrystalline cellulose, pectin, starch, and xylan) in otherwise balanced diets. We show via 16S rRNA gene profiling that these synthetic diets reduce bacterial diversity and alter the phylogenetic composition of cockroach gut microbiota in a fiber-dependent manner, regardless of the vitamin and protein content of the diet. Comparisons with cockroaches fed whole-food diets reveal that synthetic diets induce blooms in common cockroach-associated taxa and subsequently fragment previously stable microbial correlation networks. Our research leverages an unconventional microbiome model system and customizable lab-grade artificial diets to shed light on how purified polysaccharides, as opposed to nutritionally complex intrinsic fibers, exert substantial influence over a normally stable gut community.},
}

@article {pmid40111696,
year = {2025},
author = {Zeng, Y and Lin, D and Chen, A and Ning, Y and Li, X},
title = {Periodontal Treatment to Improve General Health and Manage Systemic Diseases.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {245-260},
pmid = {40111696},
issn = {0065-2598},
mesh = {Humans ; *Periodontitis/microbiology/therapy/immunology ; Dysbiosis/therapy/microbiology ; Microbiota ; Cardiovascular Diseases/therapy/microbiology/immunology ; },
abstract = {Periodontitis is increasingly recognized for its role in overall health and its associations with systemic conditions. Shared etiological factors, including microbiological, immunological, genetic, and environmental influences, have prompted interest in the potential impact of periodontal therapy on broader health outcomes. The oral microbiome plays a key role in the pathogenesis of periodontitis, with microbial imbalances (dysbiosis) contributing to inflammation and systemic disease progression. Additionally, immune responses to periodontal infection, such as chronic inflammation and dysregulated immune activity, are central to linking periodontitis with conditions like diabetes, cardiovascular disease, and autoimmune disorders. This chapter explores the connections between periodontal treatment and systemic diseases, such as diabetes, rheumatoid arthritis, cardiovascular disease, chronic kidney disease, Alzheimer's disease, digestive disorders, and respiratory disease. It also reviews the current research on the mechanisms, including microbial and immune factors, that underlie these associations. By emphasizing the role of periodontal health, the oral microbiome, and immune regulation in disease prevention and management, this chapter underscores the importance of integrated healthcare approaches to improve patient outcomes.},
}

Humans
*Periodontitis/microbiology/therapy/immunology
Dysbiosis/therapy/microbiology
Microbiota
Cardiovascular Diseases/therapy/microbiology/immunology

@article {pmid40111695,
year = {2025},
author = {Rus, MJ and Sauco Carballo, C and Faria, FD and Simon-Soro, A},
title = {Hormonal Environment Shapes the Oral Microbiome.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {225-242},
pmid = {40111695},
issn = {0065-2598},
mesh = {Humans ; *Microbiota/physiology ; *Mouth/microbiology ; *Saliva/microbiology/metabolism ; Hormones/metabolism ; Host Microbial Interactions/physiology ; Biofilms/growth & development ; Female ; },
abstract = {Hormones are present in oral fluids and undergo dynamic changes throughout life. Hormonal changes can influence the interactions between the microbial community and the host. The oral microbiome is sensitive to changes in the oral environment, and hormonal fluctuations can create conditions that favour the growth of certain types of bacteria over others. Since the gingival niche harbours the resident microbial community in the biofilm form, while saliva has a transient microbiota in the planktonic form, both could modulate the host-microbial interaction under hormonal oscillations.The microbiome and hormones have a dynamic bidirectional interaction. Specific oral microorganisms can metabolize steroid hormones, disrupting their host regulation. Hormones can serve as host-microbial crosstalk related to health and disease. Hormonal imbalances are associated with systemic diseases such as polycystic ovary syndrome, endometriosis, cortisol-related conditions and oral cancer. Elucidating the complex relationship between steroid hormones and the oral microbiome offers valuable insights into the mechanisms of the disease and potential therapeutic avenues for maintaining oral and systemic health.},
}

Humans
*Microbiota/physiology
*Mouth/microbiology
*Saliva/microbiology/metabolism
Hormones/metabolism
Host Microbial Interactions/physiology
Biofilms/growth & development
Female

@article {pmid40111694,
year = {2025},
author = {Vieira Lima, CP and Pauletto, P and Lataro, RM and De Luca Canto, G and Dame-Teixeira, N and Stefani, CM},
title = {The Oral Microbiome in Diabetes, Arterial Hypertension, and Obesity: A Scoping Review.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {201-223},
pmid = {40111694},
issn = {0065-2598},
mesh = {Humans ; *Obesity/microbiology ; *Hypertension/microbiology ; *Diabetes Mellitus, Type 2/microbiology ; *Microbiota/genetics ; *Mouth/microbiology ; Saliva/microbiology ; },
abstract = {BACKGROUND: Changes in the oral microbiome are expected in the presence of chronic conditions such as type 2 diabetes mellitus (T2D), arterial hypertension (AH), and obesity (OB).

OBJECTIVE: We aimed to map the literature regarding oral microbiome changes in people with T2D, AH, or OB compared to those without these conditions.

METHODS: This scoping review was guided by the JBI Manual for Evidence Synthesis and reported according to the PRISMA extension for scoping reviews (PRISMA-ScR). A search strategy was developed and adapted to five databases (Embase, LILACS, PubMed, Scopus, and Web of Science) and gray literature (Google Scholar and ProQuest Dissertation and Thesis). Two reviewers individually screened studies for inclusion. Data from the studies, including the molecular method to evaluate the microbiome and the type of sample, were extracted and analyzed. The focus was significant changes in phylum and genera.

RESULTS: A total of 1413 records were retrieved from databases, 86 from gray literature, and 7 from reference lists. After the screening process, 50 records were included, 28 on T2D, 8 on AH, and 12 on OB. Two studies addressed metabolic syndromes. Most studies identified the oral microbiome in saliva using 16S rRNA amplicon sequencing.

CONCLUSION: At the phylum level, Fusobacteria was enriched in ≥3 studies in people with T2D. Firmicutes enrichment was associated with T2D and OB. Genera enriched in T2D comprised Catonella, Leptotrichia, Prevotella, and Rothia. Aggregatibacter and Prevotella were enriched in OB. No phylum or genera were consistently enriched in AH.OSF protocol registration: DOI 10.17605/OSF.IO/XK72V (available at https://osf.io/z5fp4).},
}

Humans
*Obesity/microbiology
*Hypertension/microbiology
*Diabetes Mellitus, Type 2/microbiology
*Microbiota/genetics
*Mouth/microbiology
Saliva/microbiology

@article {pmid40111693,
year = {2025},
author = {Yu, X and Mankia, K and Do, T and Meade, J},
title = {Oral Microbiome Dysbiosis and Citrullination in Rheumatoid Arthritis.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {185-199},
pmid = {40111693},
issn = {0065-2598},
mesh = {*Arthritis, Rheumatoid/immunology/microbiology/metabolism ; Humans ; *Dysbiosis/microbiology/immunology ; *Citrullination ; *Microbiota/immunology ; *Mouth/microbiology/immunology ; Porphyromonas gingivalis/pathogenicity/immunology/metabolism ; Animals ; Autoimmunity ; Periodontal Diseases/microbiology/immunology/metabolism ; },
abstract = {Rheumatoid arthritis and periodontal diseases, both characterized by chronic inflammation, share many common risk factors, sparking interest in understanding their established association. Emerging research has shed light on the link between these two diseases potentially occurring through the intricate interactions within the oral microbiome. The enrichment of pathogenic strains and species in this microbial community disrupts the delicate balance of both ecological and immunological homeostasis with the host. Particular attention has been paid to the role of key pathogens, such as Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans, known for their immunomodulatory abilities. The generation of an autoimmune response against proteins modified by citrullination is known to be a key step in the pathogenesis of RA. Importantly, the bidirectional citrullination mediated by both host innate immune cells and oral bacteria generates citrullinated peptide neoepitopes, which may serve as potential triggers for the loss of tolerance and subsequent autoimmunity in susceptible individuals. This review highlights the importance of understanding the mechanisms through which oral microbiome dysbiosis and citrullination contribute to the onset and progression of RA. Insights into these mechanisms not only advance pathobiological understanding but also offer potential therapeutic targets. Furthermore, we discuss the potential impact of nonsurgical periodontal treatment in modifying disease progression or mitigating RA, underscoring the critical role of periodontal health in managing systemic inflammatory conditions.},
}

*Arthritis, Rheumatoid/immunology/microbiology/metabolism
Humans
*Dysbiosis/microbiology/immunology
*Citrullination
*Microbiota/immunology
*Mouth/microbiology/immunology
Porphyromonas gingivalis/pathogenicity/immunology/metabolism
Animals
Autoimmunity
Periodontal Diseases/microbiology/immunology/metabolism

@article {pmid40111692,
year = {2025},
author = {Gao, C and Kang, J},
title = {Oral Diseases Are Associated with Cognitive Decline and Dementia.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {171-183},
pmid = {40111692},
issn = {0065-2598},
mesh = {Humans ; *Dementia/epidemiology/etiology ; *Cognitive Dysfunction/epidemiology ; Risk Factors ; Mouth Diseases/epidemiology ; Oral Health ; },
abstract = {Common oral diseases, including periodontitis and dental caries, and their endpoint as tooth loss are controllable yet highly prevalent among adults worldwide. Cognitive decline also poses significant global public health challenges during the aging process, especially the pathological form of cognitive decline such as dementia. Dementia is irreversible and is one of the leading causes of death, disability, and dependency in the aging population. Emerging research suggests a bidirectional association between oral diseases and cognitive decline or dementia. This potential link has implications for designing better oral care plans for patients with dementia and recognizing oral diseases as modifiable risk factors for dementia prevention.This chapter provides an overview of the association between oral diseases and cognitive decline, followed by a discussion of current evidence on such associations in two directions: (1) the impact of cognitive decline or dementia on oral health and (2) the role of oral diseases as modifiable risk factors for dementia. We critically evaluate several hypotheses regarding the underlying mechanisms of this association, including (1) life-course hypothesis, (2) shared inflammation and bacterial infection mechanisms, (3) malnourishment mechanism, (4) pain pathway, and (5) sensory feedback pathway.However, the association between oral diseases and cognitive decline or dementia remains controversial due to limited high-quality evidence, particularly from biomedical research. Much of the existing evidence is from observational studies prone to confounding bias, with inconclusive questions about causation and the direction of causality.This chapter concludes by emphasizing the need for future studies with robust methodological designs, including randomized controlled trials, biomedical studies, and innovative research techniques such as Mendelian randomization. Such studies are crucial for disease prevention and enhancing patient care and quality of life. By providing a comprehensive overview, this chapter contributes to an advanced understanding of this field, addresses current study gaps, and suggests future research directions.},
}

Humans
*Dementia/epidemiology/etiology
*Cognitive Dysfunction/epidemiology
Risk Factors
Mouth Diseases/epidemiology
Oral Health

@article {pmid40111691,
year = {2025},
author = {Deng, J and Sun, C and Xu, G and Wang, B and Tzortzopoulou, E and Deng, D and Giovannetti, E},
title = {The Oral Microbiome and Cancer.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {151-170},
pmid = {40111691},
issn = {0065-2598},
mesh = {Humans ; *Mouth/microbiology ; *Microbiota ; Neoplasms/microbiology/immunology ; Mouth Neoplasms/microbiology/immunology/pathology ; Animals ; Periodontal Diseases/microbiology ; Bacteria/classification/pathogenicity ; },
abstract = {There is growing evidence suggesting a strong association between members of the oral microbiota and various types of cancer, including oral cancer, colorectal cancer, esophageal squamous cell carcinoma, and pancreatic cancer. Periodontal diseases closely associated with pathogenic bacteria in the oral cavity have been shown to be correlated with the occurrence and development of cancers. Among the periodontal disease-associated bacteria in the oral cavity, two prominent oral pathogens, Porphyromonas gingivalis and Fusobacterium nucleatum, have been found to promote tumor cell proliferation, invasion, and migration, as well as to inhibit immune cell function, thereby facilitating tumor progression. The presence of other oral pathogenic bacteria, such as Treponema denticola, Tannerella forsythia, Parvimonas micra, and Aggregatibacter actinomycetemcomitans, has also been found to be associated with cancer worsening. Oral commensal bacteria play a crucial role in maintaining the normal oral homeostasis. However, the relationship between oral commensal bacteria and the occurrence and development of cancers remains controversial. Some studies suggest an increase in oral commensal bacteria during tumor development, while others suggest an association of certain commensal bacteria with lower tumor risk. The microbiota can significantly alter responses and toxicity to various forms of cancer treatment through interactions with the human body, thereby influencing disease progression. In this chapter, we provide a concise overview of current understanding of the role of the oral microbiota in cancer.},
}

Humans
*Mouth/microbiology
*Microbiota
Neoplasms/microbiology/immunology
Mouth Neoplasms/microbiology/immunology/pathology
Animals
Periodontal Diseases/microbiology
Bacteria/classification/pathogenicity

@article {pmid40111690,
year = {2025},
author = {He, J and Cheng, L},
title = {The Oral Microbiome: A Key Determinant of Oral Health.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {133-149},
pmid = {40111690},
issn = {0065-2598},
mesh = {Humans ; *Microbiota/physiology ; *Oral Health ; *Mouth/microbiology ; Dental Caries/microbiology ; Mouth Diseases/microbiology ; Periodontal Diseases/microbiology ; Bacteria/classification/genetics ; },
abstract = {As the second largest reservoir of human microbes, the oral cavity is colonized by millions of tiny creatures collectively named as oral microbiome. Species detected in human mouth are diverse, including bacteria, fungi, viruses, and protozoa. Active bidirectional interaction exists between the oral microbiome and the host. Stresses from hosts shape the composition, distribution pattern, and the community behaviors of the oral microbiome, while any changes occurring on the oral microbiome may disrupt its symbiosis relationship with the host and ultimately lead to oral and systemic diseases that jeopardize the host's health. In this chapter, the latest understanding about the role of oral microbiome in common oral diseases, including dental caries, periodontal disease, oral candidiasis, and hyposalivation, is discussed.},
}

Humans
*Microbiota/physiology
*Oral Health
*Mouth/microbiology
Dental Caries/microbiology
Mouth Diseases/microbiology
Periodontal Diseases/microbiology
Bacteria/classification/genetics

@article {pmid40111689,
year = {2025},
author = {Mattos, MCO and Vivacqua, A and Carneiro, VMA and Grisi, DC and Guimarães, MDCM},
title = {Interaction of the Systemic Inflammatory State, Inflammatory Mediators, and the Oral Microbiome.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {121-132},
pmid = {40111689},
issn = {0065-2598},
mesh = {Humans ; *Microbiota/immunology ; *Mouth/microbiology/immunology ; *Inflammation Mediators/metabolism ; *Inflammation/microbiology/immunology ; *Periodontitis/microbiology/immunology ; Dysbiosis/microbiology/immunology ; Animals ; },
abstract = {Humans are biological units that host numerous microbial symbionts and their genomes, which together form a superorganism or holobiont. Changes in the balance of the oral ecosystem can have consequences for both general and oral health, such as cavities, gingivitis, and periodontitis. Periodontitis is initiated by a synergistic and dysbiotic microbial community that causes local inflammation and destruction of the tooth's supporting tissues, potentially leading to systemic inflammation. This inflammation caused by periodontal disease has been associated with various systemic alterations, and the immune system is largely responsible for the body's exacerbated response, which can induce and exacerbate chronic conditions. Studies indicate that subgingival microorganisms found in periodontitis reach the bloodstream and are distributed throughout the body and, therefore, can be found in distant tissues and organs. Among all diseases associated with periodontal disease, diabetes mellitus presents the strongest and most elucidated link, and its bidirectional relationship has already been demonstrated. Chronic hyperglycemia favors the worsening of periodontal parameters, while the aggravation of periodontal parameters can promote an increase in glycemic indexes. Other systemic diseases have been related to periodontitis, such as Alzheimer's, chronic kidney disease, atherosclerosis, and respiratory diseases. The importance of periodontal control may suggest a reduction in the chances of developing chronic inflammatory diseases because these two alterations often share inflammatory pathways and, for this reason, may influence each other.},
}

Humans
*Microbiota/immunology
*Mouth/microbiology/immunology
*Inflammation Mediators/metabolism
*Inflammation/microbiology/immunology
*Periodontitis/microbiology/immunology
Dysbiosis/microbiology/immunology
Animals

@article {pmid40111688,
year = {2025},
author = {Heller, D and Nery, GB and Bachi, ALL and Al-Hashimi, I},
title = {Positive Role of Saliva in the Oral Microbiome.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {103-118},
pmid = {40111688},
issn = {0065-2598},
mesh = {*Saliva/microbiology/metabolism/immunology ; Humans ; *Microbiota/physiology/immunology ; *Mouth/microbiology/immunology ; Dysbiosis/microbiology/immunology ; Salivary Proteins and Peptides/immunology/metabolism ; Immunoglobulin A, Secretory/immunology/metabolism ; Oral Health ; Antimicrobial Peptides/metabolism/immunology ; Animals ; },
abstract = {Saliva plays a pivotal role in shaping the oral microbiome and maintaining oral homeostasis and health. This chapter explores the importance of saliva in promoting eubiosis of the oral microbiome and its implications for oral and systemic health. Saliva is a dynamic fluid rich in antimicrobial components and buffering agents that contribute to the microbial balance and homeostasis within the oral cavity. It provides a cleansing mechanism that facilitates the removal of bacteria and debris and limits the growth and colonization of microorganisms. The salivary antimicrobial proteins and peptides, in combination with antibodies, predominantly secretory immunoglobulin A (sIgA), are crucial for combating microbial pathogens and preventing oral infections. Saliva also possesses a buffering mechanism that regulates the pH levels within the oral cavity, which creates an environment that is inimical for the growth of acid-producing pathogens and promotes remineralization of the teeth. Furthermore, salivary proteins and glycoproteins form an inter-face (tissue coat) over the oral mucosa and teeth to protect the oral tissue from external environmental insults, maintain tissue integrity, and promote wound healing. Understanding the positive role of saliva in the oral microbiome provides an insight into potential novel strategies for promoting oral health and combating microbial dysbiosis. Recognizing the multifaceted roles of saliva as a guardian (gatekeeper) of oral microbial balance, we can unlock the therapeutic potential of saliva in enhancing the well-being of the body and averting oral and systemic diseases.},
}

*Saliva/microbiology/metabolism/immunology
Humans
*Microbiota/physiology/immunology
*Mouth/microbiology/immunology
Dysbiosis/microbiology/immunology
Salivary Proteins and Peptides/immunology/metabolism
Immunoglobulin A, Secretory/immunology/metabolism
Oral Health
Antimicrobial Peptides/metabolism/immunology
Animals

@article {pmid40111687,
year = {2025},
author = {Washio, J and Takahashi, N},
title = {Nitrite Production from Nitrate in the Oral Microbiome and Its Contribution to Oral and Systemic Health.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {89-101},
pmid = {40111687},
issn = {0065-2598},
mesh = {Humans ; *Nitrates/metabolism ; *Nitrites/metabolism ; *Mouth/microbiology/metabolism ; *Microbiota/physiology ; Saliva/metabolism/microbiology ; Oral Health ; Animals ; },
abstract = {The metabolism of nitrate to nitrite by the oral microbiome has recently attracted considerable attention. Nitrate is abundant in the green and yellow vegetables comprising our daily diet. Nitrate is reduced to nitrite by the oral microbiome in the oral cavity, absorbed through the gastrointestinal tract after ingestion, and transferred to the bloodstream, where it is gradually reoxidized to nitrate, some of which is secreted back into the oral cavity as saliva (enterosalivary circulation). Consequently, the oral environment is constantly supplied with nitrate from food and saliva. Nitrite has antibacterial and vasodilatory effects, which may contribute to the suppression of oral or intestinal bacteria and decrease blood pressure through systemic vasodilation in the enterosalivary circulation. Thus, the nitrate metabolism of oral bacteria may play an important role in maintaining and improving both oral and systemic health. On the other hand, there has been concerns that nitrate may contribute to the production of carcinogenic substances such as nitrosamines. However, there is currently a mainstream view that this idea should be reconsidered. Given the growing number of reports showing the relationship between the oral microbiome and systemic health from the perspective of nitrate metabolism; accordingly, this review summarizes the latest findings on the mechanisms of nitrite production by the oral microbiome and its relationship with oral and systemic health.},
}

Humans
*Nitrates/metabolism
*Nitrites/metabolism
*Mouth/microbiology/metabolism
*Microbiota/physiology
Saliva/metabolism/microbiology
Oral Health
Animals

@article {pmid40111686,
year = {2025},
author = {Colombo, APV and Lourenço, TGB and de Oliveira, AM and da Costa, ALA},
title = {Link Between Oral and Gut Microbiomes: The Oral-Gut Axis.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {71-87},
pmid = {40111686},
issn = {0065-2598},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Mouth/microbiology ; *Dysbiosis/microbiology ; Animals ; Gastrointestinal Tract/microbiology ; },
abstract = {In the last decades, groundbreaking research on the human microbiome has changed our reductionist conception of the etiology and pathogenesis of several chronic diseases. As a result, we have come to appreciate the significance of a balanced microbiome in maintaining human health. In this context, the upper and lower gastrointestinal tracts (GITs) comprise the most abundant and diverse microbiotas of the human body. In addition to its diversity, functional redundancy, and temporal stability, a healthy GIT microbiome is characterized by its body site specificity. In fact, current evidence has indicated that the translocation of oral species to the gut environment through the oral-gut axis is increased in an array of illnesses, including chronic inflammatory and metabolic diseases, neurological disorders, and cancer. Oral pathogens have also been shown to promote gut dysbiosis and systemic inflammation in animal models. Yet, some level of overlapping between oral and gut microbiomes may occur without disruption of these microbial communities and loss of site specificity. The uniqueness of each host-microbiome entity may hinder our ability to define a "universal" normal GIT microbiome. Despite that, this chapter summarizes the predominant health-related taxa along the human GIT, as well as their role in the physiology and immunity of the digestive system. Some mechanisms that may lead to disturbances and relevant shifts in the oral and gut microbiomes of major inflammatory chronic diseases are also pointed out. Lastly, oral-fecal microbial signatures are presented as potential biomarkers for several oral and systemic disorders. The recognition of such symbiotic/dysbiotic microbial profiles may provide insights into the development of more accurate early diagnosis and therapeutic ecological approaches to restore the balance of the GIT microbiome.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Mouth/microbiology
*Dysbiosis/microbiology
Animals
Gastrointestinal Tract/microbiology

@article {pmid40111685,
year = {2025},
author = {Santonocito, S and Polizzi, A and Isola, G},
title = {The Impact of Diet and Nutrition on the Oral Microbiome.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {53-69},
pmid = {40111685},
issn = {0065-2598},
mesh = {Humans ; *Mouth/microbiology ; *Microbiota/physiology ; *Diet/history ; *Oral Health/history ; Nutritional Status ; },
abstract = {At present, it is well known that oral health is essential for the well-being of the body as a whole, thanks to the increasing awareness of how various oral diseases, including periodontal disease, oral carcinomas, and other conditions, have a close connection with various systemic disorders. In recent decades, studies on the oral microbiome have increasingly emphasized how the balance between the host and the microbial species that coexist there is essential for oral health at all stages of life. However, there are many factors capable of interfering with that balance, and diet is precisely one of them. The real influence of diet on the oral microbiota, and consequently on oral health, has been much debated. In this context, the observation of two key periods in human history, the Neolithic and the Industrial Revolution, has proved to be diriment. The foods and processing techniques that emerged in these two historical periods, in association with changes in customs and habits, significantly altered the central constituents of the human diet, including macronutrient proportions, glycemic load, fatty acid composition, sodium and potassium levels, micronutrient levels, dietary pH, and fiber content taken in by human beings. The introduction of these foods into the daily human routine has been linked to a decline in oral health and an increase of several other diseases, including cardiovascular diseases, inflammatory bowel disease, rheumatic diseases, many cancers, and obesity. The aim of this chapter is to update the current knowledge and further discuss the role of diet and nutrition on oral health.},
}

Humans
*Mouth/microbiology
*Microbiota/physiology
*Diet/history
*Oral Health/history
Nutritional Status

@article {pmid40111684,
year = {2025},
author = {de Barros Santos, HS and Pagnussatti, MEL and Arthur, RA},
title = {Symbiosis Between the Oral Microbiome and the Human Host: Microbial Homeostasis and Stability of the Host.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {31-51},
pmid = {40111684},
issn = {0065-2598},
mesh = {Humans ; *Symbiosis ; *Mouth/microbiology ; *Microbiota/physiology ; *Homeostasis ; *Host Microbial Interactions ; Bacteria/metabolism/genetics/classification ; Metagenomics/methods ; Oral Health ; },
abstract = {The oral cavity presents a highly diverse microbial composition. All the three domains of life, Bacteria, Eukarya, and Archaea, as well as viruses constitute the oral microbiome. Bacteria are among the most abundant microorganisms in the oral cavity, followed by viruses, fungi, and Archaea. These microorganisms tend to live in harmony with each other and with the host by preventing the colonization of oral sites by exogenous microorganisms. Interactions between the host and its microbiota are crucial for keeping ecological stability in the oral cavity and a condition compatible with oral health. This chapter focuses on describing the oral microbiota in healthy individuals based on both targeted and nontargeted genome sequencing methods and the functional activity played by those microorganisms based on metagenomic, metatranscriptomic, metaproteomic, and metabolomic analyses. Additionally, this chapter explores mutualistic and antagonistic microbe-microbe relationships. These interactions are mediated by complex mechanisms like cross-feeding networks, production of bacteriocins and secondary metabolites, synthesis of pH-buffering compounds, and the use of universal signaling molecules. At last, the role played by host-microbe interactions on colonization resistance and immune tolerance will help provide a better understanding about the harmonious and peaceful coexistence among host and microbial cells under oral health-related conditions.},
}

Humans
*Symbiosis
*Mouth/microbiology
*Microbiota/physiology
*Homeostasis
*Host Microbial Interactions
Bacteria/metabolism/genetics/classification
Metagenomics/methods
Oral Health

@article {pmid40111683,
year = {2025},
author = {Azevedo, MJ and Kaan, AM and Costa, CFFA and Sampaio-Maia, B and Zaura, E},
title = {Acquisition of the Oral Microbiome.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {13-29},
pmid = {40111683},
issn = {0065-2598},
mesh = {Humans ; *Mouth/microbiology ; *Microbiota/physiology ; Bacteria/genetics/classification/growth & development/isolation & purification ; Animals ; },
abstract = {The oral cavity hosts a diverse range of microorganisms that are essential for maintaining oral and general health. These communities include bacteria, fungi, archaea, viruses, and protozoa, and they inhabit distinct niches within the oral cavity. While most research has been dedicated to the study of bacteria, knowledge regarding the acquisition and maintenance of other members of the oral microbiota is still scarce. This chapter aims to explore the process of oral microbiota acquisition from the prenatal to the postnatal stages, emphasizing the intricate interplay between host and environmental factors that shape these microbial communities. However, it is important to acknowledge that significant gaps in knowledge persist, particularly regarding the understanding of these processes beyond bacteria.},
}

Humans
*Mouth/microbiology
*Microbiota/physiology
Bacteria/genetics/classification/growth & development/isolation & purification
Animals

@article {pmid40111682,
year = {2025},
author = {Dame-Teixeira, N and Do, T and Deng, D},
title = {The Oral Microbiome and Us.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {3-9},
pmid = {40111682},
issn = {0065-2598},
mesh = {Humans ; *Mouth/microbiology ; *Microbiota/physiology ; *Dysbiosis/microbiology ; Periodontitis/microbiology ; Animals ; Oral Health ; },
abstract = {Oral and systemic human health depend on the symbiotic relationship between the human host and its microbiome. As the second most diverse site of the human microbiome, the oral cavity is instrumental in symbiotic relationships, transforming nutrients and acting as the human body's initial barrier against pathogens. However, under certain conditions, the typically beneficial oral microbiome can become harmful. Systemic inflammatory diseases can send signals through the oral-gut axis, such as cytokines and host defensins, altering gene expression and, consequently, the composition of the oral microbiome. These changes can be responsible for causing oral diseases, such as periodontitis and candidiasis. Evidence of metabolic syndrome, including obesity, hypertension, hyperglycemia, and dyslipidemia, exacerbates oral microbiome dysbiosis. On the other hand, the oral microbiota can also influence systemic health. Inflammatory processes in the gingival structures caused by a dysbiotic oral microbiome are linked to worsen glycemic levels in diabetics, premature birth, and rheumatoid arthritis, among others. The idea for this book emerged from the need to explore the multifaceted nature of this relationship in its various dimensions. We discuss multispecies characteristics from an ecological perspective, focusing on how the host affects the microbiome and vice versa. Understanding how the oral microbiome influences human health will guide tailored strategies for disease prevention and treatment, which is discussed in the last section of the book. Looking ahead, predictive health and disease models will enable personalized therapies centered on restoring the healthy human microbiome.},
}

Humans
*Mouth/microbiology
*Microbiota/physiology
*Dysbiosis/microbiology
Periodontitis/microbiology
Animals
Oral Health

@article {pmid40111647,
year = {2025},
author = {Choi, Y and Jeong, J and Kim, M and Cha, S and Han, K},
title = {Backtracking identification techniques for predicting unclear bacterial taxonomy at species level: molecular diagnosis-based bacterial classification.},
journal = {Genes & genomics},
volume = {},
number = {},
pages = {},
pmid = {40111647},
issn = {2092-9293},
support = {RS-2024-00355393//National Institute for International Education/ ; },
abstract = {Bacterial 16S rRNA genes are widely used to classify bacterial communities within interesting environments (e.g., plants, water, human body) because they contain nine hyper-variable regions (V1-V9) reflecting a large number of sequence variation sites between species. Short-read sequencing platform (targeting partial region of 16S rRNA gene; approximately 150-500 bp) commonly used in the 16S-based microbiome study is favored by many researchers because it is economical and can generate highthroughput sequencing data faster than long-read sequencing platforms. However, this sequencing platform has technical limitations in that it cannot clarify bacterial classification at the species level compared to long-read sequencing technology, which can cover the unclassification issue due to sequence similarity between species by targeting the 16S full-length region. In recent microbiome research-related industries, species-level high-resolution microbial classification is considered a key challenge to secure microbial resources among institutions in the field. However, the long-read sequencing platforms currently offered are still under price adjustment (demanding higher cost than short-read sequencing platforms) and have the disadvantage of low base-calling accuracy compared to short-read sequencing platforms. Therefore, this brief communication introduces the'Molecular diagnosis-based bacterial classification' technology to predict candidate species by backtracking for unclassified bacterial taxonomy at the species level in the NGS-based 16S microbiome study.},
}

@article {pmid40111427,
year = {2025},
author = {Rukavina Mikusic, NL and Prince, PD and Choi, MR and Chuffa, LGA and Simão, VA and Castro, C and Manucha, W and Quesada, I},
title = {Microbiota, mitochondria, and epigenetics in health and disease: converging pathways to solve the puzzle.},
journal = {Pflugers Archiv : European journal of physiology},
volume = {},
number = {},
pages = {},
pmid = {40111427},
issn = {1432-2013},
support = {PICT2018-3965//ANPCyT FONCyT/ ; PICT 2000 Serie A 4000//ANPCyT FONCyT/ ; J029-T1 SIIP 2022-2024//ANPCyT FONCyT/ ; },
abstract = {Dysbiosis, which refers to an imbalance in the composition of the gut microbiome, has been associated with a range of metabolic disorders, including type 2 diabetes, obesity, and metabolic syndrome. Although the exact mechanisms connecting gut dysbiosis to these conditions are not fully understood, various lines of evidence strongly suggest a substantial role for the interaction between the gut microbiome, mitochondria, and epigenetics. Current studies suggest that the gut microbiome has the potential to affect mitochondrial function and biogenesis through the production of metabolites. A well-balanced microbiota plays a pivotal role in supporting normal mitochondrial and cellular functions by providing metabolites that are essential for mitochondrial bioenergetics and signaling pathways. Conversely, in the context of illnesses, an unbalanced microbiota can impact mitochondrial function, leading to increased aerobic glycolysis, reduced oxidative phosphorylation and fatty acid oxidation, alterations in mitochondrial membrane permeability, and heightened resistance to cellular apoptosis. Mitochondrial activity can also influence the composition and function of the gut microbiota. Because of the intricate interplay between nuclear and mitochondrial communication, the nuclear epigenome can regulate mitochondrial function, and conversely, mitochondria can produce metabolic signals that initiate epigenetic changes within the nucleus. Given the epigenetic modifications triggered by metabolic signals from mitochondria in response to stress or damage, targeting an imbalanced microbiota through interventions could offer a promising strategy to alleviate the epigenetic alterations arising from disrupted mitochondrial signaling.},
}

@article {pmid40111342,
year = {2025},
author = {Castonguay-Paradis, S and Demers-Potvin, É and Rochefort, G and Lacroix, S and Perron, J and Martin, C and Flamand, N and Raymond, F and Di Marzo, V and Veilleux, A},
title = {Seasonal variations in circulating endocannabinoidome mediators and gut microbiota composition in humans.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2476563},
doi = {10.1080/19490976.2025.2476563},
pmid = {40111342},
issn = {1949-0984},
mesh = {Humans ; *Seasons ; *Endocannabinoids/blood ; *Gastrointestinal Microbiome ; Female ; Male ; *Feces/microbiology ; Middle Aged ; Adult ; Longitudinal Studies ; Bacteria/classification/isolation & purification/genetics ; Quebec ; Aged ; Diet ; Feeding Behavior ; },
abstract = {BACKGROUND: The human gut microbiome-endocannabinoidome axis is crucial for several homeostatic processes, including inflammation and energy metabolism, and is influenced by many endogenous and exogenous factors, such as dietary habits. Changes in the gut microbiome in response to seasonal variations were previously reported and tentatively attributed to shifts in dietary patterns. However, there is a need for longitudinal studies in industrialized populations to comprehensively explore seasonal variations independently of lifestyle confounding factors.

OBJECTIVE: To investigate the longitudinal effects of seasonal variations on the composition of the gut microbiome and the circulating levels of endocannabinoidome mediators in humans, while elucidating the contributing factors underlying these changes.

METHODS: Plasma and fecal samples were collected at the end of both the winter and summer in a longitudinal cohort of 48 individuals living in Québec City (Canada). Dietary habits, medical history, fecal microbiota taxonomic composition and plasma levels of circulating N‑acyl‑ethanolamines (NAEs) and 2‑monoacyl-glycerols (2‑MAGs) were obtained at each time point.

RESULTS: Lower circulating levels of most NAEs were observed at the end of summer. These changes were accompanied by a reduction in the relative abundance of the Bifidobacteriaceae and Lachnospiraceae families, along with an increase in the abundance of the Bacteroidaceae and Ruminococcaceae families. These seasonal variations were not associated with concurrent changes in adiposity parameters, dietary intakes, physical activity habits, or vitamin D status. Importantly, the magnitude of the shift in gut microbiota composition from winter to summer was found to be associated with the seasonal variations in circulating endocannabinoidome (eCBome) mediators.

CONCLUSION: This study identified specific seasonal changes in gut microbiota composition and circulating levels of several NAEs, which were not associated with vitamin D status and lifestyle habits. It underscores the importance of the gut microbiota-endocannabinoidome axis in the pathophysiology of seasonal changes, and of considering seasons in clinical trials on these systems.},
}

Humans
*Seasons
*Endocannabinoids/blood
*Gastrointestinal Microbiome
Female
Male
*Feces/microbiology
Middle Aged
Adult
Longitudinal Studies
Bacteria/classification/isolation & purification/genetics
Quebec
Aged
Diet
Feeding Behavior

@article {pmid40111075,
year = {2025},
author = {Zhang, X and Gaballa, MMS and Hasan, AA and Liu, Y and Hocher, JG and Chen, X and Liu, L and Li, J and Wigger, D and Reichetzeder, C and Elitok, S and Kleuser, B and Krämer, BK and Hocher, B},
title = {Effects of High-Salt Intake on Glucose Metabolism, Liver Function, and the Microbiome in Rats: Influence of ACE Inhibitors and Angiotensin II Receptor Blockers.},
journal = {American journal of physiology. Cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpcell.01036.2024},
pmid = {40111075},
issn = {1522-1563},
support = {2022RC40//Hunan High-Level Talent Aggregation Project/ ; //Boehringer Ingelheim (Boehringer Ingelheim International GmbH)/ ; YNXM-202304//Researsch Grant of CITIC-Xiangya/ ; 202008430176//China Scholarship Council (CSC)/ ; //Deutschland-Stipendium der Charite Universitatsmedizin Berlin/ ; },
abstract = {Abstract Background: High-salt diets (HSD) are known to impact blood pressure and cardiovascular health, but their effects on glucose metabolism, liver function, and gut microbiota remain poorly understood. This study investigates how long-term HSD affects these physiological processes and evaluates the potential therapeutic effects of ACE inhibitors (ACEIs) and angiotensin II receptor blockers (ARBs). Methods: Male Sprague-Dawley rats were fed a normal salt diet (0.3% NaCl), a moderate salt diet (2% NaCl), or a high-salt diet (8% NaCl) for 12 weeks. Two subgroups in the HSD condition received telmisartan or enalapril. We assessed blood pressure, glucose homeostasis, liver inflammation, pancreatic function, and gut microbiota composition. Results: HSD rats exhibited significantly higher blood pressure (130 ± 2 mmHg in ND vs. 144 ± 4 mmHg in HSD; p < 0.01), reduced fasting insulin (1.33 ± 0.14 ng/mL in ND vs. 0.60 ± 0.05 ng/mL in HSD; p < 0.01), and gut microbiota dysbiosis, with a 71% reduction in Ruminococcus species (p = 0.018). Liver inflammation, indicated by an increase in CD68+ macrophages, was also observed in the HSD group. Telmisartan treatment significantly reduced liver inflammation but did not fully restore metabolic homeostasis. Conclusion: HSD disrupts multiple physiological systems, including glucose metabolism and liver function, partly through gut microbiota alterations. ACEIs and ARBs provided partial protection, highlighting the need for multi-targeted interventions to mitigate high-salt diet effects.},
}

@article {pmid40111053,
year = {2025},
author = {Jian, N and Yu, L and Ma, L and Zheng, B and Huang, W},
title = {BCG therapy in bladder cancer and its tumor microenvironment interactions.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0021224},
doi = {10.1128/cmr.00212-24},
pmid = {40111053},
issn = {1098-6618},
abstract = {SUMMARYBacillus Calmette-Guérin (BCG) has been the standard treatment for non-muscle-invasive bladder cancer for over 30 years. Despite its proven efficacy, challenges persist, including unclear mechanisms of action, resistance in 30%-50% of patients, and significant side effects. This review presents an updated and balanced discussion of the antitumor mechanisms of BCG, focusing on its direct effects on bladder cancer and its interactions with various cell types within the bladder tumor microenvironment. Notably, recent research on the interactions between BCG and the bladder microbiome is also incorporated. We further summarize and analyze the latest preclinical and clinical studies regarding both intrinsic and adaptive resistance to BCG in bladder cancer. Based on the current understanding of BCG's therapeutic principles and resistance mechanisms, we systematically explore strategies to improve BCG-based tumor immunotherapy. These include the development of recombinant BCG, combination therapy with different drugs, optimization of therapeutic regimens and management, and the exploration of new approaches by targeting changes in the bladder microbiota and its metabolites. These measures aim to effectively address the BCG resistance in bladder cancer, reduce its toxicity, and ultimately enhance the clinical anti-tumor efficacy. Bacterial therapy, represented by genetically engineered oncolytic bacteria, has gradually emerged in the field of cancer treatment in recent years. As the only bacterial drug successfully approved for oncology use, BCG has provided decades of clinical experience. By consolidating lessons from BCG's successes and limitations, we hope to provide valuable insights for the development and application of bacterial therapies in cancer treatment.},
}

@article {pmid40110742,
year = {2025},
author = {Dutta, S and Chatterjee, N and Gallina, NLF and Kar, S and Koley, H and Nanda, PK and Biswas, O and Das, AK and Biswas, S and Bhunia, AK and Dhar, P},
title = {Diet, microbiome, and probiotics establish a crucial link in vaccine efficacy.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-26},
doi = {10.1080/1040841X.2025.2480230},
pmid = {40110742},
issn = {1549-7828},
abstract = {Vaccination plays a critical role in public health by reducing the incidence and prevalence of infectious diseases. The efficacy of a vaccine has numerous determinants, which include age, sex, genetics, environment, geographic location, nutritional status, maternal antibodies, and prior exposure to pathogens. However, little is known about the role of gut microbiome in vaccine efficacy and how it can be targeted through dietary interventions to improve immunological responses. Unveiling this link is imperative, particularly in the post-pandemic world, considering impaired COVID-19 vaccine response observed in dysbiotic individuals. Therefore, this article aims to comprehensively review how diet and probiotics can modulate gut microbiome composition, which is linked to vaccine efficacy. Dietary fiber and polyphenolic compounds derived from plant-based foods improve gut microbial diversity and vaccine efficacy by promoting the growth of short-chain fatty acids-producing microbes. On the other hand, animal-based foods have mixed effects - whey protein and fish oil promote gut eubiosis and vaccine efficacy. In contrast, lard and red meat have adverse effects. Studies further indicate that probiotic supplements exert varied effects, mostly strain and dosage-specific. Interlinking diet, microbiome, probiotics, and vaccines will reveal opportunities for newer research on diet-induced microbiome-manipulated precision vaccination strategies against infectious diseases.},
}

@article {pmid40110651,
year = {2025},
author = {Saini, S and Sabaeifard, P and Coughlin, L and Poulides, N and Gan, S and Zhan, X and Dang, M and Koh, AY and Zia, A},
title = {Identifying Microbiota and Immune Host Factors Associated With Bleeding Risk in Children With Immune Thrombocytopenia.},
journal = {American journal of hematology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajh.27669},
pmid = {40110651},
issn = {1096-8652},
support = {1R01HL153963/NH/NIH HHS/United States ; K24AI123163/NH/NIH HHS/United States ; 20IPA35320263//American Heart Association/ ; R38HL150214/HL/NHLBI NIH HHS/United States ; },
}

@article {pmid40110597,
year = {2025},
author = {Mason, B and Sahoo, DK and Iennarella-Servantez, CA and Kathrani, A and Morgan, SM and Bourgois-Mochel, A and Bray, AM and Gabriel, V and Zdyrski, C and Groeltz, JM and Cassmann, E and Ackermann, MR and Suchodolski, JS and Mochel, JP and Allenspach, K and Jergens, AE},
title = {Effects of a Western Diet on Colonic Dysbiosis, Bile Acid Dysmetabolism and Intestinal Inflammation in Clinically Healthy Dogs.},
journal = {Journal of veterinary internal medicine},
volume = {39},
number = {2},
pages = {e70035},
doi = {10.1111/jvim.70035},
pmid = {40110597},
issn = {1939-1676},
support = {//Iowa State University Veterinary Clinical Sciences Incentive Grant Program 2021/ ; //VCA Sponsored Resident Funding/ ; },
mesh = {Animals ; Dogs ; *Dysbiosis/veterinary ; *Dog Diseases/microbiology/diet therapy ; *Bile Acids and Salts/metabolism ; *Feces/microbiology/chemistry ; Male ; Female ; *Diet, Western/adverse effects ; Inflammation/veterinary ; Colon/pathology/microbiology ; Gastrointestinal Microbiome/drug effects ; Animal Feed/analysis ; },
abstract = {BACKGROUND: Consumption of a high-fat, high-carbohydrate Western-style diet (WD) associated with obesity and inflammation in humans has not been investigated in dogs.

AIMS: To determine the effects of WD on inflammatory indices, microbiome, and fecal bile acids (BAs) in dogs.

ANIMALS: Ten adult clinically healthy dogs.

METHODS: A dietary trial compared the effects of two home-prepared diets: a high-fiber, low-fat control diet (CD) to a diet containing the macronutrient composition of WD (low-fiber, high fat). Dietary treatments were given sequentially for three feeding periods, each lasting 1 month. Outcome measures included molecular/microbiologic testing of colonic biopsies, histopathology, inflammatory biomarkers, and quantification of fecal BA following each feeding period.

RESULTS: Cell markers of apoptosis (TUNEL-positive cells: CD1, 0.36% ± 0.2%; WD, 0.79% ± 0.5%; CD2, 0.42% ± 0.3%; 95% CI) and inflammation (NF-ĸB area: CD1, 8.09% ± 3.3%; WD, 11.58% ± 3.4%; CD2 7.25% ± 3.8%; 95% CI), as well as serum high-sensitivity C-reactive protein (CD1, 2.0 ± 0.4 ng/mL; WD, 2.76 ± 0.23 ng/mL; CD2, 2.29 ± 0.25 ng/mL; 95% CI), were increased (p < 0.05) in dogs fed WD versus CD. Other perturbations seen with WD ingestion included altered (p < 0.05) colonic mucosal bacteria (bacterial counts: CD1, 301.5 ± 188.5; WD, 769.8 ± 431.9; CD2, 542.1 ± 273.9; 95% CI) and increased (p < 0.05) fecal cholic acid (median and interquartile range/IQR: CD1, 9505 [2384-33 788] peak heights; WD, 34 131 [10 113-175 909] peak heights) and serum myeloperoxidase (CD1, 46.98 ± 16.6 ng/mL; WD, 82.93 ± 33.6 ng/mL; CD2, 63.52 ± 29.5 ng/mL; 95% CI).

WD fed to clinically healthy dogs promotes colonic dysbiosis, altered fecal BA, and low-grade inflammation independent of obesity.},
}

Animals
Dogs
*Dysbiosis/veterinary
*Dog Diseases/microbiology/diet therapy
*Bile Acids and Salts/metabolism
*Feces/microbiology/chemistry
Male
Female
*Diet, Western/adverse effects
Inflammation/veterinary
Colon/pathology/microbiology
Gastrointestinal Microbiome/drug effects
Animal Feed/analysis

@article {pmid40110560,
year = {2025},
author = {Adachi, A and Zhang, F and Kanaya, S and Ono, N},
title = {Quantifying uncertainty in microbiome-based prediction using Gaussian processes with microbial community dissimilarities.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf045},
pmid = {40110560},
issn = {2635-0041},
abstract = {SUMMARY: The human microbiome is closely associated with the health and disease of the human host. Machine learning models have recently utilized the human microbiome to predict health conditions and disease status. Quantifying predictive uncertainty is essential for the reliable application of these microbiome-based prediction models in clinical settings. However, uncertainty quantification in such prediction models remains unexplored. In this study, we have developed a probabilistic prediction model using a Gaussian process (GP) with a kernel function that incorporates microbial community dissimilarities. We evaluated the performance of probabilistic prediction across three regression tasks: chronological age, body mass index, and disease severity, using publicly available human gut microbiome datasets. The results demonstrated that our model outperformed existing methods in terms of probabilistic prediction accuracy. Furthermore, we found that the confidence levels closely matched the empirical coverage and that data points predicted with lower uncertainty corresponded to lower prediction errors. These findings suggest that GP regression models incorporating community dissimilarities effectively capture the characteristics of phylogenetic, high-dimensional, and sparse microbial abundance data. Our study provides a more reliable framework for microbiome-based prediction, potentially advancing the application of microbiome data in health monitoring and disease diagnosis in clinical settings.

The code is available at https://github.com/asahiadachi/gp4microbiome.},
}

@article {pmid40110548,
year = {2024},
author = {Phiri, TN and Weatherill, JW and Monford-Sanchez, E and Serrano-Contreras, JI and Melvin, C and Kunaka, M and Chisenga, I and Ngalande, P and Mweetwa, MN and Besa, E and Haider, T and Mandal, N and Thompson, AJ and Edwards, CA and Bourke, CD and Robertson, RC and Posma, JM and Banda, R and Mwiinga, M and Kazhila, L and Katsidzira, L and Bwakura-Dangarembizi, M and Amadi, B and Garcia-Perez, I and Maitland, K and Marchesi, JR and Morrison, DJ and Frost, G and Kelly, P},
title = {Novel gastrointestinal tools (GI Tools) for evaluating gut functional capacity in adults with environmental enteropathy in Zambia and Zimbabwe: A cross-sectional study protocol.},
journal = {F1000Research},
volume = {13},
number = {},
pages = {956},
pmid = {40110548},
issn = {2046-1402},
mesh = {Humans ; Cross-Sectional Studies ; Zambia ; Adult ; Middle Aged ; Adolescent ; *Intestinal Diseases ; Zimbabwe ; Young Adult ; Aged ; Female ; Male ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Environmental enteropathy (EE) is a highly prevalent subclinical inflammatory intestinal disorder associated with growth failure, impaired neurocognitive development, poor response to oral vaccines, and micronutrient deficiencies. However, EE research and clinical trials are hampered by the lack of non-invasive tools for measuring intestinal function in detail. This study aims to develop new tools for the measurement of multiple domains of gut functional capacity.

METHODS: The GI TOOLS project is a cross-sectional study that will recruit adults aged 18-65 years with EE in Lusaka, Zambia. Each participant will undergo assessment of gut functional capacity using novel near-point-of-care tools and provide multiple samples for detailed laboratory analyses. Participants will also undergo endoscopy for collection of duodenal biopsies. Novel techniques include stable isotopes approaches to measuring digestion, absorption, and bidirectional transmucosal amino acid flux, a non-invasive fluorescence tool for real-time evaluation of gut permeability, and assessment of reverse permeation of intravenous antibiotics to be carried out separately in Zimbabwe. Stool and duodenal microbiome sequencing using MinION sequencing, metabolome analysis applied to plasma and intestinal fluids, blood immune cell phenotyping, in vitro epithelial barrier models, and duodenal immunohistochemistry will also be used to explore EE in depth. These will all be integrated with gold standard histology and mucosal morphometry, alongside lactulose permeation data, and stool and plasma biomarker analysis. The protocol has been approved by ethics committees and regulators in Zambia, Zimbabwe, and the UK. Participants will give informed consent before they can participate.

ANTICIPATED OUTCOMES: Based on this extensive phenotyping, tests will be developed which can be simplified and refined for use in adults and children with EE, and for clinical trials. Findings from this project will be disseminated through in-person meetings with caregivers and regulatory bodies, presentations at conferences and in peer-reviewed journals.},
}

Humans
Cross-Sectional Studies
Zambia
Adult
Middle Aged
Adolescent
*Intestinal Diseases
Zimbabwe
Young Adult
Aged
Female
Male
Gastrointestinal Microbiome

@article {pmid40110359,
year = {2025},
author = {Ahmed, W and Ye, W and Pan, J and Liu, S and Ji, W and Zhou, S and Wang, F and Li, Z and Mohany, M and Wang, X},
title = {Evaluation the role of Luteibacter pinisoli DP2-30 in mitigating pine wilt disease caused by Bursaphelenchus xylophilus through modulation of host microbiome.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1515506},
pmid = {40110359},
issn = {1664-462X},
abstract = {BACKGROUND AND AIM: Pine wilt disease (PWD), caused by the pine wood nematode (PWN) Bursaphelenchus xylophilus, poses a significant threat to pine forests worldwide. This study aimed to isolate bacterial strains from the rhizosphere of healthy Pinus massoniana and elucidate their biocontrol potential in mitigating PWD through direct nematicidal activity and manipulation of host microbiome.

RESULTS: We successfully isolated the rhizobacterium strain DP2-30 from rhizosphere of healthy pine plants, which was identified as Luteibacter pinisoli on the basis of morphological, biochemical, and molecular analyses. The fermentation filtrates of strain DP2-30 displayed direct nematicidal activity of >95% (corrected mortality rate) on PWN after 48 hours of treatment. The fermentation broth and filtrates of strain DP2-30 significantly inhibited PWN egg hatching by 49.38% and 43.05%, respectively. Additionally, root drenching of strain DP2-30 fermentation broth significantly reduced PWD severity in pine seedlings (2 years old), with a control effect of 62.50%. Microbiome analyses revealed significant variations in the diversity, structure, and relative abundance of bacterial and fungal communities of pine plants combined treated with DP2-30 and PWN (T2), solely treated with PWN (T1), and control (treated with water). Bacterial phyla, Proteobacteria, Actinobacteriota, Chloroflexi, Acidobacteriota, and Armatimonadota and fungal phyla Ascomycota, Basidiomycota and Mortierellomycota were dominant in the all root and stem samples. The application of L. pinisoli DP2-30 significantly increased the relative abundance of the family Rhodanobacteraceae in the roots and stems of pine seedlings. Additionally, intra-kingdom co-occurrence network analysis revealed reduced complexity in the bacterial networks but increased complexity in the fungal networks of treated plants, suggesting enhanced functional redundancy and ecosystem stability.

CONCLUSIONS: Overall, this study highlights the potential of L. pinisoli DP2-30 as an effective biocontrol agent against PWD by directly killing PWN and manipulating the host microbiota.},
}

@article {pmid40110355,
year = {2025},
author = {Lane, BR and Kuhs, MA and Zaret, MM and Song, Z and Borer, ET and Seabloom, EW and Schlatter, DC and Kinkel, LL},
title = {Foliar fungi-imposed costs to plant productivity moderate shifts in composition of the rhizosphere microbiome.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1558191},
pmid = {40110355},
issn = {1664-462X},
abstract = {Plants in grasslands navigate a complex landscape of interactions including competition for resources and defense against pathogens. Foliar fungi can suppress plant growth directly through pathogenic interactions, or indirectly via host growth-defense tradeoffs. The exclusion of foliar fungi allows the reallocation of resources from defense to growth and reproduction. In addition, plants also invest photosynthates in rhizodeposition, or root exudates, which play a significant role in shaping the rhizosphere microbial community. However, it remains unclear what impact the exclusion of foliar fungi has on the allocation of resources to rhizodeposition and the composition of the rhizosphere microbial community. Using a 6-year foliar fungicide study in plots planted with 16 species of native prairie plants, we asked whether foliar fungi influence the rhizosphere microbial composition of a common prairie grass (Andropogon gerardii) and a common legume (Lespedeza capatita). We found that foliar fungicide increased aboveground biomass and season-long plant production, but did not alter root biomass, seed production, or rhizosphere microbial diversity. The magnitude of change in aboveground season-long plant production was significantly associated with the magnitude of change in the rhizosphere microbial community in paired foliar fungicide-treated vs. control plots. These results suggest important coupling between foliar fungal infection and plant investment in rhizodeposition to modify the local soil microbial community.},
}

@article {pmid40110195,
year = {2025},
author = {Carneiro, KO and Araújo, TMT and Da Silva Mourão, RM and Casseb, SMM and Demachki, S and Moreira, FC and Dos Santos, ÂKCR and Ishak, G and Da Costa, DSA and Magalhães, L and Vidal, AF and Burbano, RMR and de Assumpção, PP},
title = {Transcriptional and microbial profile of gastric cancer patients infected with Epstein-Barr virus.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1530430},
pmid = {40110195},
issn = {2234-943X},
abstract = {INTRODUCTION: Gastric cancer (GC), which has low survival rates and high mortality, is a major concern, particularly in Asia and South America, with over one million annual cases. Epstein-Barr virus (EBV) is recognized as a carcinogen that may trigger gastric carcinogenesis by infecting the stomach epithelium via reactivated B cells, with growing evidence linking it to GC. This study investigates the transcriptional and microbial profiles of EBV-infected versus EBV-non-infected GC patients.

METHODS: Using Illumina NextSeq, cDNA libraries were sequenced, and reads were aligned to the human genome and analyzed with DESeq2. Kegg and differential analyses revealed key genes and pathways. Gene sensitivity and specificity were assessed using ROC curves (p < 0.05, AUC > 0.8). Non-aligned reads were used for microbiome analysis with Kraken2 for bacterial identification. Microbial analysis included LDA score, Alpha and Beta diversity metrics, with significance set at p ≤ 0.05. Spearman's correlation between differentially expressed genes (DEGs) and bacteria were also examined.

RESULTS: The data revealed a gene expression pattern in EBV-positive gastric cancer, highlighting immune response, inflammation, and cell proliferation genes (e.g., GBP4, ICAM1, IL32, TNFSF10). ROC analysis identified genes with high specificity and sensitivity for discriminating EBV+ gastric cancer, including GBP5, CMKLR1, GM2A and CXCL11 that play pivotal roles in immune response, inflammation, and cancer. Functional enrichment pointed to cytokine-cytokine receptor interactions, antigen processing, and Th17 immune response, emphasizing the role of the tumor microenvironment, shaped by inflammation and immunomodulation, in EBV-associated GC. Microbial analysis revealed changes in the gastric microbiota in EBV+ samples, with a significant reduction in bacterial taxa. The genera Choristoneura and Bartonella were more abundant in EBV+ GC, while more abundant bacteria in EBV- GC included Citrobacter, Acidithiobacillus and Biochmannia. Spearman's correlation showed a strong link between DE bacterial genera and DEGs involved in processes like cell differentiation, cytokine production, digestion, and cell death.

CONCLUSION: These findings suggest a complex interaction between the host (EBV+ GC) and the microbiota, possibly influencing cancer progression, and offering potential therapeutic targets such as microbiota modulation or gene regulation. Comparing with EBV- samples further highlights the specific impact of EBV and the microbiota on gastric cancer pathogenesis.},
}

@article {pmid40110165,
year = {2025},
author = {Liu, C and Zhang, J and Li, Q and Zhang, Y and Zhang, S and Yu, Z and Li, J and Li, J},
title = {Horizontal transmission of symbiotic bacteria and host selective sweep in the giant clam Tridacna crocea.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf037},
pmid = {40110165},
issn = {2730-6151},
abstract = {Giant clams, with their significant ecological importance, depend on associated bacteria for their health and development, yet the transmission modes and succession of community dynamics of these bacteria remain poorly understood. This study employed 16S rRNA gene sequencing and microscopy to investigate the transmission and community dynamics of symbiotic bacteria in the giant clam Tridacna crocea during early developmental stages (fertilized eggs, blastocyst, D-larvae, and pediveliger larvae). Fluorescence in situ hybridization and transmission electron microscopy did not detect internal symbiotic bacteria in fertilized eggs and adult gonad gametes, but scanning electron microscopy revealed microbial structures on egg surface microvilli, suggesting their role as microbial carriers. 16S rRNA sequencing confirmed microbial presence in fertilized eggs, indicating bacterial acquisition via external vertical transmission (adherence to microvilli) or horizontal transmission. Given the lack of internalized bacteria in reproductive organs, we prefer to classify the symbiotic bacteria acquisition as horizontal transmission. Microbial community analysis showed that T. crocea acquired a significant portion of its microbiome from seawater throughout its development. Before reaching the pediveliger stage, the bacterial community composition closely resembled that of the surrounding seawater, primarily featuring the family Rhodobacteraceae. As T. crocea matured, the host's selective pressure increased (e.g. deterministic assembly), which simplified the microbial community and reduced diversity. During the pediveliger stage, the genus Endozoicomonas became dominant, forming a large proportion of the bacterial community within the gonads. This highlights the ecological significance of host-microbe interactions in maintaining biodiversity and driving ecosystem stability through dynamic community assembly processes.},
}

@article {pmid40109991,
year = {2025},
author = {Xu, CC and Zhao, WX and Sheng, Y and Yun, YJ and Ma, T and Fan, N and Song, JQ and Wang, J and Zhang, Q},
title = {Serum homocysteine showed potential association with cognition and abnormal gut microbiome in major depressive disorder.},
journal = {World journal of psychiatry},
volume = {15},
number = {3},
pages = {102567},
pmid = {40109991},
issn = {2220-3206},
abstract = {BACKGROUND: Cognitive impairment is one of the common clinical manifestations of depression, causing negative distress to patients. Elevated homocysteine (Hcy) concentrations and gut microbiome dysfunction may be observed in patients with depression.

AIM: To investigate the relationship between Hcy, microbiome, and cognition in depressive patients.

METHODS: We recruited 67 patients with major depressive disorder (MDD) (MDD group) and 94 healthy controls (HCs) individuals (HCs group). Serum Hcy levels were determined using the enzyme circulation method. 16s rRNA sequencing was used to classify and identify the fecal bacteria. 17 Hamilton depression rating scale and MATRICS consensus cognitive battery were used to evaluate mood states and cognition in patients with MDD. Correlation analysis was performed to explore the correlation between fecal flora, Hcy, and depressive cognitive function.

RESULTS: Elevated serum levels of Hcy were seen in patients with MDD compared to healthy individuals. Patients with MDD indicated significant decreases in cognitive scores (P < 0.001) in six modules: Speed of processing, working memory, visual learning, reasoning and problem-solving, social cognition, and total scores. Hcy levels showed a negative correlation with processing speed, social cognition, and total MDD scores (P < 0.05). Hcy was also significantly negatively correlated with Alistipes, Ruminococcae, Tenericides, and Porphyromonas (P < 0.05).

CONCLUSION: Our results highlight that Hcy was correlated with cognition and gut microbiome in MDD. This interaction may be related to the physiological and pathological mechanisms underlying cognitive deficits in depression.},
}

@article {pmid40109976,
year = {2025},
author = {Ku, JY and Lee, MJ and Jung, Y and Choi, HJ and Park, J},
title = {Changes in the gut microbiome due to diarrhea in neonatal Korean indigenous calves.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1511430},
pmid = {40109976},
issn = {1664-302X},
abstract = {Studies on gut microbiome changes in neonatal Korean indigenous calves with diarrhea are rare. In this study, 14 normal calves and 11 calves with diarrhea were selected from Korean indigenous calves up to 30 days of age and classified into three groups at 10-day intervals (1-10, 11-20, and 21-30 days). Feces from 25 calves were collected, and the diversity, similarity, structure, and correlation of the gut microbiome were analyzed. Firmicutes, Bacteroidetes, and Proteobacteria were predominant in the taxonomic composition of the gut microbiome of the calves regardless of the presence of diarrhea. However, Proteobacteria increased and Bacteroidetes and Actinobacteria decreased in calves with diarrhea. In addition, calves with diarrhea showed a significant decrease in the diversity of the gut microbiome, especially for anaerobic microorganisms Faecalibacterium prausnitzii, Gemmiger formicilis, and Collinsella aerofaciens. The microbial communities in calves with diarrhea and normal calves were distinct. By analyzing the microorganisms that showed correlation with diarrhea and age using linear discriminant analysis effect size, at the genus level, Prevotella and Lachnospiraceae_uc were significantly related in the normal (11-20 days) group whereas Enterobacterales, Gammaproteobacteria, Enterobacteriaceae, Escherichia, and Proteobacteria were significantly associated with diarrhea in the 11-20 days group. Futhermore, the normal (21-30 days) group showed significant correlation with Blautia, Provotellaceae, Muribaculaceae, Christensenellaceae, and Catenella, whereas the diarrhea (21-30 days) group showed significant correlation with Dorea. The microorganisms associated with diarrhea in calves were mainly known as harmful microorganisms, we confirmed that there is a relationship between the increase in harmful bacteria and diarrhea. These results show that diarrhea significantly affects the gut microbiome of Korean indigenous calves. The changes in the gut microbiome of Korean indigenous calves observed in this study could be helpful in predicting and managing diarrhea calves, and furthermore, in establishing preventive measures for calf diarrhea through management of gut microbiome.},
}

@article {pmid40109720,
year = {2025},
author = {Merelim, AS and Zacca, R and Moreira-Gonçalves, D and Costa, PP and Baptista, LC},
title = {Distinct exercise modalities on GUT microbiome in sarcopenic older adults: study protocol of a pilot randomized controlled trial.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1504786},
pmid = {40109720},
issn = {2296-858X},
abstract = {BACKGROUND: Sarcopenia is a progressive and age-related skeletal muscle disease related to adverse health outcomes and to an increased economic burden. Recent evidence pinpoints the human gut microbiota (GM) as a contributing factor in the development of sarcopenia via the gut-muscle axis. To date, no study specifically analyzed the optimal type of exercise modality in older adults with sarcopenia considering the impact of GM composition in skeletal muscle mass and function. Therefore, the DEMGUTS study intents to explore the impact of three different exercise regimens on GM composition and gut-derived metabolites in older adults with sarcopenia.

METHODS: This pilot single center three-arm parallel open-label randomized control trial (RCT) will randomly assign eligible participants to: (i) moderate aerobic exercise (AER); (ii) resistance exercise (RES); or (iii) concurrent exercise training (RES + AER). Participants will engage in a supervised center-based exercise intervention (12-weeks, 3 d/week, 60 min/d), and will be assessed at (i) baseline, (ii) end of intervention (14 weeks), and (iii) at close-out (26-weeks). The primary outcome will be the change in the relative abundance of Faecalibacterium prausnitzii and other short-chain fatty acid producing bacteria after the intervention (14-weeks). A set of complementary outcomes will also be assessed to broadly characterize the impact of each exercise intervention on body composition, skeletal muscle function, functional performance and general GM composition.

CONCLUSION: Unraveling the impact of these exercise regimens on GM is crucial to help clarify the optimal exercise modality to manage sarcopenia disease, contributing to clinical guidance and enhancing exercise prescription in older adults with sarcopenia.

CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/, identifier NCT06545123.},
}

@article {pmid40109716,
year = {2025},
author = {Tian, X and Wang, L and Zhong, L and Zhang, K and Ge, X and Luo, Z and Zhai, X and Liu, S},
title = {The research progress and future directions in the pathophysiological mechanisms of type 2 diabetes mellitus from the perspective of precision medicine.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1555077},
pmid = {40109716},
issn = {2296-858X},
abstract = {Type 2 diabetes mellitus (T2DM) is a complex metabolic disorder characterized by pathophysiological mechanisms such as insulin resistance and β-cell dysfunction. Recent advancements in T2DM research have unveiled intricate multi-level regulatory networks and contributing factors underlying this disease. The emergence of precision medicine has introduced new perspectives and methodologies for understanding T2DM pathophysiology. A recent study found that personalized treatment based on genetic, metabolic, and microbiome data can improve the management of T2DM by more than 30%. This perspective aims to summarize the progress in T2DM pathophysiological research from the past 5 years and to outline potential directions for future studies within the framework of precision medicine. T2DM develops through the interplay of factors such as gut microbiota, genetic and epigenetic modifications, metabolic processes, mitophagy, NK cell activity, and environmental influences. Future research should focus on understanding insulin resistance, β-cell dysfunction, interactions between gut microbiota and their metabolites, and the regulatory roles of miRNA and genes. By leveraging artificial intelligence and integrating data from genomics, epigenomics, metabolomics, and microbiomics, researchers can gain deeper insights into the pathophysiological mechanisms and heterogeneity of T2DM. Additionally, exploring the combined effects and interactions of these factors may pave the way for more effective prevention strategies and personalized treatments for T2DM.},
}

@article {pmid40109342,
year = {2025},
author = {Zhan, P and Chen, W and Chen, J and Zhao, J and Ding, M and Fu, S and Wang, J},
title = {Commentary: Exploring the gut microbiome and immunological landscape in kidney cancer: a Mendelian randomization analysis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1506205},
pmid = {40109342},
issn = {1664-3224},
}

@article {pmid40109036,
year = {2025},
author = {Xu, Q and Xue, L and Wu, Z and Kang, S and Li, J and Wu, Y and Wu, Y and Zhao, J and Wu, R and Lv, H and Wang, J and Han, D},
title = {Dietary Qiwenghuangbo powder-enriched Limosilactobacillus reuteri protects the intestinal epithelium and alleviates inflammation via a strain-specific mechanism.},
journal = {Animal models and experimental medicine},
volume = {},
number = {},
pages = {},
doi = {10.1002/ame2.70016},
pmid = {40109036},
issn = {2576-2095},
support = {6232024//Beijing Municipal Natural Science Foundation/ ; 2021YFD1300201//National Key Research and Development Program of China/ ; 2022YFA1304201//National Key Research and Development Program of China/ ; B16044//111 Project/ ; 32125036//National Natural Science Foundation of China/ ; 32172750//National Natural Science Foundation of China/ ; 32302765//National Natural Science Foundation of China/ ; 32330100//National Natural Science Foundation of China/ ; CARS-35//China Agricultural Research System/ ; //2115 Talent Development Program of China Agricultural University/ ; },
abstract = {BACKGROUND: Qiwenghuangbo powder (QP), composed of Astragalus, Phellodendron chinensis, and Radix pulsatilla, is a traditional Chinese herbal formula, but its effects on weaned piglets remained unclear.

METHODS: Weaned piglets fed with 0.5 kg/t QP (QP1), 1 kg/t QP (QP2), low-zinc oxide (ZnO; negative control), and high-ZnO (positive control) diets in two phases, respectively, and the growth performance, intestinal morphology, cytokines, and microbial communities were profiled. The mouse models of colitis induced by Citrobacter rodentium and dextran sulfate sodium (DSS) were employed to elucidate the potential role of QP-fed enriched key species.

RESULTS: Dietary 1.0 kg/t QP alleviated diarrhea and inflammation and improved intestinal development and growth performance of weaned piglets. Moreover, this dietary intervention notably altered microbiota composition, characterized by the enrichment of Limosilactobacillus reuteri. Furthermore, out of three isolated L. reuteri, two strains could alleviate pathogen infection and intestinal inflammation, respectively. Specifically, the anti-inflammatory effect of one strain was achieved by promoting the colonization resistance of C. rodentium as significantly reduced pathogen loads. The other strain mitigated DSS-induced colitis by enhancing the goblet cell function and inhibiting the secretion of pro-inflammatory cytokines, particularly interleukin-1β (IL-1ß) and tumor necrosis factor-α (TNF-α).

CONCLUSIONS: Dietary QP improved the growth performance and intestinal health of weaned piglets by promoting the colonization of L. reuteri. The isolated commensal L. reuteri control colitis in a strain-specific mechanism, highlighting the potential of QP and L. reuteri in providing evidence for gut health promotion.},
}

@article {pmid40108947,
year = {2025},
author = {Zhang, C and Qu, L and Huang, Y and Tang, L and Ma, J and Xie, K and Wu, H},
title = {Association of Oral Microbiome Diversity With Depression Status: NHANES 2009-2012.},
journal = {Journal of public health dentistry},
volume = {},
number = {},
pages = {},
doi = {10.1111/jphd.12671},
pmid = {40108947},
issn = {1752-7325},
abstract = {OBJECTIVES: To investigate the relationship between oral microbial diversity and depression symptoms in the U.S.

METHODS: We utilized the US National Health and Nutrition Examination Survey (NHANES; 2009-2012) to assess the association between oral microbial diversity and depression symptoms. A cut-off PHQ-9 score of 15 was used to define severe depression symptoms. We conducted the multivariate linear regression to explore the association of the amplicon sequence variants (ASVs) with PHQ-9 scores. A restricted cubic spline (RCS) model was introduced to curve the dose-response relationship. A logistic regression model was used to calculate the odds ratio (OR) and 95% confidence interval (CI) of the association between ASVs and the risk of severe depression symptoms. Based on Bray-Curtis dissimilarity of beta diversity, analysis of similarity (ANOSIM) is used to assess the dissimilarity between different depression groups.

RESULTS: A total of 1497 participants were included, with 111 (7.41%) meeting the criteria for severe depression. After adjusting for confounders, we found that ASVs were negatively correlated with PHQ-9 scores (β = -0.008, p = 0.014). The RCS plot showed a linear relationship (pnon-linear = 0.232). Logistic regression showed that ASVs were associated with a decreased risk of severe depression symptoms (OR = 0.992, p = 0.003). Analysis of β diversity identified a statistically significant difference (R = 0.087, p = 0.003). Additionally, we developed a nomogram to estimate an individual's risk of severe depression symptoms.

CONCLUSIONS: Alpha diversity of the oral microbiota was associated with a reduced risk of severe depression symptoms, which could contribute to the early identification and intervention of severe depression.},
}

@article {pmid40108935,
year = {2025},
author = {O'Grady, K and Grabrucker, AM},
title = {Metal Dyshomeostasis as a Driver of Gut Pathology in Autism Spectrum Disorders.},
journal = {Journal of neurochemistry},
volume = {169},
number = {3},
pages = {e70041},
doi = {10.1111/jnc.70041},
pmid = {40108935},
issn = {1471-4159},
support = {//University of Limerick/ ; },
mesh = {Humans ; *Autism Spectrum Disorder/metabolism/pathology ; *Homeostasis/physiology ; *Gastrointestinal Microbiome/physiology ; *Brain-Gut Axis/physiology ; Animals ; Metals, Heavy/metabolism/toxicity ; Gastrointestinal Tract/metabolism/pathology ; },
abstract = {Despite being classified as neurodevelopmental disorders, in recent years, there has been a growing interest in the association between autism spectrum disorders (ASDs) and gut pathology. This comprehensive and systematic review explores a potential mechanism underlying gut pathology in ASDs, including alterations in gut microbiota, intestinal permeability, immune dysregulation, and gastrointestinal (GI) symptoms. Specifically, it delves into the role of toxic and essential metals and their interplay, affecting the development and function of the GI tract. The review also discusses the potential implications of this gut pathology in the development and management of ASDs. Studies have shown that heavy metal exposure, whether through environmental sources or dietary intake, can disrupt the delicate balance of trace elements in the gut. This disruption can adversely affect zinc homeostasis, potentially exacerbating gut pathology in individuals with ASDs. The impaired zinc absorption resulting from heavy metal exposure may contribute to the immune dysregulation, oxidative stress, and inflammation observed in the gut of individuals with ASDs. By shedding light on the multifaceted nature of gut pathology, including the impact of metal dyshomeostasis as a non-genetic factor in ASD, this review underscores the significance of the gut-brain axis in the etiology and management of ASDs.},
}

Humans
*Autism Spectrum Disorder/metabolism/pathology
*Homeostasis/physiology
*Gastrointestinal Microbiome/physiology
*Brain-Gut Axis/physiology
Animals
Metals, Heavy/metabolism/toxicity
Gastrointestinal Tract/metabolism/pathology

@article {pmid40108902,
year = {2025},
author = {Khalili, L and Park, G and Nagpal, R and Bhide, P and Salazar, G},
title = {The Impact of Akkermansia muciniphila on Mouse Models of Depression, Anxiety, and Stress: A Systematic Review and Meta-Analysis.},
journal = {Current neuropharmacology},
volume = {},
number = {},
pages = {},
doi = {10.2174/011570159X360149250225041829},
pmid = {40108902},
issn = {1875-6190},
abstract = {BACKGROUND: Akkermansia muciniphila (A. muciniphila), a bacterial species within the human gut microbiome, has shown beneficial effects on host health. Emerging research suggests that A. muciniphila also influences neurobehavioral domains through the microbiota-gut-brain axis. This meta-analysis evaluates A. muciniphila's impact on depression, anxiety, and stress in mouse models.

METHODS: We conducted a systematic search of PubMed, Science Direct, Embase, and Web of Science databases up to March 2024, identifying 15 eligible studies.

RESULTS: Supplementation with A. muciniphila, its outer membrane protein (Amuc_1100), and extracellular vesicles (EVs) alleviated anxiety, depressive-like behaviors, and enhanced memory in mice. Compared to controls, intervention groups exhibited reduced anxiety-like behaviors, including increased travel distance in the open-field test (OFT) and more time spent in the lightbox during the light-dark box (LDB) test and open arms in the elevated plus maze (EPM). Depression-like symptoms were reduced, with lower immobility time in the tail suspension and forced swim tests. Memory function also improved, and learning time was reduced in the Y-maze and Barnes circular maze tests. Serotonin levels increased significantly in the serum and hippocampus, while corticosterone levels decreased, though not significantly. The intervention reduced hippocampal and serum inflammatory markers (TNFα, IL1β, IL6) and altered gut microbiome composition, increasing Akkermansia, Roseburia, Caldicoprobacter, and Lachnospiraceae.

CONCLUSION: This meta-analysis provides evidence supporting the health-promoting effects of A. muciniphila, one of the next-generation probiotics, in alleviating neuropsychiatric disorders. Given the high prevalence and clinical significance of depression, anxiety, and stress, further investigation into the therapeutic utility of A. muciniphila is warranted.},
}

@article {pmid40108895,
year = {2025},
author = {Dagdeviren, M and Bozcal, E},
title = {Inflecting Factors on Alzheimer's Disease Progression: The Interaction of Gut Microbiome, Oxidative Stress, and Nutritional Interventions.},
journal = {Current topics in medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115680266342624241127071044},
pmid = {40108895},
issn = {1873-4294},
abstract = {Alzheimer's Disease (AD) is a complex neurological condition caused by various factors. Diet, oxidative stress, and the gut microbiota all play critical roles in the development of AD. Recent studies suggested a bidirectional relationship between the gut and the brain, emphasizing the pivotal role of the gut microbiome in influencing cognitive functions. For instance, dysbiosis, a disruption in the balance of gut microbial communities, has been linked to neuroinflammation and the accumulation of amyloid-beta plaques, hallmark features of AD. Oxidative stress, arising from an imbalance between free radicals and antioxidants, contributes significantly to AD pathology. The molecular mechanisms through which oxidative stress impacts neuronal health and exacerbates the cognitive decline in AD patients are also relevant. Moreover, nutritional interventions emerge as promising strategies to modulate these inflecting factors. Dietary components, such as antioxidants, omega-3 fatty acids, and polyphenols, exhibit neuroprotective effects, potentially mitigating AD progression. In contrast, the Western diet has a high potential to abet AD onset. Mediterranean diet and/or intermittent fasting are more valuable diets that may help delay the AD onset or progression. Limitations like individual differences affect the efficacy of nutritional interventions. As a supporting therapy, personalized diets should be applied according to the patients' special needs/microbiomes in the future. To gather current knowledge on the interconnected roles of the gut microbiome, oxidative stress, and nutritional interventions in AD is crucial. Understanding these interactions may pave the way for novel therapeutic approaches, as well as disputing the potential diets that can help improve AD patients' quality of life.},
}

@article {pmid40108741,
year = {2025},
author = {Gamboa, DA and Flynn, PJ and Horna-Lowell, ES and Pinter-Wollman, N},
title = {Social organization and physical environment shape the microbiome of harvester ants.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {29},
pmid = {40108741},
issn = {2524-4671},
support = {000886211//National Science Foundation Graduate Research Fellowship Program/ ; GM115509//Foundation for the National Institutes of Health/ ; },
abstract = {All animals harbor microbiomes, which are obtained from the surrounding environment and are impacted by host behavior and life stage. To determine how two non-mutually exclusive drivers - physical environment and social organization - affect an organism's microbiome, we examined the bacterial communities within and around nests of harvester ants (Veromessor andrei). We collected soil and nest content samples from five different ant nests. We used 16S rRNA gene sequencing and calculated alpha and beta diversity to compare bacterial diversity and community composition across samples. To test the hypotheses that physical environment and/or social organization impact ant colonies' community of microbes we compared our samples across (i) sample types (ants, brood, seeds and reproductives (winged alates), and soil), (ii) soil inside and outside the nest, and (iii) soil from different chamber types. Interestingly, we found that both the environment and social organization impact the bacterial communities of the microbiome of V. andrei colonies. Soil from the five nests differed from one another in a way that mapped onto their geographical distance. Furthermore, soil from inside the nests resembled the surrounding soil, supporting the physical environment hypothesis. However, the bacterial communities associated with the contents within the nest chambers, i.e., ants, brood, seeds, and reproductives, differed from one another and from the surrounding soil, supporting the social organization hypotheses. This study highlights the importance of considering environmental and social factors in understanding microbiome dynamics.},
}

@article {pmid40108657,
year = {2025},
author = {Ruiz-Moreno, AJ and Del Castillo-Izquierdo, Á and Tamargo-Rubio, I and Fu, J},
title = {MicrobeRX: a tool for enzymatic-reaction-based metabolite prediction in the gut microbiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {78},
pmid = {40108657},
issn = {2049-2618},
support = {101001678/ERC_/European Research Council/International ; VI.C.202.022//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; Bacteria/metabolism/classification/genetics ; Pharmaceutical Preparations/metabolism ; Enzymes/metabolism ; Software ; Biotransformation ; Metabolomics/methods ; },
abstract = {BACKGROUND: The gut microbiome functions as a metabolic organ, producing numerous enzymes that influence host health; however, their substrates and metabolites remain largely unknown.

RESULTS: We present MicrobeRX, an enzyme-based metabolite prediction tool that employs 5487 human reactions and 4030 unique microbial reactions from 6286 genome-scale models, as well as 3650 drug metabolic reactions from the DrugBank database (v.5.1.12). MicrobeRX includes additional analysis modules for metabolite visualization and enzymatic and taxonomic analyses. When we applied MicrobeRX to 1083 orally administered drugs that have been approved in at least one jurisdiction at some point in time (DrugBank), it predicted metabolites with physicochemical properties and structures similar to metabolites found in biosamples (from MiMeDB). It also outperformed another existing metabolite prediction tool (BioTransformer 3.0) in terms of predictive potential, molecular diversity, reduction of redundant predictions, and enzyme annotation.

CONCLUSIONS: Our analysis revealed both unique and overlapping metabolic capabilities in human and microbial metabolism and chemo- and taxa-specific microbial biotransformations. MicrobeRX bridges the genomic and chemical spaces of the gut microbiome, making it a valuable tool for unlocking the chemical potential of the gut microbiome in human health, the food and pharmaceutical industries, and environmental safety. Video Abstract.},
}

*Gastrointestinal Microbiome
Humans
Bacteria/metabolism/classification/genetics
Pharmaceutical Preparations/metabolism
Enzymes/metabolism
Software
Biotransformation
Metabolomics/methods

@article {pmid40108637,
year = {2025},
author = {Gangiah, TK and Alisoltani, A and Potgieter, M and Bell, L and Ross, E and Iranzadeh, A and McDonald, Z and Allali, I and Dabee, S and Barnabas, S and Blackburn, JM and Tabb, DL and Bekker, LG and Jaspan, HB and Passmore, JS and Mulder, N and Masson, L},
title = {Exploring the female genital tract mycobiome in young South African women using metaproteomics.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {76},
pmid = {40108637},
issn = {2049-2618},
support = {SP.2011.41304.038//European and Developing Countries Clinical Trials Partnership Strategic Primer/ ; },
mesh = {Female ; Humans ; South Africa ; *Mycobiome ; *Proteomics ; Adult ; Young Adult ; *Vagina/microbiology ; Fungi/classification/isolation & purification/genetics ; Vaginosis, Bacterial/microbiology ; Adolescent ; Genitalia, Female/microbiology ; Microbiota ; Candida/classification/isolation & purification/genetics ; Chromatography, Liquid ; Tandem Mass Spectrometry ; Sexually Transmitted Diseases/microbiology ; },
abstract = {BACKGROUND: Female genital tract (FGT) diseases such as bacterial vaginosis (BV) and sexually transmitted infections are prevalent in South Africa, with young women being at an increased risk. Since imbalances in the FGT microbiome are associated with FGT diseases, it is vital to investigate the factors that influence FGT health. The mycobiome plays an important role in regulating mucosal health, especially when the bacterial component is disturbed. However, we have a limited understanding of the FGT mycobiome since many studies have focused on bacterial communities and have neglected low-abundance taxonomic groups, such as fungi. To reduce this knowledge deficit, we present the first large-scale metaproteomic study to define the taxonomic composition and potential functional processes of the FGT mycobiome in South African reproductive-age women.

RESULTS: We examined FGT fungal communities present in 123 women by collecting lateral vaginal wall swabs for liquid chromatography-tandem mass spectrometry. From this, 39 different fungal genera were identified, with Candida dominating the mycobiome (53.2% relative abundance). We observed changes in relative abundance at the protein, genus, and functional (gene ontology biological processes) level between BV states. In women with BV, Malassezia and Conidiobolus proteins were more abundant, while Candida proteins were less abundant compared to BV-negative women. Correspondingly, Nugent scores were negatively associated with total fungal protein abundance. The clinical variables, Nugent score, pro-inflammatory cytokines, chemokines, vaginal pH, Chlamydia trachomatis, and the presence of clue cells were associated with fungal community composition.

CONCLUSIONS: The results of this study revealed the diversity of FGT fungal communities, setting the groundwork for understanding the FGT mycobiome. Video Abstract.},
}

Female
Humans
South Africa
*Mycobiome
*Proteomics
Adult
Young Adult
*Vagina/microbiology
Fungi/classification/isolation & purification/genetics
Vaginosis, Bacterial/microbiology
Adolescent
Genitalia, Female/microbiology
Microbiota
Candida/classification/isolation & purification/genetics
Chromatography, Liquid
Tandem Mass Spectrometry
Sexually Transmitted Diseases/microbiology

@article {pmid40108579,
year = {2025},
author = {Feng, Q and Huang, W and Zhao, X and Sheng, T and Peng, B and Meng, S and Liu, W and Ge, L and Wang, L and Pathak, JL and Jiang, Q and Lin, R and Zeng, S},
title = {Investigation of dental health and salivary microbiota characteristics of children with visual impairment in Guangzhou, China.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {408},
pmid = {40108579},
issn = {1472-6831},
support = {No.20241A010079//the General Guidelines of Guangzhou Health Science, Technology Project/ ; No.20241A010079//the General Guidelines of Guangzhou Health Science, Technology Project/ ; 201904010085//the Science and Technology Planning Project of Guangzhou/ ; 201904010085//the Science and Technology Planning Project of Guangzhou/ ; 2023E02J0004//the Guangzhou Liwan District science popularization "One District One Brand" project/ ; },
mesh = {Humans ; Child ; China ; *Saliva/microbiology ; Female ; Male ; *Microbiota ; Adolescent ; *Oral Health ; *Vision Disorders/microbiology ; Dental Caries/microbiology ; RNA, Ribosomal, 16S ; },
abstract = {BACKGROUND: The prevalence of visual impairment (VS) among children in China is increasing. The oral microbiome is crucial for maintaining homeostasis and health. This study aimed to investigate the oral health and hygiene habits of children with VS in Guangzhou and explore the differences in salivary microbiota (SM) between children with VS and healthy vision (HS).

METHOD: This study included oral health examinations and surveys of oral hygiene habits among 101 children with VS. Saliva samples from 20 children with VS and 20 with HS were analysed for oral microbiota. The 16s rRNA V3-V4 regions were sequenced using the Illumina MiSeq platform and operational taxonomic units were clustered using QIIME for statistical analysis.

RESULTS: Inadequate oral hygiene was observed among 101 children with VS, aged 6-16, who displayed a high caries rate of 92.1%. There was no significant difference in the overall composition of the salivary microbiota between the two groups. HS group had a higher abundance of Bacillota, Patescibacteria, and Spirochaetota at the phylum level; Bacilli, Negativicutes, and Saccharimonadia at the class level; and Streptococcus at the genus level. In contrast, VS group showed a greater abundance of Actinomycetota, Bacteroidota, Pseudomonadota, and Fusobacteriota (at the phylum level) and Actinomycetia, Bacteroidia, Gammaproteobacteria, Fusobacteriia, and Clostridia (at the class level), along with Rothia, Neisseria, Veillonella, Prevotella_7, Actinomyces, Leptotrichia, and Lactobacillales (at the genus level). Actinomycetota was significantly and positively correlated with gingivitis and dental caries, and Streptococcus salivarius was more abundant in children with VS.

CONCLUSION: This study underscores the importance of improving oral healthcare for schoolchildren with VS in Guangzhou, China and provides valuable insights into the characteristics of the salivary microbiota of this population, identifying potential targets for interventions aimed at enhancing oral health.},
}

Humans
Child
China
*Saliva/microbiology
Female
Male
*Microbiota
Adolescent
*Oral Health
*Vision Disorders/microbiology
Dental Caries/microbiology
RNA, Ribosomal, 16S

@article {pmid40108399,
year = {2025},
author = {Xu, J and Dong, L and Xie, X and Geng, BD and Lu, J and Dong, Y and Hu, Y and Liu, C and Mao, Y and Ge, G and Ren, Z},
title = {Human umbilical cord-derived mesenchymal stem cells improve thymus and spleen functions in D-galactose-induced aged mice.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {9470},
pmid = {40108399},
issn = {2045-2322},
support = {82160126//National Natural Science Foundation of China/ ; gzwkj2023-230//Science and Technology Fund Project of Guizhou Province Health Commission/ ; HY2402//Cooperation projects of Guizhou Medical University-Guizhong Biotechnology Co., Ltd/ ; Qiankehe Foundation-ZK 2024 General 182//Natural Science Foundation Project of Guizhou Provincial Science and Technology Department/ ; XBHJ[2024]018 & [2020]018//Guizhou Medical University Doctoral Start-up Fund/ ; },
mesh = {Animals ; *Galactose ; *Thymus Gland/metabolism ; *Mesenchymal Stem Cells/metabolism/cytology ; *Spleen/metabolism ; Mice ; *Umbilical Cord/cytology ; Humans ; *Mesenchymal Stem Cell Transplantation/methods ; Gastrointestinal Microbiome ; Aging ; Cellular Senescence ; Male ; NF-E2-Related Factor 2/metabolism ; },
abstract = {As aging progresses, the structures and functions of immune organs such as the thymus and spleen deteriorate, leading to impaired immune function and immune senescence. This study investigated the potential of umbilical cord mesenchymal stem cells (UC-MSCs) to mitigate D-galactose-induced immune senescence by enhancing the structural and functional integrity of aging immune organs and regulating the gut microbiota. The findings show that UC-MSCs treatment significantly delayed thymus and spleen atrophy and reduced the number of senescence-associated β-galactosidase (SA-β-gal) positive cells. At the molecular level, UC-MSCs treatment downregulated the expression of aging-related genes, including p16, p53, p21, and RB. It also boosted antioxidant enzyme activity, increasing the levels of catalase (CAT), superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px), while decreasing serum malondialdehyde (MDA) levels by activating the Nrf2/HO-1 pathway. Additionally, UC-MSCs treatment restored the balance of the gut microbiota. These results demonstrate that UC-MSCs significantly improve the structural and functional integrity of immune organs and enhance the composition of the gut microbiome, offering a potential strategy for delaying immune senescence.},
}

Animals
*Galactose
*Thymus Gland/metabolism
*Mesenchymal Stem Cells/metabolism/cytology
*Spleen/metabolism
Mice
*Umbilical Cord/cytology
Humans
*Mesenchymal Stem Cell Transplantation/methods
Gastrointestinal Microbiome
Aging
Cellular Senescence
Male
NF-E2-Related Factor 2/metabolism

@article {pmid40108347,
year = {2025},
author = {Bashandy, SR and Mohamed, OA and Abdalla, OA and Elfarash, A and Abd-Alla, MH},
title = {Harnessing plant growth-promoting bacteria to combat watermelon mosaic virus in squash.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {9440},
pmid = {40108347},
issn = {2045-2322},
mesh = {*Plant Diseases/microbiology/virology ; *Potyvirus/physiology ; *Cucurbita/virology/microbiology/growth & development ; *Bacteria/metabolism/genetics ; Rhizosphere ; Soil Microbiology ; Indoleacetic Acids/metabolism ; RNA, Ribosomal, 16S/genetics ; Carbon-Carbon Lyases/metabolism ; Plant Growth Regulators/metabolism ; Plant Development ; },
abstract = {Plant diseases significantly threaten global food security, with viral infections, particularly Watermelon Mosaic Virus (WMV), causing substantial losses in economically important crops such as squash. This study aims to investigate the efficacy of beneficial bacteria isolated from various plants in promoting growth and mitigating the effects of WMV in squash. Understanding the interactions between plants and beneficial microbes could provide sustainable solutions for managing viral infections in agriculture. Sixty-two bacterial isolates were obtained from the rhizosphere of basil, mint, thyme, and squash plants. Among these, six strains exhibited notable plant growth-promoting activities, including the synthesis of indole acetic acid, solubilization of phosphate and zinc, ammonia production, and activity of 1-aminocyclopropane-1-carboxylate deaminase (ACCD). Morphological observations and 16S rRNA gene sequencing identified these isolates as Pseudomonas indica, Bacillus paramycoides, Bacillus thuringiensis, Bacillus mycoides, Paenibacillus glucanolyticus, and Niallia circulans. In pot experiments, squash plants inoculated with these bacterial strains demonstrated significant reductions in disease severity after being infected with WMV. Specifically, foliar applications of the bacteria resulted in the following reductions in disease severity: B. mycoides (87%), B. thuringiensis (73%), Paenibacillus glucanolyticus (73%), Niallia circulans (70%), B. paramycoides (65%), and Pseudomonas indica (65%). Additionally, plants treated with B. mycoides showed increased plant height and shoot dry weight, indicating enhanced growth performance relative to infected controls. Statistical analysis revealed that these growth promotions and disease severity reduction were significant (p < 0.05). GC-MS analysis of the six bacterial strains revealed a diverse array of 73 chemical metabolites, including common compounds such as 9-Octadecenoic acid (Z), benzene derivatives, and cyclopentanones. These findings suggest shared metabolic pathways among the strains and indicate potential roles in ecological interactions, plant defense mechanisms, and antiviral properties. These metabolites likely contribute to the observed reductions in viral severity and enhance plant resilience. The study indicates that inoculating squash plants with specific beneficial bacteria, especially B. mycoides, through foliar or soil application can significantly decrease the severity of WMV and promote plant growth. This approach offers an environmentally friendly alternative to chemical antiviral treatments and may reduce reliance on pesticides. This research highlights the potential of using plant growth-promoting bacteria (PGPB)as a sustainable approach to control viral infections in crops. Further field trials are necessary to PGPB validate the scalability of these findings and assess their effectiveness under diverse agricultural conditions. Incorporating these beneficial microbes into agricultural practices could enhance the resilience of cropping systems, ultimately fostering sustainable agriculture and enhancing food security.},
}

*Plant Diseases/microbiology/virology
*Potyvirus/physiology
*Cucurbita/virology/microbiology/growth & development
*Bacteria/metabolism/genetics
Rhizosphere
Soil Microbiology
Indoleacetic Acids/metabolism
RNA, Ribosomal, 16S/genetics
Carbon-Carbon Lyases/metabolism
Plant Growth Regulators/metabolism
Plant Development

@article {pmid40108202,
year = {2025},
author = {Redgwell, TA and Thorsen, J and Petit, MA and Deng, L and Vestergaard, G and Russel, J and Chawes, B and Bønnelykke, K and Bisgaard, H and Nielsen, DS and Sørensen, S and Stokholm, J and Shah, SA},
title = {Prophages in the infant gut are pervasively induced and may modulate the functionality of their hosts.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {46},
pmid = {40108202},
issn = {2055-5008},
mesh = {*Gastrointestinal Microbiome ; *Prophages/genetics/physiology ; Humans ; Infant ; *Metagenome ; Virome ; Female ; Feces/microbiology/virology ; Bacteria/genetics/classification/virology ; Bacteroides/genetics/virology ; },
abstract = {Gut microbiome (GM) composition and function is pivotal for human health and disease, of which the virome's importance is increasingly recognised. However, prophages and their induction patterns in the infant gut remain understudied. Here, we identified 10645 putative prophages in 662 metagenomes from 1-year-old children in the COPSAC2010 mother-child cohort and investigated their potential functions. No core provirome was found as the most prevalent vOTU was identified in only ~70% of the samples. The most dominant cluster of vOTUs in the cohort was related to Bacteroides phage Hanky p00', and it carried both diversity generating retroelements and genes involved in capsular polysaccharide synthesis. Paired analysis of viromes and metagenomes from the same samples revealed that most prophages within the infant gut were induced and that induction was unaffected by a range of environmental perturbers. In summary, prophages are major components of the infant gut that may have far reaching influences on the microbiome and its host.},
}

*Gastrointestinal Microbiome
*Prophages/genetics/physiology
Humans
Infant
*Metagenome
Virome
Female
Feces/microbiology/virology
Bacteria/genetics/classification/virology
Bacteroides/genetics/virology

@article {pmid40108178,
year = {2025},
author = {Hong, MG and Song, EJ and Yoon, HJ and Chung, WH and Seo, HY and Kim, D and Lee, D and Seo, JG and Lee, H and Kim, SI and Kim, GJ and Kim, KN and Lee, SN and Kim, KS and Nam, YD},
title = {Clade-specific extracellular vesicles from Akkermansia muciniphila mediate competitive colonization via direct inhibition and immune stimulation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2708},
pmid = {40108178},
issn = {2041-1723},
mesh = {*Akkermansia ; *Extracellular Vesicles/metabolism/immunology ; *Gastrointestinal Microbiome ; Animals ; Immunoglobulin A/immunology ; Mice ; Humans ; Probiotics ; Mice, Inbred C57BL ; },
abstract = {Akkermansia muciniphila, a promising candidate for next-generation probiotics, exhibits significant genomic diversity, classified into several distinct clades (AmI to AmIV). Notably, a single Akkermansia clade tends to predominate within individual hosts, with co-occurrence of different clades being rare. The mechanisms driving such clade-specific exclusion remain unclear. Here, we show that extracellular vesicles (EVs) derived from AmII clade inhibit the growth of clade I (AmI), conferring a competitive advantage to AmII. Moreover, we observe clade-specific immunoglobulin A (IgA) responses, where AmII clade-specific IgAs, induced by EVs from AmII, facilitate niche occupancy and competitive exclusion of AmI. These findings provide insights into the competitive dynamics of A. muciniphila clades and suggest that future personalized microbiome interventions could be optimized by considering the clade composition of A. muciniphila in individual hosts.},
}

*Akkermansia
*Extracellular Vesicles/metabolism/immunology
*Gastrointestinal Microbiome
Animals
Immunoglobulin A/immunology
Mice
Humans
Probiotics
Mice, Inbred C57BL

@article {pmid40108151,
year = {2025},
author = {Krueger, ME and Boles, JS and Simon, ZD and Alvarez, SD and McFarland, NR and Okun, MS and Zimmermann, EM and Forsmark, CE and Tansey, MG},
title = {Comparative analysis of Parkinson's and inflammatory bowel disease gut microbiomes reveals shared butyrate-producing bacteria depletion.},
journal = {NPJ Parkinson's disease},
volume = {11},
number = {1},
pages = {50},
pmid = {40108151},
issn = {2373-8057},
support = {PF-RCE-1945//Parkinson's Foundation (Parkinson's Foundation, Inc.)/ ; PF-RCE-1945//Parkinson's Foundation (Parkinson's Foundation, Inc.)/ ; PF-RCE-1945//Parkinson's Foundation (Parkinson's Foundation, Inc.)/ ; },
abstract = {Epidemiological studies reveal that inflammatory bowel disease (IBD) is associated with an increased risk of Parkinson's disease (PD). Gut dysbiosis has been documented in both PD and IBD, however it is currently unknown whether gut dysbiosis underlies the epidemiological association between both diseases. To identify shared and distinct features of the PD and IBD microbiome, we recruited 54 PD, 26 IBD, and 16 healthy control individuals and performed the first joint analysis of gut metagenomes. Larger, publicly available PD and IBD metagenomic datasets were also analyzed to validate and extend our findings. Depletions in short-chain fatty acid (SCFA)-producing bacteria, including Roseburia intestinalis, Faecalibacterium prausnitzii, Anaerostipes hadrus, and Eubacterium rectale, as well depletion in SCFA-synthesis pathways were detected across PD and IBD datasets, suggesting that depletion of these microbes in IBD may influence the risk for PD development.},
}

@article {pmid40107863,
year = {2025},
author = {Emerson, KJ and Shaikh, SS and Bradley-Slagle, DP and Woodley, SK},
title = {The Aquatic Microbial Environment Shapes the Tadpole Microbiome and Antipredator Behavior.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icaf009},
pmid = {40107863},
issn = {1557-7023},
abstract = {Host-associated microbial communities impact the brain and behavior through the microbiota-gut-brain (MGB) axis. Most studies of the gut microbiota use mammals in biomedical contexts; much less is known regarding wildlife species. We used larval amphibians to study the impact of the aquatic microbial environment on the gut and skin microbiota, brain, and antipredator behavior. We raised Northern Leopard Frog (Lithobates pipiens) tadpoles in pond water that was autoclaved or not autoclaved (natural); other studies show that these treatments produce variation in the tadpole gut microbiota. Tadpoles were also raised in the presence of stressors: predation-derived chemical cues and corticosterone. Compared to tadpoles raised in natural pond water, tadpoles raised in autoclaved pond water had altered gut and skin microbial communities, body size, brain size, brain shape and behavioral responses to alarm pheromones. There was no effect of microbial environment or stressors on differential gene expression of the whole brain. The gut microbiota, but not the skin microbiota, was a significant predictor of behavioral endpoints. We found surprisingly few impacts of stressors on the tadpoles, although stressor treatments interacted with pond water treatments to influence the composition of the gut microbiota. Our findings demonstrate that tadpole behavior is modulated by the aquatic microbial community experienced during development in ways that are likely to affect survival.},
}

@article {pmid40107677,
year = {2025},
author = {Pasquier, JC and Plourde, M and Ramanathan, S and Chaillet, N and Boivin, G and Laforest-Lapointe, I and Allard-Chamard, H and Baron, G and Beaulieu, JF and Fülöp, T and Généreux, M and Mâsse, B and Robitaille, J and Valiquette, L and Bilodeau, S and H Buch, D and Piche, A},
title = {P robiotics i nfluencing r esponse of a ntibodies over t ime in s eniors after CO VID-19 v accine (PIRATES-COV): a randomised controlled trial protocol.},
journal = {BMJ open},
volume = {15},
number = {3},
pages = {e088231},
doi = {10.1136/bmjopen-2024-088231},
pmid = {40107677},
issn = {2044-6055},
mesh = {Humans ; Aged ; *COVID-19/prevention & control ; Aged, 80 and over ; *Probiotics/therapeutic use ; Double-Blind Method ; *SARS-CoV-2/immunology ; Male ; Female ; *COVID-19 Vaccines/immunology ; Quebec ; Antibodies, Viral/blood ; Lacticaseibacillus casei/immunology ; Lacticaseibacillus rhamnosus ; Randomized Controlled Trials as Topic ; },
abstract = {INTRODUCTION: The elderly are particularly vulnerable to morbidity and mortality from COVID-19, the disease caused by the SARS-CoV-2. Approximately 20% of the elderly showed no antibodies 3-5 months post-second dose of the COVID-19 vaccine. As probiotics have been shown to increase influenza-specific antibody levels post-influenza vaccination, we aim to reduce the percentage of participants without antibodies against the SARS-CoV-2 spike protein receptor-binding domain (anti-S1-RBD) at 6 months post-vaccination.

METHODS AND ANALYSIS: Our study design is a double-blind randomised controlled trial, using intention-to-treat analysis. Eligible participants are a purposive sample of 688 adults aged 65-89 years, in Quebec, Canada, not diagnosed with COVID-19 in the 3 months prior to recruitment and who wish to receive a government-recommended mRNA booster (Pfizer-BioNTech, Moderna) vaccine. The intervention consists of one capsule/day of a probiotic dietary supplement of Lacticaseibacillus rhamnosus and Lacticaseibacillus casei 6×10[9] CFU/capsule or a placebo, for 15 days pre-booster and post-booster vaccine. All participants provide dried blood spot samples at three timepoints (inclusion, 3 and 6 months post-vaccination) and a stool sample for microbiome analysis. A subgroup of 100 participants living near Sherbrooke, Quebec, is expected to volunteer for two onsite blood-test visits (at inclusion and 6 months post-vaccination). The primary outcome is the percentage of participants without anti-S1-RBD antibodies at 6 months post-vaccination. Secondary outcomes include longitudinal analysis of anti-S1-RBD and anti-N antibodies at three timepoints. In the subgroup, serum levels of neutralising antibodies will be determined at inclusion and 6 months post-vaccination. Probiotic and vaccine side effects are monitored. At the end of the study, we expect to identify the adjuvant effect of probiotic on vaccine-induced immune response.

ETHICS AND DISSEMINATION: The study was approved by Research Ethics Board of the Centre Intégré Universitaire de Santé et des Services Sociaux de l'Estrie- Centre Hospitalier Universitaire de Sherbrooke (CIUSSS de l'Estrie-CHUS) and the CHU de Québec-Université Laval # MP-31-2022-4598 as well as Health Canada. All participants will provide informed consent. Results will be disseminated to the scientific community and to all networks related in this research.

TRIAL REGISTRATION NUMBER: NCT05195151.},
}

Humans
Aged
*COVID-19/prevention & control
Aged, 80 and over
*Probiotics/therapeutic use
Double-Blind Method
*SARS-CoV-2/immunology
Male
Female
*COVID-19 Vaccines/immunology
Quebec
Antibodies, Viral/blood
Lacticaseibacillus casei/immunology
Lacticaseibacillus rhamnosus
Randomized Controlled Trials as Topic

@article {pmid40107222,
year = {2025},
author = {Yatera, K and Nishida, C and Mukae, H},
title = {Up-to-date nucleic acid assays for diagnosing respiratory infection.},
journal = {Respiratory investigation},
volume = {63},
number = {3},
pages = {383-393},
doi = {10.1016/j.resinv.2025.03.004},
pmid = {40107222},
issn = {2212-5353},
abstract = {Nucleic acid assays have been widely used as rapid tests for diagnosing respiratory infections during and after the coronavirus disease 2019 (COVID-19) pandemic. An ideal point-of-care diagnostic must be affordable, sensitive, specific, user-friendly, rapid/robust, equipment-free and deliverable (ASSURED), and in addition to improvements to conventional methods based on polymerase chain reaction (PCR), point-of-care testing aiming for "REASSURED" are emerging through integration with microfluidic technology. Compared to conventional immunoassays, nucleic acid assays, especially rapid nucleic acid assays as point-of-care testing, contribute to improvements in various clinical outcomes, such as diagnostic yield, turnaround time, length of hospital stay, disease treatment, and infection control management. Rapid and diverse development of new nucleic acid-based molecular diagnostic technologies, such as those based on the CRISPR/Cas system or biosensor nucleic acid assays, is expected to become increasingly diverse in the future as point-of-care testing. In addition, laboratory-based DNA sequencing technology has been used to perform microbiome analyses over a wide area and is expected to shed light on the pathological mechanisms of various respiratory infectious diseases. One example of the benefits of nucleic acid amplification analysis methods is their ability to reveal the true nature of the bacterial flora in pneumonia lesions. This has been demonstrated based on the results of 16S ribosomal RNA gene sequencing analyses using bronchoalveolar lavage fluid directly obtained from pneumonia lesions in patients with pneumonia.},
}

@article {pmid40106906,
year = {2025},
author = {Pan, H and Bi, J and Hu, H and Huang, Y and Li, A and Zhang, H and Wan, Y and Zhan, K and Wang, K and Zhao, Z and Bai, X},
title = {Chinese herbal medicine improves antioxidant capacity of chicken liver at high stocking density involved gut-liver microbiota axis based on multi-omics technologies.},
journal = {Poultry science},
volume = {104},
number = {5},
pages = {105015},
doi = {10.1016/j.psj.2025.105015},
pmid = {40106906},
issn = {1525-3171},
abstract = {Traditional Chinese Medicine (TCM), such as artemisinin, berberine and proanthocyanidin, has been considered an effective additive for broiler production. High density farming (HDF), which is the primary modern mode of chicken production, is associated with animal health problems. This work aimed to evaluate the effects of dietary TCMs (dihydroartemisinin, hydrochloride, and oligomeric proanthocyanidins) on improving the antioxidant capacity of chickens under HDF and their underlying mechanisms. A total of 360 Wuding chickens (134-day-old) were divided into five experimental groups: one normal stocking density (8 birds/m[2], control group) and four high stocking density (16 birds/m[2]), with six replicates for each group. For four HDF groups, one group was fed the basal diet, and the other three groups were fed the basal diet supplemented with 80 mg/kg dihydroartemisinin, 600 mg/kg berberine hydrochloride, and 250 mg/kg grape oligomeric proanthocyanidins, respectively. HDF increased malondialadehyde level, but decreased superoxide dismutase, glutathione and glutathione peroxidase levels in the liver of broiler; however, dietary TCMs apparently alleviated this attenuation. Dietary TCMs significantly decreased the expression of genes involved in cholesterol synthesis in the liver and the levels of tripepides in the intestine of the HDF chickens. Meanwhile, dietary TCMs significantly altered the composition of the liver microbiome in the HDF chickens, expressing by reduced Pseudomonas but enriched Bradyrhizobium. The gut microbiota of the HDF chickens was also altered following dietary TCM administration, with a decreased abundance of Microbacter margulisiae and an increased abundance of acetate synthesis genes. Association analysis of the multi-omics results revealed negative correlations between liver cholesterol synthesis and antioxidant factors that could be regulated by gut microbiota-produced short-chain fatty acids. Furthermore, alleviating of oxidative stress by dietary TCMs also showed significant correlations with the liver microbiome, which could be mediated by tripeptides produced by the gut microbiota. These results indicated that dietary TCM is beneficial in improving antioxidant defenses in HDF chickens and interpreted the mechanisms of action of TCM from the perspective of modern science.},
}

@article {pmid40106821,
year = {2025},
author = {Yang, CC and Washio, J and Lin, YC and Hsu, ML and Wang, DH and Tsai, FT and Lin, YM and Tu, HF and Chang, HC and Takahashi, N},
title = {Microbiome Signatures and Dysbiotic Patterns in Oral Cancer and Precancerous Lesions.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.15317},
pmid = {40106821},
issn = {1601-0825},
support = {112-2314-B-A49-027//the National Science and Technology Council, Taiwan/ ; 111-2314-B-A49-028-MY2//the National Science and Technology Council, Taiwan/ ; 111-2314-B-A49-026-MY3//the National Science and Technology Council, Taiwan/ ; 112-2314-B-A49-058//the National Science and Technology Council, Taiwan/ ; 111-2314-B-A49-087-MY3//the National Science and Technology Council, Taiwan/ ; 21H03151//the Japan Society for the Promotion of Science/ ; 20K10241//the Japan Society for the Promotion of Science/ ; 23K18349//the Japan Society for the Promotion of Science/ ; 23K21499//the Japan Society for the Promotion of Science/ ; //the National Yang Ming Chiao Tung University and Ministry of Education (MOE), Taiwan/ ; },
abstract = {BACKGROUND: The oral microbiome has been shown to be associated with the development of oral squamous cell carcinoma (OSCC). Research has primarily focused on elucidating the oncogenic mechanisms of specific pathogens by comparing the microbiomes of OSCC and normal tissues. However, the characteristics of the microbiome in the precancerous state remain less understood, as does the influence of metabolic and environmental factors on OSCC-associated microbiomes.

METHODS: In this study, we analyzed mucosa-associated microbiomes in normal, precancerous, and OSCC lesions from a cohort of 51 patients using 16S rRNA amplicon sequencing. We investigated compositional changes in the microbiome, including the specific abundances and co-occurrences of OSCC-associated bacteria.

RESULTS: Our findings indicate that the microbiome associated with precancerous lesions is indistinguishable from that of the normal mucosa, whereas the OSCC microbiome significantly differs from both normal and precancerous conditions. Specifically, the OSCC microbiome harbors less Streptococcus, coupled with an increase in amino-acid-degrading anaerobes such as Fusobacterium and Prevotella. The metabolic properties of individual microbes reported suggest that the overrepresentation of OSCC-specific bacteria is a result of metabolic adaptation to tumor microenvironments, although this possibility needs to be experimentally confirmed.

CONCLUSIONS: Our results demonstrate oral microbiome patterns across OSCC progression, offering insights into microbial ecological perspectives.},
}

@article {pmid40106235,
year = {2025},
author = {Frenn, M and Salzman, N and Lam, V and Holtz, M and Moosreiner, A and Garnier-Villarreal, M and Singh, M},
title = {Childhood Obesity Body Mass Index and Gut Microbiome: A Cluster Randomized Controlled Pilot Feasibility Study.},
journal = {Childhood obesity (Print)},
volume = {},
number = {},
pages = {},
doi = {10.1089/chi.2024.0344},
pmid = {40106235},
issn = {2153-2176},
abstract = {Background: Prebiotic fiber has been examined as a way to foster gut bacteria less associated with obesity. Tests of prebiotic fiber in reducing obesity have occurred mainly in animals, adults, and Caucasians when the highest obesity rates are in African American and Latinx youth. Response to prebiotic fiber is determined by the pre-existing intestinal microbiota. The type of microbiota varies based on diet and physical activity (PA), so it is important to examine acceptability and response to prebiotic fiber in those most at risk for obesity. Methods: This cluster randomized controlled feasibility trial included an online program designed to improve diet and PA along with administration of prebiotic fiber for 12 weeks in 123 4th and 5th grade students where 98% were eligible for free or reduced fee lunch. Of these 56% were male; 71% Latinx; 15% African American; and 14% Other. Results: A decrease in body fat (BF) was associated with higher pre-test BF. Lower BMI was associated with a decrease in fecal Tenericutes and an increase in Actinobacteria. Conclusion: Prebiotic fiber was evaluated in additional studies. Determining those most responsive to prebiotic fiber can also permit individual recommendations for greater inclusion in usual diet choices.},
}

@article {pmid40105993,
year = {2025},
author = {Ge, Y and Yang, H and Fu, Y and Zhou, J and Cheng, Z and Fan, X and Yu, Y},
title = {A Mendelian randomization study to reveal gut-disc axis: causal associations between gut microbiota with intervertebral disc diseases.},
journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society},
volume = {},
number = {},
pages = {},
pmid = {40105993},
issn = {1432-0932},
support = {No.cstc2021jcyj-msxmX0853//Natural Science Foundation of Chongqing, China/ ; No.2024ZYZD006//Chongqing Traditional Chinese Medicine scientific research project (Joint project of Chongqing Health Commission and Science and Technology Bureau)/ ; Grant No.KJQN202215120//The Science and Technology Research Program of Chongqing Municipal Education Commission/ ; },
abstract = {PURPOSE: Emerging evidence suggests a link between gut microbiota and intervertebral disc diseases (IDDs); however, the causal relationships remain unclear. This study aimed to evaluate the causal effects of gut microbiota on the risk of cervical disc disorders (CDD), other intervertebral disc disorders (OIDD), pyogenic intervertebral disc infections, and discitis, shedding light on the potential "gut-disc axis".

METHODS: Genetic variation data for 202 gut microbiota taxa were obtained from the Dutch Microbiome Project, and disease outcome data were sourced from the FinnGen consortium. A Mendelian Randomization (MR) approach was employed to assess causal relationships, using genetic variants as instrumental variables. Sensitivity analyses, including tests for pleiotropy, heterogeneity, and reverse causation, ensured robust findings.

RESULTS: The study identified 20 gut microbial taxa with significant associations to IDDs. Notably, taxa within the Erysipelotrichaceae family showed consistent protective effects against OIDD after Bonferroni correction (P < 0.05). Associations between several species and specific diseases, such as Alistipes senegalensis with CDD and Ruminococcus lactaris with discitis, were also observed. Sensitivity analyses confirmed no evidence of confounding or reverse causation.

CONCLUSION: This study provides evidence of causal relationships between specific gut microbiota and IDDs, supporting the existence of a "gut-disc axis." The findings suggest that microbial dysbiosis may influence spinal health through systemic inflammation and immune regulation. These insights open new possibilities for microbiota-targeted interventions, such as probiotics or dietary modifications, to prevent or manage IDDs. However, further research is required to validate these therapeutic strategies.},
}

@article {pmid40105301,
year = {2025},
author = {Qiu, W and Kang, J and Ye, Z and Yang, S and Tu, X and Xie, P and Ge, J and Ping, W and Yuan, J},
title = {Arbuscular mycorrhizal fungi build a bridge for soybeans to recruit Pseudomonas putida.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70064},
pmid = {40105301},
issn = {1469-8137},
support = {42322708//National Natural Science Foundation of China/ ; 42277297//National Natural Science Foundation of China/ ; HST2022TR004//the Scientific Research Project of Ecological Environment Protection of Heilongjiang Provincial Department of Ecological Environment, China/ ; 2023-KYYWF-1448//the Basic Scientific Research Operating Expenses of Colleges and Universities in Heilongjiang Province, China/ ; PL2024D015//Heilongjiang Provincial Natural Science Foundation of China/ ; },
abstract = {The assembly of the rhizosphere microbiome determines its functionality for plant fitness. Although the interactions between arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) play important roles in plant growth and disease resistance, research on the division of labor among the members of the symbionts formed among plants, AMF, and PGPR, as well as the flow of carbon sources, is still insufficient. To address the above questions, we used soybean (Glycine max), Funneliformis mosseae, and Pseudomonas putida KT2440 as research subjects to establish rhizobiont interactions and to elucidate the signal exchange and division of labor among these components. Funneliformis mosseae can attract P. putida KT2440 by secreting cysteine as a signaling molecule and can promote the colonization of P. putida KT2440 in the soybean rhizosphere. Colonized P. putida KT2440 can stimulate the l-tryptophan secretion of the host plant and can lead to the upregulation of genes involved in converting methyl-indole-3-acetic acid (Me-IAA) into IAA in response to l-tryptophan stimulation. Collectively, we decipher the tripartite mechanism of rhizosphere microbial community assembly via cross-kingdom interactions.},
}

@article {pmid40104597,
year = {2025},
author = {Zhang, Z and Wang, J and Dang, S and Liu, X and Zhang, Y and Zhang, H},
title = {The worldview of Akkermansia muciniphila, a bibliometric analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1500893},
pmid = {40104597},
issn = {1664-302X},
abstract = {Akkermansia muciniphila (A. muciniphila), a critical bacterium within the gut microbiota, plays a key role in human health and immunomodulation. Since its identification in 2004, A. muciniphila has emerged as a significant agent in treating metabolic diseases, gastroenterological diseases, and tumor immunotherapy. Its rapid ascent in scientific translation underscores its importance in gut microbiome research. However, there has been a lack of visualization and analysis of the rapidly occurring commercialization in this field, which has critically hindered insights into the current knowledge structure and understanding of the cutting-edge of the discipline. This study employs the Web of Science Core Collection (WOSCC) and Innography platforms to provide the first comprehensive analysis of A. muciniphila's academic progresses and commercialization over the past two decades, highlighting its growing prominence in global health research. Our analysis delineates that, following the academic trajectory, the evolution of A. muciniphila patents from foundational research through to application development and maturity, with particular emphasis on its expansive potential in emerging fields, including gastroenterological disorders, non-alcoholic fatty liver disease, cancer immunotherapy, stress management, and neurodegenerative disease treatment. Concluding, A. muciniphila presents as a next-generation probiotic with vast implications for human health. Our findings provide essential insights for future research and product development, contributing to the advancement of this burgeoning field.},
}

@article {pmid40104591,
year = {2025},
author = {Yang, S and Liu, H and Liu, Y},
title = {Advances in intestinal epithelium and gut microbiota interaction.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1499202},
pmid = {40104591},
issn = {1664-302X},
abstract = {The intestinal epithelium represents a critical interface between the host and external environment, serving as the second largest surface area in the human body after the lungs. This dynamic barrier is sustained by specialized epithelial cell types and their complex interactions with the gut microbiota. This review comprehensively examines the recent advances in understanding the bidirectional communication between intestinal epithelial cells and the microbiome. We briefly highlight the role of various intestinal epithelial cell types, such as Paneth cells, goblet cells, and enteroendocrine cells, in maintaining intestinal homeostasis and barrier function. Gut microbiota-derived metabolites, particularly short-chain fatty acids and bile acids, influence epithelial cell function and intestinal barrier integrity. Additionally, we highlight emerging evidence of the sophisticated cooperation between different epithelial cell types, with special emphasis on the interaction between tuft cells and Paneth cells in maintaining microbial balance. Understanding these complex interactions has important implications for developing targeted therapeutic strategies for various gastrointestinal disorders, including inflammatory bowel disease, metabolic disorders, and colorectal cancer.},
}

@article {pmid40104590,
year = {2025},
author = {Pakostova, E and Falagan, C and Mazuelos Rojas, A},
title = {Editorial: Exploring processes and applications of metal-microbe interactions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1575076},
doi = {10.3389/fmicb.2025.1575076},
pmid = {40104590},
issn = {1664-302X},
}