@article {pmid41465246,
year = {2025},
author = {Sokolova, EA and Smirnova, NV and Fedorets, VA and Khlistun, IV and Mishukova, OV and Tromenschleger, IN and Savenkov, OA and Saprikin, OI and Rogaev, EI and Buyanova, MD and Filippova, IM and Mayorova, TM and Glukhova, MA and Ivanovna, MM and Manakhov, AD and Voronina, EN},
title = {Microbial Consortium Application Under Temperature Stress: Effects on the Rhizosphere Microbiome and Plant Growth.},
journal = {International journal of molecular sciences},
volume = {26},
number = {24},
pages = {},
doi = {10.3390/ijms262411814},
pmid = {41465246},
issn = {1422-0067},
support = {075-15-2025-473//Ministry of Science and Higher Education of the Russian Federation (the Federal Scientific-technical programme for genetic technologies development for 2019-2030)/ ; },
mesh = {*Rhizosphere ; Soil Microbiology ; *Microbiota ; *Microbial Consortia ; *Stress, Physiological ; *Plant Development ; Crops, Agricultural/growth & development/microbiology ; Temperature ; Bacteria/genetics ; Triticum/growth & development/microbiology ; Fagopyrum/growth & development/microbiology ; },
abstract = {The aim of the present study was to investigate the effect of a synthetic microbial consortium (SMC) containing five functionally different bacterial strains (Rahnella aquatilis, Rothia endophytica, Stenotrophomonas indicatrix, Burkholderia contaminans, Lelliotia amnigena) on the growth and development of three agricultural crops (wheat, buckwheat, and rapeseed) on two soil types (chernozem and gray forest soil) under field conditions. The experiment was conducted from June to September 2024 under extreme field conditions, with temperatures reaching 43.8 °C. This study evaluates SMC efficacy under severe abiotic stress, reflecting increasingly common climate extremes. Metagenomic data analysis showed that the introduced strains did not establish stable populations in the soil, possibly due to heat-induced bacterial mortality, though other factors including competition with indigenous microflora and lack of protective formulations may have also contributed. No statistically significant effects on plant morphometric parameters were observed. The extreme temperature and water stress conditions appear to have been the dominant limiting factors, overriding any potential benefits from microbial inoculation, as evidenced by the lack of response to mineral fertilizer application as well. Crop-specific effects were revealed: when cultivating rapeseed on chernozem, a significant increase in available phosphorus content was noted (from 278 ± 45 to 638 ± 92 mg/kg with SMC application, p < 0.001).},
}

*Rhizosphere
Soil Microbiology
*Microbiota
*Microbial Consortia
*Stress, Physiological
*Plant Development
Crops, Agricultural/growth & development/microbiology
Temperature
Bacteria/genetics
Triticum/growth & development/microbiology
Fagopyrum/growth & development/microbiology

@article {pmid41465245,
year = {2025},
author = {Guo, P and Qin, W and Song, W and Chen, H},
title = {Spatial Multi-Omics Analysis of the Qianqiu Goat Gut Microbiome and Metabolome.},
journal = {International journal of molecular sciences},
volume = {26},
number = {24},
pages = {},
doi = {10.3390/ijms262411815},
pmid = {41465245},
issn = {1422-0067},
support = {WJ24CYHXM06//Wanjiang Emerging Industry Technology Development Center 2024 Industrialization Project/ ; 22576206//National Natural Science Foundation of China Natural/ ; },
mesh = {Animals ; *Goats/microbiology/metabolism ; *Gastrointestinal Microbiome/genetics ; *Metabolome ; *Metabolomics/methods ; RNA, Ribosomal, 16S/genetics ; Rumen/microbiology/metabolism ; Multiomics ; },
abstract = {This study profiled the rumen (RM), small intestine (SI), and large intestine (LI) of 24 samples collected from eight 6-month-old Qianqiu goats (body weight 28.40 ± 1.80 kg), with the samples equally divided into three groups. A combination of methods was used, including 16S rRNA sequencing, untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics, Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and weighted gene co-expression network analysis-based module detection (WGCNA) with network integration. An uncommon composition of organisms dominated the SI: the hydrogenotrophic methanogens Methanobrevibacter (SI 24.51%; RM 1.92%; LI 2.19%) and Methanosphaera (SI 0.43%; RM 0.02%; LI 0.02%), together with the acetogen Acetitomaculum (SI 1.58%; RM 0.34%; LI 0.11%), were markedly more abundant compared to the RM or LI. Correlation and pathway analyses indicated that Methanobrevibacter was positively correlated with a steroid-type lipid metabolite (r = 0.52, p < 0.05) and with bile-acid-related metabolites. Acetitomaculum was positively correlated with several metabolites: 4-Hydroxyphenyl 4-hydroxybenzoate (r = 0.79, p < 0.05), 2-Aminoethyl dihydrogen phosphate (r = 0.76, p < 0.05), 1-Myristoyl-2-stearoyl-sn-glycero-3-phosphocholine (r = 0.76, p < 0.05), and 1,2-Dioleoyl-sn-Glycero-3-Phosphocholine (r = 0.74, p < 0.05). Together, these data define a small-intestinal microbial-metabolite module in Qianqiu goats characterized by elevated abundances of specific methanogens and acetogens in the SI. Specific positive correlations were identified between these taxa and metabolites associated with lipids and bile acids.},
}

Animals
*Goats/microbiology/metabolism
*Gastrointestinal Microbiome/genetics
*Metabolome
*Metabolomics/methods
RNA, Ribosomal, 16S/genetics
Rumen/microbiology/metabolism
Multiomics

@article {pmid41465235,
year = {2025},
author = {Kim, H and Kim, H and Lee, Y and Park, C and Cho, B and Son, S and Kim, H and Kim, G and Park, J and Park, H},
title = {Lactobacillus delbrueckii subsp. lactis CKDB001 Ameliorates Scopolamine-Induced Cognitive Impairment Through Metabolic Modulation.},
journal = {International journal of molecular sciences},
volume = {26},
number = {24},
pages = {},
doi = {10.3390/ijms262411804},
pmid = {41465235},
issn = {1422-0067},
support = {HU22C0150//The Korea Dementia Research Project through the Korea Dementia Research Center (KDRC), funded by the Ministry of Health & Welfare and Ministry of Science and ICT/ ; },
mesh = {Animals ; *Cognitive Dysfunction/chemically induced/metabolism/therapy/microbiology ; Mice ; Gastrointestinal Microbiome/drug effects ; *Scopolamine/adverse effects ; Male ; *Lactobacillus delbrueckii/physiology ; Mice, Inbred ICR ; Donepezil/pharmacology ; Hippocampus/metabolism/drug effects ; *Probiotics/pharmacology ; },
abstract = {Microbiome-derived metabolites have emerged as key mediators of the gut-brain axis, influencing cognitive function and neuroprotection. This study investigated whether Lactobacillus delbrueckii subsp. lactis CKDB001 alleviates scopolamine-induced memory impairment through metabolic modulation, and how its effects compare with those of donepezil. ICR mice were administered CKDB001 or donepezil for 4-5 weeks and evaluated through behavioral, microbiome, metabolomic, and molecular analyses. CKDB001 significantly improved spatial working memory in a dose-dependent manner, with the high-dose group showing improvements comparable to those of the donepezil-treated group, while passive avoidance showed a non-significant but positive trend. Both CKDB001 and donepezil modulated gut microbial composition, leading to a partial divergence from the scopolamine-disrupted community structure, with CKDB001 inducing dose-dependent intestinal colonization. Metabolomic profiling revealed that both treatments increased tryptophan-derived indole metabolites and altered lipid and short-chain fatty acid metabolite profiles, although these effects were more pronounced in CKDB001-treated mice. At the molecular level, both CKDB001 and donepezil reduced hippocampal tau phosphorylation, downregulated glycogen synthase kinase-3 (GSK-3) signaling, enhanced intestinal tight-junction proteins, and partially normalized acetylcholinesterase activity, with CKDB001 restoring AChE levels more closely toward the normal control. Together, these findings suggest that CKDB001 mitigates cognitive deficits through coordinated modulation of microbial, metabolic, and neuronal pathways, offering a microbiome-based therapeutic approach that may provide benefits comparable to donepezil with potentially fewer limitations.},
}

Animals
*Cognitive Dysfunction/chemically induced/metabolism/therapy/microbiology
Mice
Gastrointestinal Microbiome/drug effects
*Scopolamine/adverse effects
Male
*Lactobacillus delbrueckii/physiology
Mice, Inbred ICR
Donepezil/pharmacology
Hippocampus/metabolism/drug effects
*Probiotics/pharmacology

@article {pmid41465180,
year = {2025},
author = {Raber, J and O'Niel, A and Kasschau, KD and Pederson, A and Robinson, N and Guidarelli, C and Chalmers, C and Winters-Stone, K and Sharpton, TJ},
title = {Exercise, APOE Genotype, and Testosterone Modulate Gut Microbiome-Cognition Associations in Prostate Cancer Survivors.},
journal = {Genes},
volume = {16},
number = {12},
pages = {},
doi = {10.3390/genes16121507},
pmid = {41465180},
issn = {2073-4425},
support = {CCSG CPCP-2023-002//National Institute of Health USA/ ; },
mesh = {Humans ; Male ; *Prostatic Neoplasms/genetics/microbiology/therapy ; *Gastrointestinal Microbiome/genetics ; *Testosterone/metabolism ; Aged ; Cancer Survivors ; Middle Aged ; *Cognition ; *Apolipoproteins E/genetics ; Genotype ; *Exercise/physiology ; Saliva ; },
abstract = {Background: Men treated with androgen deprivation therapy (ADT) for prostate cancer are at risk for cognitive decline. Patient genetics and endocrine state may shape gut microbiome features that relate to cognition. Methods: We studied a subsample of 79 prostate cancer survivors with prior ADT exposure previously enrolled in a randomized controlled exercise trial comparing three training modalities (strength training, Tai Chi training, or stretching control) who completed an additional food-frequency questionnaire and remote Montreal Cognitive Assessment (MoCA) and provided saliva and stool for APOE genotyping, salivary testosterone, and 16S rRNA sequencing. We used beta regression for MoCA (scaled 0-1), linear models for testosterone, alpha diversity regressions, PERMANOVA for beta diversity, and DESeq2 for genus-level differential abundance, with false-discovery correction. Results: Compared to post-stretching control, post-strength training testing was associated with higher MoCA scores whereas post-Tai Chi testing was not. APOE ε4 carriers exhibited a greater testosterone increase with strength training than non-carriers. Testosterone, and its interactions with exercise modality and APOE ε2 status, was related to presence/absence-based community structure; APOE ε4 interacted with exercise intervention to influence alpha diversity. At the genus level, exercise was linked to lower levels of Bacteroidota taxa (including Muribaculaceae) and higher levels of Enterobacteriaceae; APOE ε4 status was linked to higher Megamonas and lower Rikenellaceae RC9 levels; and higher salivary testosterone levels were linked to higher Prevotellaceae taxa and Succinivibrio levels. Higher MoCA scores were associated with lower abundances of several Firmicutes genera. Conclusions: Endocrine state and APOE genotype may condition the gut microbiome's response to exercise intervention in ADT-treated prostate cancer survivors, with downstream associations with cognition. These findings could inform precision survivorship strategies pairing strength training with genotype- and hormone-informed microbiome monitoring to optimize cognitive performance.},
}

Humans
Male
*Prostatic Neoplasms/genetics/microbiology/therapy
*Gastrointestinal Microbiome/genetics
*Testosterone/metabolism
Aged
Cancer Survivors
Middle Aged
*Cognition
*Apolipoproteins E/genetics
Genotype
*Exercise/physiology
Saliva

@article {pmid41465120,
year = {2025},
author = {Borrego-Ruiz, A and Borrego, JJ},
title = {Addiction Susceptibility: Genetic Factors, Personality Traits, and Epigenetic Interactions with the Gut Microbiome.},
journal = {Genes},
volume = {16},
number = {12},
pages = {},
doi = {10.3390/genes16121447},
pmid = {41465120},
issn = {2073-4425},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Epigenesis, Genetic ; *Substance-Related Disorders/genetics/microbiology ; *Personality/genetics ; *Genetic Predisposition to Disease ; *Behavior, Addictive/genetics/microbiology ; },
abstract = {Despite valuable insights into the individual roles of genetic factors and personality traits, their combined contribution to addiction susceptibility remains insufficiently characterized. Within this framework, the potential influence of epigenetic mechanisms, particularly those mediated by the gut microbiome, also remains underexplored. This comprehensive review aims to address these gaps in an integrative manner by examining: (i) the association of gene regulation with personality traits; (ii) the genetics of substance use disorders; (iii) the roles of genes and personality in addiction; and (iv) epigenetic influences on addiction, with a particular focus on the role of the gut microbiome. Genetic influences on personality act primarily via regulatory variants that modulate gene expression during neurodevelopment, shaping cognitive, emotional, and behavioral traits that contribute to individual differences. Substance use disorders share partially overlapping genetic foundations, with specific loci, heritability estimates, and causal pathways differing across substances, reflecting both shared vulnerability and substance-specific genetic influences on addiction susceptibility. Impulsivity, novelty-seeking, and stress responsiveness are heritable personality traits that interact to shape susceptibility to substance use disorders, with genetic factors modulating risk across different forms of addiction. Environmental factors, early-life stress, and social influences interact with the gut microbiome to shape neurobiological and behavioral pathways that modulate addiction risk. These interactions highlight the multifactorial nature of substance use disorders, in which epigenetic, microbial, and psychosocial mechanisms converge to influence susceptibility, progression, and maintenance of addictive behaviors.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Epigenesis, Genetic
*Substance-Related Disorders/genetics/microbiology
*Personality/genetics
*Genetic Predisposition to Disease
*Behavior, Addictive/genetics/microbiology

@article {pmid41464979,
year = {2025},
author = {Yang, W and Han, N and Zhang, X},
title = {Eurotium cristatum Ameliorates Glucolipid Metabolic Dysfunction of Obese Mice in Association with Regulating Intestinal Gluconeogenesis and Microbiome.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {24},
pages = {},
doi = {10.3390/foods14244273},
pmid = {41464979},
issn = {2304-8158},
support = {32502233//National Natural Science Foundation of China/ ; },
abstract = {Eurotium cristatum (EC), a fungus derived from Fu brick tea, exhibits anti-obesity potential, but its mechanisms regulating intestinal gluconeogenesis (IGN) remain unclear. This study aimed to elucidate whether EC alleviates obesity and glucolipid metabolic disorders by modulating the gut microbiota and activating the IGN pathway. The 8-week EC administration at low (10[4] CFU/mL), medium (10[6] CFU/mL), and high doses (10[8] CFU/mL) ameliorated high-fat-diet (HFD)-induced metabolic abnormalities, including aberrant weight gain, dyslipidemia, glucose intolerance and hepatic injury with effects showing a dose-dependent trend. EC treatment significantly activated IGN, as indicated by increased colonic levels of short-chain fatty acids (SCFAs) and succinate (key IGN substrates) and the upregulation of IGN-key enzymes (PEPCK, FBPase, and G6Pase). In addition, EC treatment significantly alleviated the HFD-induced gut dysbiosis by reducing the Firmicutes/Bacteroidetes ratio and enriching beneficial bacteria such as Lachnospiraece_NK4A136_group, Bacteroidota and Alloprevotella. Non-targeted metabolomics analysis revealed that EC significantly altered the linoleic acid metabolism, specifically decreasing the relative levels of bile acid and chenodeoxycholic acid (p < 0.01) while increasing those of linoleic acid and ricinoleic acid (p < 0.05). EC treatment reshaped the gut microbiome, promoted the production of beneficial metabolites (e.g., SCFAs), and consequently activated the IGN pathway, ultimately ameliorating host glucose and lipid metabolic disorders. Our findings provide mechanistic insights into the anti-obesity effects of EC, suggesting its potential for further investigation as a dietary intervention for metabolic diseases.},
}

@article {pmid41464971,
year = {2025},
author = {Yang, Y and Guo, L and Li, Y and Ji, M and He, T and Hou, K and Li, J and Zhang, H and Shi, Z and Zhang, H},
title = {Environmental and Rhizosphere Microbiome Drivers of Metabolic Profiles in Gastrodia elata: An Integrative Analysis of Soil, Metabolomics and Anti-Inflammatory Readouts.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {24},
pages = {},
doi = {10.3390/foods14244265},
pmid = {41464971},
issn = {2304-8158},
abstract = {BACKGROUND: Gastrodiae Rhizoma, the dried tuber of Gastrodia elata Bl. (Orchidaceae), is a traditional Chinese medicinal (TCM) and edible plant. Its quality formation is closely associated with rhizosphere microorganisms; however, the specific underlying mechanisms remain unclear.

METHODS: Tubers and rhizosphere soils were collected from seven major production regions of G. elata. Soil physicochemical properties were analyzed, and integrative analyses combining soil microbiome and untargeted metabolome profiling were conducted. The anti-inflammatory activity of G. elata extracts was evaluated using a RAW264.7 macrophage model. Multivariate statistical approaches, including OPLS-DA and correlation network analysis, were used to decipher relationships among environmental factors, microbial communities, metabolic profiles, and bioactivities.

RESULTS: A total of 39,250 bacterial ASVs and 10,544 fungal ASVs were identified. The bacterial community, dominated by Proteobacteria and Acidobacteria, was strongly influenced by soil chemical factors, including pH and total nitrogen. The fungal community, primarily composed of Ascomycota and Basidiomycota, exhibited marked sensitivity to altitudinal gradients. Correlation analysis revealed that key secondary metabolites, including flavonoids and phenolic acids, along with their anti-inflammatory activities, were significantly associated with rhizosphere microorganisms such as Edaphobaculum, Hypocrea, and Pseudomonas.

CONCLUSIONS: Our findings outline the pathways connecting environmental factors, the microbiome, and functional metabolites in G. elata, highlighting the importance of environmental-microbial interactions in determining metabolic outcomes. This work provides new insights into the ecological and molecular mechanisms behind the quality formation of this medicinal plant.},
}

@article {pmid41464936,
year = {2025},
author = {Choe, H and Shin, CY and Lim, JS and Park, JS and Park, JW and Kim, WJ and Park, YI and Ree, J},
title = {Evaluation of Potential Anti-Diabetic Synbiotic Formulation of Lacticaseibacillus rhamnosus BST.L-601 Using db/db Mice.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {24},
pages = {},
doi = {10.3390/foods14244230},
pmid = {41464936},
issn = {2304-8158},
support = {//Gyeonggido Business & Science Accelerator (GBSA)/ ; },
abstract = {Probiotics have been studied for their potential to treat chronic diseases. This study examined the use of Lacticaseibacillus rhamnosus BST.L-601 as an anti-diabetic symbiotic with sweet potato for fermentation. The medium supplemented with sweet potato showed increased productivity and enhanced storability. The anti-diabetic effect of fermented BST.L-601 was evaluated using the C2C12 myotube and a type 2 diabetes mellitus (T2DM)-induced db/db (Lepr[db]/Lepr[db]) mouse model. Treatment with heat-killed BST.L-601 increased glucose uptake by 125% and α-glucosidase inhibition in a dose-dependent manner without cytotoxicity for myotubes. 8 weeks of oral administration of BST.L-601 led to anti-diabetic activities in various biomarkers in the mouse model, including lowered fasting blood glucose by 88% and elevated mRNA expression of glucose metabolism-related factors IRS-1 (510%) and GLUT4 (181%) from skeletal muscle. Moreover, the improvement of induced T2DM in mice was supported by blood serum analysis. Immunohistochemistry showed increased insulin and decreased glucagon secreted from β and α cells in the pancreas islet. Microbiota analysis demonstrated elevated microbiome diversity in mice treated with BST.L-601. Furthermore, the safety and probiotic properties of the strain were confirmed. These results suggest that BST.L-601 fermented with sweet potato could be a functional symbiotic used to improve diabetes, particularly T2DM.},
}

@article {pmid41464856,
year = {2025},
author = {Sylwestrzak, T and Ciosek, M and Pastuszak, K and Jastrzębski, T},
title = {Fecal Short-Chain Fatty Acids in Colorectal Cancer Patients Versus Healthy Controls: A Systematic Review and Meta-Analysis.},
journal = {Journal of clinical medicine},
volume = {14},
number = {24},
pages = {},
doi = {10.3390/jcm14248949},
pmid = {41464856},
issn = {2077-0383},
abstract = {Background: Short-chain fatty acids (SCFAs), the main microbial fermentation products in the colon, have immunometabolic and anti-neoplastic properties. Alterations in fecal SCFA profiles have been proposed as potential non-invasive biomarkers for colorectal cancer (CRC), but previous findings remain inconsistent. This systematic review and meta-analysis aimed to determine whether fecal acetate, propionate, and butyrate concentrations differ between patients with CRC and healthy individuals. Methods: A comprehensive search of PubMed, Web of Science and Cochrane Library was conducted on 18 September 2025. Eligible studies were observational, included adults with histologically confirmed CRC and healthy controls, and reported fecal concentrations of at least one SCFA quantified using validated analytical methods. Two independent reviewers performed study screening, data extraction, and risk-of-bias assessment. Random-effects models were applied to calculate pooled standardized mean differences (SMDs) with 95% confidence intervals (CIs). Results: Thirteen studies met inclusion criteria for qualitative synthesis, and four (141 CRC cases, 98 controls) were eligible for meta-analysis. Compared with healthy controls, patients with CRC had significantly lower fecal acetate (pooled SMD -0.37; 95% CI -0.63 to -0.10; p = 0.006; I[2] = 0%) and butyrate (pooled SMD -0.59; 95% CI -1.10 to -0.07; p = 0.026; I[2] = 64.4%), whereas propionate did not differ significantly (pooled SMD -0.02; 95% CI -0.85 to 0.82; p = 0.971; I[2] = 89%). Conclusions: CRC is associated with reduced fecal butyrate and, to a lesser extent, acetate, suggesting impaired microbial fermentation. Propionate shows no consistent difference. SCFA profiling currently lacks sufficient standardization and validation for clinical application. Future harmonized, longitudinal studies integrating diet, microbiome, and metabolomic data are warranted to confirm SCFAs as reproducible biomarkers of CRC.},
}

@article {pmid41464714,
year = {2025},
author = {Nijs, J and Ahmed, I and Vandeputte, D and R Goodin, B and Adetayo, T and Kindt, S and Vanroose, M and Elma, Ö and Johansson, E and Logghe, T and Van Akeleyen, J and Goossens, Z and Labie, C and Silva, F and Lahousse, A and Huysmans, E and Núñez-Cortés, R},
title = {In the Mouth or in the Gut? Innovation Through Implementing Oral and Gastrointestinal Health Science in Chronic Pain Management.},
journal = {Journal of clinical medicine},
volume = {14},
number = {24},
pages = {},
doi = {10.3390/jcm14248812},
pmid = {41464714},
issn = {2077-0383},
abstract = {Recent scientific advances point towards an important role for oral and gastrointestinal health in people with chronic pain. Poor oral health (e.g., periodontitis, tooth loss) is observed in subgroups of the chronic pain population, including abdominal pain, low back pain, fibromyalgia, and rheumatoid arthritis. In addition to poor oral health, studies have also revealed altered intestinal microbiota compositions in various types of chronic pain, including people with chronic low back pain, knee osteoarthritis, visceral pain, fibromyalgia, tinnitus, and migraine. While overweight/obesity contributes to the likelihood of gut dysbiosis, normal-weight individuals with chronic pain also more often present with poor gut health. Both gastrointestinal and oral health problems (e.g., periodontitis, tooth loss) are increasingly recognized across multiple chronic pain conditions, including abdominal pain, low back pain, fibromyalgia, and rheumatoid arthritis. This perspective paper provides an overview of the requirements for integrating oral and gastrointestinal health in chronic pain management. First and foremost, oral and gastrointestinal health issues need to be recognized as common chronic pain comorbidities that require tailored treatment. Next to recognition of the issue, individuals seeking care for chronic pain need to be screened routinely for these oral and gastrointestinal comorbidities. In terms of management, the following options are suggested: (1) providing oral and gastrointestinal health science education; (2) considering the possible interplay between the gut microbiome and drug treatment (including polypharmacy); (3) expanding the importance of dietary interventions; and (4) considering the potential interplay with other lifestyle factors (e.g., chronic insomnia, overweight/obesity, depression and anxiety). To inform the implementation of these suggestions, longitudinal cohort studies investigating the role of oral and gastrointestinal health in people with chronic pain, as well as studies exploring possible (modifiable) factors that affect the oral and/or gut microbiome, are needed. This includes the bidirectional interplay between the gut microbiome and drugs commonly prescribed to patients with chronic pain. Likewise, adequately powered and controlled clinical trials evaluating the effectiveness of possible treatments for oral and/or gastrointestinal comorbidities in people with chronic pain represent another research priority. Such randomized clinical trials can not only examine the possible causal link between poor oral/gut health and treatment outcomes, but also inform the development of new, innovative ways to improve care for people with chronic pain.},
}

@article {pmid41464345,
year = {2025},
author = {Gaia-Oltean, AI and Boitor, D and Pop, LA and Galea, G and Telecan, T and Micu, R},
title = {Non-Invasive Methods for Early Diagnosis of Endometriosis-A Comprehensive Narrative Literature Review.},
journal = {Healthcare (Basel, Switzerland)},
volume = {13},
number = {24},
pages = {},
doi = {10.3390/healthcare13243276},
pmid = {41464345},
issn = {2227-9032},
abstract = {Endometriosis is a common gynecological pathology, with an incidence of nearly 10% in patients of reproductive age, and is still underdiagnosed. A thorough and well-spread diagnostic study of endometriosis based on epigenetic factor dysregulation can highlight potential areas for improvement. To quantify the potential and utility of non-invasive tools in the early diagnosis of endometriosis, an overview of current knowledge on epigenetic factors, based on DNA and RNA, is presented. Among these tools, it is important to highlight the role of miRNAs (microRNAs), cfDNA (cell-free DNA), and rRNAs (ribosomal RNAs), which are small molecules involved in endometriosis and numerous other pathologies. To evaluate their potential and utility in endometriosis, a salivary miRNA diagnostic test was conducted, the cfDNA methylation patterns of fragmented DNA circulating in bodily fluids (e.g., plasma) were analyzed, and cervical and uterine microbiomes were profiled for bacterial rRNA in patients with clinical suspicion of incipient endometriosis. Specific molecular profiles associated with endometriosis were analyzed. The first profile, a 109-miRNA saliva signature, was validated as a product of miRNA biomarkers and artificial intelligence modeling. In addition, peripheral blood cfDNA methylation biomarkers were identified by investigating nine genes in a molecular signature that requires validation. A profile was also obtained from cervical swabs and uterine washes, including molecular analysis of 16S rRNA amplicon sequencing to evaluate alterations in the cervical bacterial community. This review aims to optimize the integration of a non-invasive diagnostic tool for early endometriosis diagnosis. Genetic biomarkers can be correlated with clinical factors to improve diagnostic accuracy. Of the assessed diagnostic tools, salivary miRNA tests, a peripheral blood cfDNA methylation biomarker, and a microbiome rRNA signature may be useful for early diagnosis of endometriosis, as well as, implicitly, therapeutic attitude and follow-up.},
}

@article {pmid41464202,
year = {2025},
author = {Holmgaard, DB and Nebrich, L and Uslu, B and Schouw, CH and Dargis, R and Pedersen, HP and Fuursted, K and Nielsen, HV and Christensen, JJ and Nielsen, XC and Poulsen, LM},
title = {Comparison of Cultures and 16S/18S Amplicon-Based Microbiome Analyses for Diagnosing Nosocomial Pneumonia in Patients Admitted to the Intensive Care Unit-An Exploratory Study.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {24},
pages = {},
doi = {10.3390/diagnostics15243202},
pmid = {41464202},
issn = {2075-4418},
support = {REG-48-2014//Region Zealand/ ; },
abstract = {Background: Nosocomial pneumonia (NP) is a significant cause of morbidity and mortality in intensive care unit (ICU) patients. Prior antibiotic use, polymicrobial infections, and the limitations of conventional microbiological methods often complicate an accurate diagnosis. Bronchoalveolar lavage (BAL) and tracheal suction (TS) are commonly used methods for collecting respiratory samples; however, their diagnostic accuracy can vary. Additionally, microbiome analysis using 16S/18S rRNA gene sequencing provides an alternative approach for identifying pathogens that are difficult to culture. This study aimed to compare the diagnostic value of routine culturing and microbiome analysis in identifying pathogens in ICU patients with NP. Methods: A prospective cohort study was conducted in 23 critically ill patients at Zealand University Hospital. Samples from TS and BAL were collected from patients with suspected NP. Both culturing and 16S/18S rRNA gene amplicon-based microbiome analysis were performed to identify pathogens. Findings were compared between the two types of samples and between the two analysis methods. Results: A total of 46 samples were analyzed (23 TS and 23 BAL). Culture results showed complete concordance in 60.9% of cases and partial concordance in 21.7% between results from TS and BAL. Discrepancies often involved low-virulence organisms, such as Staphylococcus epidermidis and Candida albicans. Microbiome analysis revealed a broader spectrum of microbial diversity, detecting pathogens such as Pasteurella canis and Tropheryma whipplei that were previously missed by culture methods. In 34.8% of the samples, the pathogen identified by microbiome analysis was also detected by culture. However, microbiome analysis also identified additional microorganisms in 17.4% of the cases, which were not detected by culture. When comparing microbiome results between TS and BAL, 16 out of 23 (69.5%) showed complete concordance. Conclusions: The findings were similar in TS and BAL, both for culture and 16S/18S amplicon-based microbiome analyses. Microbiome analysis using 16S/18S rRNA gene sequencing provided new insights into NP patients, identifying pathogens that were previously undetected by conventional culturing methods. Combining microbiome analysis with traditional culture techniques could enhance the diagnostic accuracy for NP. Further studies are needed to refine diagnostic thresholds and assess the clinical impact of microbiome-based diagnostics.},
}

@article {pmid41463926,
year = {2025},
author = {Do, ADT and Alharbi, K and Perera, R and Asnayanti, A and Alrubaye, A},
title = {Preliminary Investigation of Cecal Microbiota in Experimental Broilers Reared Under the Aerosol Transmission Lameness Induction Model.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {24},
pages = {},
doi = {10.3390/ani15243641},
pmid = {41463926},
issn = {2076-2615},
support = {PG104703//Arkansas Biosciences Institute/ ; },
abstract = {Bacterial chondronecrosis with osteomyelitis (BCO), and its associated lameness, is one of the most common and devastating issues the poultry industry constantly faces, both globally and domestically. Leveraging the currently accepted "leaky gut" model of pathogenesis, this study aims to evaluate the cecal community of broilers reared under the aerosol transmission BCO induction model. A trial involving 1320 Cobb 500 broilers was conducted using the same induction model for 56 d with the following treatments: (1) positive control (PC)-untreated birds on wire-flooring pens; (2) negative control (NC)-untreated birds on litter-flooring pens; (3) LOW-birds treated with probiotic Enterococcus faecium spray on day-of-hatch (2.0 × 10[9] CFU/bird); and (4) HIGH-birds treated with LOW spray combined with probiotic Bacillus amyloliquefaciens/Bacillus subtilis inclusion in the diet (492.1 mg/kg). Cecal contents were collected from six birds per treatment on d14, d28, d42, and d56 of the experiment; then, DNA was extracted and sent for 16 s V3-V4 amplicon sequencing. Returned sequences were assembled and taxonomically assigned, after which diversity indices were analyzed (including alpha, beta, and abundance). No significant effect was found between all treatments and positive/negative control groups in all timepoints, but timepoints were significantly different from each other in both alpha and beta diversity indices (p < 0.05). Abundance analysis also showed a high Bacillota:Bacteroidota ratio (average 18.87; p < 0.0001) with Bacillota (Firmicutes) dominating at 95.57% on average across all treatments, followed by Bacteroidota at 5.06% and Pseudomonadota at 2.59%. These findings characterize in detail the cecal microbiome in populations of broilers reared under the novel aerosol transmission induction model, offering further insights and possibilities into studies of BCO etiology and pathology.},
}

@article {pmid41463923,
year = {2025},
author = {Sakarnyte, L and Spinkyte, R and Merkeviciene, L and Siugzdiniene, R and Ruzauskas, M},
title = {Next-Generation Sequencing Insights into the Oral Microbiome and Antibiotic Resistance Genes in Grey Wolves (Canis lupus).},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {24},
pages = {},
doi = {10.3390/ani15243639},
pmid = {41463923},
issn = {2076-2615},
abstract = {The oral microbiome of apex predators such as grey wolves (Canis lupus) is colonised by complex microbial communities and plays a crucial role in the health of wild mammals, but remains poorly understood. In this study, a single pooled sample mixed from oral samples of 17 wolves (Canis lupus) hunted in Lithuania was investigated for the determination of a variety of oral microbiota, providing the first metagenomic insight into wolf oral microbiomes in Baltic countries. The aim of this study was to identify the zoonotic and antimicrobial resistance potential of the oral microbiota. The results revealed diverse microbiomes associated with periodontal health as well as microbiomes related to the environment. Unique microbial taxa potentially reflect the nutritional and ecological interactions of carnivores. Shotgun metagenomic sequencing yielded a total of 18,726,406 raw reads, and following quality trimming and filtering, 86.01% of these (16,106,613) were retained. Among the total reads, 45.15% (8,455,255) were identified as host-derived and were removed. The most common oral bacterial genera were Pseudomonas (50%) and Psychrobacter (22.6%). Metagenomic reads for zoonotic pathogens, including Salmonella, Mycobacterium spp., Yersinia, Coxiella burnetii, Corynebacterium pseudotuberculosis, and others, were also detected, suggesting that grey wolves are potential natural reservoirs of zoonotic infections. Genes encoding antimicrobial resistance to many classes of antibiotics were also detected. This research contributes to understanding wolf dietary habits, oral health, the carriage and possible risk of transmitting AMR, and social interactions.},
}

@article {pmid41463903,
year = {2025},
author = {Williams, S and Domingues, F and Manu, H and Gomez, A and Johnston, L},
title = {Effects of a Feed Sanitizer in Sow Diets on Sow and Piglet Performance.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {24},
pages = {},
doi = {10.3390/ani15243618},
pmid = {41463903},
issn = {2076-2615},
support = {Research contract//Anitox Corporation/ ; },
abstract = {This study evaluated effects of Termin-8[®], a formaldehyde, propionic acid, and terpene-based feed sanitizer, on the performance, health, and gut microbiome of sows and nursing piglets. One hundred and seven mixed-parity sows were allocated to control diets (n = 53) or diets containing 0.55% sanitizer (n = 54) from day 80 of gestation until approximately day 19 postpartum. Performance metrics, scours, and fecal microbiome composition via 16S rRNA sequencing were assessed. Feed sanitizer supplementation had no significant effects on sow body weight, backfat depth, feed intake, wean-to-estrus interval, litter size or weight at weaning, or piglet diarrhea incidence. However, stillborn pig weight was significantly reduced in the sanitized group (p = 0.010). Gut microbiome changed drastically from gestation to weaning in both groups (R[2] > 0.20, p < 0.001), but the taxa and functions that fluctuated largely differed in each group. At weaning, both groups exhibited significantly different microbiome compositions (R[2] = 0.06, p < 0.001). Feed sanitizer in sows did not influence the piglet microbiome. Supplementing formaldehyde-based feed sanitizer to sow diets did not significantly impact overall performance or health but moderately influenced sow gut microbiome composition, warranting further investigation into its potential functional implications.},
}

@article {pmid41463799,
year = {2025},
author = {Chen, J and Ai, G and Xiong, P and Song, W and Liu, G and Wei, Q and Chen, X and Zou, Z and Song, Q},
title = {Dietary Fagopyrum dibotrys Extract Supplementation: Impacts on Growth Performance, Immune Response, Intestinal Morphology, and Microbial Community in Broiler Chickens Infected with Escherichia coli O157.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {24},
pages = {},
doi = {10.3390/ani15243515},
pmid = {41463799},
issn = {2076-2615},
support = {JXSNKYJCRC202333//the Agricultural Scientific and Technological Innovation Project of Jiangxi Academy of Agricultural Sciences/ ; 32360847//the National Natural Science Foundation of China/ ; JXARS-12//Jiangxi Province Modern Agricultural Industry Technology System Construction Special Project/ ; },
abstract = {This study explored the efficacy of dietary Fagopyrum dibotrys extract (FDE) in mitigating Escherichia coli O157 (E. coli) infections in broilers. A total of 240 one-day-old male Shengze 901 broilers were randomly allocated to four groups (with 10 broilers per group): CON (basal diet), COLI (basal diet + E. coli challenge), FDE (basal diet + 500 mg/kg FDE), and FDEC (basal diet + 500 mg/kg FDE + E. coli challenge). The results showed that E. coli challenge reduced the average daily gain (ADG) and average daily feed intake (ADFI), increased the feed conversion ratio (FCR) and cecal E. coli load, impaired the intestinal mucosa, and induced intestinal inflammatory responses (p < 0.05). FDE supplementation improved growth performance, increased duodenal villus height and villus/crypt ratio; reduced serum interleukin (IL)-1β, tumor necrosis factor-α (TNF-α), diamine oxidase (DAO), and endotoxin levels; and lowered cecal E. coli counts (p < 0.05). Molecularly, FDE supplementation upregulated Occludin, Claudin-1, and ZO-1 gene expressions, and downregulated jejunal TLR4 and MyD88 mRNA levels. Microbiome analysis revealed that FDE increased the relative abundance of Faecalibacterium and alleviated the E. coli-induced reduction in Clostridia_UCG-014. In conclusion, dietary supplementation with 500 mg/kg FDE could mitigate colibacillosis-related intestinal damage and inflammatory responses.},
}

@article {pmid41463747,
year = {2025},
author = {Priputnevich, T and Denisov, P and Zhigalova, K and Muravieva, V and Shabanova, N and Gordeev, A and Zubkov, V and Bembeeva, B and Isaeva, E and Nikolaeva, A and Sukhikh, G},
title = {The Impact of Antimicrobial Therapy on the Development of Microbiota in Infants.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/antibiotics14121245},
pmid = {41463747},
issn = {2079-6382},
support = {122020900123-4//Ministry of Health of the Russian Federation/ ; },
abstract = {Background. The establishment and diversity of the gut microbiota during early childhood are fundamental for immune regulation and metabolic processes, with factors such as prematurity, delivery method, antibiotic treatment, and breastfeeding significantly impacting microbiome development and potential health outcomes. Objectives/Methods. This comparative study examined the gut microbiota composition in children aged 6-8 and 9-12 months, born via spontaneous labor at ≥38 weeks' gestation, who either did not receive antibacterial therapy or required beta-lactam antibiotics. The composition of the colonic microbiota was analyzed in these fecal samples using a quantitative real-time PCR (qRT-PCR). Results. Significant differences in microbiota composition were observed between groups. Children treated with antibiotics exhibited a statistically significant reduction in alpha diversity indices (Shannon and Simpson), along with decreased colonization of key functionally important microorganisms, including obligate anaerobic bacteria such as Faecalibacterium prausnitzii, Clostridium leptum, Bacteroides spp., and metabolically active Bifidobacteria (B. bifidum, B. breve, B. longum). Conclusions. These microbiota alterations may adversely affect child health by diminishing microbial balance and functional potential, especially during this critical period of immune and metabolic development. The decline in anti-inflammatory, short-chain fatty acid-producing bacteria elevates the risk for allergic, atopic, dysbiotic, and metabolic conditions. Recognizing these impacts underscores the importance of strategies to supports microbiota restoration after antibiotic use, such as probiotics, prebiotics, and dietary interventions. Further research should focus on microbiota recovery dynamics to facilitate early intervention and optimize pediatric health outcomes. Overall, understanding antibiotic effects on gut microbiota can guide more judicious treatment approaches, reducing long-term health risks.},
}

@article {pmid41463743,
year = {2025},
author = {Almazán-Catalán, J and Carpizo-Zaragoza, P and Penalba-Iglesias, D and Sánchez, ML and González-Reguero, D and Bueno, S and Robas-Mora, M and Varela-Moreiras, G and Partearroyo, T and Jiménez-Gómez, P},
title = {Gut Resistome and Hearing Loss in Young Adults: A Preliminary Study on the Interplay Between Microbial Resistance and Auditory Health.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/antibiotics14121241},
pmid = {41463743},
issn = {2079-6382},
support = {MCP24TPC//CEU-Banco Santander/ ; },
abstract = {Background: Hearing loss (HL) affects more than 1.5 billion people worldwide and represents a major global health concern. Recent evidence suggests that alterations in gut microbial composition and antimicrobial resistance (AMR) may be linked to inflammatory and metabolic pathways that could influence auditory physiology. Objectives: This study aimed to explore the relationship between auditory function and the antimicrobial resistance in the gut microbiome of young adults. Methods: Fecal and auditory data were collected from young adults. Auditory function was assessed through pure-tone audiometry, and participants were classified according to the presence or absence of HL based on the American Speech-Language-Hearing Association (ASHA) criteria. Bacterial resistance was analyzed under aerobic and anaerobic conditions using disk diffusion and E-test methods to determine minimum inhibitory concentrations (MICs) for a panel of antibiotics. Gut microbiota composition was further characterized using quantitative polymerase chain reaction (qPCR) to quantify 15 key microbial taxa. Results: Overall, 40.9% of participants presented some degree of HL, with mild or slight HL being more frequent in women (53.3%) than in men (14.3%). Participants with HL exhibited significantly higher MICs for nalidixic acid, amoxicillin, and ciprofloxacin, as well as trends toward increased MIC variability for several other agents. Principal component analysis demonstrated distinct clustering of individuals without HL and greater dispersion among those with HL, suggesting higher interindividual variability in resistance profiles. These findings suggest potential associations between antimicrobial resistance and auditory function, possibly mediated through gut microbiome alterations. qPCR analyses demonstrated that Faecalibacterium prausnitzii abundance was significantly higher in individuals with HL and in those exhibiting greater resistance to amoxicillin. Conclusions: These findings provide preliminary evidence connecting the gut resistome with auditory function, supporting the emerging concept of a gut-ear-brain axis and underscoring the need for further research into microbiome-related mechanisms underlying HL.},
}

@article {pmid41463508,
year = {2025},
author = {Liu, Q and Qu, Y and Jiang, S and Guo, X and Xing, Y and Zheng, J and Dong, Z and Yu, W and Zhang, G},
title = {Corncob Returning Enhances Soil Fertility and Rhizosphere Microbiome Functions to Improve Growth and Nutrient Uptake of Eleutherococcus sessiliflorus in Cold Agroecosystems.},
journal = {Biology},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/biology14121735},
pmid = {41463508},
issn = {2079-7737},
support = {20250203140SF//the Key R&D Project of the Natural Science Foundation of Jilin Province/ ; ZKP202202//the Climbing Project of Changchun University/ ; },
abstract = {Corncob residues, an abundant but underutilized organic resource in Northeast Asia, offer substantial potential for improving soil health and plant productivity. This study investigates the effects of corncob returning on soil physicochemical properties, microbial processes, and the performance of Eleutherococcus sessiliflorus in a cold-temperate region (Jilin Province, China). The treatments included no-amendment control (CK), corncob incorporation (CI), and corncob mulching (CM). Corncob returning significantly increased soil organic carbon, moisture content, and the availability of N-P-K, while reducing soil bulk density, thus improving soil structure and nutrient availability. Both CI and CM treatments enhanced microbial biomass C, N, and P, as well as nutrient-cycling enzyme activities (β-glucosidase, urease, and alkaline phosphatase), accelerating C-N-P turnover in the rhizosphere. These improvements resulted in enhanced plant nutrient status and significant gains in biomass, with plant height and fruit number increasing by up to 44% and 136%, respectively. Multivariate analysis and PLS-SEM revealed that soil improvements strongly stimulated enzyme activity (path coefficient = 0.956), and enhances the microbial niche, thereby promoting plant traits through nutrient release (enzyme → plant path coefficient = 0.694). Microbial functional activity, rather than microbial richness, plays a more crucial role in plant growth promotion. Collectively, these findings underscore that corncob returning improves E. sessiliflorus performance through a soil biochemical activation pathway mediated by microbial metabolism and enzymatic nutrient release. This study provides strong evidence supporting corncob recycling as a cost-effective, environmentally sustainable approach for improving medicinal plant production and advancing circular agriculture in cold-region ecosystems.},
}

@article {pmid41463469,
year = {2025},
author = {Sá, C and Brígido, C and Fidalgo, C and Pires, A and Alves, A and Figueira, E and Cardoso, P},
title = {Influence of Plant Developmental Phase and Irrigation Level on Cultivable Microbiome of Maize Root.},
journal = {Biology},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/biology14121694},
pmid = {41463469},
issn = {2079-7737},
support = {UID/50006 + LA/P/0094/2020//FCT - Fundação para a Ciência e a Tecnologia I.P./ ; 2020.05872.BD//FCT - Fundação para a Ciência e a Tecnologia I.P./ ; 2023.06755.CEECIND//FCT - Fundação para a Ciência e a Tecnologia I.P./ ; CEEC-IND/01373/2018//FCT - Fundação para a Ciência e a Tecnologia I.P./ ; CEECIND/00093/2018//FCT - Fundação para a Ciência e a Tecnologia I.P./ ; 2022.00500.CEECIND//FCT - Fundação para a Ciência e a Tecnologia I.P./ ; },
abstract = {Plant growth-promoting bacteria can help plants survive in stressful environments. Here, we describe the isolation of root-surface and endophytic bacteria from maize roots at two different phases of the plant life cycle (vegetative and reproductive), grown under three different water regimes (100%, 50%, and 0%). Isolates were typed using BOX-PCR to identify unique genetic fingerprints, resulting in a total of 400 strains. These strains were screened for osmotic stress tolerance using 15% polyethylene glycol 6000. Isolates were also tested for bacterial plant growth-promoting traits, including the ability to produce siderophores, indole-3-acetic acid synthesis, and phosphate solubilization, both in the presence and absence of osmotic stress. The results showed that in the reproductive phase, a higher percentage of endophytic and rhizoplane bacteria were tolerant to osmotic stress. Additionally, the highest values of alginate and siderophore production by rhizoplane bacteria were also observed in the reproductive phase. These findings suggest that isolation of maize bacteria should consider the plant's developmental phase and hydric stress conditions to effectively select bacterial strains that enhance crop resilience in drought-affected areas.},
}

@article {pmid41463425,
year = {2025},
author = {Wang, F and Song, W and Wang, D and Huang, Z and Shan, M and Sun, S and Jin, Z and Lu, J and Ji, Y and Sun, K and Li, Z},
title = {Investigating the Dynamic Variation of Skin Microbiota and Metabolites in Bats During Hibernation.},
journal = {Biology},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/biology14121648},
pmid = {41463425},
issn = {2079-7737},
support = {YDZJ202401501ZYTS//Jilin Provincial Natural Science Foundation/ ; 32430066//National Natural Science Foundation of China/ ; 32300425//National Natural Science Foundation of China/ ; 32171525//National Natural Science Foundation of China/ ; 31961123001//National Natural Science Foundation of China/ ; 32171481//National Natural Science Foundation of China/ ; 202310193005//Innovation and Entrepreneurship Training Program for College Students in Jilin Province/ ; S202410193089//Innovation and Entrepreneurship Training Program for College Students in Jilin Province/ ; S202510193059//Innovation and Entrepreneurship Training Program for College Students in Jilin Province/ ; },
abstract = {Pseudogymnoascus destructans (Pd) invades the skin tissue of bats, leading to severe population declines. The skin microbiome plays a crucial role in protecting hosts from fungal infection and exhibits pronounced spatiotemporal dynamics in its structure and function. Meanwhile, metabolites derived from microbial communities reflect the host physiological state and participate in microbe-pathogen interactions. In this study, we investigated the spatiotemporal dynamics of skin bacterial communities and metabolites during hibernation in Rhinolophus ferrumequinum by integrating 16S rRNA sequencing with untargeted metabolomics and experimentally verified the antifungal effects of microbially derived potential metabolites against Pd. Our results revealed that the structure of the skin bacterial community varied significantly across sampling contexts, with its assembly primarily governed by stochastic processes. Bacterial diversity reached its lowest level during middle hibernation, accompanied by a simplified co-occurrence network dominated by cooperative or mutualistic interactions. Additionally, metabolomic analyses demonstrated systematic metabolic remodeling of bat skin across hibernation stages, marked by significant enrichment of multiple pathways closely involved in host antimicrobial defense. Furthermore, metabolite profiles differed across locations, and the abundance patterns of several metabolites were strongly correlated with Pd infection levels. Integrated analyses identified multiple metabolites that showed significant correlations with bacterial genera capable of synthesizing the corresponding compounds. In vitro validation confirmed that nine metabolites effectively inhibited the growth of Pd, among which melatonin exhibited the strongest antifungal activity. Collectively, this study reveals the dynamics of the skin microbiome and metabolites of R. ferrumequinum during hibernation, providing novel insights into the defensive role of skin-associated microbes and metabolites in maintaining population health and resilience against fungal pathogens.},
}

@article {pmid41463367,
year = {2025},
author = {Biţă, A and Scorei, IR and Soriano-Ursúa, MA and Pisoschi, CG and Biţă, CE and Dincă, L and Ştefănescu, S and Racu, MV and Pinzaru, I and Florescu, C and Hădăreanu, DR and Siloşi, CA and Neamţu, J and Gheonea, DI and Mogoşanu, GD and Zorilă, MV},
title = {Boron Bioavailability Revisited: From Plasma-Accessible Species to Microbiota-Accessible Complexes-Implications for Nutritional Essentiality.},
journal = {Biomolecules},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/biom15121711},
pmid = {41463367},
issn = {2218-273X},
mesh = {Humans ; *Boron/metabolism/pharmacokinetics/blood ; *Gastrointestinal Microbiome ; Biological Availability ; Animals ; Prebiotics ; },
abstract = {Boron (B) remains one of the least understood trace elements in human nutrition. Traditionally regarded as non-essential, its biological role has been reevaluated in light of emerging microbiome research. We provide a narrative synthesis of mechanistic, preclinical, and clinical studies to assess whether the colonic actions of B meet accepted criteria for nutritional essentiality. This review revisits B bioavailability through a dual-pathway framework distinguishing plasma-accessible boron (PAB)-small, fully absorbable species with transient systemic effects-from microbiota-accessible boron complexes (MABCs)-indigestible conjugates that reach the colon intact. Evidence indicates that PAB exerts short-term metabolic modulation, whereas MABCs act as prebiotic cofactors that stabilize microbial quorum sensing (autoinducer-2-borate; AI-2B), reinforce the colonic mucus barrier through borate-diol crosslinking, and support host-microbiota symbiosis. Deficiency or low intake of MABCs leads to dysbiosis, barrier fragility, and low-grade inflammation along gut-organ axes-effects reversible by MABC-rich diets. Analytical and clinical tools are proposed to discriminate between PAB and MABC pathways, including fecal B/speciation, AI-2B assays, and mucus-penetration markers. Recognizing B's essentiality as a microbiota-dependent nutrient reframes its nutritional assessment, guiding future dietary guidelines and prebiotic design toward the microbiome-mucus interface.},
}

Humans
*Boron/metabolism/pharmacokinetics/blood
*Gastrointestinal Microbiome
Biological Availability
Animals
Prebiotics

@article {pmid41463053,
year = {2025},
author = {N F Guimarães, G and Dos Santos Cardoso, F and Gamboa, L and W Barrett, D and Gonzalez-Lima, F},
title = {Abdominal Photobiomodulation and the Gut-Brain Axis: A Systematic Review of Mechanistic and Translational Evidence.},
journal = {Biomedicines},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/biomedicines13123042},
pmid = {41463053},
issn = {2227-9059},
abstract = {Background/Objectives: Bidirectional communication between the gut and brain is central to neurological and psychiatric health, and abdominal photobiomodulation (PBM) has emerged as a promising non-invasive way to modulate this axis by targeting intestinal mitochondria, epithelial integrity, and the microbiota. We systematically reviewed preclinical and clinical evidence on abdominal PBM, alone or in combined protocols, reporting microbiome, metabolic, or neurobehavioral outcomes. Methods: Following PRISMA 2020 recommendations, we searched MEDLINE, Scopus, Web of Science, and ScienceDirect through May 2025 for animal and human studies applying PBM to the abdomen and reporting gut-related, metabolic, or brain-related outcomes. Results: Nine studies met the eligibility criteria (five human, four animal). Human trials, mainly in Parkinson's and Alzheimer's disease, used 630-904 nm light and reported gains in mobility, balance, cognition, and olfaction; one trial also showed microbiota modulation with a decreased Firmicutes:Bacteroidetes ratio. Animal models revealed cognitive improvement, reduced neuroinflammation, dopaminergic neuroprotection, and microbial rebalancing. Mechanistic findings converged on enhanced mitochondrial bioenergetics, redox and anti-inflammatory signaling, vagal activation, and short-chain fatty acid-mediated effects. Conclusions: Current evidence, though limited by small samples, heterogeneous dosimetry, combined treatment sites, and few sham-controlled human trials, suggests that abdominal PBM can influence the gut-brain axis through converging mitochondrial, immune, and microbial mechanisms. Adequately powered randomized trials with standardized dosimetry, validated mechanistic biomarkers, and integrative multi-omics analyses are needed to clarify causal pathways and optimize translational applications.},
}

@article {pmid41463040,
year = {2025},
author = {Velikic, G and Supic, G and Maric, DL and Puletic, M and Maric, MD and Barac, B and Maric, DM},
title = {Stem Cell and Exosome Therapy in Wound Healing: Traps, Paradoxes, and Tricks Transforming Paradigms.},
journal = {Biomedicines},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/biomedicines13123030},
pmid = {41463040},
issn = {2227-9059},
abstract = {Cell therapies hold great promise for advancing wound healing; however, translating this promise into consistent clinical benefit has proven elusive. Numerous trials have failed to reproduce the robust outcomes suggested by preclinical studies, reflecting a landscape marked by hidden traps. These include the hostile wound microenvironment, the cytotoxicity of antimicrobial dressings, poor retention and engraftment, immune clearance, and the paradoxical risk of fibrosis and scarring. Across these challenges emerge paradoxes that redefine how traps are understood. The Scarring Paradox reveals that MSCs and EVs may either suppress or reinforce fibrosis, depending on the niche context. The Immune Double-Edged Sword captures the duality of clearance and regenerative modulation. These paradoxes illustrate that traps are not static obstacles but dynamic inflection points. Recognition of these paradoxes has inspired tricks: protective biomaterial carriers, preconditioning strategies, engineered exosomes, and combinatorial therapies with anti-fibrotic, neuromodulatory, or microbiome-targeted adjuncts. Case studies illustrate how classical traps manifest in clinical practice and how paradoxes guide innovation. Emerging adjuncts, ranging from herbal bioactives and bioelectric modulation to circadian synchronization and digital twins, point toward more unconventional but increasingly plausible frameworks for niche control. This perspective review demonstrates that the future of regenerative wound therapy depends not on avoiding traps but on reframing them through paradoxes and converting them into tricks. Stem cell and exosome therapy is thus moving beyond a linear "promise versus failure" narrative toward a systemic, context-aware, programmable approach in which paradoxes drive conceptual renewal and transformative paradigms in wound care.},
}

@article {pmid41463036,
year = {2025},
author = {Andriankaja, OM and Whiteheart, S and Mattos, MBA},
title = {Biological Plausibility Between Long-COVID and Periodontal Disease Development or Progression.},
journal = {Biomedicines},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/biomedicines13123023},
pmid = {41463036},
issn = {2227-9059},
abstract = {Background: Long COVID (LC) is a multi-system disorder with persistent symptoms following SARS-CoV-2 infection. The presence of SARS-CoV-2 in the oral cavity and periodontium raises questions about its potential impact on periodontal health. Methods: A comprehensive literature search was conducted in PubMed using terms related to LC (e.g., "long-COVID," "post-acute sequelae of SARS-CoV-2 infection," "PASC," "post-COVID-19," "long-haul COVID") and oral/periodontal diseases (e.g., "periodontal disease," "periodontitis," "gingiva," "oral disease," "dental"), filtered for English-language full-text articles published from 2019 to 2024. The search yielded 260 articles, which were supplemented with targeted searches on pathogenesis, immune mechanisms, microbiome alterations, and clinical outcomes, resulting in approximately 248 studies included in this review. Results: LC exhibits systemic immunoinflammatory dysregulation, including neutrophil activation, elevated pro-inflammatory cytokines, and complement activation, overlapping with mechanisms implicated in periodontitis. LC also leads to gastrointestinal and pulmonary dysbiosis, with potential effects on oral microbial communities. Gingival epithelium and periodontal ligament cells express ACE2, which is increased in periodontitis, facilitating viral entry. LC has been associated with reactivation of herpesviruses, such as Epstein-Barr virus, which are linked to autoimmune disorders and periodontitis. Conclusions: LC may act as a systemic risk factor for periodontitis. This review provides the theoretical foundation for the interactions between LC and oral health and highlights priorities for future epidemiologic and mechanistic research to better understand these relationships.},
}

@article {pmid41462944,
year = {2025},
author = {Radić, M and Belančić, A and Vučković, M and Fajkić, A and Rogoznica Pavlović, M and Radić, J},
title = {Eradication of Small Intestinal Bacterial Overgrowth in Systemic Sclerosis: Current Treatment and Perspectives-A Narrative Review.},
journal = {Biomedicines},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/biomedicines13122932},
pmid = {41462944},
issn = {2227-9059},
abstract = {Small intestinal bacterial overgrowth (SIBO) is a major yet underrecognized driver of gastrointestinal morbidity in systemic sclerosis (SSc). Disordered motility, fibrosis, and dysbiosis promote microbial stasis, malabsorption, and malnutrition, contributing substantially to impaired quality of life and survival. Diagnostic accuracy remains limited: jejunal aspirate culture is invasive, whereas breath testing offers only moderate sensitivity and specificity. Empirical antibiotic therapy yields transient symptom relief, but recurrence is common, and evidence guiding optimal eradication strategies is sparse. Adjunctive measures, including probiotics, prokinetics, and dietary interventions, remain variably applied, with heterogeneous outcomes across studies. Novel microbiome-targeted, neuromodulatory, and antifibrotic therapies are emerging as promising mechanism-based options. Bearing this in mind, this narrative review aims to consolidate current knowledge on SIBO eradication in SSc. We first outline the pathophysiological rationale and clinical relevance of bacterial overgrowth. We then synthesize available evidence for treatment strategies, appraise barriers to durable remission, and discuss implications for multidisciplinary management. Finally, we highlight emerging approaches, including microbiome-directed therapies, novel prokinetics, and antifibrotic interventions, and define priorities for future clinical research.},
}

@article {pmid41462928,
year = {2025},
author = {Abdelbadiee, S and Yoon, G and Pearman, K and Kumar, A and Harvey, PR},
title = {Understanding How Mental Health Influences IBD Outcomes: A Review of Potential Culprit Biological Mechanisms.},
journal = {Biomedicines},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/biomedicines13122916},
pmid = {41462928},
issn = {2227-9059},
abstract = {Inflammatory bowel disease (IBD) includes Crohn's disease (CD) and ulcerative colitis (UC). Similar to other chronic diseases, IBD is associated with negative mental health outcomes. The prevalence of anxiety and depression with IBD is increasing in western societies and there is a growing body of evidence suggesting a bidirectional relationship which remains poorly understood. This review seeks to distil current evidence on the epidemiology, biological mechanisms and microbial changes through which anxiety and depression may lead to worse IBD outcomes. The literature demonstrates that a prior diagnosis of depression is associated with an increased risk of developing IBD. Co-morbid anxiety or depression doubles the odds of adverse outcomes in IBD. Antidepressants appear to have class dependent effects on modulating disease activity in IBD with co-morbid depression. Chronic stress may drive IBD through a number of mechanisms, including inducing the hypothalamic pituitary axis, glucocorticoid resistance, increasing intestinal permeability, and releasing inflammatory cytokines. Alterations in the microbiome on either a genus or species' level has been shown to be affected by and have an impact on both mental health illness and IBD activity. Further research with high quality longitudinal follow-up data is required to clarify causal associations of anxiety/depression and IBD onset as well as measure the impact of different antidepressant classes and microbiome targeted strategies on disease progression and outcomes.},
}

@article {pmid41462435,
year = {2025},
author = {Zhang, H and Wang, D and Li, C and Xu, F and Cao, X and Bao, B and Zhao, M and Liu, X},
title = {Comprehensive Evaluation of the Antihyperuricemic Effect of Red Kidney Bean Anthocyanins and Molecular Screening of the Lead Candidate.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c14579},
pmid = {41462435},
issn = {1520-5118},
abstract = {This study aimed to investigate the effects of red kidney bean (Phaseolus vulgaris L.) anthocyanins (RKBA) on alleviating hyperuricemia (HUA) and screen the lead candidate. First, RKBA effectively inhibited XOD in vitro. Then, in vivo results showed that RKBA significantly reduced serum uric acid (UA) levels, protected kidney function, and alleviated inflammation and tissue damage. Mechanistically, RKBA down-regulated XOD, ADA, and 5'-NT while modulating urate transporters URAT1, GLUT9, and OAT3, thereby rebalancing UA metabolism. Additionally, it reshaped the gut microbiome (particularly enriching Ligilactobacillus and Dubosiella) and elevated short-chain fatty acids. Subsequently, the UPLC-ESI-MS/MS-based anthocyanin-targeted omics identified and quantified 42 anthocyanins. Integrating molecular docking and dynamics simulation, pelargonidin-3,5-diglucoside was selected as the lead candidate owing to its high abundance and strong affinity for XOD. Pelargonidin-3,5-diglucoside has not been reported as an antihyperuricemic nutraceutical before; hence, this study lays a foundation for future in vivo validation.},
}

@article {pmid41462375,
year = {2025},
author = {Zhang, Y and Zhou, K and Chen, X and Zhang, H and Han, J and Ning, K},
title = {A temporal-aware machine learning framework enables microbial community dynamics prediction with personalized precision.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {261},
pmid = {41462375},
issn = {2049-2618},
support = {Grant No. 2023YFA1800900 and 2018YFC0910502//National Key R&D Program of China/ ; Grant Nos. 32071465, 31871334, 81827901//the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Machine Learning ; *Precision Medicine/methods ; *Gastrointestinal Microbiome ; *Microbiota ; Infant ; Bacteria/classification/genetics ; },
abstract = {BACKGROUND: Accurately forecasting the dynamic behavior of microbial communities from sparse longitudinal data remains a critical challenge for microbiome-based precision medicine and ecological monitoring. Most existing models depend on data interpolation and assume population-level dynamics, which limits their ability to capture personalized microbial changes in real-world scenarios.

RESULTS: We propose MicroProphet, a personalized temporal-aware framework capable of accurately forecasting microbial abundance trajectories from incomplete longitudinal observations without requiring data imputation. Powered by a time-aware Transformer architecture, MicroProphet reconstructs subject-specific microbial trajectories using only the initial 30% of observed time points, capturing critical transitional states through an attention mechanism. We demonstrated its robust cross-ecosystem generalizability across synthetic communities, human gut microbiomes, infant gut development, and corpse decomposition. The framework consistently achieves high predictive accuracy and biological interpretability. In clinical contexts, the framework enables early detection of disease-associated microbial shifts and supports timing optimization for microbiome-targeted interventions. In forensic settings, it accurately infers decomposition timelines from early microbial signals.

CONCLUSIONS: By transforming incomplete, noisy microbiome data into actionable, individualized forecasts, MicroProphet lays the foundation for a new class of temporal-aware systems in microbial ecology and precision health.},
}

Humans
*Machine Learning
*Precision Medicine/methods
*Gastrointestinal Microbiome
*Microbiota
Infant
Bacteria/classification/genetics

@article {pmid41462337,
year = {2025},
author = {Chen, S and Yuan, F and Fang, H and Gouda, M and Wu, W and Zhang, H and Ma, Z and Feng, L and Wang, M and Liu, Y},
title = {Integrating microbiome and machine learning for precision diagnosis of rice bakanae disease.},
journal = {Plant methods},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13007-025-01486-2},
pmid = {41462337},
issn = {1746-4811},
support = {U21A20219//National Natural Sciences Foundation of China/ ; 2023YFD2000103//National Key Research and Development Project/ ; 226-2024-00191//Fundamental Research Funds for the Zhejiang Provincial Universities/ ; },
abstract = {Bakanae is a fungal rice disease that is threatening global rice production, causing severe yield losses. The plant microbiome plays a significant role in plant stress resistance, but its high-dimensional characteristics have not been fully exploited. Therefore, we integrated the microbiome and machine learning (ML) to diagnose bakanae disease in this study. We found significant correlations between Gammaproteobacteria and Bacteroidia and the severity of bakanae disease. We constructed different diagnosis models based on random forests (RF), support vector machines (SVM), and convolutional neural networks (CNN) on 88 biological replicates with an independent test set. We found that the RF model demonstrated strong performance across four taxonomic levels, with an accuracy of 88.9% and an F1 score of 94.1%. Notably, a Bray-Curtis dissimilarity-based extraction method was proposed to rapidly screen practical information from the original microbial community, which can enhance the model performance to a certain extent. According to phenotypic data, the disease severity of infected samples was classified into two levels (high and low infected levels) using the K-means clustering method. In the diagnosis of infection severity based on the family level, the model's prediction accuracy reached 77.8%. Collectively, these findings highlight that the combination of microbiome with ML can advance diagnostic strategies for bakanae disease, providing new avenues for precision agriculture.},
}

@article {pmid41462238,
year = {2025},
author = {Serbanescu, MA and Wright, MC and Elebasy, M and Shi, P and Arnold, JW and Haines, KL and White, JR and Surana, NK and Wischmeyer, PE},
title = {Impact of fiber-containing enteral nutrition on microbial community dynamics in critically ill trauma patients: a pilot-randomized trial.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {706},
pmid = {41462238},
issn = {1741-7015},
support = {1R35GM156920-01/NH/NIH HHS/United States ; },
mesh = {Humans ; *Enteral Nutrition/methods ; *Critical Illness/therapy ; Pilot Projects ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome/drug effects ; *Dietary Fiber/administration & dosage ; Double-Blind Method ; Prospective Studies ; *Wounds and Injuries/therapy/microbiology ; Adult ; *Dysbiosis/microbiology ; Prebiotics/administration & dosage ; Aged ; Oligosaccharides/administration & dosage ; },
abstract = {BACKGROUND: Gut microbial dysbiosis is common in the intensive care unit and certain derangements, like expansion of Enterobacteriaceae and other potential pathogens (pathobionts), are associated with increased morbidity. In other populations, dysbiosis is improved by enteral nutrition supplemented with prebiotic short-chain fructooligosaccharides (scFOS-EN). The impact of scFOS-EN on the microbiota in critical illness is unknown and difficult to predict in a dysbiotic environment. Thus, we conducted a pilot randomized control trial (RCT) in critically ill trauma patients to evaluate the effects of scFOS-EN versus a fiber-free enteral formula (NF-EN) on gut microbial dynamics.

METHODS: In this single-center, prospective, double-blind RCT, mechanically ventilated trauma ICU patients received scFOS-EN or a similar fiber-free formula (NF-EN). Microbial communities in longitudinally collected stool samples were characterized using 16S rRNA gene sequencing. We used linear mixed-effects models to assess microbial dynamics in the 10-day study period after scFOS-EN or NF-EN initiation, as well as a time-informed dimensionality reduction method to identify patient-specific temporal responses and clinical correlates and network approaches for microbe:microbe interactions.

RESULTS: A total of 57 stool samples were analyzed from 17 patients (7 NF-EN, 10 scFOS-EN). All participants had profound baseline dysbiosis and received broad-spectrum antibiotics. Compared to NF-EN, scFOS-EN was associated with an accelerated loss of Bifidobacterium (- 0.6%/day p = .026) and Firmicutes (3.5%/day, p < .001) and greater increases in several Bacteroidaceae members, with expansion of pathobiont Enterobacteriaceae (0.3%/day, p = .003) unique to scFOS-EN participants. Detrimental microbial responses to scFOS-EN, including high Enterobacteriaceae burden, were dictated by pre-existing and ongoing antibiotic exposure and associated with enhanced microbial competition.

CONCLUSIONS: In the dysbiotic gut of critically ill trauma patients, the effect of scFOS-EN is context-dependent. Prior exposure to anaerobic antibiotics appears to modify the microbial response from beneficial to detrimental. These findings challenge a universal approach to prebiotic therapy and underscore the need for personalized nutritional strategies in the ICU.

TRIAL REGISTRATION: The trial was prospectively registered at ClinicalTrials.gov (Identifier: NCT03153397; first posted May 15, 2017) prior to participant enrollment and approved by the Duke Health Institutional Review Board (IRB Pro00081414).},
}

Humans
*Enteral Nutrition/methods
*Critical Illness/therapy
Pilot Projects
Male
Female
Middle Aged
*Gastrointestinal Microbiome/drug effects
*Dietary Fiber/administration & dosage
Double-Blind Method
Prospective Studies
*Wounds and Injuries/therapy/microbiology
Adult
*Dysbiosis/microbiology
Prebiotics/administration & dosage
Aged
Oligosaccharides/administration & dosage

@article {pmid41462094,
year = {2025},
author = {Alaeddini, Z and Nemati, I and Gholizadeh, S},
title = {Deciphering gut microbial impact in coronary artery disease through multimodal computational approaches.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {802},
pmid = {41462094},
issn = {1471-2180},
}

@article {pmid41461922,
year = {2025},
author = {Jin, S and Cenier, A and Wetzel, D and Arefaine, B and Moreno-Gonzalez, M and Stamouli, M and Mohamad, M and Lupatsii, M and Ríos, E and Lee, S and Zamalloa, A and Chokshi, S and Mardinoglu, A and Shoaie, S and Beraza, N and Patel, VC and Schirmer, M},
title = {Microbial collagenase activity is linked to oral-gut translocation in advanced chronic liver disease.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41461922},
issn = {2058-5276},
support = {426120468//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; BBS/E/F/000PR13632//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/CCG1860/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 268211/1134579//Foundation for Liver Research/ ; },
abstract = {Microbiome perturbations are associated with advanced chronic liver disease (ACLD), but how microorganisms contribute to disease mechanisms is unclear. Here we analysed metagenomes of paired saliva and faecal samples from an ACLD cohort of 86 individuals, plus 2 control groups of 52 healthy individuals and 14 patients with sepsis. We identified highly similar oral and gut bacterial strains, including Veillonella and Streptococcus spp., which increased in absolute abundance in the gut of patients with ACLD compared with controls. These microbial translocators uniquely share a prtC gene encoding a collagenase-like proteinase, and its faecal abundance was a robust ACLD biomarker (area under precision-recall curve = 0.91). A mouse model of hepatic fibrosis inoculated with Veillonella and Streptococcus prtC-encoding patient isolates showed exacerbation of gut barrier impairment and hepatic fibrosis. Furthermore, faecal collagenase activity was increased in patients with ACLD and experimentally confirmed for the prtC gene of translocating Veillonella parvula. These findings establish mechanistic links between oral-gut translocation and ACLD pathobiology.},
}

@article {pmid41461857,
year = {2025},
author = {Xie, Y and Pan, J and Li, D and Wang, Q and Sun, Y and Wang, S},
title = {MVPHI: a multi-view learning framework for predicting complex microbial interactions.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-32359-2},
pmid = {41461857},
issn = {2045-2322},
support = {No. 2022FY101100//Science & Technology Fundamental Resources Investigation Program/ ; },
abstract = {Bacteriophages (phages) are viruses that infect bacteria. As the natural regulators of microbial communities, it plays a crucial role in microbiome turnover. Predicting phage-bacteria interactions (PBIs), as well as bacteria-bacteria interactions (BBIs) is essential for advancing microbiome research. Given the high cost and risk of wet-lab techniques, computational biology and bioinformatics methods are reasonable alternatives. However, existing approaches suffer from the low predictive accuracy and poor efficiency. In this study, we proposed a multi learning-based model named MVPHI for predicting complex microbial interactions. More specifically, we first construct a heterogeneous multi-attributed microbial network (MAMN) based on pathogenic bacteria and associated phages. Next, MVPHI introduces three different view microbial characteristics for training the model, including the statistical-view, textual-view and topology-view features. Experimental results on seven benchmark datasets indicated that MVPHI achieves superior performance compared with the six variant models and eight baseline algorithms. Moreover, case study and protein docking experiments further demonstrated the robustness and generalization of our model. In conclusion, the proposed MVPHI model has potential ability to predict novel PBIs and BBIs, and can also provide valuable insights for phages screening and bacterial community research.},
}

@article {pmid41461744,
year = {2025},
author = {Cho, H and Nam, H and Kim, HE and Kim, JE and Park, JI and Park, J and Kim, YC and Lee, JP and Kim, DK and Joo, KW and Kim, YS and Kim, BS and Park, S and Lee, H},
title = {Gut microbiome and metabolite signatures for predicting acute kidney transplant rejection: a prospective study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {44709},
pmid = {41461744},
issn = {2045-2322},
support = {2021R1I1A1A01060190//National Research Foundation grants funded by the Korean government/ ; 2018R1A3B1052328//National Research Foundation grants funded by the Korean government/ ; 2022R1A2C2011190//by National Research Foundation grants funded by the Korean government/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Kidney Transplantation/adverse effects ; Female ; Male ; Prospective Studies ; Middle Aged ; *Graft Rejection/metabolism/microbiology/diagnosis/etiology ; Adult ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Metabolomics/methods ; Dysbiosis/microbiology ; *Metabolome ; },
abstract = {Acute rejection (AR) remains a significant challenge in kidney transplantation (KT) despite advances in immunosuppressive treatment. Recognizing the critical influence of the gut microbiome on modulating host immunity, we investigated the association between gut dysbiosis and AR in KT recipients. A total of 97 patients with KT were prospectively enrolled from two centers, and their samples were collected at multiple time points, such as pre-transplant (n = 97), three months (n = 66), and twelve months (n = 37) post-transplant. Microbial profiling was performed using 16S rRNA sequencing and fecal metabolomics was done via nuclear magnetic resonance spectroscopy. Thirty-three patients developed AR after KT, exhibiting reduced bacterial richness and diversity compared with KT recipients without AR. In addition, these patients had increased Escherichia-Shigella and decreased Phascolarctobacterium abundance. Pathway analysis identified 47 enriched pathways in AR patients, notably those involved in lipopolysaccharide biosynthesis and short-chain fatty acid metabolism. Consistent results were obtained from stool metabolomics, showing reduced propionate and lactate concentrations compared with patients without AR. Finally, combining pre-KT bacterial and fecal metabolite features with clinical parameters significantly improved AR prediction accuracy. Our results suggest that integrating clinical, microbial, and metabolomic data may provide a more holistic patient care regimen across both pre- and post-transplant phases.},
}

Humans
*Gastrointestinal Microbiome
*Kidney Transplantation/adverse effects
Female
Male
Prospective Studies
Middle Aged
*Graft Rejection/metabolism/microbiology/diagnosis/etiology
Adult
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Metabolomics/methods
Dysbiosis/microbiology
*Metabolome

@article {pmid41461645,
year = {2025},
author = {Moradi, J and Berggreen, E and Gerdts, E and Kringeland, E and Bolstad, AI and Bunæs, DF and Bertelsen, RJ},
title = {Taxonomic and functional signatures of smoking and periodontitis severity in the subgingival microbiome of older adults.},
journal = {npj aging},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41514-025-00319-9},
pmid = {41461645},
issn = {2731-6068},
support = {318443//Research Council of Norway/ ; 318443//Research Council of Norway/ ; 318443//Research Council of Norway/ ; 318443//Research Council of Norway/ ; 318443//Research Council of Norway/ ; },
abstract = {Periodontitis and smoking are major contributors to oral and systemic health deterioration in aging adults. This study investigated the combined effects of smoking status and periodontitis severity on the subgingival microbiome in 1107 individuals aged 69-72 using shotgun metagenomic sequencing. Smoking was linked to reduced microbial diversity, enrichment of periodontal pathogens, and depletion of health-associated commensals, while increasing periodontitis severity was associated with broader dysbiotic shifts, including enrichment of canonical pathogens. The presence of overlapping taxa suggests shared dysbiotic pathways that may accelerate disease progression in older adults. Notably, the combination of smoking and severe periodontitis was characterized by enrichment of key pathogens, such as Tannerella forsythia, Fusobacterium nucleatum, Actinomyces israelii, and Mogibacterium timidum. Although former smokers showed fewer opportunistic pathogens than current smokers, their microbiomes remained altered compared to never smokers, suggesting persistent differences potentially related to past smoking. Functional profiling revealed largely additive effects of smoking and periodontitis, with enrichment of lipopolysaccharide biosynthesis, proteolysis, and sulfur metabolism, alongside depletion of commensal biosynthetic functions. Overall, the findings highlight the persistent and additive impacts of smoking and periodontitis on the subgingival microbiome, underscoring the importance of addressing both exposures jointly in long-term oral health strategies for older adults.},
}

@article {pmid41461600,
year = {2025},
author = {Chen, S and Luo, Y and Wei, G and Liu, S},
title = {Molecular Mimicry at the Gut-Immune Interface: A Mechanistic Link to Type 1 Diabetes.},
journal = {Immunology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imm.70091},
pmid = {41461600},
issn = {1365-2567},
abstract = {Type 1 diabetes (T1D) arises from T cell-mediated destruction of pancreatic β-cells. However, genetic susceptibility alone cannot account for the increasing incidence and earlier onset of T1D, suggesting a substantial contribution from environmental factors, particularly the gut microbiota. This review synthesises recent human, multiomics and experimental evidence linking gut microbiota dysbiosis and microbial metabolites to β-cell autoimmunity. We focus on two converging mechanisms: (1) metabolite-driven disruption of intestinal barrier integrity and immune regulation, and (2) molecular mimicry between microbial peptides and islet autoantigens that activate autoreactive T cells. Across human cohorts and animal models, T1D-associated dysbiosis features reduced short-chain fatty acid (SCFA)-producing bacteria (e.g., Faecalibacterium, Roseburia) and increased pro-inflammatory taxa (e.g., Bacteroides, Streptococcus spp.). SCFA deficiency compromises Treg induction and gut barrier stability, facilitating antigen translocation. Several gut-derived peptides, such as the Parabacteroides distasonis hprt4-18 peptide, share sequence homology with insulin and other islet antigens, activate insulin-reactive T cells and accelerate diabetes in NOD mice, supporting a role for molecular mimicry. Interventional approaches including FMT, probiotics and prebiotics show promise but remain heterogeneous; their efficacy is highly strain-, timing- and context-dependent and translation from animal studies to humans is still limited. Therapeutically targeting the gut-islet axis, through modulation of microbiota, microbial metabolites or cross-reactive antigens, offers potential for disease prevention or adjunctive treatment. We highlight emerging biomarkers, including MAIT-cell phenotypes, antimicrobial peptide reactivity and microbiome-derived functional signatures, and emphasise the need for stratified clinical trial designs based on age, genotype and baseline microbiota composition to address current variability. The microbiota-metabolite-molecular mimicry axis provides a coherent mechanistic framework linking gut dysbiosis to T1D pathogenesis. Advancing these insights into clinical application will require rigorous, genotype-stratified human studies and standardised, transparent methodological approaches.},
}

@article {pmid41461596,
year = {2025},
author = {Alqassim, AY},
title = {Confronting neglected tropical vector-borne diseases in a changing world: a review of challenges and opportunities.},
journal = {Pathogens and global health},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/20477724.2025.2609157},
pmid = {41461596},
issn = {2047-7732},
abstract = {Neglected tropical vector-borne diseases (NTVBDs) pose a significant global health challenge, disproportionately affecting low- and middle-income countries. This review begins by defining NTVBDs and their classification criteria, providing a comprehensive overview of their geographical distribution, vectors, and causative agents. Climate change, socioeconomic factors, and land-use changes are changing NTVBD transmission dynamics, with temperature increases expanding vector ranges and creating new transmission hotspots in previously unsuitable regions. The review examines both established vector control approaches and emerging technologies, including CRISPR-based gene editing, artificial intelligence, and microbiome manipulation for NTVBD control. Housing improvements have shown particular promise, with studies demonstrating significant reductions in vector presence through structural interventions. Sustainable control programs emphasize community-based and culturally appropriate interventions, with gender-responsive approaches enhancing both intervention coverage and women's economic empowerment. The review explores the integration of NTVBD control with existing health systems through formal coordination mechanisms and sustainable financing frameworks beyond traditional donor-dependent models. Recent field initiatives addressing the psychological dimensions of NTVBDs highlight the importance of comprehensive approaches that extend beyond physical symptoms. To address the complex challenges of NTVBDs in a rapidly changing world, the review concludes that a multidisciplinary approach integrating technological innovation with social and ecological considerations is essential. Future research should examine the long-term effects of climate change on NTVBD dynamics, develop broadly protective vaccines, optimize integrated control strategies, and investigate innovative funding mechanisms for resource-limited settings.},
}

@article {pmid41461486,
year = {2026},
author = {Kang, S and Lee, JY and Cho, KS},
title = {Bacterial and fungal metagenomes associated with atmospheric particulates in Republic of Korea: Comparison of PM2.5 and TSP larger than PM2.5.},
journal = {Journal of environmental sciences (China)},
volume = {161},
number = {},
pages = {400-410},
doi = {10.1016/j.jes.2025.08.021},
pmid = {41461486},
issn = {1001-0742},
mesh = {*Particulate Matter/analysis ; Republic of Korea ; Bacteria/genetics ; *Air Pollutants/analysis ; *Environmental Monitoring ; Particle Size ; *Fungi/genetics ; *Metagenome ; *Air Microbiology ; Microbiota ; Air Pollution/statistics & numerical data ; },
abstract = {Particulate matter (PM) significantly contributes to air pollution, potentially causing health issues, with PM-associated microorganisms implicated in some cases. While studies have explored microbial concentration and structure in PM based on particle size, comprehensive analysis of microbial functional traits and environmental influences is limited. This study evaluated microbial concentrations and diversity in PM with a diameter of 2.5 µm or lower (PM2.5) and total suspended particles (TSP) greater than PM2.5 (PM>2.5) samples relative to air temperature and other factors. DNA extracted from PM2.5 and PM>2.5 filters was sequenced to characterize bacterial and fungal community structures and functional genes. Results showed that microbial concentrations and diversity were greater in PM>2.5, with similar dominant species across PM sizes. Higher air temperatures correlated with increased microbial concentrations and diversity in PM>2.5, attributed to enhanced microbial growth. An Asian dust event from the Mongolian desert disrupted the PM microbiome. Despite consistent species dominance, gene function analysis revealed abundant drug resistance pathways in bacterial communities of both particle types, while pathotroph prevalence was higher in PM2.5 fungal communities. These findings indicate that PM2.5 microbial community analysis suffices for understanding PM ecosystems, offering valuable insights for air quality management and microbial pollution control, especially concerning potential pathogens.},
}

*Particulate Matter/analysis
Republic of Korea
Bacteria/genetics
*Air Pollutants/analysis
*Environmental Monitoring
Particle Size
*Fungi/genetics
*Metagenome
*Air Microbiology
Microbiota
Air Pollution/statistics & numerical data

@article {pmid41461451,
year = {2026},
author = {Xiao, S and Zheng, C and Yang, J and Zhang, W and Fang, H and Wu, X and Han, L},
title = {Responses and regulatory mechanisms of soil microbiome and antibiotic resistome to carbendazim and ZnO nanoparticles.},
journal = {Pesticide biochemistry and physiology},
volume = {217},
number = {},
pages = {106891},
doi = {10.1016/j.pestbp.2025.106891},
pmid = {41461451},
issn = {1095-9939},
mesh = {*Zinc Oxide/pharmacology/toxicity ; *Soil Microbiology ; *Microbiota/drug effects ; *Benzimidazoles/pharmacology ; *Carbamates/pharmacology ; Plasmids/genetics ; *Soil Pollutants ; *Fungicides, Industrial/pharmacology ; *Nanoparticles ; Bacteria/drug effects/genetics ; *Metal Nanoparticles ; *Drug Resistance, Microbial/genetics/drug effects ; Reactive Oxygen Species/metabolism ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Exogenous pollutants may alter the profile of antibiotic resistance genes (ARGs) in soil. Substantial application of a fungicide carbendazim (CBD) and ZnO nanoparticles (nZnO) in modern agriculture has led to serious combined pollution in soil. Here, the degradation characteristics of CBD, the diversity and abundance of ARGs and their dissemination and regulatory mechanisms were investigated in response to individual and combined applications of CBD and nZnO. CBD initially degraded fast and then slowly in soil, and nZnO slightly delayed the degradation of CBD. CBD and nZnO significantly changed the soil bacterial community structure. Meanwhile, CBD and nZnO significantly increased the abundance of ARGs, especially for multidrug and beta-lactam resistance genes. The relative abundance of plasmids significantly increased in CBD and nZnO treatments, and the elevation in soil ARG abundance was associated with the increase in plasmid-borne ARG abundance, suggesting that plasmid-mediated horizontal gene transfer might contribute to the dissemination of ARGs. Moreover, the intergenus and intragenus conjugative transfer frequency of plasmid RP4 in the CBD and nZnO treatments increased by up to 9.4-fold of the control. Additionally, the cell membrane permeability and intracellular reactive oxygen species content of recipient and donor bacteria in the CBD and nZnO treatments increased by up to 1.6-fold of the control, which facilitated plasmid-mediated conjugative transfer of ARGs. It is concluded that CBD and nZnO can alter soil microbiome and improve antibiotic resistome by accelerating conjugative plasmid-mediated ARGs propagation.},
}

*Zinc Oxide/pharmacology/toxicity
*Soil Microbiology
*Microbiota/drug effects
*Benzimidazoles/pharmacology
*Carbamates/pharmacology
Plasmids/genetics
*Soil Pollutants
*Fungicides, Industrial/pharmacology
*Nanoparticles
Bacteria/drug effects/genetics
*Metal Nanoparticles
*Drug Resistance, Microbial/genetics/drug effects
Reactive Oxygen Species/metabolism
Anti-Bacterial Agents/pharmacology

@article {pmid41461446,
year = {2026},
author = {Yuan, Y and Li, C and Yang, L and Zhao, Y and Xu, C and Tao, J},
title = {Harnessing rhizosphere bacteria for fungal disease management in Paeonia lactiflora.},
journal = {Pesticide biochemistry and physiology},
volume = {217},
number = {},
pages = {106885},
doi = {10.1016/j.pestbp.2025.106885},
pmid = {41461446},
issn = {1095-9939},
mesh = {*Rhizosphere ; *Paeonia/microbiology ; *Plant Diseases/microbiology/prevention & control ; Alternaria ; Soil Microbiology ; Bacillus subtilis/physiology ; *Bacteria/metabolism ; },
abstract = {Paeonia lactiflora Pall., a traditional Chinese ornamental flower, holds significant aesthetic and economic value but remains highly susceptible to fungal diseases. In this study, eight candidate biocontrol bacteria (SY1-SY8) were isolated and identified from the rhizosphere soil of P. lactiflora, and their antagonistic effects against four major fungal pathogens were evaluated using plate confrontation assays, fermentation broth antagonism tests, and pot experiments. Among these isolates, Bacillus subtilis SY8 exhibited the most significant inhibitory effect against all four pathogens. Treatment with SY8 significantly reduced the incidence of black spot disease caused by Alternaria alternata FSY1 and enhanced the activities of phenylalanine ammonia-lyase and polyphenol oxidase in P. lactiflora leaves. Additionally, SY8 treatment reduced the abundance of pathogenic fungi in both the phyllosphere and endophytic compartments, while increasing the diversity and evenness of the phyllosphere bacterial community, thereby promoting more complex microbial interactions. Metabolomic analysis revealed that SY8 substantially altered key metabolic pathways in P. lactiflora leaves, including carbon metabolism, amino acid biosynthesis, and the citric acid cycle. These metabolic shifts collectively enhance the antioxidant capacity, cellular repair mechanisms, and disease resistance of plants. Furthermore, metabolomic profiling of the SY8 fermentation broth identified specific bioactive metabolites associated with its antagonistic activity against FSY1. SY8 significantly enhanced the resistance of P. lactiflora to black spot disease in by increasing the activities of defense-related enzymes, modifying the rhizosphere microbial community, and regulating metabolic pathways. These findings underscore the potential of SY8 as a promising biocontrol agent for managing fungal diseases in P. lactiflora.},
}

*Rhizosphere
*Paeonia/microbiology
*Plant Diseases/microbiology/prevention & control
Alternaria
Soil Microbiology
Bacillus subtilis/physiology
*Bacteria/metabolism

@article {pmid41461420,
year = {2026},
author = {Cao, W and Yang, S and Wang, J and Chen, S and Byarlay, M and Shi, X and Li-Byarlay, H and Ma, C},
title = {Field-realistic cyfluthrin exposure alters multi-omics profiles in Bombus terrestris: Implications for wild pollinator health.},
journal = {Pesticide biochemistry and physiology},
volume = {217},
number = {},
pages = {106896},
doi = {10.1016/j.pestbp.2025.106896},
pmid = {41461420},
issn = {1095-9939},
mesh = {Animals ; Bees/drug effects/metabolism ; *Pyrethrins/toxicity ; *Nitriles/toxicity ; *Insecticides/toxicity ; Gastrointestinal Microbiome/drug effects ; Transcriptome/drug effects ; Pollination/drug effects ; Metabolome/drug effects ; Multiomics ; },
abstract = {Cyfluthrin is effective in mitigating crop damage caused by pests. However, its residues in bee colonies pose potential threats to the health and fitness of bumblebees. While previous studies have shown significant physiological effects of cyfluthrin on honeybees, its effects on bumblebees remain poorly understood. In this study, bumblebees were exposed to 30 and 120 μg/kg cyfluthrin (two field-level concentrations) for 10 days. We assessed the effects of chronic cyfluthrin exposure on bumblebee survival, sucrose solution consumption, body weight and midgut pathology. Multi-omics analyses were performed, encompassing the gut microbiome and metabolome, as well as the head transcriptome and proteome. The results demonstrated that exposure to cyfluthrin at a concentration of 120 μg/kg significantly reduced the survival probability of bumblebees. Hematoxylin-Eosin staining revealed damage to the midgut microvilli. 16S rRNA sequencing indicated a significant decrease in the relative abundance of the core gut microbiota, Bifidobacterium. Metabolomic analysis of the gut further revealed a significant reduction in multiple beneficial metabolites (crustecdysone, creatine and retinol palmitate). Head transcriptomics showed significant downregulation of genes associated with the tyrosine metabolism pathway and fatty acid β-oxidation. Furthermore, proteomic analysis of the head revealed a significant upregulation of apoptosis-related proteins, alongside a significant downregulation of proteins involved in immune responses and glycosaminoglycan biosynthesis. These findings highlight the need for cautious pesticide application in agricultural systems and emphasize the importance of considering sublethal effects on pollinators - particularly through disruptions to the gut and head.},
}

Animals
Bees/drug effects/metabolism
*Pyrethrins/toxicity
*Nitriles/toxicity
*Insecticides/toxicity
Gastrointestinal Microbiome/drug effects
Transcriptome/drug effects
Pollination/drug effects
Metabolome/drug effects
Multiomics

@article {pmid41461407,
year = {2026},
author = {Shahid, M},
title = {Molecular engineering and in-silico biotechnological innovations for microbial degradation of persistent pesticides.},
journal = {Pesticide biochemistry and physiology},
volume = {217},
number = {},
pages = {106833},
doi = {10.1016/j.pestbp.2025.106833},
pmid = {41461407},
issn = {1095-9939},
mesh = {*Pesticides/metabolism ; Biodegradation, Environmental ; *Biotechnology ; Metabolic Engineering ; Soil Microbiology ; Bacteria/metabolism/genetics ; Computer Simulation ; },
abstract = {The persistence of recalcitrant pesticides in agricultural soils poses a serious threat to environmental and public health. Conventional remediation methods often have limited efficiency and, sustainability. Whereas, microbial degradation provides an eco-friendly and attractive alternative. This review highlights advances in molecular and biotechnological tools driving microbial pesticide degradation. It also emphasizes key genes, enzymatic pathways, and resilient microbes driving recalcitrant pesticide degradation. This review discusses the integration of next-generation sequencing, multi-omics platforms, CRISPR-Cas editing, synthetic biology, and AI-driven metabolic engineering in advancing microbial pesticide degradation. It also highlights progress in rhizosphere microbiome research, bioinformatics pipelines, and field-scale validation. The transition from lab to field highlights precision bioremediations' potential for sustainable pesticide management.},
}

*Pesticides/metabolism
Biodegradation, Environmental
*Biotechnology
Metabolic Engineering
Soil Microbiology
Bacteria/metabolism/genetics
Computer Simulation

@article {pmid41461310,
year = {2025},
author = {Sun, C and Zhu, J and Sun, X and Zhang, Z and Sun, Y and Jin, Y and Wu, T},
title = {Targeting the human gut microbiome: a comparative review of probiotics, prebiotics, synbiotics, and postbiotics.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.12.032},
pmid = {41461310},
issn = {2090-1224},
abstract = {BACKGROUND: The human gut microbiome plays a central role in regulating host health, serving as a core hub for systemic physiological interactions. Dysregulation of the gut microbiome is implicated in a wide spectrum of local and systemic diseases. Research has evolved from establishing associations to elucidating the mechanistic roles of gut microbes and developing targeted strategies for their modulation, with a growing emphasis on their bidirectional communication with other organ systems.

AIM OF REVIEW: This review aims to synthesize current knowledge on the composition and function of the gut microbiome, its functional crosstalk with the host, and its integral role in both health and disease. A major focus is placed on critically evaluating the mechanisms, efficacy, and applications of key microbiome-directed interventions-probiotics, prebiotics, synbiotics, and postbiotics-in maintaining or restoring gut-centric ecological balance.

The gut microbiome acts as a dynamic microbial organ essential for digestion, immune maturation, and metabolic homeostasis. Dysbiosis, characterized by a loss of beneficial microbes and an overgrowth of potential pathogens, is a critical factor in the pathogenesis of gastrointestinal disorders, metabolic diseases, and other systemic conditions. The gut microbiome engages in continuous bidirectional communication with distant organs, including the oral cavity, lungs, skin, and urinary tract, via specific axes (e.g., gut-oral, gut-lung, gut-skin), thereby exerting widespread influence on host physiology. Probiotics, prebiotics, synbiotics, and postbiotics represent complementary strategies to counteract dysbiosis and reestablish gut ecological integrity, ranging from introducing live beneficial bacteria to utilizing inactivated microbial cells and their bioactive metabolites. Enhancing the translational potential of these interventions requires deeper mechanistic insights and robust clinical validation.},
}

@article {pmid41461285,
year = {2025},
author = {Bharathi, S and Soundara Rajan, YAPA and Prakash, S and Immanuel, G and Ramasubburayan, R},
title = {Pathobionts in the microbiome: Drivers of disease and targets for treatment.},
journal = {Microbial pathogenesis},
volume = {211},
number = {},
pages = {108268},
doi = {10.1016/j.micpath.2025.108268},
pmid = {41461285},
issn = {1096-1208},
abstract = {Pathobionts are commensal inhabitants of the human microbiome that can transition to a pathogenic state under specific genetic or environmental conditions. They have recently gained attention for their impact on various clinical conditions. This review discusses the key factors behind pathobiont emergence, including microbial dysbiosis, antibiotic use, dietary influences, immune dysfunction and host genetics. It provides a comprehensive overview of pathobionts associated with the gut, oral cavity, and vaginal microbiomes highlighting their roles in disease pathogenesis. A significant focus is also placed on the involvement of pathobiont in immune-related disorders. Furthermore, current and advanced therapeutic strategies aimed at mitigating the effects of pathobionts, such as faecal microbiota transplantation, phage therapy, probiotics and prebiotics, along with their advantages and limitations, were highlighted. Thus, the integrated perspective combining microbial ecology, host immunity, and therapeutic strategies outlines the need for targeted, microbiome-based interventions to address the complex behaviour of pathobionts.},
}

@article {pmid41461264,
year = {2025},
author = {Mannon, PJ and Benson, AK and Schnable, J and Ding, W and Juritsch, AF and Rose, DJ},
title = {Food as Medicine: Enhancing Crop Breeding and Food Processing to Shift the Gut Microbiome for Prevention and Treatment of Chronic Diseases.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101298},
doi = {10.1016/j.tjnut.2025.101298},
pmid = {41461264},
issn = {1541-6100},
abstract = {Prebiotics are useful tools for shifting the gut microbiome and metabolome to confer immune, metabolic and preventive benefit for human disease. However, there are emerging concerns about methods for discovering optimal candidate compounds and their sustainable production for long-term success in targeting mechanisms of disease. In this perspective we review the current state of prebiotics moving from nutrition to function in health, highlighting the opportunities for using food as medicine in treating a model disease, inflammatory bowel disease, discussing the ways crop breeding can be used to identify and improve the functional (beyond nutritional) value of a prebiotic and the critical role that food processing plays in sustaining the integrity and scalability of the prebiotic compound while influencing consumer adoption of these agents. This information supports a trajectory for the future of "food as medicine" to be moving from population-scale dietary guidelines to personalized or precision nutrition guidelines, from "eat more fiber" to "eat this specific type of fiber that has been enhanced in and processed from this specific genotype of food crop". This could include developing "designer fibers" by crop breeding to develop panels of genotypes with different fiber structures that deliver reliable shifts in the microbiome and metabolome for most patients with the targeted disease. Finally, there needs to be a commitment to sustainability of the plant-derived product so that future generations will have access to the same benefits of the food as medicine initially developed for disease prevention and treatment.},
}

@article {pmid41461105,
year = {2025},
author = {Dias, MF and Freitas, APA and Collares, SF and Santos, RMS and Nogueira, YJA and Júnior, AMÁ and Martins, TC and Rocha, PMB and Romano-Silva, MA and de Miranda, DM},
title = {Gut Microbiota, Antipsychotics, and Metabolic Alterations in Children and Adolescents: Protocol for a Longitudinal Observational Study.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e77374},
pmid = {41461105},
issn = {1929-0748},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Adolescent ; Child ; *Antipsychotic Agents/adverse effects/pharmacology/therapeutic use ; Longitudinal Studies ; Prospective Studies ; Male ; Female ; Metabolome/drug effects ; Observational Studies as Topic ; },
abstract = {BACKGROUND: Over the past decade, numerous studies have emphasized the important role of gut microbiota (GM) in maintaining the body's homeostasis. Imbalances in GM have been linked to many dysfunctions, such as metabolic and neurodevelopmental disorders. GM can be influenced by many factors, among them the use of certain medications, such as second-generation antipsychotics (SGAs), and, in turn, act upon the endocrine, immune, and nervous systems. Despite the growing interest in the microbiota-gut-brain axis, significant gaps remain in our understanding of how SGAs affect GM and the host metabolic profile.

OBJECTIVE: This study aims to build on the current knowledge on the impact of SGAs on clinical parameters, microbial and metabolic profiles, and behavior of children and adolescents undergoing treatment with SGAs.

METHODS: This is a prospective longitudinal study, in which the effects of SGAs will be assessed before and 3 to 6 months after their introduction. An integrated approach will be used, encompassing clinical data (such as weight, lipid profile, and glucose levels); microbiome and metabolome analyses; emotional, behavioral, and sleep patterns (assessed through psychiatric scales); and dietary habits.

RESULTS: This project was funded in November 2023 and will start data collection in January 2026. It is expected to be completed in 2027.

CONCLUSIONS: This study is expected to provide insights into the multidimensional effects of SGAs on children and adolescents, including clinical data, GM microbial profile, metabolism, and behavior. The findings may contribute to a better understanding of treatment impacts and provide information on more personalized therapeutic strategies.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Adolescent
Child
*Antipsychotic Agents/adverse effects/pharmacology/therapeutic use
Longitudinal Studies
Prospective Studies
Male
Female
Metabolome/drug effects
Observational Studies as Topic

@article {pmid41461020,
year = {2025},
author = {Palmiotti, A and Bertolini, A and Fiorotto, R},
title = {Pathophysiology of cystic fibrosis-related liver disease.},
journal = {Current opinion in gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {41461020},
issn = {1531-7056},
abstract = {PURPOSE OF REVIEW: Cystic fibrosis liver disease (CFLD) is a significant nonpulmonary complication of cystic fibrosis, affecting approximately 5-10% of patients. It encompasses a spectrum of hepatic abnormalities ranging from mild, transient elevations in liver enzymes to advanced CFLD (aCFLD), which is marked by clinically relevant portal hypertension due to cirrhotic or noncirrhotic liver pathology. This review focuses on aCFLD as the clinically meaningful form of the disease and summarizes recent mechanistic insights into its pathogenesis that may inform the development of targeted therapeutic strategies.

RECENT FINDINGS: CFLD pathogenesis has been traditionally linked to defective bile secretion. Emerging evidence, however, highlights additional contributors, including cholangiocyte immune dysregulation, gut dysbiosis, and intestinal barrier dysfunction, which together promote hepatic inflammation. Furthermore, recent studies underscore the role of vascular alterations independent of cirrhosis, specifically noncirrhotic portal hypertension, as the main clinical feature in aCFLD. These findings support a multifactorial, multihit model of disease in the pathogenesis of CFLD.

SUMMARY: The complex interplay of these factors suggests that effective treatment for aCFLD may require a multifaceted approach. Advances in understanding the gut-liver axis and vascular contributions provide new therapeutic targets. Future research should focus on validating these findings and evaluating the efficacy of cystic fibrosis transmembrane conductance regulator modulators and microbiome-targeted treatments in altering the course of CFLD.},
}

@article {pmid41460655,
year = {2025},
author = {Oso, TA and Ahmed, MM and Okesanya, OJ and Adebayo, UO and Obadeyi, KB and Othman, ZK and Lucero-Prisno, DE},
title = {Exploring the gut-brain-microbiome axis in Alzheimer's disease: Integrating metagenomics, metabolomics, and artificial intelligence for next-generation biomarker discovery.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {},
number = {},
pages = {13872877251407700},
doi = {10.1177/13872877251407700},
pmid = {41460655},
issn = {1875-8908},
abstract = {Alzheimer's disease (AD), a progressive neurodegenerative disorder, is increasingly understood as a multifactorial condition influenced by systemic and environmental factors beyond the central nervous system. A growing body of evidence shows that the gut-brain-microbiome axis (GBMA), a complex bidirectional communication network, is involved in neural, endocrine, immune, and metabolic pathways in AD pathogenesis. This narrative review synthesizes emerging insights into the role of gut microbiota dysbiosis in promoting neuroinflammation, amyloid-β aggregation, blood-brain barrier disruption, and cognitive decline. We explored recent advancements in metagenomics and metabolomics for profiling microbial communities and their functional metabolites linked to AD. Alterations in microbe-derived compounds, such as short-chain fatty acids and tryptophan metabolites, influence neurodevelopment, glial activation, and mitochondrial dysfunction. Multi-omics integration, enhanced by artificial intelligence (AI), enables precise biomarker discovery, patient stratification, and the development of personalized therapeutic strategies. Translational opportunities include microbiome-based diagnostics, probiotic therapy, and stratified interventions. However, clinical translation faces challenges such as methodological heterogeneity, inter-individual microbiome variation, data governance issues, and algorithmic bias. We emphasize the need for diverse reference panels, longitudinal multimodal cohorts, and shared AI-ready datasets to enhance the reproducibility and global equity of research. Strategic investment in integrative, ethically governed, and interdisciplinary approaches is essential to unlock the full therapeutic and diagnostic potential of GBMA in AD.},
}

@article {pmid41460370,
year = {2025},
author = {Wang, G and Li, X and Ren, P and Ai, Q and Wang, Z},
title = {Integrative Microbiome-Genetic Analysis Reveals Mechanisms of Fishmeal-Free Feed Adaptability in Large Yellow Croaker (Larimichthys crocea).},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {28},
number = {1},
pages = {6},
pmid = {41460370},
issn = {1436-2236},
mesh = {Animals ; *Perciformes/microbiology/genetics/physiology ; *Gastrointestinal Microbiome/genetics ; *Animal Feed/analysis ; Diet/veterinary ; RNA, Ribosomal, 16S/genetics ; Polymorphism, Single Nucleotide ; Bacteria/classification/genetics ; Adaptation, Physiological/genetics ; },
abstract = {To address the challenge of fishmeal shortage and improve the utilization of fishmeal-free (FMF) diets in large yellow croaker (Larimichthys crocea), we conducted an integrative analysis combining host genetics and gut microbiota. A 28-day indoor feeding trial was performed with 185 fish using an FMF-based diet, during which single nucleotide polymorphism (SNP) genotyping and feed efficiency evaluations were conducted. The V3-V4 regions of the 16S rRNA gene were sequenced from both distal (DI) and proximal (PI) intestinal segments. Significant microbial contributions (microbiability) were only observed for daily feed intake (DFI) and residual feed intake (RFI). Microbiability estimates reached 0.25 (DI) and 0.17 (PI) for DFI, while RFI in DI exhibited higher microbiability (m[2] = 0.11) than heritability (h[2] = 0.08). In contrast, correlations between host genetic variation and microbial community distances were extremely weak. We further identified heritable microbial taxa, including Lactococcus, Alicyclobacillus acidoterrestris, and Bacillus, as well as microbial biomarkers such as Lactococcus, Listeria, Methylobacterium, and Alicyclobacillus acidoterrestris, which were significantly associated with FMF feed adaptation. These findings highlight the complementary roles of host genetics and gut microbiota in shaping FMF feed utilization in marine fish, and provide valuable targets for selective breeding of strains with enhanced adaptability to plant-based diets.},
}

Animals
*Perciformes/microbiology/genetics/physiology
*Gastrointestinal Microbiome/genetics
*Animal Feed/analysis
Diet/veterinary
RNA, Ribosomal, 16S/genetics
Polymorphism, Single Nucleotide
Bacteria/classification/genetics
Adaptation, Physiological/genetics

@article {pmid41460363,
year = {2025},
author = {Wang, C and Li, H and Wang, T and Li, X and Liu, J and Deng, A and Jiao, X},
title = {The gut-eye axis in blinding eye diseases: microbiota-driven immune dysregulation and immunomodulatory therapies.},
journal = {International ophthalmology},
volume = {46},
number = {1},
pages = {57},
pmid = {41460363},
issn = {1573-2630},
support = {2024BSQD05//the Doctoral Startup Fund of the Affiliated Hospital of Shandong Second Medical University/ ; ZR2025QC815//the Shandong Provincial Natural Science Foundation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/immunology ; Animals ; Probiotics/therapeutic use ; Dysbiosis ; *Immunomodulation ; *Eye Diseases/therapy/microbiology/immunology ; },
abstract = {PURPOSE: To synthesize recent (2020-2025) advances on how gut, oral, and ocular-surface microbiota contribute to major blinding eye diseases, dry eye disease (DED), non-infectious uveitis, glaucoma, optic neuropathy, age-related macular degeneration (AMD), and diabetic retinopathy (DR), and to evaluate the therapeutic potential of microbiome-based interventions.

METHODS: PubMed and Web of Science were searched (January 2020-October 2025) using the terms "gut microbiota", "ocular diseases", and "immunomodulatory therapies". Eligible studies included original human and animal research demonstrating microbial dysbiosis or testing microbiome-directed therapies. Data were synthesized thematically across microbial composition, immune-metabolic mechanisms, and intervention outcomes.

RESULTS: Across all six diseases, dysbiosis was consistently characterized by depletion of anti-inflammatory taxa such as Akkermansia, Ruminococcaceae, and other short-chain fatty acid (SCFA) producers, with enrichment of pro-inflammatory bacteria including Proteobacteria, Staphylococcus, and Porphyromonas gingivalis. These changes were associated with increased intestinal permeability, systemic lipopolysaccharide (LPS) and trimethylamine N-oxide (TMAO), Th17 (T helper 17)/Treg (regulatory T cell) imbalance, and loss of SCFA-mediated neuroprotection. Probiotics containing Lactobacillus or Bifidobacterium improved tear stability and reduced inflammation in preclinical and pilot clinical studies, while high-fiber diets ameliorated lesions in age-related macular degeneration (AMD) and diabetic retinopathy (DR). Fecal microbiota transplantation confirmed microbial causality but revealed donor-dependent effects, and engineered Lactobacillus expressing angiotensin-converting enzyme 2 (ACE2) or Ang-(1-7) preserved retinal integrity in diabetic models.

CONCLUSIONS: Microbial dysbiosis acts as a common driver of immune-metabolic dysfunction in blinding eye diseases. Microbiome-targeted strategies show promising efficacy in experimental systems, but large, longitudinal human trials are needed for clinical translation.},
}

Humans
*Gastrointestinal Microbiome/physiology/immunology
Animals
Probiotics/therapeutic use
Dysbiosis
*Immunomodulation
*Eye Diseases/therapy/microbiology/immunology

@article {pmid41459968,
year = {2025},
author = {Nishimura, Y and Okumura, K and Oiki, S and Ogura, K and Hashimoto, W},
title = {Molecular evolution and diversity of isomerase-reductase clusters involved in the bacterial metabolism of glycosaminoglycans.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0081725},
doi = {10.1128/msphere.00817-25},
pmid = {41459968},
issn = {2379-5042},
abstract = {Glycosaminoglycans (GAGs), comprising uronic acids and amino sugars, are widely distributed in human tissues such as the intestine and oral cavity. Various bacteria colonize these tissues by assimilating GAGs. During GAG degradation, 4-deoxy-l-threo-5-hexosulose uronate (DHU) is produced. Pectin, an abundant plant component, is also degraded into DHU. DHU is metabolized in a stepwise manner by the isomerase KduI or its nonhomologous isofunctional enzyme DhuI, followed by the reductase KduD or DhuD, belonging to the same reductase-dehydrogenase family. Previous studies have found that the genes encoding isomerase and reductase (kduI-kduD and dhuD-dhuI, respectively) are usually organized in clusters. Therefore, it was believed that the kduI-kduD and dhuD-dhuI clusters evolved independently. However, the discovery of a hybrid kduI-dhuD cluster raised questions regarding the evolution of these clusters. This study investigated the diversity of clusters through a pan-genomic phylogenetic analysis across 3,550 bacterial strains. Among 16 possible cluster structures, 10 types were involved in DHU metabolism. Bacteroidota possessed a hybrid-type kduI-dhuD cluster, while Bacillota, but not Pseudomonadota or Bacteroidota, possessed the cluster dhuD-dhuI. Using public data sets from the human fecal microbiome and environmental habitats, we detected the prevalence of kduI-dhuD and dhuD-dhuI clusters in gut microbes. Although DHU is generated from oligomerized GAG degradation by unsaturated glucuronyl hydrolase (UGL), the UGL gene was frequently found in pathogenic strains containing kduD-kduI, dhuD-dhuI, kduI-dhuD, or dhuD-kduI, indicating that the acquisition of these clusters is advantageous for human colonization.IMPORTANCEGlycosaminoglycans (GAGs), crucial components of the extracellular matrix, play vital roles in host infection by pathogenic bacteria and host colonization by commensal bacteria. The dhuD-dhuI cluster is well conserved within certain phyla, and it appears to have a strong association with GAG metabolism. In contrast, kduI-containing clusters are more widely distributed across bacterial species. Based on the possession ratios of genes encoding the enzymes involved in the production of 4-deoxy-l-threo-5-hexosulose uronate, this study indicates that the substrates differ depending on the specific cluster type.},
}

@article {pmid41459926,
year = {2025},
author = {Bu, F and Zhang, K and Song, B and He, L and Lu, Z and Yuan, X and Chen, C and Jiang, F and Tao, Y and Zhang, W and Zhang, D and Chen, Y and Wang, Q},
title = {Akkermansia muciniphila alleviates experimental colitis through FXR-mediated repression of unspliced XBP1.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0158925},
doi = {10.1128/msystems.01589-25},
pmid = {41459926},
issn = {2379-5077},
abstract = {UNLABELLED: Endoplasmic reticulum (ER) stress-related mucin depletion could be involved in the pathogenesis of ulcerative colitis (UC). Akkermansia muciniphila (A. muciniphila) uses mucin as its sole energy source and shows potential in the treatment of colitis. However, the effects and underlying mechanisms of A. muciniphila on colonic epithelial ER stress in colitis are largely unknown. Colitis was induced by adding 2.5% dextran sulfate sodium (DSS) in drinking water. Mice were orally administered A. muciniphila (3*10[^]7, 3*10[^]8 cfu/day) once daily for 10 days during DSS intervention. Ultra high performance liquid chromatography q-exactive orbitrap high-resolution mass spectrometry (UHPLC-Q-Orbitrap-HRMS)-based metabolomic analyses were performed on feces. 16S rRNA sequencing was used to quantify and characterize the gut microbiota of mice. Metabolomic analysis showed that P-hydroxyphenyl acetic acid (p-HPAA), the metabolite with the highest variable importance in projection (VIP) score that was elevated by A. muciniphila, was negatively correlated with acetic acid levels and exhibited a potential inhibitory effect on ER stress. Additionally, A. muciniphila supplementation decreases the abundance of Parasutterella, a genus implicated in bile acid homeostasis. By restoring the levels of deoxycholic (DCA) and ursodeoxycholic acid (UDCA), A. muciniphila administration normalized the bile acid pool size and composition altered by colitis. A. muciniphila supplementation protected colon shortening and histological injury in wild-type (WT) mice, but not in farnesoid X receptor-null (FXR[-/-]) mice. Mechanistically, our results demonstrate that A. muciniphila alleviates DSS-induced colitis by targeting inositol requiring enzyme 1α(IRE1α) and unspliced XBP1 (XBP1u) within the ER stress pathway, with the regulation of XBP1u being FXR-dependent. Supplementation with A. muciniphila at appropriate doses may, thus, offer a promising therapeutic strategy for Ulcerative colitis (UC).

IMPORTANCE: UC is a chronic inflammatory disease in which inflammation begins in the rectum and extends proximally throughout the colon. A.muciniphia is significantly reduced in UC patients and shows promise as a next-generation probiotic. However, the mechanisms behind its protective effects are not fully understood. Our study reveals that A. muciniphila alleviates experimental colitis by reshaping the gut microbiome and correcting imbalances in bile acid metabolism. Crucially, we identify a novel mechanism where A. muciniphila acts through the host bile acid receptor FXR to suppress a specific ER stress pathway (XBP1u) in colon cells, thereby helping to restore the intestinal barrier. These findings provide a scientific basis for using A. muciniphila as a targeted therapeutic strategy for UC.},
}

@article {pmid41459925,
year = {2025},
author = {Ruzickova, M and Palkovicova, J and Nesporova, K and Rysava, M and Pariza, R and Krejci, S and Literak, I and Dolejska, M},
title = {From ecology to evolution: plasmid- and colicin-mediated persistence of antibiotic-resistant Escherichia coli in gulls.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0166325},
doi = {10.1128/msystems.01663-25},
pmid = {41459925},
issn = {2379-5077},
abstract = {UNLABELLED: Antimicrobial resistance (AMR) in wildlife is an emerging concern within the One Health concept. Gulls, due to their synanthropic behavior and long-distance migration, are recognized as vectors and secondary reservoirs of resistant bacteria. These birds can facilitate the environmental spread of resistant strains across ecosystem boundaries. Understanding their role in shaping microbial communities is essential for assessing the broader ecological impact. This study investigates the persistence and competitive dynamics of cephalosporin-resistant Escherichia coli in Caspian gulls (Larus cachinnans) captured at their breeding colony at a water reservoir and subsequently monitored in captivity for three months, representing the longest in vivo experiment of its kind conducted on wild birds. We observed sustained colonization and long-term shedding of resistant E. coli throughout the entire study, marking the longest documented carriage of resistant bacteria in wild birds to date. Notably, rapid dissemination of various E. coli sequence types (STs) with CTX-M-1 was observed, with ST11138 rapidly outcompeting other strains, including the initially dominant ST11893. Genomic analyses revealed that ST11138 harboured F24:A-:B1 and IncI1/ST3/CTX-M-1 plasmids encoding colicins and corresponding immunity genes, likely conferring a competitive advantage. Our findings underscore the role of bacteriocin-mediated interactions in shaping microbial communities and highlight the importance of plasmid-encoded traits in the persistence of resistant strains in wildlife. Importantly, our findings underscore the ecological novelty of longitudinal in vivo tracking of AMR persistence in natural hosts and highlight the need to consider ecological and microbiome-level interactions when assessing the environmental dimension of AMR under the One Health concept.

IMPORTANCE: Antimicrobial resistance (AMR) in wildlife is an emerging concern within the One Health framework, with gulls recognised as important vectors and secondary reservoirs of resistant bacteria. Due to their synanthropic behavior and long-distance migration, these birds can facilitate the spread of resistant strains across ecosystems. However, the role of wildlife in resistance dynamics remains underexplored, especially in long-term, natural settings. Our study is unique in its scope and duration, representing the longest in vivo experiment of its kind conducted on wild birds. By capturing these processes in live hosts under naturalistic conditions and across an extended period, our study provides rare and ecologically grounded insights into how AMR is maintained outside clinical or laboratory settings. Our findings show sustained colonisation and long-term shedding of resistant E. coli, with strain ST11138 outcompeting others. Genomic analyses reveal plasmid-encoded traits, highlighting the ecological and evolutionary mechanisms underlying resistance maintenance in wildlife.},
}

@article {pmid41459804,
year = {2026},
author = {van Kalkeren, CAJ and van Deuren, T and Coenjaerds, MMJ and Galazzo, G and Barnett, DJM and Penders, J and Hartmann, B and Holst, JJ and Canfora, EE and Blaak, EE},
title = {Effects of a slowly fermentable fiber mixture against the background of a high-protein diet on insulin sensitivity and metabolic health in individuals with overweight: a randomized, placebo-controlled trial.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2606473},
doi = {10.1080/19490976.2025.2606473},
pmid = {41459804},
issn = {1949-0984},
mesh = {Humans ; *Dietary Fiber/metabolism/administration & dosage ; Male ; *Overweight/metabolism/diet therapy/microbiology ; *Insulin Resistance ; Female ; Adult ; Fermentation ; Middle Aged ; Gastrointestinal Microbiome ; *Diet, High-Protein ; Fatty Acids, Volatile/metabolism ; Dietary Supplements ; Obesity/metabolism ; Solanum tuberosum/chemistry ; },
abstract = {The gut microbiota ferments dietary fibers, producing short-chain fatty acids (SCFA). Enhanced SCFA production in the distal colon has been linked to improved cardiometabolic health. However, most fibers are fermented proximally, resulting in increased protein fermentation distally, producing metabolites putatively harmful to metabolic health. This 12-week randomized, placebo-controlled trial aimed to improve metabolic health through increasing distal SCFA production while inhibiting proteolytic fermentation using a fiber supplement that increased distal SCFA production in vitro. We assessed the effects of daily potato fiber/sugar beet pectin supplementation (fiber, n = 19) versus maltodextrin (placebo, n = 21), both added to a high-protein diet (25E% protein, ±45% plant-based), on peripheral insulin sensitivity (IS) in adults with overweight/obesity. Secondary outcomes included tissue-specific IS, body composition, microbial composition and functionality, substrate metabolism, and gut permeability. Peripheral IS tended to decrease after fiber supplementation compared to placebo (p = 0.081), while whole-body IS significantly decreased (p = 0.034). Fiber mitigated the increase in insulin-mediated carbohydrate oxidation (p = 0.027) and decrease in fat oxidation (p = 0.006) that occurred in the placebo group. Additionally, fiber prevented an increase in protein oxidation (p = 0.048), while increasing colonic gut permeability (p = 0.046) and plasma interleukin-6 (p = 0.025). Body composition, microbial composition, and fecal and circulating metabolites remained unchanged. In conclusion, fibers combined with a high-protein diet reduced (peripheral) IS and decreased metabolic flexibility compared to placebo. Reduced protein oxidation after fiber may reflect diminished amino acid bioavailability. Additionally, coadministration of fiber and protein may compromise gut barrier function and inflammatory responses. More research investigating the interplay between dietary fibers and proteins is needed.},
}

Humans
*Dietary Fiber/metabolism/administration & dosage
Male
*Overweight/metabolism/diet therapy/microbiology
*Insulin Resistance
Female
Adult
Fermentation
Middle Aged
Gastrointestinal Microbiome
*Diet, High-Protein
Fatty Acids, Volatile/metabolism
Dietary Supplements
Obesity/metabolism
Solanum tuberosum/chemistry

@article {pmid41459742,
year = {2025},
author = {Kwon, Y and Choi, J and Kim, SH and Kim, PJ and Lee, SM and Cha, JK and Park, H and Kang, JW and Jo, SM and Kwak, YS and Kim, D and Kim, WJ and Lee, JH and Ryu, CM},
title = {Rice gs3 allele and low-nitrogen conditions enrich rhizosphere microbiota that mitigate methane emissions and promote beneficial crop traits.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf284},
pmid = {41459742},
issn = {1751-7370},
abstract = {Methane emissions from rice paddies represent a critical environmental concern in agriculture. Although genetic strategies for mitigating emissions have gained attention, the specific microbial and molecular mechanisms remain underexplored. Here, we investigated how the gs3 loss-of-function allele in the near-isogenic rice line Milyang360 modulates rhizosphere and endosphere microbial communities under distinct nitrogen regimes. Field experiments revealed that Milyang360 consistently reduced methane emissions compared with its parental line, Saeilmi, particularly under low-nitrogen conditions. Integrated plant transcriptomic and rhizosphere metagenomic analyses, including the reconstruction of Metagenome-Assembled Genomes, demonstrated that the gs3 allele upregulated genes related to root hair elongation or promoting microbial symbiosis. This physiological change limited substrate availability for methanogens and facilitated the colonization by beneficial microorganisms. Consequently, we observed a functional shift in the microbiome, characterized by the enrichment of methanotrophs and nitrogen-fixing bacteria. This microbial restructuring was most prominent under low-nitrogen conditions, indicating a strong genotype by environment interaction. Our findings highlight the gs3 allele's dual role in reducing methane emissions and improving nitrogen use efficiency by recruiting a beneficial microbiome. This study provides a clear mechanistic link between a plant gene and rhizosphere ecology, offering a promising genetic target for developing sustainable, low emission rice cultivars.},
}

@article {pmid41459728,
year = {2026},
author = {Parthasarathy, A and Li, T and Edelblum, KL},
title = {Crosstalk between the microbiota and intestinal γδ T cell compartments in health and IBD.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2604908},
doi = {10.1080/19490976.2025.2604908},
pmid = {41459728},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Inflammatory Bowel Diseases/immunology/microbiology ; Humans ; *Receptors, Antigen, T-Cell, gamma-delta/immunology/metabolism/genetics ; *Intestinal Mucosa/immunology/microbiology ; *Intraepithelial Lymphocytes/immunology ; Mice ; Bacteria/immunology ; Peyer's Patches/immunology/microbiology ; *T-Lymphocytes/immunology ; },
abstract = {Unconventional T cells expressing the γδ T cell receptor (TCR) are abundant within the intestine and largely function as 'first responders' to injury, infection and inflammation. To this end, murine γδ T cells are highly compartmentalized within the intestinal mucosa based on the expression of their Vγ chain and their effector function. The activation status also differs among these γδ T cell populations to ensure a timely and appropriate response within their local microenvironment. In this review, we will examine the role of γδ T cell populations in the epithelium (i.e. intraepithelial lymphocytes), the lamina propria and Peyer's patches and discuss the influence of the gut microbiota on the maintenance and effector function of each compartment. We will also highlight how γδ T cells contribute to the host response to luminal bacteria and how this reciprocal crosstalk is disrupted in the context of inflammatory bowel disease (IBD). An enhanced understanding of how γδ T cells function within distinct mucosal compartments and their regulation by commensal bacteria may lead to the development of novel microbiome-based therapies for IBD.},
}

Animals
*Gastrointestinal Microbiome/immunology
*Inflammatory Bowel Diseases/immunology/microbiology
Humans
*Receptors, Antigen, T-Cell, gamma-delta/immunology/metabolism/genetics
*Intestinal Mucosa/immunology/microbiology
*Intraepithelial Lymphocytes/immunology
Mice
Bacteria/immunology
Peyer's Patches/immunology/microbiology
*T-Lymphocytes/immunology

@article {pmid41459531,
year = {2025},
author = {Nikolaidis, CG and Gyriki, D and Stavropoulou, E and Karlafti, E and Didangelos, T and Tsigalou, C and Thanopoulou, A},
title = {Targeting the TLR4 axis with microbiota-oriented interventions and innovations in diabetes therapy: a narrative review.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1701504},
pmid = {41459531},
issn = {1664-3224},
mesh = {Humans ; *Toll-Like Receptor 4/metabolism/immunology ; *Gastrointestinal Microbiome/immunology/drug effects ; Fecal Microbiota Transplantation ; *Diabetes Mellitus, Type 2/therapy/immunology/microbiology/metabolism ; Animals ; Signal Transduction ; NF-kappa B/metabolism ; *Diabetes Mellitus, Type 1/therapy/immunology/microbiology/metabolism ; Insulin Resistance ; },
abstract = {The gut microbiota-Toll-like receptor 4(TLR4)-nuclear factor kappa B(NF-κB) signaling is a key controller of low-grade chronic inflammation and insulin resistance in type 1 (T1DM) and type 2 diabetes mellitus (T2DM). While TLR4-mediated inflammation contributes to both T1DM and T2DM, the bulk of microbiota-targeted interventions have been studied in T2DM. The focus of the current review is on T2DM, with relevant parallels in T1DM noted where appropriate. Modulation of this pathway by dietary natural bioactive molecules, fecal microbiota transplantation (FMT), and technological innovations hold therapeutic promise for the reconstitution of metabolic and immune homeostasis. Agents like celastrol, berberine, paeoniflorin, and licorice extract exhibit anti-inflammatory and antidiabetic effects by TLR4/Myeloid differentiation primary response 88(MyD88)/NF-κB signaling inhibition. FMT enhanced β-cell function and insulin sensitivity with evidence of immune-metabolic modulation. New technologies, like ingestible biosensors and gut-on-chip platforms, allow real-time monitoring and precision modulating of the microbiota. Gastric bypass-induced microbial remodeling is linked to long-term glycemic benefit. Pharmacological, surgical, and technological manipulation of gut microbiota-immune interactions is a potential complementary strategy to diabetes. The future encompasses personalized microbiota-matching, controlled FMT regimens, and incorporation of digital therapeutics into microbiome-based precision medicine.},
}

Humans
*Toll-Like Receptor 4/metabolism/immunology
*Gastrointestinal Microbiome/immunology/drug effects
Fecal Microbiota Transplantation
*Diabetes Mellitus, Type 2/therapy/immunology/microbiology/metabolism
Animals
Signal Transduction
NF-kappa B/metabolism
*Diabetes Mellitus, Type 1/therapy/immunology/microbiology/metabolism
Insulin Resistance

@article {pmid41459520,
year = {2025},
author = {Ariizumi, H and Shimazui, M and Ogawa, C and Kaneki, M and Saito, N and Mura, E and Suzuki, R and Tsurui, T and Iriguchi, N and Ishiguro, T and Hirasawa, Y and Shimokawa, M and Ohkuma, R and Kubota, Y and Horiike, A and Wada, S and Yoshimura, K and Murakami, K and Tsunoda, T},
title = {Vinegar intake in patients undergoing immune checkpoint inhibitor therapy: food frequency questionnaire study.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1640603},
pmid = {41459520},
issn = {1664-3224},
mesh = {Humans ; Female ; Male ; *Immune Checkpoint Inhibitors/therapeutic use ; Aged ; Middle Aged ; *Acetic Acid/administration & dosage ; *Neoplasms/drug therapy/immunology ; Surveys and Questionnaires ; Gastrointestinal Microbiome ; Dietary Fiber ; Treatment Outcome ; Aged, 80 and over ; Japan ; Adult ; },
abstract = {INTRODUCTION: The gut microbiome is increasingly recognized as a key modulator of immune checkpoint inhibitor (ICI) efficacy. Dietary factors, particularly fibers, may influence the microbiome and thus affect the ICI response. Although Western studies have suggested a link between high fiber intake and better outcomes, this relationship remains unclear in Japanese populations with different dietary habits. This study investigated dietary components associated with ICI response in Japanese patients with cancer.

METHODS: In total, 32 patients with carcinomas treated with ICIs were enrolled. Nutritional customs before ICI infusion were analyzed using a food frequency questionnaire.

RESULTS: Among the 331 dietary items, only vinegar (acetic acid) intake showed an independent association with the treatment response. Higher vinegar consumption correlated with significantly lower odds of nonresponse (P = 0.017). In contrast, total and fermentable dietary fiber intake showed no significant association with ICI efficacy or survival outcomes.

CONCLUSIONS: Higher vinegar intake is associated with better ICI response in Japanese patients, whereas fiber has a limited effect. Thus, tailored dietary strategies are needed for optimal outcomes.},
}

Humans
Female
Male
*Immune Checkpoint Inhibitors/therapeutic use
Aged
Middle Aged
*Acetic Acid/administration & dosage
*Neoplasms/drug therapy/immunology
Surveys and Questionnaires
Gastrointestinal Microbiome
Dietary Fiber
Treatment Outcome
Aged, 80 and over
Japan
Adult

@article {pmid41459433,
year = {2025},
author = {Bhojiya, AA and Saurabh, A and Jain, D},
title = {Editorial: Microbial therapeutics: harnessing the human microbiome for disease treatment and prevention.},
journal = {Frontiers in medical technology},
volume = {7},
number = {},
pages = {1751147},
doi = {10.3389/fmedt.2025.1751147},
pmid = {41459433},
issn = {2673-3129},
}

@article {pmid41459350,
year = {2025},
author = {Agusti, S and Alothman, A and Jin, P and Stanschewski, CS and Díaz-Rúa, R and Emwas, AH and Singh, U and Jaremko, M},
title = {Host metabolite production and microbiome dynamics: effects of long-term diatom adaptation to warming.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf103},
pmid = {41459350},
issn = {2730-6151},
abstract = {Marine diatoms contribute significantly to global oceanic primary production, constituting ~25% of earth production but are susceptible to the impacts of ocean warming. While organisms' adaptation to rising temperatures may mitigate these impacts, it could also disrupt species interactions, including those between hosts and their microbiomes. In our study, we examined thermal performance and diversity changes in the microbiome of the tropical diatom Chaetoceros tenuissimus after long-term adaptation to ambient (LA) and warming (LW) temperatures. We observed notable shifts in the metabolomic profile, with amino acids accumulating after LW adaptation and sugars accumulating after LA, while lipids content remained unchanged. After LW, the microbiota increased maximum growth rate without changing its temperature optimum. Roseovarius sp. dominated the microbiome community at both LA (49.6%) and LW strains (42.8%) proving a strong partnership. Extinctions were highest under warming occurring in the low-abundant genera, but different partners developed increasing richness, with changes induced in the core microbiome. Short-term warming, however, resulted in decreased richness. Beta diversity was associated with long-term adaptation instead of assay temperature. Our findings align with general plant species association models, suggesting that long-term evolution of mutualisms enhances diversity and strength, particularly under warming in the marine partnership studied here. Our experimental results highlight the importance of examine long-term coevolution of host- microbiome partnerships to improve our understanding of consequences of warming.},
}

@article {pmid41459349,
year = {2025},
author = {Nandi, S and Stephens, TG and Walsh, K and García-Camps, R and Villalpando, MF and Sellares-Blasco, RI and Zubillaga, AL and Croquer, A and Bhattacharya, D},
title = {Shifts in the microbiome and virome are associated with stony coral tissue loss disease (SCTLD).},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf226},
pmid = {41459349},
issn = {2730-6151},
abstract = {Stony coral tissue loss disease (SCTLD) is a rapidly spreading lethal coral disease, the etiology of which remains poorly understood. In this study, using deep metagenomic sequencing, we investigated microbial and viral community dynamics associated with SCTLD progression in the Caribbean stony coral Diploria labyrinthiformis. We assembled 264 metagenome-assembled genomes and correlated their abundance with disease phenotypes, which revealed significant shifts in both the prokaryotic microbiome and virome. Our results provide clear evidence of microbial destabilization in diseased corals, suggesting that microbial dysbiosis is an outcome of SCTLD progression. We identified DNA viruses in our dataset that increase in abundance in SCTLD-affected corals and are present in existing coral data from other Caribbean regions. In addition, we identified the first putative instance of asymptomatic/resistant SCTLD-affected corals. These are apparently healthy colonies that share the viral profile of diseased individuals. However, these colonies contain a different prokaryotic microbiome than do diseased corals, suggesting microbe-induced resilience (i.e. beneficial microbiome) to SCTLD. Finally, utilizing differential abundance analysis and gene inventories, we propose a mechanistic model of SCTLD progression, in which viral dynamics may contribute to microbiome collapse. These findings provide novel insights into SCTLD pathogenesis and offer consistent molecular signals of disease across diverse geographic sites, presenting new opportunities for disease monitoring and mitigation.},
}

@article {pmid41459229,
year = {2025},
author = {Mulec, J and Pašić, L and Oarga-Mulec, A},
title = {Metabolic traits of sediment bacteria in karst caves in the light of environmental changes.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1724116},
pmid = {41459229},
issn = {1664-302X},
abstract = {INTRODUCTION: Karst subterranean systems are vulnerable ecosystems that have not yet been studied adequately at the microbial functional level. Cave sediments deposited over different time periods host diverse microbial communities that play a critical role in nutrient cycling and pollutant degradation.

METHODS: In this study, we investigated microbial diversity and metabolic capacity in recently deposited alluvial sediments and an ancient palaeo-river deposit in a karst cave system. Using 16S rRNA gene amplicon metagenomic analysis, community-level physiological profiling (CLPP), and chemical characteristics of the environment, the influence of key environmental factors on microbial community composition and substrate degradation, concentrating particularly upon sediment age, oxygen availability, and temperature, was assessed.

RESULTS: The results showed different microbiome compositions and metabolic characteristics between sites. The old alluvial sediment exhibited low taxonomic and functional diversity, accompanied by elevated heavy-metal concentrations, suggesting that sediment age might act as a geochemical filter, limiting microbial function. In contrast, a periodically flooded site showed high metabolic versatility and taxonomic diversity, emphasizing the ecological role of hydrological pulses in maintaining functional microbial diversity. CLPP metrics linked community structure to functional potential, revealing adaptive traits in key taxa such as Polaromonas, Methylibium, and Beggiatoa.

DISCUSSION: These results demonstrated the value of integrating functional and taxonomic approaches in subsurface environments and provide insights into microbial resilience, biogeochemical processes, and the potential for applied environmental use.},
}

@article {pmid41459217,
year = {2025},
author = {Li, P and Wang, M and Zhang, H and Gao, X and Chen, L and Chen, H and Xu, Q and Chen, W and Liu, W and Dai, M},
title = {Integrative metagenomic and metabolomic profiling identifies gut microbial and metabolite signatures associated with lymph node metastasis in pancreatic cancer.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1706084},
pmid = {41459217},
issn = {1664-302X},
abstract = {BACKGROUND: Lymph node metastasis (LNM) is a prognostic factor in pancreatic cancer. The association between the gut microbiota and LNM remains unexplored. This study aimed to characterize the gut microbiota and metabolomic profiles associated with LNM and to investigate their potential as predictive biomarkers.

METHODS: Fecal samples from pancreatic cancer patients undergoing surgery were analyzed using metagenomic sequencing and untargeted metabolomics. The patients were categorized into LNM and non-LNM (NLNM) groups. Differential microbiome taxa were analyzed using the DESeq2 package. Random forest predictive models were developed based on metagenomic and metabolomic data, with performance assessed using leave-one-out cross-validation (LOOCV).

RESULTS: A total of 26 patients with LNM and 29 patients without LNM were included. Principal coordinates analysis (PCoA) revealed significant differences in microbiota composition between the two groups (Anosim, p = 0.047). The absolute counts of Ruminococcus gnavus and Blautia wexlera were significantly decreased in LNM. Tryptophan-derived metabolites, indole-3-lactic acid (3-ILA) and indole-3-acrylic acid (3-IA), were downregulated in LNM. Functional pathway analysis showed downregulation of tryptophan metabolism in LNM, while cancer-related pathways were upregulated. Correlation analysis revealed a significant positive association between Ruminococcus gnavus and 3-ILA/3-IA levels. Moreover, Ruminococcus gnavus was positively correlated with CD8[+] T cells. Predictive models based on the gut microbiota and metabolites distinguished LNM from NLNM, with AUC values of 0.854 and 0.940, respectively.

CONCLUSION: The gut microbiota and metabolites exhibit significant alterations during lymph node metastasis in pancreatic cancer, especially Ruminococcus gnavus, Blautia wexlera, and tryptophan metabolites (3-ILA and 3-IA). Gut microbial and metabolite signatures may serve as potential non-invasive biomarkers for predicting LNM in pancreatic cancer. Further functional validation is required to determine whether and how the gut microbiota and metabolites may mediate lymph node metastasis.},
}

@article {pmid41459215,
year = {2025},
author = {Liu, P and Zhang, Y and Chen, X and Tang, L and Xu, W and Wang, G and Zhang, D and Liu, J},
title = {Effect of IFN-τ on intestinal flora and metabolomics of Escherichia coli-mediated endometritis in mice.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1687781},
pmid = {41459215},
issn = {1664-302X},
abstract = {Endometritis is a common reproductive disease in dairy cows, which can lead to low fertility or infertility and cause significant economic losses to the dairy farming industry. IFN-τ is a type I interferon that may exert significant anti-inflammatory effects in inflammatory diseases. With breakthroughs in microbial mapping sequencing and metabolomics, the role between gut flora and host metabolism and disease has been revealed from a completely new perspective. Therefore, the aim of this study was to investigate the role of IFN-τ in a mouse model of E. coli-induced endometritis by 16S rRNA sequencing and LC-MS untargeted metabolomics, the results showed that IFN-τ could affect the flora structure of the mouse intestine. The E. coli-induced endometritis in mice was found to be associated with five different metabolites and three potential metabolic pathways by LC-MS non-targeted metabolomics, which were the major players in the metabolic pathways, namely Arginine biosynthesis, Pyruvate metabolism, Arginine and proline metabolism. This may be an important metabolic pathway for IFN-τ intervention in endometritis mice. Combining the results of gut flora and metabolomics analyses suggest that changes in metabolic pathways may be influenced by gut flora. We hypothesize that IFN-τ is likely to exert its anti-inflammatory effects by regulating the levels of Oscillospira and Clostridium flora in the gut, which in turn affects the expression of five differential metabolites in uterine tissues.},
}

@article {pmid41459155,
year = {2025},
author = {Starodubova, A and Leonov, G and Shaposhnikova, N and Varaeva, Y and Livantsova, E and Fotin, D and Kirichenko, T and Bagheri Ekta, M and Markina, Y and Koshechkin, S and Orekhov, A and Nikityuk, D},
title = {Gut and oral microbiome profiles in patients with obesity and ischemic heart disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1695279},
pmid = {41459155},
issn = {2235-2988},
mesh = {Humans ; *Obesity/microbiology/complications ; Male ; *Myocardial Ischemia/microbiology/complications ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; *Mouth/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Aged ; *Microbiota ; Adult ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/chemistry/genetics ; },
abstract = {BACKGROUND: Ischemic heart disease (IHD) and obesity are major contributors to global mortality. Both conditions are linked to systemic inflammation, dyslipidemia, and microbiota alterations. This study examines the relationship between the composition of the gut and oral microbiota, obesity, and IHD to gain insight into the interconnections between these factors.

METHODS: The study included 182 participants divided into four groups based on obesity and IHD status. Anthropometric and biochemical analyses were performed. Oral and gut microbiomes were analyzed using 16S rRNA sequencing.

RESULTS: Obesity and IHD were associated with distinct microbiota compositions. Obesity-IHD subjects showed elevated levels of gut Streptococcus, Intestinibacter, alongside reduced Citrobacter, Ruthenibacterium, Parabacteroides, and Flavonifractor. The oral microbiota exhibited decreased Alloprevotella, Capnocytophaga, Prevotellamassilia, and Campylobacter in Obesity-IHD. Correlation analysis highlighted associations between microbial taxa (e.g., Blautia, Oscillibacter) and clinical parameters like BMI, blood pressure, and cholesterol.

CONCLUSIONS: This study demonstrates that obesity and IHD are linked to unique microbiota alterations. Microbial dysbiosis may contribute to the pathogenesis of these conditions and should be considered as a therapeutic target in the development of personalized treatment strategies of the obesity and associated cardiovascular complications.},
}

Humans
*Obesity/microbiology/complications
Male
*Myocardial Ischemia/microbiology/complications
Female
*Gastrointestinal Microbiome
Middle Aged
RNA, Ribosomal, 16S/genetics
Dysbiosis/microbiology
*Mouth/microbiology
*Bacteria/classification/genetics/isolation & purification
Aged
*Microbiota
Adult
DNA, Bacterial/genetics/chemistry
DNA, Ribosomal/chemistry/genetics

@article {pmid41459154,
year = {2025},
author = {Chen, W},
title = {Editorial: Natural compounds from plant: microbiome-targeted therapeutic strategy for gastrointestinal disorders.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1736556},
doi = {10.3389/fcimb.2025.1736556},
pmid = {41459154},
issn = {2235-2988},
}

@article {pmid41459150,
year = {2025},
author = {Chavez-Bueno, S and Lawrence, SM},
title = {Editorial: Advancing understanding of neonatal bacterial infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1746698},
pmid = {41459150},
issn = {2235-2988},
}

@article {pmid41459147,
year = {2025},
author = {Tye, KD and Liu, X and Huang, C and Li, C and Wu, C and Lin, J and Yu, Y and Lin, X},
title = {Probiotic modulation of maternal gut and milk microbiota and potential implications for infant microbial development in the perinatal period.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1715989},
pmid = {41459147},
issn = {2235-2988},
mesh = {Humans ; *Probiotics/administration & dosage ; Female ; Pregnancy ; *Gastrointestinal Microbiome/drug effects ; *Milk, Human/microbiology ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Adult ; Infant, Newborn ; Infant ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: Probiotics are live microorganisms that may enhance or restore gut microbiota. They are often recommended during pregnancy and infancy for potential benefits, but evidence is inconclusive. This study aimed to investigate probiotic supplementation's effects on maternal and infant gut and milk microbiota and its link to nutrient intake during pregnancy.

METHOD: A total of 23 pregnant women were enrolled and divided into a probiotic group (n = 11) and a non-probiotic control group (n=12). Probiotic effects were evaluated through fecal and milk microbiota analysis via 16S rRNA gene sequencing. Nutrient intake data were collected to assess differences linked to probiotics. Key microbiota diversity and richness were analyzed using linear discriminant analysis effect size (LEfSe) and weighted gene co-expression network analysis (WGCNA) to explore associations with diet and sample characteristics. Predictive microbial pathway characteristics were identified using time series analysis, random forest algorithms, and logistic regression models.

RESULTS: Nutrient intake did not significantly differ between groups, and overall microbial diversity and richness were stable. However, LEfSe revealed distinct genera in both maternal gut and milk microbiota linked to probiotic intake. WGCNA identified microbial modules correlated with specific nutrient patterns and sampling conditions. Predictive genus clusters associated with probiotics demonstrated robust classification performance, suggesting functional shifts in microbial communities with potential implications for immune programming in early life.

CONCLUSION: Probiotic supplementation during pregnancy may modulate key microbial taxa in maternal gut and milk, potentially influencing microbial recognition and immune signaling in the maternal-infant dyad. These findings highlight complex diet-microbiota-immune interactions within reproductive and lactational systems, offering insights into strategies for enhancing maternal and neonatal health resilience.},
}

Humans
*Probiotics/administration & dosage
Female
Pregnancy
*Gastrointestinal Microbiome/drug effects
*Milk, Human/microbiology
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Adult
Infant, Newborn
Infant
Bacteria/classification/genetics/isolation & purification

@article {pmid41459064,
year = {2025},
author = {Anderson, M and Hrivnak, W and Prak, K and Stockert, A},
title = {Potential effects of cinnamon on cancer prevention and progression.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1717834},
pmid = {41459064},
issn = {2296-861X},
abstract = {Cinnamon has been used medicinally for centuries, but recently in vitro research has suggested it may have a role in cancer prevention and potentially treatment. The search for alternative and subjunctive therapies is essential due to the public demand and the increasing cost of healthcare. Here we review the biologically active components of cinnamon and discuss the methods of potential cinnamon activity against cancer, including: transcription factor regulation and kinase activity. Nuclear Factor kappa B (NFκB) is a stress sensitive transcription factor that regulates transcription of genes involved in tumor progression and is inhibited by cinnamon components. Another way that cinnamon inhibits tumor growth is by suppression of transcription factor activator protein 1 (AP1) which interacts with genes responsible for apoptosis, metastasis and inflammation. Hypoxia-inducible transcription factor 1 (HIF1) and vascular endothelial growth factor (VEGF) are involved in angiogenesis, especially in the tumor microenvironment. The HIF1-VEGF pathway is a target of cinnamaldehyde, a compound found in cinnamon. Nuclear factor erythroid related factor 2 (Nrf2) is also examined and has been indicated to affect cancer progression and potentially provide preventative measures; various cinnamon derivatives target Nrf2. A cinnamaldehyde derivative has been implicated in a reduction of the mitogen-activated protein kinases (MAPKs), which are a group of kinases that regulate proliferation. Additionally, cinnamon components have been tied to cancer prevention by positively affecting the gut microbiome and inhibiting inflammation. The review concludes with a discussion of the future research needed, including the need for clinical studies and potential risk associated with cinnamon intake.},
}

@article {pmid41459062,
year = {2025},
author = {Li, W and Gunn, A and Zheng, X and Ma, J and Sheng, N and Wang, B},
title = {Exploring human milk oligosaccharides: mechanisms linking gut function to cognitive development in human and pig physiology.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1700954},
pmid = {41459062},
issn = {2296-861X},
abstract = {Human milk oligosaccharides (HMOs) are emerging as key modulators of host physiology, with growing evidence supporting their role in shaping gut microbial communities and influencing neurocognitive outcomes. This review critically examines the impact of HMOs on gut health and behavioral responses, focusing on the complex relationship between HMOs and host physiology in both human and pigs. Given their anatomical, physiological, and microbiome similarities to humans, pigs serve as a valuable translational model for investigating the functional roles of HMOs. We summarize experimental methodologies employed in HMO research and highlight findings that demonstrate HMO-induced alterations in microbial diversity, gut integrity, and cognitive performance. Potential mechanisms of action, including gut-brain axis signaling, immune modulation, and microbial metabolite production, are explored. This review concludes by identifying current knowledge gaps and proposing future research directions aimed at elucidating HMO structure-function relationships, with implications for advancing both human nutrition and animal health.},
}

@article {pmid41459056,
year = {2025},
author = {Auclair-Ouellet, N and Kassem, O and Bronner, S and Oula, ML and Binda, S},
title = {Leveraging microbiome-based interventions to improve the management of neurodegenerative diseases: evidence for effects along the microbiota-gut-brain axis.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1699884},
pmid = {41459056},
issn = {2296-861X},
abstract = {The microbiota-gut-brain axis (MGBA) has recently emerged as a useful model for the understanding of the onset and progression of neurodegenerative diseases (NDDs). Microbiome-based interventions using biotic supplements (probiotics, prebiotics, synbiotics, postbiotics) can modulate the MGBA and constitute relevant solutions to help reduce the risk of neurological changes associated with NDDs and manage symptoms. This narrative review provides a summary of the functioning of the MGBA and of its interactions with disease processes involved in the onset and progression of NDDs. Microbiome-based interventions and their mechanisms of action are reviewed, and important considerations for the design of interventions are discussed. Next, preclinical and clinical studies on the potential of microbiome-based interventions in Alzheimer's disease (AD), Parkinson's disease (PD), Multiple Sclerosis (MS), Amyotrophic Lateral Sclerosis (ALS), and Huntington's disease (HD) are reviewed. Evidence related to biomarkers of pathology (e.g., beta-amyloid or alpha-synuclein protein depositions), neuroinflammation, and metabolic activity is summarized, along with emerging evidence for the improvement of clinical symptoms and disease trajectories. Overall, preclinical studies show that microbiome-based supplements have significant positive effects on mechanisms and pathways involved in the pathophysiology of NDDs. Clinical studies show that these interventions provide important benefits both in terms of biomarkers and clinical symptoms. However, evidence is limited in some key clinical areas, such as mental wellbeing in AD and cognition in PD, and for the management of clinical symptoms in ALS and HD overall. Gaps in knowledge and open questions as well as perspectives for future research are discussed.},
}

@article {pmid41458968,
year = {2025},
author = {Jing, Y and Huicong, D and Xuanchi, G and Cao, L and Huanhuan, Z and Yongze, G},
title = {Fraxin modulates lipid metabolism as well as gut flora to avert NAFLD.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1657966},
pmid = {41458968},
issn = {1663-9812},
abstract = {BACKGROUND: Public healthcare systems are heavily burdened by non-alcoholic fatty liver disease (NAFLD), which is the leading "chronic liver disorder" around the globe. Fraxin, a natural compound extracted from Fraxini cortex in traditional Chinese medicine, exerts hepatoprotective effects. However, the mechanism by which fraxin alleviates NAFLD remains elusive. This research looks into fraxin's therapeutic potential in NAFLD management using an integrated experimental and pharmacological strategy.

METHODS: First, network pharmacology was used to identify core therapeutic targets of fraxin for NAFLD. Second, we built protein-protein interaction (PPI) networks, followed by "Gene Ontology (GO)" along with "Kyoto Encyclopedia of Genes and Genomes (KEGG)" pathways. Molecular docking validated the interaction of fraxin with its predicted targets. To confirm fraxin's therapeutic effect in vivo, we built a "methionine-choline-deficient" (MCD) diet-induced NAFLD mouse model. Comprehensive assessments included liver function tests, hepatic triglyceride content, inflammatory marker measurement, mRNA expression for key lipid metabolism enzymes through reverse transcription-polymerase chain reaction, fatty acid translocase/cluster of differentiation 36 (FAT/CD36) expression through Western blotting, and 16S ribosomal RNA sequencing to assess changes in metabolic dysfunction and the gut microbiota.

RESULTS: Network pharmacology identified 34 potential fraxin targets in NAFLD. GO and KEGG analyses suggested that fraxin primarily treats NAFLD by modulating lipid metabolism and atherosclerosis-related signaling pathways. In vivo, fraxin significantly lowered liver index and visceral fat accumulation, reduced serum levels of "interleukin-6 (IL-6)," "aspartate aminotransferase," "tumor necrosis factor-α (TNF-α)" and "alanine aminotransferase," and decreased hepatic TG content. Furthermore, fraxin downregulated IL-6 and TNF-α expression and lowered the gene and protein levels of FAT/CD36, controlling key targets in signaling pathways related to lipid metabolism and atherosclerosis. Additionally, fraxin altered the gut microbial composition, reducing the Firmicutes/Bacteroidota ratio while increasing the abundance of Bacteroidota, Bacteroidia, Bacteroidales, Prevotellaceae, and Alloprevotella. Therefore, fraxin attenuated gut microbiota dysbiosis in mice caused by the MCD diet.

CONCLUSION: Fraxin alleviates MCD diet-induced NAFLD by controlling lipid metabolism as well as restoring the homeostasis of gut microbiota.},
}

@article {pmid41458802,
year = {2025},
author = {Brasse, P and Zerdka, J and Staszkiewicz, K and Staszkiewicz, KK and Piszka, M and Kwapien, E and Bartkowski, J and Kubicka, M and Czarnecki, F},
title = {Intermittent Fasting: Efficacy, Safety, and Its Impact on Body Weight, Glucose Metabolism, and Gut Microbiota.},
journal = {Cureus},
volume = {17},
number = {11},
pages = {e97773},
pmid = {41458802},
issn = {2168-8184},
abstract = {Intermittent fasting (IF) has gained significant attention as a nutritional strategy with potential health-promoting effects. It typically involves periodic restriction of calorie intake or limiting the daily eating window. Growing scientific interest has led to a wide range of clinical and observational research exploring its biological and metabolic impacts. Existing studies suggest that IF may positively influence metabolic health, weight management, and cellular processes. However, the breadth of findings varies, and questions remain regarding its long-term safety and effectiveness across diverse populations, especially individuals with chronic conditions. A comprehensive evaluation of the current evidence is therefore warranted. An analysis of 55 publications, including clinical trials, observational studies, and review articles, was conducted. These sources were examined to assess the effects of various forms of IF on metabolic health, diabetes-related outcomes, gut microbiome composition, and broader physiological functions. Across most studies, IF was associated with moderate but clinically meaningful weight loss, enhanced insulin sensitivity, reductions in blood pressure, and improvements in lipid profiles. Some evidence also pointed to beneficial changes in gut microbiota, decreased oxidative stress, and increased autophagy activity. Comparisons with traditional caloric restriction indicate similar levels of effectiveness and safety, with IF potentially offering better adherence for certain individuals. Despite these promising outcomes, the current evidence base lacks long-term studies and comprehensive evaluations in specific clinical populations, limiting conclusions about sustained benefits and generalizability. IF appears to be a promising approach for the prevention and management of obesity and metabolic disorders. Its combination of physiological benefits and relative ease of implementation makes it an appealing strategy. Nonetheless, further long-term and population-specific research is needed to fully establish its safety, durability, and applicability across diverse groups.},
}

@article {pmid41458699,
year = {2025},
author = {Chavhan, PKB and Sayeed, MS and Saiyad, SS and Shah, MN and Ekambaram, G and Panchal, H and B H, G and Js, S},
title = {Lactose Intolerance in Irritable Bowel Syndrome: Prevalence, Subtype Correlations, and Clinical Predictors in an Indian Cohort.},
journal = {Cureus},
volume = {17},
number = {11},
pages = {e97697},
pmid = {41458699},
issn = {2168-8184},
abstract = {Irritable bowel syndrome (IBS) and lactose intolerance (LI) frequently coexist, complicating diagnosis and management due to overlapping abdominal pain, bloating, and altered bowel habits. This study aimed to quantify LI prevalence in IBS and delineate clinical predictors to inform targeted care. We conducted a single-center observational study (July 2021-December 2022) at a tertiary hospital in North India, enrolling 100 adults with Rome IV-defined IBS. Standardized hydrogen breath testing identified lactose malabsorption; demographic, dietary, and symptom data were collected, and associations were evaluated using chi-square tests and logistic regression with a prespecified α = 0.05. LI was present in 38 (38%) IBS patients in this study. The diarrhea-predominant (IBS-D) subtype showed the strongest association with LI (OR = 5.92; 95% CI 2.1-16.8; p < 0.001), whereas the constipation-predominant (IBS-C) subtype was least affected. Higher habitual lactose intake (≥26 g/day) correlated with greater symptom frequency (p < 0.001). The cohort's mean age was 36.8 ± 11.4 years, and most reported symptoms for ≥1 year, underscoring chronicity. No significant associations were observed with sex or BMI categories. These findings demonstrate that unrecognized LI contributes substantially to symptom burden in Indian IBS populations, particularly IBS-D. Incorporating structured dietary assessment and selective breath testing into diagnostic algorithms can reduce misclassification, avoid unnecessary pharmacotherapy, and enable individualized lactose restriction. The study provides population-specific evidence supporting diet-responsive, precision strategies for IBS care and highlights the value of simple, noninvasive diagnostics in resource-constrained settings. Prospective multicenter trials integrating microbiome and dietary interventions are warranted to refine subtype-specific, nutrition-based management.},
}

@article {pmid41458698,
year = {2025},
author = {Darwish, S and Razdolsky, N and Ditty, K and Torres, A and Mathew, S and Ali, S and Izhar, A and Ghazzawi, J and Phillips, C and Braun, A and Costin, JM},
title = {The Effects of Vaginal Virome on Women's Health: A Scoping Review.},
journal = {Cureus},
volume = {17},
number = {11},
pages = {e97876},
pmid = {41458698},
issn = {2168-8184},
abstract = {While research on the vaginal microbiome (VMB) has focused mainly on its bacteriome, the role of viral communities remains largely understudied. Given the vaginal virome's potential influence on disease susceptibility and progression, understanding its exact role in different health outcomes is crucial. The objective of this scoping review was to analyze studies on the vaginal virome's influence on women's health, the virome's interactions with other microbes, assess the limitations of these studies, and highlight gaps to guide future studies and treatments in the field of gynecological health. The review was conducted using previously gathered literature on the impact of the vaginal virome among reproductive-aged women in developed countries. Articles were sourced from Ovid MEDLINE, Embase, and World of Science using the following search string: vaginal virome AND reproductive health OR infections OR pregnancy outcomes. Articles were screened using the PCC framework as follows: influence of the vaginal virome on women's health (Concept) in women aged 18 and older (Population) in developed countries (Context). Of the 352 articles originally identified, 10 studies met the inclusion criteria and were utilized in this scoping review. The vaginal virome contains a diverse array of viruses and bacteriophages that impact human papillomavirus (HPV) infection persistence and subsequent progression to cervical cancer, pregnancy outcomes, and the inflammatory response. In bacterial vaginosis, reductions in Lactobacillus-targeting bacteriophages have the potential to contribute to dysbiosis. Hormonal fluctuations throughout the menstrual cycle influence both bacterial and viral populations, potentially affecting infection susceptibility and overall vaginal health. During pregnancy, higher viral diversity is associated with preterm birth risk, and immune modulation by the virome may impact susceptibility to infections like HPV. Analysis of the included studies indicates the need for continued investigation of the manner in which the vaginal virome interacts with other aspects of the microenvironment to influence women's health. This scoping review highlights the new and emerging role of the vaginal virome in women's health, highlighting its relationship with other microbes and clinical significance. These findings underscore the importance of the vaginal virome in reproductive health, suggesting that further research is needed to better understand its role and guide effective prevention and treatment strategies.},
}

@article {pmid41458627,
year = {2025},
author = {Ma, J and Tao, M and Zhang, W and Zhou, L and Zhang, H and Li, F and Zhang, H and Yao, D and Lu, W and Wang, M},
title = {Tirzepatide modulates gut microbiota homeostasis to protect against diabetic kidney disease.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1715024},
pmid = {41458627},
issn = {2296-889X},
abstract = {PURPOSE: This study evaluated the effect of Tirzepatide on metabolic profiles, kidney function, and gut microbiota composition in mice with diabetic kidney disease (DKD) and clarify the relationship between gut microbiota alterations and the renoprotective effects.

METHODS: Seven-week-old diabetic db/db mice and db/m controls were randomly assigned to three groups: db/db, db/db-T, and db/m. In the db/db-T group, mice received 10 nmol/kg Tirzepatide injections for a duration of 8 weeks. Biochemical and histopathological analyses were used to assess body weight, blood glucose, lipid profile, hepatic and renal function, and renal histopathological changes in mice. An antibiotic-pretreated group (ABX-db/db-T) was established to explore the impact of gut microbiome depletion on the therapeutic effects of Tirzepatide.The composition of gut microbiota was determined through 16S rRNA gene sequencing to assess microbial differences among groups.

RESULTS: Tirzepatide notably decreased fasting blood glucose (FBG), food intake, body weight, glycated hemoglobin A1c (HbA1c), blood lipid levels, and liver function markers, while improving renal function in mice. The renoprotective effects of Tirzepatide were attenuated following gut microbiota depletion. Microbiota analysis revealed that Tirzepatide could reverse dysbiosis and reshape the gut microbial ecosystem. Tirzepatide treatment raised the proportion of beneficial genera, Clostridium_sensu_stricto_1 and Romboutsia, while reducing potentially pathogenic genera, Erysipelatoclostridium and Bacteroides. Moreover, these microbiota changes were significantly correlated with serum creatinine and urinary albumin/creatinine ratio.

CONCLUSION: Tirzepatide improves renal function and metabolic parameters in DKD mice through gut microbiome regulation. The underlying mechanism involves the modulation of gut-renal axis through the optimization of microbial composition, promoting the development of beneficial bacteria while inhibiting harmful microbes. These results establish a foundational understanding for the use of Tirzepatide in DKD and suggest that combined interventions targeting the gut microbiota may have potential clinical value.},
}

@article {pmid41458603,
year = {2025},
author = {Oh, B and Lamoury, G and Carroll, S and Morgia, M and Boyle, F and Pavlakis, N and Clarke, S and Guminski, A and Menzies, A and Diakos, C and Moore, K and Baron-Hay, S and Eade, T and Molloy, M and Back, M},
title = {The gut microbiome as a potential predictive biomarker for breast cancer: emerging association and geographic differences.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1666830},
pmid = {41458603},
issn = {2234-943X},
abstract = {BACKGROUND: The gut microbiome may influence breast cancer (BC) development by modulating estrogen metabolism, immune responses, and microbial metabolites. Altered microbial patterns have been reported in BC, but their value as predictive biomarkers remains uncertain.

METHODS: We reviewed 13 case-control studies that compared gut microbiome composition in women with and without BC, focusing on diversity, compositional shifts, and geographic variation.

RESULTS: Reduced microbial richness (alpha diversity, the number and balance of bacterial species) was observed in more than half of the studies, although findings were not uniform. Differences in community composition (beta diversity) were common. Across studies, BC was consistently associated with elevated Bacteroides and reduced Faecalibacterium, a genus linked to anti-inflammatory effects. Other recurrent findings included enrichment of Eggerthella and Blautia in BC, though results for several taxa were inconsistent. Geographic variation was evident: Eggerthella was enriched in U.S. cohorts, Blautia in European cohorts, and in Chinese cohorts, Prevotella was elevated while Akkermansia was reduced.

CONCLUSIONS: Despite heterogeneity, converging evidence supports reduced diversity and shifts in select taxa, particularly enrichment of Bacteroides and depletion of Faecalibacterium, as emerging features of the BC microbiome. Geographic differences underscore the influence of host and environmental factors. These findings suggest biomarker potential but highlight the need for larger, longitudinal, and standardized studies to establish causality and clinical utility.},
}

@article {pmid41458324,
year = {2025},
author = {Harcęko-Zielińska, E and Górska, A and Romantowski, J and Małgorzewicz, S and Gruchała-Niedoszytko, M and Wypych, TP and Gutowska-Owsiak, D and Abouali, R and Chełmińska, M and Niedoszytko, M},
title = {Changes in the Gut Microbiome is Influenced by the Level of Control and Treatment in Asthma.},
journal = {Journal of asthma and allergy},
volume = {18},
number = {},
pages = {1857-1867},
pmid = {41458324},
issn = {1178-6965},
abstract = {BACKGROUND: The influence of intestinal microorganisms on the development and course of allergic diseases has recently been the subject of intensive research, but studies describing changes in the intestinal microbiome of asthma patients in response to altering factors are still scarce.

OBJECTIVE: (1) the analysis of eating habits composition of intestinal microbiota and BMI in asthma patients compared to the control group, (2) the comparison of the results of the analyzed parameters in asthma patients and in the control group, (3) the analysis of asthma treatment results depending on the composition of intestinal microbiota.

METHODS: Clinical stool isolates were cultured and genetic material was sequenced. The study included 49 subjects with asthma and a control group of 18 healthy volunteers. Clinical data was collected through questionnaires on the most frequently reported symptoms and the FFQ questionnaire. The composition of intestinal microbiota was determined using the traditional breeding method (the serial dilution method was used) followed by 16S rRNA sequencing.

RESULTS: Patients with asthma reported the greatest severity of clinical symptoms in all the body systems examined.The most common cause of the aberrant stool test results was E. coli, with titers <10[6]. The was no difference in the dietary habits between the asthma patients and the control group. Alpha and beta diversity, was significantly lower in asthma patients compared to the control group. Asthma patients had lower abundance of Faecalibacterium vs healthy volunteers. Statistically significant depletion of Oscilospirales, Anaerovoracaceea, was demonstrated in patients with uncontrolled asthma compared to controlled and partially controlled asthma. In patients taking glucocorticoids (oral and inhaled) enriched intestinal microbiota in Anaerovoracaceae and Christensenellaceae and depleted Faecalibacterium were observed.

CONCLUSION: Patients with asthma showed less richness and diversity in the composition of their intestinal microbiota compared to the control group.},
}

@article {pmid41458320,
year = {2025},
author = {Ghiotto, G and Francescato, L and Biancalani, MA and Treu, L and Campanaro, S},
title = {Hydrogen excess drives metabolic reprogramming and viral dynamics in syngas-converting microbiomes.},
journal = {Environmental science and ecotechnology},
volume = {28},
number = {},
pages = {100637},
pmid = {41458320},
issn = {2666-4984},
abstract = {Microbial communities drive essential bioprocesses, including the conversion of synthesis gas into biomethane, a sustainable energy source that supports circular carbon economies. In anaerobic environments, specialized consortia of bacteria and archaea facilitate syngas methanation through syntrophic interactions, where hydrogenotrophic methanogens play a central role in reducing carbon dioxide and monoxide with hydrogen. However, imbalances in gas ratios, particularly excess hydrogen, can disrupt these interactions and impair overall efficiency. Yet, the molecular mechanisms underlying microbial responses to such imbalances remain poorly understood. Here we show that hydrogen excess triggers profound metabolic and viral remodeling in a thermophilic anaerobic microbiome, leading to reduced methane yields and ecological instability. This reprogramming involves transcriptional downregulation of methanogenesis genes in the dominant archaeon Methanothermobacter thermautotrophicus, coupled with upregulation of CRISPR-Cas and restriction-modification systems that correlate with diminished activity of an associated phage, indicating activated host defenses against viral threats. Concurrently, bacterial species such as those from Tepidanaerobacteraceae enhance carbon fixation via the Wood-Ljungdahl pathway, serving as electron sinks to mitigate redox imbalance. These adaptive responses highlight the microbiome's resilience mechanisms under stress, revealing viruses as both stressors and selective forces in syntrophic systems. Such insights advance our understanding of microbiome dynamics in bioconversion processes and guide the engineering of more stable microbial consortia for optimized syngas-to-methane conversion amid variable feedstocks.},
}

@article {pmid41458082,
year = {2025},
author = {Njom Nlend, AE and Nkwelle Mekone, I and , },
title = {Human Milk Oligosaccharides, Microbiome, Antiretroviral Therapy and HIV Infected Mothers: Reasons to Still Promote Breastfeeding in HIV Context of Lactating Countries, a Mini-Narrative Review.},
journal = {Sage open pediatrics},
volume = {12},
number = {},
pages = {30502225251408582},
pmid = {41458082},
issn = {3050-2225},
abstract = {Breastfeeding is the preferred feeding for newborns during the first 6 months of life and until the age of 2 years or beyond. The benefits of breastfeeding remain significant, even in cases of HIV infection. The introduction of antiretroviral therapy(ART) has greatly reduced the risk of HIV transmission from mother to child through breastfeeding. As a result, breast milk is recommended for infants born to HIV-positive mothers, regardless of the mother's HIV status. Nevertheless, breastfeeding still poses a risk of HIV transmission in the era of eliminating vertical transmission. This mini-narrative review will highlight the continued benefits of breast milk for both HIV-infected and uninfected infants, focussing on the changes in bioactive components of breast milk, such as human milk oligosaccharides, and their effects on the gut microbiota. Additionally, this review will recommend strategies to improve safe breastfeeding practices in the context of HIV when mothers are receiving ART.},
}

@article {pmid41457605,
year = {2025},
author = {Lin, X and Li, C and Xu, X and Jiang, J},
title = {[Synthetic microbiome design: applications and challenges from theoretical construction to environmental bioremediation].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {41},
number = {11},
pages = {4298-4320},
doi = {10.13345/j.cjb.250436},
pmid = {41457605},
issn = {1872-2075},
mesh = {*Biodegradation, Environmental ; *Microbiota/physiology ; *Synthetic Biology/methods ; *Environmental Pollutants/metabolism/isolation & purification ; },
abstract = {As artificially constructed microbial communities with specific functions, synthetic microbiomes have shown great application potential in bioremediation in recent years. Compared with single strains, synthetic microbiomes have significant advantages in mineralizing complex pollutants and simultaneously metabolizing multiple pollutants. The construction of synthetic microbiomes involves various strategies and methods, which contribute to the design of microbial communities with diverse functions and adaptability to different environments. Conventional experiment-based studies on synthetic microbiomes often struggle to systematically elucidate the complex metabolic interactions among microbial community members, which limits the design and application of synthetic microbiomes. Genome-scale metabolic model (GSMM) technology has paved new avenues for the design, construction, and functional optimization of synthetic microbiomes. This review concentrates on the advantages of synthetic microbiomes in bioremediation and the current theories and strategies involved in the design and construction of synthetic microbiomes, and highlights the application potential of GSMMs in the design of synthetic microbiomes and the bioremediation of polluted environments. This paper can provide a theoretical basis and technical support for the research on synthetic microbiomes and their application in environmental bioremediation.},
}

*Biodegradation, Environmental
*Microbiota/physiology
*Synthetic Biology/methods
*Environmental Pollutants/metabolism/isolation & purification

@article {pmid41457383,
year = {2025},
author = {Wu, X and Wang, D and Mao, X and Dong, B and Wang, Y},
title = {Microbiome-Driven Resistance in Cervical Cancer Therapy: From Mechanistic Dissection to Clinical Translation.},
journal = {Expert reviews in molecular medicine},
volume = {},
number = {},
pages = {1-45},
doi = {10.1017/erm.2025.10029},
pmid = {41457383},
issn = {1462-3994},
}

@article {pmid41457316,
year = {2025},
author = {Zhao, C and Chang, X and Fan, L and Jiang, L and Zhong, R},
title = {Innovative manure via hyper-thermophilic fermentation coupled with heat-resistant phosphate-solubilizing Bacillus inoculation promotes phosphorus transformation by assembling keystone taxa in the oat rhizosphere.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0120825},
doi = {10.1128/aem.01208-25},
pmid = {41457316},
issn = {1098-5336},
abstract = {UNLABELLED: Phosphorus forms and distribution in organic manures vary under different treatment conditions, thereby exerting distinct effects on the soil microbiome and soil phosphorus transformation process. This study examined the effects of a novel manure treated with hyper-thermophilic fermentation combined with Bacillus strain inoculation, compared with raw and composted manure, on the oat rhizosphere microbiome and phosphorus transformation across different soil types in a controlled pot experiment. Our findings demonstrate that hyper-thermophilic fermentation with Bacillus inoculation not only promotes the survival and abundance of the bacterial genus Bacillus but also selectively enriches the hyper-thermophilic bacterial genus Thermobifida in the fermented manure. Notably, the application of hyper-thermophilic fermented manure led to a significant enrichment of keystone species like Bacillus and Thermobifida across both soil types, relative to other manure applications. These genera emerged as key drivers of available phosphorus, phosphatase activity, and differential metabolites in the rhizosphere, exhibiting a synergistic effect on soil phosphorus transformation. Fermented manure exhibited superior performance relative to conventional composted manure, as it increased the phosphorus uptake rate of oats by 35.5% in black soil and 27.9% meadow soil, respectively, over a single growing season. Additionally, among all organic manures, the application of fermented manure significantly enhanced the sequestration of phosphorus from manure in the soils, with 78.0% in black soil and 56.9% in meadow soil. This consequently reduced P loss to 13.6% and 34.4% in the respective soil types.

IMPORTANCE: Phosphate-solubilizing microorganisms (PSMs) are frequently proposed as catalysts for promoting phosphorus recycling; however, their performance is often inefficient or ineffective in the context of a circular bioeconomy within agricultural systems. This study introduces innovative concepts and methodologies by integrating hyper-thermophilic fermentation with heat-resistant phosphate-solubilizing Bacillus inoculation, thereby enhancing the effective phosphorus recovery and utilization from manure waste in sustainable agricultural practices.},
}

@article {pmid41457314,
year = {2025},
author = {Hosmer, M and Wright, RJ and McCavour, C and Keys, K and Sterling, S and Langille, MGI and Rohde, J},
title = {Lime amendment to chronically acidified forest soils results in shifts in prokaryotic communities.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0217124},
doi = {10.1128/aem.02171-24},
pmid = {41457314},
issn = {1098-5336},
abstract = {A consequence of past acid rain events has been chronic acidification of Nova Scotian forests, leading to a loss of essential nutrients and subsequent decreases in forest productivity and biodiversity. Liming-supplementing forests with crushed limestone-can restore essential nutrients to acidified soils and increase the pH of soils and the carbon capture by forests through the promotion of tree growth. Liming treatments are often assessed through tree growth measurements, although little is known about how microorganisms respond to these changes in pH and nutrient availability. Understanding the impacts of liming on microbial communities will help determine whether liming is a good remediation strategy for Nova Scotia. A pilot study evaluating liming in acidified forests in Nova Scotia began in 2017. Microbiome analysis (prokaryotic 16S and fungal ITS2 rRNA gene amplicon sequencing) of three different horizons (depths; upper forest floor, lower forest floor, and upper B horizon) of soil in a softwood forest area showed significant differences between lime-treated and control soils for the prokaryotic but not fungal communities, particularly in the uppermost soil horizon. Several genera from the Alphaproteobacteria class were significantly higher in abundance in treated than control soils, whereas genera from the Acidobacteriia (previously Acidobacteriae) class were significantly lower in abundance in treated versus control soils. Soil chemistry analysis of the same three horizons showed a significant increase in base cations and pH of the uppermost soil horizon in control versus treatment sites.IMPORTANCEForests are increasingly being managed with an emphasis on understanding how forests function. Lime amendments are used to promote forest health and increase resilience to climate change. To date, only a handful of studies have analyzed the effects of liming on microbial communities in forest soils. Our study combines soil chemistry with prokaryotic and fungal communities of limed and control soils. Shifts in microbial composition that are coincident with liming may provide early indications of the effectiveness of liming and provide insight into the roles of microbes in forest health.},
}

@article {pmid41457274,
year = {2025},
author = {Catry, A and Abrouk, D and Fierling, N and Mendoza, AIS and Rey, M and Vesga, P and Heiman, CM and Garrido-Sanz, D and Bouffaud, ML and Buscot, F and Giongo, A and Smalla, K and Comte, G and Keel, C and Muller, D and Moënne-Loccoz, Y},
title = {Biogeography influences plant-microbe interactions and natural soil suppressiveness to black root rot disease of tobacco.},
journal = {Genome biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13059-025-03911-0},
pmid = {41457274},
issn = {1474-760X},
support = {BiodivERsA3 ERA-Net SuppressSOIL//Biodiversa+/ ; grant SuppressSOIL no. ANR19-EBI3-0007//Agence Nationale de la Recherche/ ; grant SuppressSOIL no. 31BD30_186540//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; grant no. 51NF40_180575//NCCR Microbiomes/ ; BU 941/30-1//Deutsche Forschungsgemeinschaft/ ; project DiControl 031A560A-F//Bundesministerium für Bildung und Forschung/ ; },
abstract = {BACKGROUND: In disease-suppressive soils, the rhizosphere microbiota protects plants from root disease(s). However, the soil microbiome follows distinct spatial patterns, and the biogeographic factors shaping plant-microbe interactions and soil suppressiveness remain poorly understood. Here, we use Swiss and Savoie soils suppressive or conducive to Thielaviopsis basicola-mediated black root rot of tobacco, to test the hypothesis that plant-microbe interactions and suppressiveness are influenced by both the geological origin and geographic positioning of soils. Soils are compared based on tobacco health, soil physicochemistry and organic matter profiles, taxonomic and functional microbial diversity, and plant physiological responses.

RESULTS: Soil physicochemistry and metabolomic profiling of soil organic matter show differences based on suppressiveness status, soil geology and geography. The taxonomic (metabarcoding of prokaryotes and fungi) and functional (metagenomics) diversity of the tobacco rhizosphere reveals that the microbiota is influenced by geography and geology which, in turn, affects suppressiveness. Additionally, shoot metabolomics shows that tobacco responses are impacted by soil geography and geology, particularly in Savoie soils regarding two nicotinic derivatives.

CONCLUSIONS: Overall, suppressiveness is influenced by both the geological origin and geographic positioning of the soils, with distinct patterns in the two regions. In Swiss soils, suppressiveness is primarily associated with major differences in rhizosphere microbiota composition and functions between suppressive and conducive soils. In contrast, in Savoie soils, suppressiveness is linked to distinct plant physiological responses (pointing to induced systemic resistance) rather than strong microbial shifts. This study highlights the importance of considering the biogeographic features shaping disease-suppressive soils and their microbiota-plant interactions.},
}

@article {pmid41415463,
year = {2025},
author = {Hinzke, T and Kunath, BJ and Blakeley-Ruiz, JA and Korenek, A and Vintila, S and Wilmes, P and Kleiner, M},
title = {Evaluation of statistical approaches for differential metaproteomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41415463},
issn = {2692-8205},
support = {P30 DK034987/DK/NIDDK NIH HHS/United States ; R35 GM138362/GM/NIGMS NIH HHS/United States ; },
abstract = {Metaproteomics characterizes and compares molecular phenotypes of organisms in communities by comprehensively analyzing their protein expression profiles using statistical methods. However, not all statistical methods are suitable for determining differentially abundant protein groups in metaproteomic analyses. Statistical challenges in metaproteomics include: data sparsity, non-normality, compositionality, and large between-sample variability. These challenges can potentially be addressed with several data processing steps, including imputation, normalization, transformation, and selection of the appropriate statistical tests. The potential combinations of different processing methods create a complex matrix of analysis options and it is currently unclear how these combinations impact the results of statistical tests on metaproteomic data. To determine what data processing methods and statistical tests are best for identifying differentially abundant proteins in metaproteomics datasets, we generated a set of thirteen metaproteomic samples with known compositions, known differences, and differing levels of complexity. These defined metaproteomes address the general challenges outlined above, using various scenarios in metaproteomic data analyses. We compared over 110 different statistical analysis combination options, including regression-based tools, general statistics inference, and machine learning techniques. Our work enables improved assessment of statistical methods for metaproteomics by establishing a framework for testing statistical approaches, including comprehensive raw mass spectrometry data and reproducible benchmarking code. We found that several combinations within the frameworks of limma, edgeR, MaAslin2, custom linear and Bayesian linear models, and random forests all offer suitable evaluation options, and highlight key recommendations for differential expression analysis in metaproteomics.},
}

@article {pmid41457176,
year = {2025},
author = {Paul, D and Talukdar, D and Kapuganti, RS and Gupta, V and Narendrakumar, L and Jana, P and Kumar, P and Singh, J and Kumari, S and Basak, C and Kamboj, K and Bakshi, S and Lal, S and Tanwar, S and Kumar, R and Babele, P and Bajpai, M and Kumar, Y and Mutreja, A and Mandal, S and Wadhwa, N and Banerjee, SK and Das, B},
title = {Antibiotic contamination and antimicrobial resistance dynamics in the urban sewage microbiome in India.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-68034-3},
pmid = {41457176},
issn = {2041-1723},
support = {RAD/22017/19/2022-KGD-DBT//Department of Biotechnology, Ministry of Science and Technology (DBT)/ ; GCI-13012/2/2025-GCl//Department of Biotechnology, Ministry of Science and Technology (DBT)/ ; },
abstract = {The emergence and spread of antimicrobial resistance (AMR) in clinically important bacterial pathogens has severely compromised the effectiveness of commonly used antibiotics in healthcare. Acquisition and transmission of AMR genes (ARGs) are often facilitated by sublethal concentrations of antibiotics in microbially dense environments. In this study, we use sewage samples (n = 381) collected from six Indian states between June and December 2023 to assess the concentration of eleven antibiotics, microbial diversity, and ARG richness. We find antibiotics from seven drug classes and detect over 2000 bacterial amplicon sequence variants (ASVs). Metagenomic (n = 220) and isolated genome sequences (n = 305) of aerobic and anaerobic bacterial species identify 82 ARGs associated with 80 mobile genetic elements (MGEs). These MGEs are predominantly present in multidrug-resistant (MDR) bacterial pathogens. Comparative core genome analysis of MDR bacterial isolates (n = 7166) shows strong genetic similarity between sewage-derived strains and clinical pathogens. Our results highlight sewage as a significant reservoir for ARGs, where genetic exchanges occur and facilitate the evolution and spread of AMR pathogens in both community and healthcare settings. Additionally, the dipstick-based assay developed for ARGs detection can be used for sewage surveillance in low-resource settings for better understanding of resistance prevalence.},
}

@article {pmid41457081,
year = {2025},
author = {Priyadarshani, HMC and Mierzejewska-Sinner, E and Kózka, B and Giebułtowicz, J and Urbaniak, M},
title = {Benomyl modulates paracetamol bioaccumulation and endophytic microbiome diversity in zucchini.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-33977-6},
pmid = {41457081},
issn = {2045-2322},
support = {2023/51/B/NZ9/00540//Narodowe Centrum Nauki/ ; },
abstract = {Paracetamol, a widely used analgesic and antipyretic, has emerged as a prevalent environmental pollutant that poses risks to various organisms, including plants. Phytoremediation, particularly the use of Cucurbitaceae family plants, offers a promising, eco-friendly approach to mitigate such pollutants. This study investigated the bioaccumulation of paracetamol in zucchini (Cucurbita pepo cv. Atena Polka) and explored the role of the fungicide benomyl in modulating paracetamol bioaccumulation. Additionally, the impacts of these compounds on zucchini health (measured by biomass, chlorophyll content, and phenolic compound concentrations) and on the diversity of the endophytic microbiome (assessed via the Biolog EcoPlate™ and identification of isolated endophytes via 16S rRNA gene sequencing) were evaluated. Four treatments were assessed over a 28-day cultivation period: control (no pharmaceutical or fungicide), paracetamol (25 mg/kg) (P), paracetamol + benomyl (P + B), and benomyl alone (B). The results revealed that paracetamol accumulated significantly more in the roots of the P variant, but notably, the P + B variant presented a 24-fold increase in paracetamol concentration in aboveground tissues compared with the P variant. The bioaccumulation factors indicated that benomyl significantly enhanced the translocation of paracetamol to aerial parts in the P + B variant. Compared with the control, all the treatments reduced plant biomass, with the lowest values observed in the P variant. The chlorophyll content, in turn, was the highest in the P + B treatment, suggesting that benomyl helped mitigate oxidative stress. The levels of phenolic compounds, particularly flavonoids and phenylpropanoids, were elevated in the P variant, indicating a stress response. Additionally, the endophytic microbial community showed diminished diversity in the P variant. In the P + B variant, in turn, the microbial diversity measured via Biolog Ecoplates and 16S rRNA gene sequencing was greater. Our findings demonstrate that benomyl significantly enhanced the accumulation of paracetamol in the aerial parts of zucchini while promoting the resilience of plants and their associated endophytic bacteria and improving their potential for the phytoremoval of pharmaceutical pollutants.},
}

@article {pmid41457079,
year = {2025},
author = {Moraskie, M and Li, S and Codina, JR and Roshid, MHO and Núño, K and O'Connor, G and Dikici, E and Deo, S and Beurel, E and Daunert, S},
title = {DPO production by gut commensals suggests a broader role in bacterial communication and host-microbiome interactions.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00886-5},
pmid = {41457079},
issn = {2055-5008},
abstract = {The quorum-sensing molecule 3,5-dimethylpyrazine-2-ol (DPO), known for regulating biofilm formation in Vibrio cholerae, has unknown distribution among commensal bacteria. We screened 37 bacterial strains using a validated biosensor and found widespread production. Inoculating mice with high producers elevated gut DPO levels, highlighting DPO's potential influence on gut microbiota. These findings expand DPO's ecological relevance and underscore quorum sensing as a potentially critical influence on microbiome function and host-microbe interactions.},
}

@article {pmid41456898,
year = {2025},
author = {Mao, C and Zhang, Q and Zhang, J and Li, X},
title = {Omics Analysis of Lignin Degradation by the Gut Microbiomes of Wood-Eating Hypomeces squamosus Fabricius.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70208},
doi = {10.1002/mbo3.70208},
pmid = {41456898},
issn = {2045-8827},
support = {E5290504//"First Action Plan for Attracting Talents" of the Chinese Academy of Sciences-Category B/ ; },
mesh = {*Lignin/metabolism ; *Gastrointestinal Microbiome ; Animals ; Wood/metabolism ; Metabolic Networks and Pathways/genetics ; *Isoptera/microbiology/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; },
abstract = {Microbial degradation of lignin is important to carbon cycling. The gut microbiome of wood-feeding Hypomeces squamosus Fabricius has been shown to degrade lignin efficiently. However, the specific degradation mechanisms remain incompletely understood. In this study, we investigated the mechanism of lignin degradation using omics comparative analysis, focusing on differentially expressed genes and metabolic pathways in the gut microbiome of insects fed with a lignin-rich diet. The dominant genus taxon was Pantoea (29.82%), which was predominant in insects fed with high lignin-containing Iris ensata Thunberg, whereas Wolbachia and Enterobacter were predominant in insects fed with cabbage leaves (MHS_K group). Furthermore, expression levels of carbohydrate-active enzymes from the auxiliary activities (AAs) families in the MHS_I group were 1.18 times higher than those in the MHS_K group. These mainly included lignin peroxidase and manganese peroxidase of the AA2 family, vanillyl-alcohol oxygenase of the AA4 family, and 1,4-benzoquinone reductase of the AA6 family. Expression levels of multiple genes encoding aromatic compound-degrading genes (2303 accounted for 75.76% of the total upregulated genes) were found, including about 0.03% was related to lignin degradation. Genes MHS-HN_11398_2 (protocatechuate 2,3-dioxygenase) and MHS-HN_4821_1 (muconolactone d-isomerase) were enriched in the MHS_I group. Three lignin-degrading pathways were found: ortho-cleavage and meta-cleavage of catechol, as well as ring-opening of protocatechuate. This study provides a comprehensive and theoretical evidence of the gut microbiome roles of H. squamosus Fabricius in lignin degradation.},
}

*Lignin/metabolism
*Gastrointestinal Microbiome
Animals
Wood/metabolism
Metabolic Networks and Pathways/genetics
*Isoptera/microbiology/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification

@article {pmid41456824,
year = {2025},
author = {Quan, H and Ouyang, J and Fu, X and Lin, D and Wu, Q and Li, D and Li, Y and Yang, F and Wu, S and Li, C and Mao, W},
title = {Elucidating the Therapeutic Mechanism of Orthosiphon aristatus in Hyperuricemic Nephropathy: An Integrated Microbiome-Metabolomics Approach.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121115},
doi = {10.1016/j.jep.2025.121115},
pmid = {41456824},
issn = {1872-7573},
abstract = {Hyperuricemic nephropathy (HN) remains challenging to treat due to the limitations, including variable efficacy and side effects, of conventional drugs. Orthosiphon aristatus (O. aristatus), used for over 2000 years in Dai medicine to treat kidney disorders by "clearing heat and promoting diuresis," shows strong potential for HN management. However, its mechanisms of action against HN remain unclear.

AIM OF THE STUDY: This study aimed to elucidate the nephroprotective effects and underlying mechanisms of O. aristatus against HN using an integrated strategy focusing on the gut-kidney axis.

METHODS: A rat model of HN was established by combined oral administration of potassium oxonate (750 mg/kg) and uric acid (300 mg/kg) daily for 7 weeks. Model rats were treated with a low- or high-dose aqueous extract of O. aristatus (3.125 or 6.25 g/kg/day), using allopurinol (5 mg/kg/day) as a positive control. Renal function was assessed by measuring serum levels of uric acid, creatinine, and urea nitrogen. Renal pathological injury and fibrosis were evaluated through histopathological examination (H&E and Masson's trichrome staining), immunohistochemistry (α-SMA, vimentin), and transmission electron microscopy. To elucidate the underlying mechanisms, an integrated multi-omics approach was employed: gut microbiota composition was profiled by metagenomic sequencing, and metabolic alterations in cecal content and kidney tissue were characterized using UPLC-MS-based metabolomics. Furthermore, the protein expression of key targets involved in intestinal barrier function (Occludin, Claudin-1) and the IDO1/AhR signaling pathway was validated by Western blot analysis.

RESULTS: O. aristatus treatment significantly ameliorated renal dysfunction and pathological injury, as demonstrated by marked reductions in serum uric acid (sUA), creatinine (Scr), and blood urea nitrogen (BUN) levels (all p < 0.001), alongside attenuated tubular injury and fibrosis. Concurrently, it restored gut microbiota diversity (e.g., increased Shannon index, p < 0.05) and composition, characterized by an enrichment of beneficial Prevotella and a reduction in Bacteroides. Integrated metabolomics analysis further linked these effects to the rectification of tryptophan metabolism, manifested by decreased renal kynurenine levels (p < 0.01) and enhanced intestinal barrier integrity (e.g., elevated Occludin and Claudin-1, p < 0.05). Collectively, our results delineate that the renoprotective effect of O. aristatus is mediated through the suppression of the renal IDO1/kynurenine/AhR pro-fibrotic signaling axis, unveiling a novel gut microbiota-metabolite-kidney interaction mechanism.

CONCLUSION: This study elucidates that the renoprotective effect of O. aristatus against HN is mediated through modulation of the gut-kidney axis, by restoring microbial ecology, reprogramming host tryptophan metabolism, and subsequently inhibiting the IDO1/kynurenine/AhR pro-fibrotic pathway.},
}

@article {pmid41456636,
year = {2025},
author = {Koppali, SR and Vadia, N and Varma, P and Mishra, S and Joshi, N and Bansal, P and Al-Hasnaawei, S and Chauhan, AS and Jain, H and Nathiya, D and Devi, A and Jayasingh Chellammal, HS and Gupta, P and Wal, P and Koppula, S},
title = {Neurodevelopmental origins of neurodegeneration: a lifespan perspective on brain vulnerability.},
journal = {Brain research},
volume = {},
number = {},
pages = {150134},
doi = {10.1016/j.brainres.2025.150134},
pmid = {41456636},
issn = {1872-6240},
abstract = {Neurodegenerative disorders-including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis-are increasingly understood to have origins in early neurodevelopmental disturbances. This review examines how genetic, epigenetic, and environmental factors impact brain development during critical periods, predisposing individuals to neurodegeneration later in life. Prenatal and early-life exposures such as maternal stress, malnutrition, infection, and environmental toxins can alter key developmental processes, leading to long-term vulnerability. Mechanistic pathways linking early-life disruptions to neurodegenerative outcomes include persistent mitochondrial dysfunction, chronic neuroinflammation, increased oxidative stress, and aberrant synaptic pruning, all of which contribute to progressive neuronal damage and dysfunction. The gut-brain axis is also discussed as a key intermediary, where early microbiota dysbiosis alters neuroimmune signaling and inflammatory responses, modulating susceptibility to age-related neurological disorders. In this context, the review highlights emerging molecular and imaging biomarkers capable of detecting subtle neurodevelopmental deviations that may precede clinical symptoms by decades. The paper emphasizes the need for early-life interventions, including maternal nutritional optimization, management of prenatal stress, and microbiome-targeted strategies, as potential tools to reduce long-term neurological risk. Furthermore, it proposes the integration of precision medicine approaches aimed at individualized risk assessment and therapeutic targeting of developmental pathways. Adopting a lifespan perspective, this review argues for a paradigm shift from reactive to preventive strategies in neurology. Understanding the developmental roots of neurodegeneration opens new avenues for research and intervention, enabling resilience and reducing disease burden through early diagnostics and tailored therapeutics across the lifespan.},
}

@article {pmid41456557,
year = {2025},
author = {Li, Y and Chen, Y and Du, Z and Guo, Y and Zhang, W and Xu, X and Liu, Z and Duan, H and Duan, X and Zhang, A and Zhou, A and Li, X and Makinia, J},
title = {Oriented butyrate production through a novel bacteria-yeast microbiome: batch verification, key electron donor identification, and long-term validation.},
journal = {Bioresource technology},
volume = {443},
number = {},
pages = {133892},
doi = {10.1016/j.biortech.2025.133892},
pmid = {41456557},
issn = {1873-2976},
abstract = {Recovering butyrate from organic waste enables its high-value conversion, aligning with the principles of a circular economy. Traditional butyrate fermentation emphasizes carbohydrates and protein degradation, with limited focus on chain elongation (CE). This study, for the first time, systematically evaluated the effects of different Saccharomyces cerevisiae (SC) concentrations (1, 2, 4, 6, and 8 g/L) on ethanol production (a key electron donor) and subsequent CE for butyrate synthesis, identifying 2 g/L as the optimal SC dosage. At this concentration, butyrate production reached 15.41 ± 2.84 g COD/L, which was 2.72 times higher than that of the blank. Metabolic pathway analysis revealed that yeast not only enhanced substrate degradation (＞90 %) but also facilitated the in situ generation and utilization of ethanol. 16S rRNA indicated 54.10 % relative abundance of butyrate-producing bacteria (Clostridium). Long-term tests found that adding SC reversed the halt in production from prolonged distiller yeast inoculum, stabilising output at 15 g COD/L. Metagenomic analysis revealed that SC inoculation primarily enriched Clostridium luticellarii and Clostridium tyrobutyricum. In addition to raising reverse β-oxidation gene abundance, this treatment also enhanced lactate utilization genes, thereby strengthening acetyl-CoA to butyrate conversion. Through further experiments involving different electron donor ratios and long-term operation, this study highlights the critical role of yeast-bacteria synergy in enhancing butyrate synthesis, providing a theoretical foundation and technical strategy for food waste valorization in line with circular economy principles.},
}

@article {pmid41456402,
year = {2025},
author = {Lyte, JM},
title = {Stress neurophysiology in poultry: A functional framework for the application of microbiome science in poultry production.},
journal = {Poultry science},
volume = {105},
number = {2},
pages = {106181},
doi = {10.1016/j.psj.2025.106181},
pmid = {41456402},
issn = {1525-3171},
abstract = {Over the last two decades, scientific interest in the poultry microbiome has skyrocketed with a role ascribed for the microbiome in virtually every aspect of poultry health and production. While substantial progress has been made in revealing important correlations that can be used as a roadmap for utilization in a production setting, much remains to be understood in way of causality of the microbiome for the bird. In other words, correlation does not mean causation and there exists an overwhelming need to identify causal mechanisms if new microbiome-based modalities are to be implemented in poultry production. Therefore, this review discusses the need for function-driven hypotheses that provide an evidence-based framework when approaching poultry microbiome research. Considering that the impact of stress on both the bird and microbiome is well-appreciated across poultry species, pre-harvest stress is taken as a prototypical example of where the use of function-driven hypotheses can help bridge basic to applied microbiome-based science to benefit poultry production. Practical examples are provided and summarized herein, in which this approach can be applied ranging from areas of foodborne pathogen carriage to performance. Central to this aim is the interdisciplinary field of Microbial Endocrinology as it represents the intersection of microbiology and neurophysiology. Microbial Endocrinology has demonstrated that monoamine neurochemical systems can serve as mechanistic routes of host-microbe interaction, providing an evidence-based platform for identification of causal relationships between microbial taxa and the host. Interventions can therefore be designed to modulate these causal pathways to benefit the bird. While emphasis is given towards the nexus of gastrointestinal neurophysiology and the gut microbiome, this review also highlights the intersection of neurochemistry and the microbiome along the respiratory and reproductive tracts. The need for widespread adoption of best practices methodologies in microbiome research experimental design is integrated into function-driven hypotheses herein. It is anticipated that the cooperative use of directed hypotheses and the implementation of robust experimental design will accelerate the application of microbiome-based solutions in poultry production.},
}

@article {pmid41456367,
year = {2025},
author = {Peraza, P and Martinez-Boggio, G and Naya, H and Sotelo-Silveira, J and Navajas, EA},
title = {Predictive ability and mediation effects of the rumen microbiome on feed efficiency and methane traits in Hereford beef cattle.},
journal = {Animal : an international journal of animal bioscience},
volume = {20},
number = {1},
pages = {101730},
doi = {10.1016/j.animal.2025.101730},
pmid = {41456367},
issn = {1751-732X},
abstract = {The ruminant genome exerts moderate control over rumen microbial composition, which is a major determinant of feed efficiency and methane emissions. However, the integration of new omics data, whether for phenotypic prediction, selective breeding, or both, is still under discussion. This study aimed to (1) estimate the heritability and microbiability for residual feed intake (RFI), dry matter intake (DMI), BW, and methane yield (MY); (2) assess the predictive ability of models including host genome and microbiome information; and (3) evaluate the mediation effects of the rumen microbiome on feed efficiency and performance traits. The data set consisted of 537 Hereford bulls and steers with RFI, DMI, and BW records, as well as a subset of them (n = 123) with MY records. All animals were genotyped using 100 k single-nucleotide polymorphism panels, and rumen microbial abundances were determined through enzyme-restriction reduced representation sequencing (ER-RRS) analysis. Heritability estimates ranged from 0.18 for RFI to 0.36 for BW, while microbiability values were moderate (0.16-0.32), indicating that both host genetics and the microbiome significantly contribute to trait variation. We found that the use of genome and rumen microbiome information improved predictive ability for BW (r = 0.48-0.52), as assessed by Pearson's correlation between observed and predicted values, but not for RFI (r = 0.15-0.14), DMI (r = 0.72-0.73), or MY (r = 0.68-0.69). We also identified several amplicon sequence variants (ASVs) with moderate genetic control and potential mediation effects on RFI, DMI, and BW. However, given the large number of tests performed, these findings should be interpreted with caution due to the increased risk of false positives. Interestingly, our findings show better results for the use of rumen microbiome for selective breeding than for phenotypic prediction in beef cattle. Additionally, we highlighted that using genomics and rumen microbiome data within structural equation models provides new biological insights into animal performance. However, the assumption of no environmental covariance between the host and the microbiome is strict but necessary. Further exploration includes the use of instrumental auxiliary variables that allow for the inclusion of the environmental covariance between the traits of interest.},
}

@article {pmid41456362,
year = {2025},
author = {Islam, MT and Yang, F and Komladzei, S and Akhter, M and Sardiu, ME and Li, Y},
title = {Integrative machine learning reveals hidden and emerging co-regulatory gene networks for multi-phase glioblastoma outcome prediction.},
journal = {European journal of cancer (Oxford, England : 1990)},
volume = {234},
number = {},
pages = {116197},
doi = {10.1016/j.ejca.2025.116197},
pmid = {41456362},
issn = {1879-0852},
abstract = {BACKGROUND: Glioblastoma (GBM) is a highly prevalent and aggressive type of brain tumor characterized by profound molecular complexity and poor prognosis. While conventional biomarker studies focus on highly significant genes or proteins associated with cancer outcomes, the contribution of gene-gene co-regulation to GBM progression remains unclear.

METHODS: This study employs an application of integrative machine learning approach, utilizing a high-dimensional transcriptomic profile that considers gene-gene co-regulations to identify predictive gene networks involved in GBM occurrence and 1-year survival prediction. We further integrate these network models with both empirical protein-protein interaction (PPI) data and random walk-based information flow analysis across the PPI landscape.

RESULTS: This dual-layered approach uncovers gene modules that bridge transcriptional co-regulation with functional connectivity at the protein level. This integration highlighted several hub genes, including both strong and weak (e.g. BSN, RHOC, ANXA1, CSF1R, and ITGAM), that emerged as key molecular connectors involved in critical GBM processes such as immune response and neuronal signaling. Notably, these hub genes also exhibited cross-disease associations with traits including gut microbiome composition, type 2 diabetes, coronary artery disease, and other cancers, underscoring their systemic biological relevance.

CONCLUSION: Overall, our findings through the computational approach underscore the significance of co-regulatory gene networks in GBM biology. It also demonstrates how integrating transcriptomic and protein-level interactions can refine prognostic modeling, advance biomarker discovery, and inform future therapeutic development.},
}

@article {pmid41455981,
year = {2025},
author = {Zhang, X and Liu, J and Li, Y and Ding, J},
title = {Long-term continuous cropping reshapes soybean rhizosphere microbiome and metabolome to alleviate allelopathic stress and enhance disease suppression.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02311-7},
pmid = {41455981},
issn = {2049-2618},
support = {ZD2023C001//Key Project of Heilongjiang Provincial Natural Science Foundation/ ; 2023ZYCX01//Department of Agriculture and Rural Affairs of Heilongjiang Province/ ; 32372048//the National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Continuous cropping obstacles (CCO) pose a persistent threat to global soybean sustainability, yet paradoxically attenuate under prolonged monoculture. To explore this, we investigated the soil-plant-microbiome dynamics across 1-year, short-term continuous cropping (STCC, 7-13 years), and long-term continuous cropping (LTCC, 19-25 years) systems.

RESULTS: Our results reveal that LTCC reduces the accumulation of allelopathic autotoxin by 49.06% (P < 0.05) and enriches beneficial rhizosphere metabolites (e.g., antibiotics, monoterpenes, and glycoside compounds), driving a shift in the microbial community towards taxa with pathogen-suppressive and nutrient-cycling functions. LTCC cultivated a microbiome with enhanced genes for stress resistance and nutrient uptake. Conversely, STCC exacerbates CCO stress, with microbial dysbiosis peaking at 13 years (Simpson index down 15.4%). Notably, 25-year LTCC restores ecosystem stability and enzyme activity, restructuring microbial communities with pathogen-suppressive and nutrient-cycling functions. By reintroducing depleted taxa including Pseudomonas, Burkholderia, and Enterobacter spp., we constructed a synthetic community, SC7. SC7 boosted soil enzymes and root nodules to shield plants from stress, increasing yield by 4.83% and mimicking long-term system advantages.

CONCLUSIONS: This study demonstrates the self-repair capacity of soybean monoculture. It bridges the gap between mechanistic insights, specifically the microbiome-metabolite feedback, and actionable solutions, such as SC7 inoculation. As a result, it advances sustainable intensification strategies for global soybean production. Video Abstract.},
}

@article {pmid41455937,
year = {2025},
author = {Almuhayya, S and Aldehalan, F and Alzamil, L and Ibrahem, K and Alharbi, SR and Aldawood, E},
title = {Vaginal microbiome knowledge and hygiene practices among women in Saudi Arabia: a cross-sectional study.},
journal = {BMC public health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12889-025-26075-9},
pmid = {41455937},
issn = {1471-2458},
}

@article {pmid41455887,
year = {2025},
author = {Tariq, H and Dutilleul, P and Geddes-McAlister, J and Geitmann, A and Smith, DL},
title = {Plant growth-promoting Bacillus strains modulate early soybean development via proteome remodeling.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-07972-y},
pmid = {41455887},
issn = {1471-2229},
abstract = {Plant adaptation to environmental stress involves tightly regulated cellular, molecular, and biochemical responses. Among these, microbe-assisted strategies have gained attention, particularly the role of the plant microbiome (phytomicrobiome) in promoting growth and stress resilience. Soybean (Glycine max), a major agricultural crop, actively recruits beneficial microbes through root-secreted secondary metabolites, fostering symbiotic interactions with endophytic bacteria. However, the direct and indirect impacts of root-associated endophytes on plant development remain incompletely understood. In this study, we investigated three Bacillus strains (HT1, HT2, and HT3) isolated previously from the soybean root microbiome.16 S rRNA analysis indicates that HT1 and HT2 are closely related to the Bacillus velezensis and HT3 to the Bacillus thuringiensis lineage although more detailed analyses are warranted for genus identification. These strains were selected for their demonstrated plant growth-promoting and biocontrol activities. Bacillus-HT1 and HT2 significantly enhanced soybean seed germination, while Bacillus-HT3 promoted leaf area expansion significantly compared to the control, indicating strain-specific developmental effects. To elucidate the molecular basis of these effects, we conducted shotgun proteomic profiling of soybean leaves. Enrichment analysis revealed distinct functional signatures, with Bacillus HT1 and HT2 associated with pathways linked to cellular component organization, microtubule dynamics, and organelle function, and Bacillus-HT3 inducing broader enrichment of photosynthesis, chloroplast organization, and biosynthetic processes. These findings suggest that HT1 and HT2 promote early developmental transitions, while HT3 enhances vegetative growth through large-scale metabolic reprogramming. Notably, proteins such as anthranilate synthase and proteasome subunit alpha type were differentially abundant, pointing to the potential involvement of auxin biosynthesis and ubiquitin-proteasome-mediated regulation but, the actual roles of these pathways remain to be validated. These findings provide mechanistic insights into how specific Bacillus strains modulate soybean development at the molecular level and highlight their potential for use as bio-inoculants to enhance crop productivity and resilience under stress conditions.},
}