@article {pmid41339392,
year = {2025},
author = {Muratore, E and Conti, G and Fabbrini, M and Zama, D and Decembrino, N and Muggeo, P and Mura, R and Perruccio, K and Leardini, D and Barone, M and Zecca, M and Cesaro, S and Brigidi, P and Turroni, S and Masetti, R},
title = {Distinct functional and compositional properties in the gut microbiome of children with acute lymphoblastic leukaemia identified by shotgun metagenomics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43082},
pmid = {41339392},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Child ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology ; Male ; Female ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; Adolescent ; Bacteria/genetics/classification ; Case-Control Studies ; },
abstract = {Acute lymphoblastic leukaemia (ALL) represents the most common childhood malignancy, and emerging evidence underscores the impact of the gut microbiome (GM) on its pathogenesis. In this study, we used shotgun metagenomics to investigate the GM of 30 ALL patients at diagnosis-19 with B-ALL and 11 with T-ALL-and compared them to 176 healthy controls (HCs). When considered as a single ALL group versus HCs, clear compositional differences emerged: ALL patients exhibited higher relative abundances of Enterococcus faecium, oral commensals such as Rothia dentocariosa, and multiple opportunistic species, whereas HCs were enriched in short-chain fatty acid producers like Anaerostipes hadrus and Intestinibacter bartlettii. Functionally, the ALL GM relied more on protein and amino acid catabolism, while HCs possessed enhanced pathways for carbohydrate and folate metabolism. These findings broadly align with 16S rRNA-based analyses from previous publications, though some discrepancies highlight differences in technique-driven resolution. In contrast, comparing the two major molecular phenotypes-B-ALL and T-ALL-revealed only minimal taxonomic and functional differences, primarily confined to BAs metabolism pathways. Overall, our results indicate that children with ALL at the time of diagnosis already display a dysbiotic signature, bolstering the notion that a disturbance in GM development during childhood may be linked to the multistep pathogenesis model of ALL.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Child
*Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology
Male
Female
Child, Preschool
RNA, Ribosomal, 16S/genetics
Adolescent
Bacteria/genetics/classification
Case-Control Studies

@article {pmid41339319,
year = {2025},
author = {Harrison, LC and Allnutt, TR and Hanieh, S and Roth-Schulze, AJ and Ngui, KM and Stone, NL and Bandala-Sanchez, E and Backshell, L and Gurruwiwi, G and Gondarra, V and Couper, JJ and Craig, ME and Davis, EA and Huynh, T and Soldatos, G and Wentworth, JM and Vuillermin, P and Penno, MAS and Biggs, BA and , },
title = {Indigenous infants in remote Australia retain an ancestral gut microbiome despite encroaching Westernization.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9904},
pmid = {41339319},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Australia ; Female ; Male ; Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; Infant, Newborn ; Indigenous Peoples ; Metagenome ; },
abstract = {Studies of traditional Indigenous compared to 'Western' gut microbiomes are underrepresented, and lacking in young children, limiting knowledge of early-life microbiomes in different cultural contexts. Here we analyze the gut metagenomes of 50 Indigenous Australian infants (median age }

Humans
*Gastrointestinal Microbiome/genetics
Infant
Australia
Female
Male
Bacteria/genetics/classification/isolation & purification
Feces/microbiology
Infant, Newborn
Indigenous Peoples
Metagenome

@article {pmid41339176,
year = {2025},
author = {Khan, S and Zobairi, A and Pouwels, S and Celik, A and Ugale, S and Parmar, C},
title = {Theories and concepts of physiological mechanisms in metabolic and bariatric surgery, beyond restriction and malabsorption: a narrative review.},
journal = {Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.soard.2025.10.017},
pmid = {41339176},
issn = {1878-7533},
abstract = {Metabolic and Bariatric surgery (MBS) has become an essential treatment for severe obesity and associated comorbidities, particularly type 2 diabetes mellitus (T2DM), with substantial benefits in weight loss, improved glycemic control, and cardiovascular risk reduction. The International Diabetes Federation (IDF) recognizes MBS as an effective option for individuals with obesity with T2DM due to its ability to improve insulin sensitivity and lower inflammation. These surgeries induce metabolic improvements through distinct mechanisms that affect gut hormone secretion, nutrient absorption, and energy balance. These interventions modulate key gut hormones like glucagon-like peptide-1 (GLP-1), ghrelin, and leptin, which influence appetite, glucose metabolism, and fat storage. Moreover, MBS alters the gut microbiome, contributing to enhanced metabolic function and the resolution of obesity-related conditions. Theories such as the Foregut-Hindgut Hypothesis, Ileal Brake Mechanism, and Gastric Center Hypothesis further try explain these metabolic changes. Understanding these theories and the physiological alterations they provoke is crucial for optimizing patient care and advancing the future of obesity treatments, offering insights into mechanisms that go beyond simple weight loss to address complex metabolic disorders.},
}

@article {pmid41338872,
year = {2025},
author = {Soule, K and Nelson, N and Wiemels, J and Gallant, R},
title = {Impact of infection and microbial exposures on pediatric cancer.},
journal = {Current problems in pediatric and adolescent health care},
volume = {55},
number = {9},
pages = {101819},
doi = {10.1016/j.cppeds.2025.101819},
pmid = {41338872},
issn = {1538-3199},
mesh = {Humans ; Child ; *Neoplasms/epidemiology/microbiology/immunology ; *Gastrointestinal Microbiome/immunology ; Environmental Exposure/adverse effects ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/epidemiology/immunology ; Female ; Incidence ; },
abstract = {The etiology of pediatric cancer is likely multifactorial including a combination of genetic alterations and environmental exposures. Infection and antigenic exposures have been identified as contributors to the development of pediatric cancers particularly acute lymphoblastic leukemia (ALL), the most common pediatric malignancy. Viral infections such as Epstein-Barr virus (EBV) and human papilloma virus (HPV) have a well-established association with Hodgkin lymphoma (EBV), Burkitt lymphoma (EBV), and head and neck cancers (HPV). More recent evidence suggests CMV is associated with glioblastoma multiforme and ALL. The incidence of pediatric cancer is much lower than the incidence of these viral infections, indicating that there are likely other factors at play. Aside from these specific viral infections, antigenic exposures in general have been associated with pediatric cancers as well. Early life antigenic exposures are known to impact the gut microbiome which is a crucial component to developing a competent immune system. Higher microbial exposure in early life, such as vaginal delivery (versus cesarean delivery), daycare attendance, and breastfeeding have been associated with lower incidence of pediatric ALL, and this effect is hypothesized to be mediated by the gut microbiome. In this review, we highlight the association between infection, antigenic exposures, and pediatric cancer and potential underlying mechanisms that facilitate this association.},
}

Humans
Child
*Neoplasms/epidemiology/microbiology/immunology
*Gastrointestinal Microbiome/immunology
Environmental Exposure/adverse effects
*Precursor Cell Lymphoblastic Leukemia-Lymphoma/epidemiology/immunology
Female
Incidence

@article {pmid41338496,
year = {2025},
author = {Sheridan, L and Hutton, P and Noble, G and Nobari, B},
title = {An in vitro investigation into the effects of postbiotic supplementation on stabilising equine hindgut pH.},
journal = {Journal of equine veterinary science},
volume = {},
number = {},
pages = {105746},
doi = {10.1016/j.jevs.2025.105746},
pmid = {41338496},
issn = {0737-0806},
abstract = {BACKGROUND: Dysbiosis of the intestinal microbiome is a precursor to hindgut acidosis. As microbial diversity and fermentation are influenced by diet, including a postbiotic could help maintain healthy gastrointestinal microbes and reduce acidosis risk.

AIMS/OBJECTIVES: It was hypothesised that including a postbiotic in batch culture would reduce the degree of pH decline and lactate accumulation during fermentation.

METHODS: In vitro batch cultures with faecal inoculant were prepared with either low starch (LS) or high glucose (G) substrate to represent normal and acidic fermentation. Saccharomyces cerevisiae derived postbiotic was added at 280 μg (T1), corresponding to the recommended daily feeding rate for a 500 kg horse adjusted to the dry matter of the incubated substrate, and 560 μg (T2), representing twice this rate, and incubated for 48 h to assess effects on pH, gas, volatile fatty acids (VFAs), ammonia (NH₃), and D-lactate production.

RESULTS: Substrate G showed a faster decline in pH (P <0.001) than LS at 6 and 12 h post incubation. Postbiotic concentration had a positive linear relationship with pH in G and observed higher (P <0.001) pH for T1 at 6 h, and T2 at 6 and 12 h. Production of propionic, and acetic acids was increased (P <0.001) with postbiotic at 12 h and 36 h, and butyric acid at 36 h (P = 0.05). D-lactate production was greater in G than LS (P <0.001) at 12 h and lower at 36 h (P <0.001). Postbiotics reduced lactate at 12 and 36 h (P <0.001) in LS.

CONCLUSION: The addition of postbiotic could reduce the severity of pH decline in high non-structural carbohydrate rations and increase VFAs, however acidosis was not prevented.},
}

@article {pmid41337904,
year = {2025},
author = {Niu, X and Ma, L and Zhou, Z and Li, Y and Shi, A and Weng, L and Xing, H},
title = {Composition of gut microbiota and alcohol-related liver disease: A systematic review and meta-analysis.},
journal = {Drug and alcohol dependence},
volume = {278},
number = {},
pages = {112988},
doi = {10.1016/j.drugalcdep.2025.112988},
pmid = {41337904},
issn = {1879-0046},
abstract = {BACKGROUND AND OBJECTIVES: The intestinal microbiome has been identified as a key factor influencing the development and prognosis of alcohol-related liver disease (ARLD). This article aims to systematically review and meta-analyze the alterations in the gut microbiome associated with ARLD, providing a comprehensive overview of these changes.

METHODS: PubMed, Embase, and Web of Science databases were systematically searched from January 1, 2015, to September 1, 2024, with the search limited to studies published in English and Chinese. Articles meeting the inclusion criteria-providing gut microbiota analysis and reporting changes in diversity and abundance-were selected through a two-stage screening process. Data extraction was conducted independently by two reviewers to ensure accuracy and reliability.

RESULTS: We compared gut microbiota differences between ARLD patients and healthy individuals, focusing on α-diversity, β-diversity, and microbial abundance. Among 17 studies, α-diversity indices showed a significant decrease in Shannon index (SMD=-0.63, 95 % CI= [-1.40, -0.14]), p < 0.001), Chao1 (SMD=-1.20, 95 % CI= [-1.67, -0.74], p = 0.022), and OTUs (SMD=-1.14, 95 % CI= [-1.55, -0.73], p = 0.010), with no significant differences observed in Simpson index, ACE, inverse Simpson, or Pielou evenness. Of 21 studies on β-diversity, 16 reported significant differences between ARLD and healthy controls. Most findings indicate a reduction in anti-inflammatory microorganisms and an enrichment of pro-inflammatory microorganisms in ARLD patients.

CONCLUSION: The study revealed that intestinal microbiome changes in ARLD patients are characterized by decreased microbial diversity, a reduction in anti-inflammatory microbiota, and an enrichment of pro-inflammatory bacteria. These findings highlight the intestinal microbiome as a promising target for potential ARLD treatment strategies.},
}

@article {pmid41338335,
year = {2025},
author = {Ono, N and Ito, Y and Aoki, S and Shiohama, A and Sasaki, T and Kurokawa, R and Suda, W and Amagai, M and Kubo, A},
title = {Microbial Dysbiosis and Foot Odor in Nagashima-Type Palmoplantar Keratosis: Improvement with Topical Benzoyl Peroxide.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2025.11.011},
pmid = {41338335},
issn = {1523-1747},
abstract = {Nagashima-type palmoplantar keratosis (NPPK; also referred to as SERPINB7-palmoplantar epidermal differentiation disorder) is the most common form of palmoplantar keratoderma in East Asia. It is characterized by erythematous hyperkeratosis, palmoplantar hyperhidrosis, and a distinctive foot odor that significantly impairs quality of life. In this study, we aimed to clarify the etiology of this odor by investigating the plantar microbiome and evaluating the therapeutic effects of topical benzoyl peroxide (BPO). Compared with healthy controls, individuals with NPPK exhibited significantly higher objective odor scores, increased bacterial load, especially in the intertoe area, and reduced microbial diversity. Corynebacterium and Staphylococcus were the predominant dysbiotic flora species. The topical application of BPO significantly reduced foot odor and bacterial load, increased microbial diversity, and selectively decreased Corynebacterium abundance, particularly that of C. tuberculostearicum. These changes correlate with the species-specific susceptibility of skin-resident bacteria to BPO. Our findings suggest that microbial dysbiosis, especially the overgrowth of Corynebacterium species, is central to the pathogenesis of foot odor in NPPK. Topical BPO is a promising therapeutic intervention for mitigating dysbiosis and its associated foot odor. This study highlights the potential of microbiome-targeted therapies for symptom relief in inherited skin disorders such as NPPK.},
}

@article {pmid41338170,
year = {2025},
author = {Egea, LG and Jiménez-Ramos, R and Rodríguez-Arias, L and Infantes, E},
title = {Successive stressors alter microbiome composition and reduce resilience in the eelgrass Zostera marina.},
journal = {Marine environmental research},
volume = {214},
number = {},
pages = {107748},
doi = {10.1016/j.marenvres.2025.107748},
pmid = {41338170},
issn = {1879-0291},
abstract = {Seagrass meadows are among the most threatened ecosystems worldwide, facing multiple anthropogenic stressors that often occur in succession. While plant-physiological responses to multiple stressors are well documented, the role of microbial symbionts in mediating consecutive stressors events remains poorly understood. Using a mesocosm experiment, Zostera marina (eelgrass) was exposed to sequential stressors: nutrient enriched sediments (NE; 70 mg of total N per 100 gDW sediment[-1] for 28 days), followed by a simulated marine heatwave (MHW, 23.3 °C for 15 days) and subsequent storm event (25 cm/s flow, 12 days). Nutrient enrichment resulted in a microbiome shift, specifically a 49.2-fold enrichment of sulfur-oxidizing Arcobacteraceae and a 4.7-fold increase in Sulfurimonadaceae, suggesting possible microbiome-mediated responses mitigating sulfide toxicity. In contrast, warming responses were primarily physiological: aboveground biomass increased by 41.5 % and net production increased by 37.1 % (mg FW shoot[-1] day[-1]), with synergistic effects under combined enrichment and heat stress (up to 175 % higher production), indicating that temperature outweighs nutrient stress. Storm exposure triggered a 114 % increase in belowground biomass via root elongation, which increases the resilience of these plants to higher flow velocities, but this acclimation was diminished by 51 % in plants previously exposed to the MHW, indicating environmental legacy effects. Our results demonstrate that eelgrass resilience depends critically on stressors sequence, where legacy effects alter both plant-microbe interactions and physiological responses. These findings emphasize the need to incorporate both a consecutive-stressor approach and microbiome dynamics into seagrass research and conservation strategies under climate change.},
}

@article {pmid41338072,
year = {2025},
author = {Jose, S and Lohith Kumar, DH and Malla, MA and Featherston, J and Bux, F and Kumari, S},
title = {Insights into microbial community, nitrogen‑phosphorus metabolism from metagenomic and metabolomic analysis of microalgal-cyanobacterial consortium-based bioinoculants.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181092},
doi = {10.1016/j.scitotenv.2025.181092},
pmid = {41338072},
issn = {1879-1026},
abstract = {The intensification of agriculture through chemical fertilizers has led to severe environmental consequences. This study provides a comprehensive investigation on chemical fertilizer, vermiculite and on microalgal-cyanobacterial consortia (bioinoculants) influencing soil microbial community. Chemical fertilizer application significantly altered the microbial community, suppressing the dominant phylum Proteobacteria to 48.3 % abundance from 60.9 % in the control soil. The bioinoculant treatments maintained a high Proteobacteria abundance (58.9 %-59.7 %) and fostered a growth-oriented, anabolic strategy. The 50:50 mix treatment uniquely promoted the fungal phylum Basidiomycota to 18.2 % abundance and showed the highest investment in the Glycolysis/Gluconeogenesis pathway (23.0 %). Chemical fertilizer treatment upregulated genes for rapid nitrogen assimilation (glnA, Log2FC = 0.60) and phosphorus starvation response (phoB, Log2FC = 0.65; pstS, Log2FC = 0.83). The enhanced energy production and conversion (11.83 %), amino acid transport and metabolism (11.20 %), and fatty acid biosynthesis (45.3 %) was observed in bioinoculant treatment. Unlike chemical fertilizer treatment, bioinoculant treatment led to the accumulation of the osmoprotectant trehalose and structural membrane lipids, while the 50:50 mix was uniquely characterized by a higher abundance of xylose. These findings demonstrate that the microalgal-cyanobacterial consortium can enhance nutrient recycling, and potentially boost soil health by reshaping the soil microbiome and metabolic functions, offering a promising strategy for sustainable agriculture.},
}

@article {pmid41337959,
year = {2025},
author = {Dong, D and Xie, Z and Wang, B and Ou, W and Tang, Y and Yang, J and Guo, Y and Fa, X},
title = {Effects of a forage-native multi-PGPM consortium symbiotic system on rhizosphere ecology and microbial regulation for remediating PAHs-contaminated very-high-altitude coal mines.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140653},
doi = {10.1016/j.jhazmat.2025.140653},
pmid = {41337959},
issn = {1873-3336},
abstract = {The very-high-altitude coal mines face polycyclic aromatic hydrocarbons (PAHs) pollution, yet studies on microbial degradation of PAHs in this region remain scarce. In this study, a native multi-plant growth-promoting microorganism consortium (N-M-PGPM-C, comprising four Tibetan Plateau strains: Trichoderma, Bacillus, Pseudomonas, and Floccularia luteovirens) was constructed. Their effects on forage growth, PAHs degradation, rhizosphere microbes, and soil metabolites were systematically investigated via high-throughput sequencing and LC-MS/MS metabolomics. The results showed that the N-M-PGPM-C significantly improved forage growth (93.81 %-120.05 % increase in dry weight compared to single PGPM treatment), degraded aromatic compounds in the rhizosphere soil, and enriched seven plant-beneficial microorganisms (e.g., Lysinibacillus, Solibacillus). In addition, it promoted the colonization and proliferation of two strains from the N-M-PGPM-C (i.e., Trichoderma by 3.20-fold and Bacillus by 9.41-fold) by reshaping the rhizosphere microbial community. According to the metabolomic analysis, the N-M-PGPM-C modulated 114 metabolites, enriching pathways for bisphenol, toluene, and benzoate degradation. The metabolite 2'-deoxyguanosine was strongly correlated with the enrichment of seven plant-beneficial microorganisms such as Lysinibacillus and Solibacillus and synergized with Trichoderma and Bacillus. Laboratory validations confirmed that Trichoderma and Bacillus possess intrinsic PAH-degrading capabilities, and exogenous application of 2'-deoxyguanosine significantly alleviated PAH stress in forages. These findings reveal the mechanism by which the N-M-PGPM-C remediates PAH contamination through the forage- native multi-PGPM consortium symbiotic system, providing a promising strategy for ecological restoration in the very-high-altitude regions.},
}

@article {pmid41337711,
year = {2025},
author = {Babu, R and Kaur, M and Sharma, S and Sureshan, CS and Garg, R and Baweja, S and Rastogi, M and Singh, SP and Varshney, M and Patil, NS and Pamecha, V and Sarin, SK and Bihari, C},
title = {Baseline oral microbiome associated with post-living donor liver transplant early complications within 6 months.},
journal = {Liver transplantation : official publication of the American Association for the Study of Liver Diseases and the International Liver Transplantation Society},
volume = {},
number = {},
pages = {},
doi = {10.1097/LVT.0000000000000779},
pmid = {41337711},
issn = {1527-6473},
abstract = {BACKGROUND AND AIMS: Oral dysbiosis noted in chronic liver disease (CLD). This may play a role in post-liver transplantation (LT) outcomes. This study aimed to assess the baseline oral microbiome and its association with early complications (EC) within 6 months after liver transplantation (LT).

METHODS: This prospective longitudinal study included 94 CLD recipients (CR) and their living donors. Patients were managed with a standardized immunosuppressive regimen and monitored for 6 months post-LT EC rejection, infection, biliary complications (BCs), and death. Pre- and post-LT saliva samples were processed for bacterial sequencing, qPCR validation, and cytokine profiling. The association between microbial abundance and EC was assessed.

RESULTS: At baseline, CR exhibited a lower Bacteroidota and a higher abundance of Bacillota compared to donors. Streptococcaceae and Veillonellaceae were enriched in CR compared to their respective donors (p<0.05, each). On follow-up, post-LT early complications were noted in 35/94 patients. Prominent Bacillota, Bacteroidetes, and Actinomycetota were noted at baseline in those who developed rejection, infection, and BC, respectively. Species-level analysis, followed by qPCR validation, revealed complication-specific baseline microbial signatures: E. marmotae (FC 3.9) for rejection, P. salivae (FC 71) for infections, and Rothia (FC 301) and Lactobacillus rhamnosus (FC 51) in BC. The baseline enrichment of Prevotella_7_sp2, Klebsiella pneumoniae, and Staphylococcus was associated with sepsis-related mortality. Recipients with post-LT EC showed pro-inflammatory links (Prevotella with IL-2, Streptococcus with IL-8).

CONCLUSION: Baseline oral microbiome profiles were differentially abundant among individuals who developed post-LT early complications. Incorporating microbial signatures may enable noninvasive risk stratification after LT.},
}

@article {pmid41337660,
year = {2025},
author = {Silva, IB and Puig-Domingo, M},
title = {The impact of thyroid disorders on the gut microbiome: emerging mechanisms and clinical relevance.},
journal = {Archives of endocrinology and metabolism},
volume = {70},
number = {Spe1},
pages = {e250075},
doi = {10.20945/2359-4292-2025-0075},
pmid = {41337660},
issn = {2359-4292},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/immunology ; *Thyroid Diseases/microbiology/immunology/metabolism ; Dysbiosis/microbiology/immunology ; Thyroid Gland/metabolism/immunology ; Animals ; Clinical Relevance ; },
abstract = {The thyroid-gut axis represents a dynamic interaction between the intestinal microbiota and thyroid function, with growing evidence linking gut dysbiosis to thyroid diseases. The gut microbiome, comprising over 100 trillion microorganisms, influences immune modulation, iodine metabolism, and thyroid hormone regulation. Short-chain fatty acids, produced by beneficial gut bacteria, support immune homeostasis and thyroid function, while pathogenic bacteria and lipopolysaccharides trigger inflammatory pathways that impair thyroid activity. Alterations in gut microbiota composition have been associated with autoimmune thyroid diseases, including Hashimoto's thyroiditis and Graves' disease. Dysbiosis increases intestinal permeability, antigen exposure, and immune activation, exacerbating thyroid autoimmunity. A reduction in short-chain fatty acids-producing bacteria weakens immune tolerance, promoting inflammatory cytokine release and autoantibody production. Recent studies highlight microbial metabolites such as tryptophan derivatives and their role in immune regulation. Gut dysbiosis is also implicated in thyroid nodules and cancer. Decreased butyrate-producing bacteria and increased inflammatory bacterial taxa have been observed in thyroid malignancies. Microbiota influence iodine and selenium bioavailability, essential for thyroid hormone synthesis, and modulate sodium-iodide symporter expression, affecting thyroid cancer response to radioactive iodine therapy. Microbiome-targeted interventions, including probiotics, prebiotics, dietary modifications, and fecal microbiota transplantation, may restore microbial balance, enhance immune regulation, and improve thyroid treatments. This review synthesizes our current understanding of the thyroid-gut axis, indicating that the intestinal microbiota and its metabolites may act directly or indirectly on the thyroid gland, highlighting potential clinical implications and paving the way for therapeutic strategies targeting the intestinal microbiota.},
}

Humans
*Gastrointestinal Microbiome/physiology/immunology
*Thyroid Diseases/microbiology/immunology/metabolism
Dysbiosis/microbiology/immunology
Thyroid Gland/metabolism/immunology
Animals
Clinical Relevance

@article {pmid41337497,
year = {2025},
author = {Camara, PEAS and Gonçalves, VN and Pellizzari, FM and Lopes, FAC and Convey, P and Ramada, MHS and Paiva, TDS and Carvalho-Silva, M and Rosa, LH},
title = {Eukaryotic diversity associated with the phycosphere of the seaweed Ulvaria obscura (Kützing) Gayral (Chlorophyta, Ulvophyceae) in the Svalbard Archipelago, Arctic region assessed using DNA metabarcoding.},
journal = {Anais da Academia Brasileira de Ciencias},
volume = {97},
number = {4},
pages = {e20240808},
doi = {10.1590/0001-3765202520240808},
pmid = {41337497},
issn = {1678-2690},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *Seaweed/classification ; Arctic Regions ; Svalbard ; *Chlorophyta/classification/genetics ; },
abstract = {Microorganisms often occur in association with macroalgae, with the term "phycosphere" referring to the seaweed surface where they may be present. Phycosphere represents a poorly explored niche of marine diversity, especially in the polar regions. DNA metabarcoding provides a new and accessible method for the detection of DNA from different organisms, especially applicable for poorly known groups where taxonomic expertise is limited or unavailable. In this study we used DNA metabarcoding to provide an initial survey of eukaryotic communities associated with marine macroalgae obtained from the shores of Svalbard. Samples of Ulvaria obscura were sequenced and the DNA reads found were assigned to 75 taxa of six Kingdoms and 17 phyla: Chromista (Ciliophora, Haptophyta, Ochrophyta, Oomycota and Chrysophyta), Fungi (Ascomycota, Basidiomycota, Chytridiomycota, Mortierellomycota and Rozellomycota), Holozoa (Ichthyosporia), Metazoa (Cnidaria), Protozoa (Cercozoa, Discosea and Heterolobosea) and Viridiplantae (Bryophyta and Chlorophyta). The most abundant group was Viridiplantae, followed by Fungi. Our environmental DNA study confirmed that the phycosphere of U. obscura shelters a rich and complex microbiome, suggesting that Arctic macroalgae provide a hotspot of currently undescribed polar biodiversity. Additionally, our results were obtained during the first official Brazilian Arctic expedition, representing a historic step for the Brazilian Antarctic Program (PROANTAR).},
}

*DNA Barcoding, Taxonomic/methods
*Biodiversity
*Seaweed/classification
Arctic Regions
Svalbard
*Chlorophyta/classification/genetics

@article {pmid41336154,
year = {2025},
author = {Zhan, B and He, D and Yang, X and Zhang, Z and Yan, S},
title = {FNatPred: A Data-Driven Approach for Distinguishing Between NAT and Tumor on the Fungal Microbiome.},
journal = {IEEE transactions on computational biology and bioinformatics},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/TCBBIO.2025.3639775},
pmid = {41336154},
issn = {2998-4165},
abstract = {OBJECTIVE: The role of fungal microbiota in human carcinogenesis remains largely uncharacterized. Recent evidence suggests normal adjacent tissue (NAT) represents an intermediate state between healthy and malignant tissues, highlighting its potential for early cancer detection. Discriminating fungal compositional profiles between tumor and NAT is thus critical for elucidating fungal involvement in oncogenesis. However, the high similarity between tumor and NAT mycobiota poses significant analytical challenges.

METHOD: To overcome this limitation, we developed a two-level ensemble discriminative model. Base-level classifiers, trained using rigorously filtered fungal microbiota data (based on prevalence, abundance, and quality metrics) via Random Forest, generate initial predictions. A meta-level classifier then integrates these base predictions, transforming high-dimensional, sparse fungal feature data into a low-dimensional, dense representation optimized for discrimination. Model implementation and analysis code are available at: https://github.com/cskyan/FNatPred.

RESULTS: Our approach achieved clear separation between tumor and NAT mycobiomes across multiple cancer types, with particularly pronounced discrimination in colorectal cancer (CRC). The proposed model significantly outperformed existing methods in tumor-NAT classification, demonstrating an average AUC improvement of approximately 10%.},
}

@article {pmid41335478,
year = {2025},
author = {Yin, C and Xu, L and Wei, Z and Zhao, Y and Bai, R and Gao, G and Fan, Y and Li, Y and Sun, W and Li, X and Pi, Y},
title = {Gut microbiota and bile acid profiles in purebred vs. crossbred sows: links to oxidative stress and inflammation in late gestation.},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
doi = {10.1099/mgen.0.001579},
pmid = {41335478},
issn = {2057-5858},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Oxidative Stress ; Female ; Pregnancy ; *Bile Acids and Salts/metabolism/analysis ; Swine/microbiology ; *Inflammation/metabolism/microbiology ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology/chemistry ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Understanding the interactions between gut microbiota, bile acid (BA) metabolism and systemic health is critical for supporting gestational physiological stability in sows, especially during the physiologically demanding late gestation period. Although physiological advantages vary by breed in late-gestation sows, the microbiota-related mechanisms underlying these differences remain poorly understood. This study compared serum antioxidant enzyme activity, oxidative damage markers, inflammatory cytokine levels, gut microbiota composition (analysed via 16S rRNA sequencing), and BA profiles (assessed through targeted metabolomics) between purebred large white (LW) and large white×landrace (LW×LR) crossbred sows during late gestation. Results showed that LW×LR crossbred sows exhibited significantly higher serum superoxide dismutase (SOD) activity and IL-10 levels, alongside reduced IL-6 levels (P<0.05), indicating enhanced antioxidant and anti-inflammatory capacity. Gut microbiota analysis revealed greater alpha diversity (Shannon indices) and a lower Simpson index, along with distinct beta diversity (P<0.05) in crossbred sows, with notable enrichment of functional taxa such as Treponema and Prevotella. Additionally, faecal concentrations of modified BAs, specifically 3-oxolithocholic acid and 7-ketolithocholic acid, were significantly elevated, correlating with increased abundance of gut microbiota encoding BA: Na[+] symporter (BASS family) proteins, as well as the increased 7-α-hydroxysteroid dehydrogenase activity (P<0.05). In contrast, LW sows exhibited enrichment of Terrisporobacter and Clostridium sensu stricto 1, alongside accumulation of primary (e.g. chenodeoxycholic acid) and unconjugated BAs (e.g. deoxycholic acid) (P<0.05). Correlation analysis demonstrated that the accumulation of Terrisporobacter and primary BAs was positively correlated with exacerbation of inflammation. In conclusion, under intensive production conditions, significant differences in the gut microbiota-BA axis between LW and LW×LR crossbred sows may underlie variations in oxidative stress and inflammatory status during late pregnancy. These findings provide valuable insights into microbiome-BA-host associations underlying the physiological advantages (enhanced antioxidant and anti-inflammatory capacity) of crossbred sows.},
}

Animals
*Gastrointestinal Microbiome/genetics
*Oxidative Stress
Female
Pregnancy
*Bile Acids and Salts/metabolism/analysis
Swine/microbiology
*Inflammation/metabolism/microbiology
RNA, Ribosomal, 16S/genetics
Feces/microbiology/chemistry
Bacteria/classification/genetics/isolation & purification

@article {pmid41335477,
year = {2025},
author = {Riskumäki, M and Ruuskanen, MO and Mäenpää, K and Ruokolainen, L and Mäkelä, MJ and Jousilahti, P and Vartiainen, E and Ottman, N and Laatikainen, T and Haahtela, T and Alenius, H and Fyhrquist, N and Sinkko, H},
title = {Shotgun metagenomics reveals distinct skin microbial species in allergen-sensitized individuals.},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
doi = {10.1099/mgen.0.001527},
pmid = {41335477},
issn = {2057-5858},
mesh = {Humans ; *Metagenomics/methods ; *Allergens/immunology ; *Skin/microbiology/virology ; Finland ; Adolescent ; *Microbiota/genetics ; Male ; Russia ; Female ; *Hypersensitivity/microbiology/immunology ; Malassezia/genetics/isolation & purification ; Immunoglobulin E/immunology ; Bacteria/genetics/classification ; Child ; },
abstract = {The Karelian region, which spans the border between Finland and Russia, presents distinct environmental exposures and lifestyles on either side of the governmental border. In the more urbanized Finnish Karelia, allergic diseases are markedly more prevalent than in the more rural Russian Karelia. Prior studies, based on amplicon sequencing, have demonstrated major differences in skin microbiotas between the two populations. However, compositional differences in microbiota between sensitized and non-sensitized (NS) individuals have not been characterized. Here, in a selected population of 112 allergen-sensitized and NS adolescents, we used shotgun metagenomics to characterize the prokaryotic, eukaryotic and viral species in the skin potentially involved in allergic sensitization via distinct environmental exposures. In the more urban Finnish Karelia, the microbiome species composition was associated with IgE-mediated allergen sensitization status, while in the more rural Russian Karelia, the composition was associated with exposure to furry pets. Finnish participants showing high IgE-mediated sensitization to common allergens (allergen-specific IgE >7.5 kU/L) had less Cutibacterium acnes and Malassezia in their skin and displayed weaker interconnectedness of the microbial co-occurrence network compared with NS participants. Moreover, Malassezia restricta strain-level differences were related to allergen sensitization in both Finnish and Russian participants. In summary, we found distinct skin microbiomes between allergen-sensitized and NS participants and tracked the bacterial and fungal species associated with the degree of allergic sensitization in the more urbanized part of the Karelian region. These findings provide new insights into the factors that shape the human skin microbiome and influence allergic diseases.},
}

Humans
*Metagenomics/methods
*Allergens/immunology
*Skin/microbiology/virology
Finland
Adolescent
*Microbiota/genetics
Male
Russia
Female
*Hypersensitivity/microbiology/immunology
Malassezia/genetics/isolation & purification
Immunoglobulin E/immunology
Bacteria/genetics/classification
Child

@article {pmid41335295,
year = {2025},
author = {Jayanandan, M and Veeraraghavan, VP and Govindarajan, S and Mariyappa Subramani, S},
title = {Development of oral dysbiosis following use of antimicrobial mouthwashes: a systematic review.},
journal = {Odontology},
volume = {},
number = {},
pages = {},
pmid = {41335295},
issn = {1618-1255},
abstract = {The oral microbiome maintains the oral and systemic health. The extensive use of antimicrobial mouthwashes to control biofilm-related diseases has increased the concerns about their effect on microbial ecology. Specific formulations may cause microbial shifts which influences both the oral and systemic physiology in an individual. This systematic review evaluates the oral dysbiosis development after antimicrobial mouthwash use and correlates the microbial changes with clinical and systemic outcomes. A comprehensive search in various databases like PubMed, Scopus, etc. (till March 2025) was done. It identified 14 relevant studies from a total of 681 screened records. Risk of bias was assessed using ROB2, ROBINS-I, CRIS, and NOS tools, with data extracted on microbial diversity, taxonomic changes, nitrate reduction capacity, and antibiotic resistance. The findings showed that chlorhexidine caused the greatest dysbiosis and reduces the microbial diversity by 40-60%, with increasing Streptococcus spp. two-to-threefold, and elevating antibiotic resistance gene prevalence. Cetylpyridinium chloride and polyhexamethylene biguanide showed milder effects, thus preserving 70-80% of commensals, while herbal and plant-based rinses (o-cymen-5-ol, StellaLife®, Rosella) reduced pathogens by 25-40% without disrupting the balance. Fluoride-arginine formulations promote beneficial bacteria by 30-50% but marginally upregulated resistance genes, whereas mechanical hygiene methods maintained over 90% microbial diversity. Suppression of nitrate-reducing bacteria was associated with reduced nitric oxide bioavailability, potentially increasing vascular and cognitive risks. Hence, antimicrobial mouthwashes especially chlorhexidine induces significant dysbiotic shifts, while herbal, postbiotic, and mechanical alternatives demonstrate safer, microbiome thereby preserving the effects which is suitable for long-term oral health maintenance.},
}

@article {pmid41335130,
year = {2025},
author = {Wang, K and Xu, Z and Ma, J and Zheng, M and Zhang, Y and Lin, Z and Ji, T},
title = {Evaluating preservation effects on honeybee gut microbiota inocula.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0275425},
doi = {10.1128/spectrum.02754-25},
pmid = {41335130},
issn = {2165-0497},
abstract = {UNLABELLED: The honeybee (Apis mellifera) gut microbiota serves as a model for host-microbe studies, as germ-free bees enable a relatively sterile system. Fresh gut homogenates are optimal for colonization, but immediate use may be limited by practical considerations, such as pathogen screening and the need to minimize repeated preparation for animal welfare. In this study, we systematically evaluated how short-term preservation conditions influence the colonization efficiency and structural integrity of the honeybee gut microbiota. Gut homogenates were prepared and either used immediately, refrigerated for one day or three days, or frozen for seven days with or without glycerol, before being fed to germ-free bees. Colonization outcomes were assessed by combining absolute quantification of bacterial 16S ribosomal RNA gene copy numbers with diversity indices and community composition analyses. Survival rates of inoculated bees did not differ significantly among treatments, but bees receiving inocula refrigerated for three days showed reduced gut mass, suggesting compromised microbial activity. Absolute quantification revealed that total bacterial loads were broadly maintained, yet taxon-specific responses varied, with Gilliamella showing marked sensitivity to freezing. Discrepancies between relative and absolute measurements highlighted the importance of absolute quantification for accurately evaluating colonization. Overall, inocula retained the ability to establish the characteristic core microbiota under all preservation conditions. Notably, refrigeration for one day preserved community features without any detectable differences from freshly prepared inocula, whereas longer refrigeration and freezing introduced measurable perturbations. These results provide methodological guidance for honeybee microbiota transplantation experiments and underscore the necessity of absolute quantification in microbiome research.

IMPORTANCE: The gut microbes of honeybees are essential for their nutrition, immunity, and overall health. To study these microbes, scientists often use germ-free bees colonized with gut communities from donor bees. Fresh preparations are ideal, but repeated preparation is time-consuming, requires pathogen checks, and may involve sacrificing many bees. In this study, we tested practical preservation methods and found that both refrigerated and frozen samples retained the ability to colonize germ-free bees. However, one day of refrigeration preserved microbial abundance and composition most similar to fresh samples, whereas longer refrigeration and freezing introduced detectable changes. These findings provide researchers with clear guidance for preparing standardized microbial inocula while also minimizing repeated dissection of donor bees, thereby improving both experimental reproducibility and animal welfare.},
}

@article {pmid41335096,
year = {2025},
author = {Ji, X and Qian, Q and Zhang, H and Cai, Q and Zhang, K and Xiao, J and Jiang, X and Li, M},
title = {ResMicroDb: a comprehensive database and analysis platform for the human respiratory microbiome.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1194},
pmid = {41335096},
issn = {1362-4962},
support = {2024YFC2607900//National Key R&D Program of China/ ; 2022YFA1304300//National Key R&D Program of China/ ; 2024YFC2607900//National Key R&D Program of China/ ; 32300078//National Natural Science Foundation of China/ ; XDA0460404//Chinese Academy of Sciences/ ; XDA0460202//Chinese Academy of Sciences/ ; },
abstract = {The respiratory microbiome plays an important role in maintaining human health. Despite the rapid growth of literature and publicly accessible data on the respiratory microbiome, a large-scale, well-curated database is still lacking. Here, we introduced ResMicroDb, a comprehensive database and analysis platform for the human respiratory microbiome. ResMicroDb contains 106 464 samples from 514 projects, spanning 10 sample sites, 72 sample types, and 146 phenotypes. Notably, it includes ~7-fold more respiratory samples than existing multi-body-site resources. To improve the reusability and accessibility of data, a standardized bioinformatics pipeline was employed to generate taxonomic profiles, and 32 metadata fields were manually curated. ResMicroDb also provides 11 908 microbe-disease associations, identified from 132 case-control studies, to deepen the understanding of microbiome-disease relationships. Additionally, ResMicroDb offers three tools for in-depth analysis: "Microbiome Composition" for visualizing taxonomic profiles of user-selected samples; "Sample Similarity Search" for inferring the characteristics of new samples by comparing them to the database based on similarity; and "Cross-study Analysis" for identifying common and specific microbial characteristics across cohorts, phenotypes and sample sites. ResMicroDb serves as a versatile and valuable resource for advancing a broad spectrum of respiratory microbiome research and clinical relevance. ResMicroDb is freely accessed at https://resmicrodb.cncb.ac.cn.},
}

@article {pmid41334942,
year = {2025},
author = {Butorac, K and Banić, M and Zucko, J and Leboš Pavunc, A and Novak, J and Jerić, I and Balog, T and Kralj, M and Penava, L and Ceilinger, M and Šušković, J and Kos, B},
title = {Modulation of the Gut Microbiota of Diabetes-Induced Mice Through Curcumin-Enriched Dietary Fibers Intervention.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70350},
doi = {10.1002/mnfr.70350},
pmid = {41334942},
issn = {1613-4133},
support = {IP-2019-04-2237//Hrvatska Zaklada za Znanost/ ; IP-2024-05-6548//Hrvatska Zaklada za Znanost/ ; KK.01.1.1.01.0002//European Commission/ ; OP KK.01.1.1.07.0040//European Commission/ ; },
abstract = {This study aimed to investigate the effect of innovative dietary fiber mixtures, comprised predominantly of resistant dextrin together with insoluble citrus fibers, fructooligosaccharides, long-chain inulin, and gum arabic, with or without curcumin or resveratrol/grape seed extract, on the intestinal microbiota of a mouse model with T2DM. The applied innovative formulations resulted in the desired changes in the distribution of gut microbiome species associated with T2DM, as revealed by QIIME2 and additionally confirmed by ANCOM. This effect was particularly pronounced in the curcumin-supplemented formulation, as evident from the enrichment of the Verrucomicrobiota representative Akkermansia muciniphila and short-chain fatty acid producers Faecalibaculum and Dubosiella, while also leading to a decrease in Patescibacteria, as well as Chlamydia muridarum, Desulfovibrio, Candidatus Saccharimonas, and Alistipes species. The administration of the examined innovative dietary fiber formulations statistically reduced the alpha diversity and altered the beta diversity of the gut microbiota in a mouse model with T2DM, in terms of abundance and presence of species analyzed with MicrobiomeAnalyst. Due to the strong influence on the composition of the gut microbiota, the innovative dietary formulations can be further evaluated for inclusion in food for special medical purposes specifically designed for the dietary management of diabetes.},
}

@article {pmid41334921,
year = {2025},
author = {Marinos, G and Zimmermann, J and Taubenheim, J and Kaleta, C},
title = {Virtual Colon: spatiotemporal modeling of metabolic interactions in a computational colonic environment.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0139125},
doi = {10.1128/msystems.01391-25},
pmid = {41334921},
issn = {2379-5077},
abstract = {Host-microbial metabolic interactions have been recognized as an essential factor in host health and disease. Genome-scale metabolic modeling approaches have made important contributions to our understanding of the interactions in such communities. One particular such modeling approach is BacArena, in which metabolic models grow, reproduce, and interact as independent agents in a spatiotemporal metabolic environment. Here, we present a modeling application of BacArena, a virtual colonic environment, which reveals spatiotemporal metabolic interactions in a computational colonic environment. This environment resembles the crypt space together with the mucus layers, the lumen, and fluid dynamics. Our proof-of-principle experiments include mono-colonization simulations of context-specific colonic cells and simulations of context-specific colonic cells with the SIHUMIx minimal model microbiome. Our simulations propose host-microbial and microbial-microbial interactions that can be verified based on the literature. Most importantly, the Virtual Colon offers visualization of interactions through time and space, adding another dimension to the genome-scale metabolic modeling approaches. Lastly, like BacArena, it is freely available and can be easily adapted to model other spatially structured environments (http://www.github.com/maringos/VirtualColon).IMPORTANCEInteractions between the human body and gut microbes are crucial for health and disease. We present the Virtual Colon, an extension of the individual-based microbiome modeling approach BacArena that mimics key features of the colon, including the crypts, mucus layers, lumen, and fluid flow. Using this model, we simulate gut environments including host cells with bacterial species alone and with a simplified gut microbiota (SIHUMIx). These simulations reveal patterns of host-microbe and microbe-microbe interactions that align with known findings. A key strength of the Virtual Colon is its ability to show how interactions unfold over time and space, offering new insights beyond traditional modeling approaches. The Virtual Colon is freely available and can be adapted to other structured biological environments (http://www.github.com/maringos/VirtualColon).},
}

@article {pmid41334892,
year = {2025},
author = {Bhatnagar, M and Burney, R and Bedawi, EO},
title = {Managing treatment failure in pleural infection.},
journal = {Expert review of respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1080/17476348.2025.2600106},
pmid = {41334892},
issn = {1747-6356},
abstract = {INTRODUCTION: Pleural infection is a common condition associated with significant morbidity, mortality, and prolonged hospital stay. Whilst antibiotics and chest tube drainage comprise initial management, over one-third of patients experience medical treatment failure, necessitating intrapleural enzyme therapy (IET) or surgery. This review examines advances in diagnosis and management of treatment failure in pleural infection.

AREAS COVERED: A literature search of PubMed, Embase, and Cochrane Library (January 2005- April 2025) was performed using keywords related to pleural infection, diagnostics, biomarkers, and treatment interventions. Treatment failure emerged as a multifactorial process involving delayed presentation, structural and physiological barriers such as increased pleural fluid viscosity, septation formation, pleural thickening, and biofilm development, alongside host factors and microbiological complexity. We review current strategies including antibiotics, chest tube drainage, IET (tPA + DNase), and surgical options, alongside emerging modalities such as next-generation sequencing, pleural biopsy, medical thoracoscopy, saline irrigation, and indwelling catheters.

EXPERT OPINION: Early identification of treatment failure within 48 hours is crucial for guiding escalation. A precision medicine approach integrating microbiological, radiological, and host-response data may redefine standards of care and improve outcomes. Future priorities include early risk stratification, biomarker-guided therapy, microbiome-informed antibiotic strategies, and improving global access to effective treatments.},
}

@article {pmid41334814,
year = {2025},
author = {López-Gutiérrez, JC and López-Hernández, D and Toro, M},
title = {Arbuscular Mycorrhizal Fungi and Phosphorus-mobilizing Microorganisms Mediate Organic Phosphorus Cycling in Tropical Savanna Soils.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf135},
pmid = {41334814},
issn = {1574-6968},
abstract = {In highly weathered tropical soils, organic phosphorus (Po) constitutes a primordial reservoir for plant P-nutrition. We studied the dynamics of Po fractions, soil phosphatase activity and P-mobilizing microflora in root compartments of non-mycorrhizal (rhizosphere and bulk soil) and mycorrhizal (mycorrhizosphere and hyphosphere) Urochloa brizantha plants growing in rhizoboxes with a low P-sorbing Entisol and a high P-sorbing Ultisol from native neotropical savannas. Inoculation with native arbuscular mycorrhizal fungi resulted in an improvement in plant P-status, particularly in the high P-sorbing soil, that coincided with transformations in more recalcitrant P fractions, a higher phosphatase activity and a higher proportion of P-solubilizing and P-mineralizing organisms in mycorrhizal compartments. We provide evidence for a mycorrhizospheric effect in low P-fertility soils that allows plants to access specific P-pools via symbiosis with arbuscular mycorrhizal fungi.},
}

@article {pmid41334655,
year = {2025},
author = {Zhang, K and Dong, H and Bian, T},
title = {Multi-omics integration and precision medicine in chronic prostatitis: from molecular mechanisms to clinical translation.},
journal = {Systems biology in reproductive medicine},
volume = {71},
number = {1},
pages = {618-629},
doi = {10.1080/19396368.2025.2586609},
pmid = {41334655},
issn = {1939-6376},
mesh = {Humans ; *Prostatitis/therapy/genetics/diagnosis/metabolism/microbiology ; Male ; *Precision Medicine ; Chronic Disease ; *Proteomics ; *Genomics ; *Metabolomics ; Translational Research, Biomedical ; Animals ; Multiomics ; },
abstract = {Chronic prostatitis (CP) imposes a considerable global disease burden, with notable regional disparities in China and significant associated healthcare costs. Traditional classification systems, particularly type III subtypes, are hindered by high symptom heterogeneity and low treatment response rates. Recent advances in multi-omics approaches have elucidated the molecular mechanisms underlying CP, including genomic and epigenetic regulation, transcriptomic and immune microenvironment interactions, metabolomic and microbiome interplay, as well as proteomic and neural remodeling. Precision diagnostic techniques are evolving, integrating multi-omics biomarkers, imaging, and functional assessments for molecular subtyping and clinical translation. Targeted therapeutic strategies are emerging, focusing on immune microenvironment modulation, neuro-immune cross-intervention, and microbiome modulation. However, challenges in clinical translation remain, including technical bottlenecks in integrating dynamic multi-omics data and limitations of animal models. To address these issues, complementary strategies between real-world evidence and traditional randomized controlled trials are proposed. Looking forward, future directions include the development of AI-driven multimodal high-precision diagnostic systems and innovative combination therapies involving targeted, immunotherapeutic, and neuro-stimulatory approaches.},
}

Humans
*Prostatitis/therapy/genetics/diagnosis/metabolism/microbiology
Male
*Precision Medicine
Chronic Disease
*Proteomics
*Genomics
*Metabolomics
Translational Research, Biomedical
Animals
Multiomics

@article {pmid41334604,
year = {2025},
author = {Cui, X and Ding, Z and Ji, Y and Wang, X and Wang, Y and Yuan, Z and Zhang, Y and Liu, K and Liu, Y},
title = {The combination of gut microbiota and metabolomics reveals the effects of polysaccharides from Schisandra chinensis on microbiota and metabolic profile in Alzheimer's disease rats.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70361},
pmid = {41334604},
issn = {1097-0010},
support = {//National Natural Science Foundation of China Young Scientists Fund/ ; },
abstract = {BACKGROUND: Polysaccharide from Schisandra chinensis (SPJ) can attenuate the progression of Alzheimer's disease (AD) by regulating changes in gut microbiota and its metabolites, but the mechanism of action is unclear. This study aimed to investigate the anti-AD effects and regulatory mechanisms of SPJ in an Aβ25-35-induced AD model from the perspective of the 'microbe-gut-brain' axis.

RESULTS: The results showed that SPJ improved spatial learning memory ability, pathological changes in the hippocampal CA1 region and intestinal barrier integrity, and modulated the composition and abundance of gut microbiota in AD rats. Meanwhile, SPJ also regulated phenylalanine, tyrosine, and tryptophan biosynthesis, and linoleic acid, α-linolenic acid, phenylalanine, and arachidonic acid metabolism in AD rats. Furthermore, correlation analysis revealed a correlation between gut microbes and metabolites.

CONCLUSION: In short, via the 'microbe-gut-brain' axis, SPJ ameliorates cognitive deficits, spatial memory loss, and neuroinflammation in AD rats. © 2025 Society of Chemical Industry.},
}

@article {pmid41334554,
year = {2025},
author = {Nabthonglang, J and Gomez, A and Rutschke, S and Santativongchai, P and Kosonsiriluk, S and Studniski, M and Wileman, B and Navanukraw, C and Boukherroub, K},
title = {Effect of bardoxolone methyl on the lower reproductive tract microbiome in turkey breeder hens.},
journal = {Frontiers in physiology},
volume = {16},
number = {},
pages = {1703742},
pmid = {41334554},
issn = {1664-042X},
abstract = {INTRODUCTION: Fertility decline in aging turkey breeder hens is associated with reduced sperm storage in the uterovaginal junction (UVJ), inflammation, oxidative stress, and tissue aging. The mucosal microbiome is an important contributor to subfertility, with shifts in immune function, inflammation, and oxidative stress linked to microbial changes. Bardoxolone methyl, a potent activator of the nuclear erythroid 2-related factor 2 (NRF2) pathway, enhances antioxidant defenses and reduces inflammation. This study investigated if bardoxolone methyl treatment alters the microbial composition and diversity of the UVJ and vagina in turkey hens.

METHODS: Forty turkey hens (59 weeks old) were randomly assigned to a bardoxolone methyl group (n = 20) or a control group (n = 20). Birds received intramuscular tail injections of bardoxolone methyl or vehicle, every other day for two weeks. Swabs from the UVJ and vagina (VAG) were collected for 16S rRNA sequencing. Microbial diversity, differential taxonomic composition, and predicted functional pathways were assessed using QIIME2, PICRUSt2, and R-based statistical packages. Microbiome profiles revealed significant differences between UVJ and VAG communities.

RESULTS: The VAG showed higher bacterial richness, while both sites were dominated by Firmicutes, Proteobacteria, Thermoproteota, and Actinobacteriota phyla, indicator species analyses identified enrichment of Staphylococcus and Escherichia in UVJ, and Lactobacillaceae in VAG. Bardoxolone methyl did not significantly alter global alpha diversity but selectively modulated unweighted beta diversity and low-abundance taxa, enriching Corynebacterium in UVJ and rare taxa like Armatimonadota and Omnitrophota in the VAG. Functional predictions indicated bardoxolone methyl's association with enrichment of pathways including energy metabolism, nucleotide biosynthesis, protein quality control, and redox balance, particularly in the UVJ.

DISCUSSION: This study provides the first characterization of the turkey lower reproductive tract microbiome, revealing tissue-specific communities and functional profiles between the UVJ and vagina. Bardoxolone methyl treatment did not alter overall microbial diversity, but selectively enriched low-abundance taxa and metabolic pathways related to energy metabolism, nucleotide biosynthesis, and stress resilience, particularly in the UVJ. These findings indicate that bardoxolone methyl treatment can finetune microbial functional capacity without destabilizing overall community structure. The results also highlight the importance of considering tissue-specific differences and functional potential when investigating reproductive function.},
}

@article {pmid41334445,
year = {2025},
author = {Jing, M and Jiang, Y},
title = {Microbiome-mediated crosstalk between T2DM and MASLD: a translational review focused on function.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1677175},
pmid = {41334445},
issn = {1664-2392},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/metabolism/complications ; *Gastrointestinal Microbiome/physiology ; Animals ; *Non-alcoholic Fatty Liver Disease/microbiology/metabolism ; *Fatty Liver/microbiology/metabolism ; },
abstract = {Type 2 diabetes mellitus (T2DM) and metabolic dysfunction-associated steatotic liver disease (MASLD) frequently co-occur and aggravate one another through shared pathways of insulin resistance, low-grade inflammation and disordered lipid handling. Framing their interaction through the gut-liver-pancreas axis, this review synthesizes recent progress with a function-first emphasis, moving beyond taxonomic lists to the microbial outputs most consistently linked to dual metabolic-hepatic endpoints. We summarize how short-chain fatty acids (SCFAs), bile acids (BAs), lipopolysaccharide (LPS) and other microbe-associated molecular patterns, branched-chain amino-acid (BCAA) catabolites, trimethylamine N-oxide (TMAO) and endogenous ethanol reach the liver via portal inflow or the enterohepatic BA cycle and act on epithelial, immune and endocrine interfaces, including the farnesoid X receptor (FXR), G-protein-coupled BA receptor 1 (TGR5) and fibroblast growth factor 19/15 signaling. Mechanistic routes-barrier dysfunction and endotoxaemia; SCFA signaling with effects on enteroendocrine tone and substrate flux; BA remodeling that resets hepatic and pancreatic set-points; and nitrogen/choline and ethanol pathways that promote lipotoxic injury-offer biologically coherent explanations for parallel trajectories of hyperglycemia and steatosis/inflammation. We appraise therapeutic modulation spanning diet and fermentable substrates, live biotherapeutics/postbiotics, BA-targeting drugs, fecal microbiota transplantation and metabolic/bariatric surgery, and we outline clinically actionable biomarker opportunities using function-based panels (fermentative capacity, BA transformation, inflammatory ligands, nitrogen/methyl flux) integrated with host metabolites and genetics for diagnosis, risk stratification and response prediction. By advocating standardized reporting, careful control of diet/medications and composite metabolic-hepatic endpoints in prospective trials, this review provides a practical framework to accelerate translation from association to targeted prevention and therapy that improves glycemic control and MASLD activity in parallel.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology/metabolism/complications
*Gastrointestinal Microbiome/physiology
Animals
*Non-alcoholic Fatty Liver Disease/microbiology/metabolism
*Fatty Liver/microbiology/metabolism

@article {pmid41334216,
year = {2025},
author = {Szabó, S and Kovács-Weber, M and Pap, TI and Dolányi, Á and Pajor, F and Bodnár, Á and Vajda, T and Heincinger, M and Szabó, RT},
title = {Effect of postbiotics on the production parameters of rearing goose.},
journal = {Veterinary and animal science},
volume = {30},
number = {},
pages = {100541},
pmid = {41334216},
issn = {2451-943X},
abstract = {Our aim was to measure the mortality, live body weight, feed conversion, intake and detect the weight and stiffness of the liver, liver colour, breast and thigh weight as an effect of the dry form of Burain® postbiotic supplementation in rearing goose. The goslings were allocated into 5 equal groups: control (without supplementation), group 1 (1 g/kg postbiotic during the starter and grower period), group 2 (2 g/kg postbiotic during the starter and grower period), group 3 (0.2 g/kg postbiotic during the starter and grower period), group 4 (1 g/kg postbiotic during the starter period). Granulated feed and drinking water were provided ad libitum to all rearing goose. Supplementation significantly increased body weight in group 2 (6321.84±664.9 g) on week 8. Group 2 showed a significantly reduced feed conversion ratio (1.51±0.04), while groups 1 and 4 exhibited significantly lower daily feed intake than the control during the starter phase. There were no significant differences among groups in foie gras parameters or in thigh and breast weights. The liver weight and stiffness were found to be significantly positively correlated in each treatment group. The supplementation made a significant difference in the parameters of b* and L* for liver colour, but not for a* values. The impact of postbiotic supplementation in the rearing period is extended to weeks. Further investigations are needed to connect information from rearing to the fattening phase and the gut microbiome in goose.},
}

@article {pmid41334169,
year = {2025},
author = {Kashyap, AS and Manzar, N and Chaudhary, P and Ali, S},
title = {Editorial: Unravelling microbial interactions in plant health and disease dynamics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1716380},
doi = {10.3389/fmicb.2025.1716380},
pmid = {41334169},
issn = {1664-302X},
}

@article {pmid41334162,
year = {2025},
author = {Elbehiry, A and Marzouk, E and Abalkhail, A},
title = {Antimicrobial resistance at a turning point: microbial drivers, one health, and global futures.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1698809},
pmid = {41334162},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) is a major health threat of the 21st century, undermining the effectiveness of modern medical interventions and reversing decades of progress in infection control. Its drivers include microbial evolution, horizontal gene transfer, inappropriate use in human and veterinary medicine, agricultural practices, environmental reservoirs, and uneven regulation. This review integrates microbial, clinical, and environmental perspectives within a One Health framework. At the microbial level, resistance arises through mutation, gene transfer, and biofilm-associated tolerance, with soil, wastewater, and wildlife serving as conduits for spreading resistance elements. Advances in diagnostics-including matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), whole-genome sequencing (WGS), digital PCR, and CRISPR-based assays are transforming detection and surveillance, but deployment remains uneven, particularly in low- and middle-income countries. Antimicrobial stewardship now extends beyond hospitals, supported by decision support systems, artificial intelligence (AI), and community programs; however, gaps in surveillance capacity and policy implementation continue to limit impact. One Health linkages connect agricultural use, wastewater, and wildlife exposure with human risk, embedding clinical decisions within ecological and veterinary contexts. Persistent gaps include fragmented regulation, limited involvement of microbiologists in policy development, and weak incentives for antibiotic innovation. Priority directions include biomarker-guided prescribing, CRISPR-directed antimicrobials, microbiome-sparing therapeutics, and genomics-informed surveillance that integrates clinical and environmental data. Positioning the clinical microbiology laboratory as an operational hub can align rapid diagnostics, interpretive reporting, antimicrobial stewardship, and integrated surveillance (GLASS, EARS-Net, NARMS, and wastewater/wildlife monitoring) on a common platform. Clear reporting triggers and concise case vignettes can translate laboratory results into actionable bedside decisions and policy measures across diverse resource settings, with measurable benefits for patient outcomes and public health.},
}

@article {pmid41333884,
year = {2025},
author = {Sousa, LM and Izquierdo, VS and Cappellozza, BI and Moriel, P},
title = {Maternal supplementation with Bacillus-based direct-fed microbials altered the maternal and offspring fecal microbiome.},
journal = {Translational animal science},
volume = {9},
number = {},
pages = {txaf145},
pmid = {41333884},
issn = {2573-2102},
abstract = {This study evaluated the effects of maternal supplementation of a Bacillus-based direct-fed microbial (DFM) on fecal microbiome of heifer-calf pairs. At the start of the study (day 0), 72 pregnant Brangus crossbred beef heifers (20 to 22 mo of age) were stratified by body weight (BW; 431 ± 31 kg) and body condition score (BCS; 6.0 ± 0.36) and randomly allocated into 1 of 12 bahiagrass pastures (1 ha and 6 heifers/pasture). Treatments were assigned to pastures and consisted of heifers supplemented with 1 kg/hd/d of soybean hulls added (BAC) or not (CON) with DFM containing Bacillus subtilis 810 and B. licheniformis 809 (3 g/hd/d; 6.6 × 10[9] colony forming unit; Bovacillus; Novonesis, Lyngby, Denmark) from day 0 to 242 (139 ± 4 d prepartum to 104 ± 4 d postpartum). Calves were early weaned on day 242 and then allocated to drylot pens and fed the same diet until day 319. On days 271 and 287, calves were vaccinated against pathogens associated with bovine respiratory disease. Fecal samples were collected from 3 heifers per pasture on days 0, 90 and 180 and from 2 to 3 calves per pen on days 242 and 272. Shannon and Simpson diversity indexes tended to be greater (P = 0.09) for BAC vs. CON heifers. Clostridium and Blautia relative abundances on day 90 and average Mogibacterium relative abundance were lower (P ≤ 0.03) for BAC vs. CON heifers, whereas Bacteroides and Porphyromonas relative abundances tended (P ≤ 0.08) to be greater for BAC vs. CON heifers. Shannon diversity index did not differ (P ≥ 0.14) between CON and BAC calves, whereas Simpson diversity index remained constant (P = 0.98) for CON calves from day 242 to 272 but increased (P = 0.02) for BAC calves from day 242 to 272. Effects of maternal treatment × day tended (P = 0.06) to be detected for Paraprevotella genus, which Paraprevotella relative abundance on day 242 was lower (P = 0.05) for BAC vs. CON calves on day 242, and did not differ (P = 0.89) between treatments on day 272. Relative abundance of Bacteroides was greater (P = 0.01), whereas Slackia was lower (P < 0.01) for BAC vs. CON calves. Blautia, Butyrivibrio, and Methanobrevibacter relative abundance tended (P = 0.08) to be lower for BAC vs. CON calves. In conclusion, exclusive maternal supplementation with a Bacillus-based DFM during gestation and early lactation modulated the fecal microbiota of both heifers and their offspring.},
}

@article {pmid41333806,
year = {2025},
author = {Al Bataineh, MT and Dash, NR and Mysara, M and Saeed, O and Alkhayyal, N and Talaat, IM and Bendardaf, R and Saber-Ayad, M},
title = {Metagenomic analysis of gut microbiota in colorectal adenocarcinoma in the MENA region.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1634631},
pmid = {41333806},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Metagenomics ; Male ; Female ; Middle Aged ; *Adenocarcinoma/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Aged ; DNA, Bacterial/genetics/chemistry ; Middle East ; Feces/microbiology ; Phylogeny ; DNA, Ribosomal/genetics/chemistry ; },
abstract = {BACKGROUND: Growing evidence suggests that gut microbiota plays a role in the development of colorectal cancer (CRC), and a few bacterial strains have been linked to carcinogenesis. Contrary to the Western population, the relationship between pro-cancer microorganisms and CRC among Middle Eastern individuals remains largely unexplored. Ninety-eight samples from Middle Eastern individuals with and without CRC were subjected to microbial profiling based on the 16S rRNA gene.

RESULTS: The CRC group exhibited a more complex gut microbiota with clusters that were significantly distinct from those of the control group. The taxonomic orders Caulobacterales, Rhizobiales, Sphingomonadales, and Burkholderiales, along with the genera Recibecterium and Sphingobium, were overrepresented in the CRC samples based on differential abundance testing between the CRC and control groups. Utilizing 16S-based functional prediction, we identified a significant enrichment of pathways vital for pentose and glucuronate interconversions, metabolism of terpenoids and polyketides, spliceosome, and dTMP kinase pathways within the CRC group. Moreover, we observed a link between Herbaspirillum huttiense and the pathways regulating the actin cytoskeleton; this intriguing connection may provide insights into the molecular mechanisms underlying cytoskeletal rearrangement and carcinogenesis triggered by H. huttiense.

CONCLUSIONS: The findings of this study support the connection between gut microbiota and the development of CRC and highlight region-specific microbial signatures that may serve as non-invasive diagnostic biomarkers or predictive tools for early screening in Middle Eastern populations, where CRC is increasingly diagnosed at advanced stages. These insights could inform the development of microbiome-based screening panels and personalized prevention strategies adapted to the MENA region's unique genetic, dietary, and environmental profiles.},
}

Humans
*Colorectal Neoplasms/microbiology
*Gastrointestinal Microbiome/genetics
RNA, Ribosomal, 16S/genetics
*Metagenomics
Male
Female
Middle Aged
*Adenocarcinoma/microbiology
*Bacteria/classification/genetics/isolation & purification
Aged
DNA, Bacterial/genetics/chemistry
Middle East
Feces/microbiology
Phylogeny
DNA, Ribosomal/genetics/chemistry

@article {pmid41333804,
year = {2025},
author = {Waechter, C and Wilkens, JN and Fehse, L and Heider, D and Sassani, K and Chatzis, G and Weyand, S and Pankuweit, S and Luesebrink, U and Soufi, M and Pöling, J and Braun, T and Ausbuettel, F and Ruppert, V},
title = {Comparative analysis of full-length 16s ribosomal RNA gene sequencing in human oropharyngeal swabs using primer sets with different degrees of degeneracy.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1658615},
pmid = {41333804},
issn = {2235-2988},
mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *Oropharynx/microbiology ; *Microbiota/genetics ; *DNA Primers/genetics ; *Bacteria/genetics/classification/isolation & purification ; Sequence Analysis, DNA/methods ; DNA, Bacterial/genetics ; Saliva/microbiology ; },
abstract = {BACKGROUND: Full-length 16S rRNA gene sequencing using nanopore technology has become increasingly relevant for profiling complex microbial communities, including the human oral microbiome. Primer selection plays a critical role in amplification bias and taxonomic resolution, yet remains insufficiently investigated for oropharyngeal samples.

METHODS: We conducted a comparative analysis of two primer sets with differing degrees of degeneracy - Oxford Nanopores (ONT) standard 27F primer (27F-I) and a more degenerate variant (27F-II) - for full-length 16S rRNA gene sequencing of 80 human oropharyngeal swab samples using ONTs MinION Mk1C. Alpha diversity and taxonomic profiles were statistically compared between primer sets and benchmarked against a large-scale salivary microbiome dataset (n=1,989) from healthy individuals.

RESULTS: Primer choice significantly impacted microbial community composition and diversity. The more degenerate primer set 27F-II yielded significantly higher alpha diversity (Shannon index: 2.684 vs. 1.850; p < 0.001) and detected a broader range of taxa across all phyla. The taxonomic profiles generated with 27F-II strongly correlated with the reference dataset (Pearson's r = 0.86, p < 0.0001), whereas profiles generated with 27F-I showed weak correlation (r = 0.49, p = 0.06). 27F-I overrepresented Proteobacteria and underrepresented key genera such as Prevotella, Faecalibacterium, and Porphyromonas.

CONCLUSION: Our findings demonstrate that primer degeneracy has a substantial effect on taxonomic resolution and biodiversity estimates in oropharyngeal 16S rRNA gene sequencing. The more degenerate 27F-II primer set seams to more faithfully captures the complexity of the human oropharyngeal microbiome and aligns more closely with population-level reference data. These results underscore the importance of careful primer selection and support the adoption of degenerate primers as a methodological standard in nanopore-based oral microbiome research.},
}

Humans
*RNA, Ribosomal, 16S/genetics
*Oropharynx/microbiology
*Microbiota/genetics
*DNA Primers/genetics
*Bacteria/genetics/classification/isolation & purification
Sequence Analysis, DNA/methods
DNA, Bacterial/genetics
Saliva/microbiology

@article {pmid41333317,
year = {2025},
author = {Ullah, S and Wu, C and Zou, X and Zhong, Y and Ahmad, A and Jan, AU and Cong, Y and Chen, Y and Li, L},
title = {Understanding microbiota-driven oncogenesis: The role of metabolites in tumorigenesis.},
journal = {iScience},
volume = {28},
number = {12},
pages = {113945},
pmid = {41333317},
issn = {2589-0042},
abstract = {The gut microbiota profoundly influence human health through its composition and metabolic activity, which are shaped by diet and host factors. Disruption of this equilibrium, known as dysbiosis, has been implicated in cancer development. Microbial metabolites act as key mediators connecting the gut microbiome to tumor progression by altering the tumor microenvironment and modulating signaling pathways in tumor and immune cells. This review examines the mechanistic links between the gut microbiota, its metabolites, and tumorigenesis, emphasizing how microbial metabolism of host- and diet-derived compounds affects oncogenic and genotoxic processes in colorectal cancer (CRC). It also explores how dietary and host factors modulate microbial composition and function, influencing cancer susceptibility. Understanding these interconnected processes provides conceptual insight into the microbiota-cancer axis and highlights opportunities for microbiome-targeted interventions in cancer prevention and therapy.},
}

@article {pmid41333064,
year = {2025},
author = {Zhao, B and Sun, J and Xiang, L and Su, Z},
title = {Exercise as a modulator of gut microbiota for improvement of sleep quality: a narrative review.},
journal = {Frontiers in neuroscience},
volume = {19},
number = {},
pages = {1639099},
pmid = {41333064},
issn = {1662-4548},
abstract = {Sleep quality is a cornerstone of physical and mental well-being, yet millions of individuals worldwide suffer from chronic sleep disturbances. Recent developments in microbiome research have shown that the microbiota-gut-brain axis regulates sleep by two-way communication between the gut and brain. Exercise is well-documented for its beneficial impact on sleep, yet emerging evidence indicates that one mechanism by which it achieves this may involve the modulation of gut microbiota. This narrative review examines the developing triadic relationship among exercise, gut microbiota, and sleep. It examines how exercise influences microbial diversity, the production of sleep-related metabolites like serotonin, GABA, and SCFAs, and immune responses that collectively shape sleep architecture. Additionally, the review highlights physiological factors influenced by exercise-such as gut motility, intestinal barrier function, and bile acid metabolism-that may impact the gut ecosystem and, in turn, sleep. Although encouraging results, deficiencies persist in our comprehension of the specific mechanisms connecting these domains. This review underscores the need for interdisciplinary research and suggests that targeting the gut microbiota via customized exercise interventions presents a promising, non-pharmacological strategy for enhancing sleep quality.},
}

@article {pmid41332906,
year = {2025},
author = {Zhao, Z and Lu, L and Yi, Y and Gao, N and Hu, J and Han, G and Ma, X},
title = {Gut microbiota signature in a cohort of Chinese patients with rosacea.},
journal = {Biochemistry and biophysics reports},
volume = {44},
number = {},
pages = {102361},
pmid = {41332906},
issn = {2405-5808},
abstract = {BACKGROUND: Rosacea is a chronic inflammatory skin disease characterized by diverse symptoms and variable clinical progression, which can significantly impair patients' quality of life and mental health. The exact etiology of rosacea remains elusive. It has been hypothesized that specific microorganisms may trigger symptom onset and play crucial roles in the pathogenesis of the disease.

OBJECTIVE: We performed a case-control study to investigate the gut microbiome of rosacea patients compared to controls matched by age, sex in China.

METHODS: The study cohort comprised eight patients diagnosed with rosacea and eight age- and sex-matched healthy controls residing in Beijing. Metagenomic sequencing was performed using on a llumina Novaseq 6000 platform. Hospital Anxiety and Depression Scale was used to evaluate the severity of anxiety and depression of rosacea patients. Skindex-16 score was used to assess dermatology-specific health-related quality of life (HrQoL) in patients with rosacea. The clinical evaluation of acne was done using the ECLA score.

RESULTS: The rosacea patients showed higher HADS and Skindex-16 score (15.375 ± 1.302 and 46 ± 9.75 respectively) vs healthy controls (3.425 ± 1.308 and 0 respectively). A clear distinction was observed between the rosacea group and the control group, characterized by a significant increase in the abundance of Turicibacter_sp._TJ11, Turicibacter_sp._H121,Turicibacter_sp._TA25,Turicibacter_sp._T129,Ruminococcus_sp._AF18-22,Ruminococcus_sp._CAG:379,Ruminococcus_sp._AM2829LB,Ruminococcus_callidus, Ruminococcus_sp._AM36-18,Ruminococcus_sp._AF43-11,Ruminococcus_sp._AM28-41,Streptococcus sp. 23.2,Streptococcus infantarius, Streptococcus vestibularis, Streptococcus salivarius, Streptococcus gordonii, Clostridium_sp._CAG:798, Clostridium_tertium, Alistipes_sp._Z76 and Lachnospiraceae_bacterium_XBB2008in the rosacea group. In contrast, reduced levels were detected in the rosacea group for Clostridium_sp._AF12-41, Clostridium_sp._CAG:299, Clostridium_sp._OM05-5BH,Clostridium_sp._AF24-2LB, Clostridium_sp._AM18-55, Clostridium_sp._CAG:43, Clostridium_sp._OM047,Clostridium_sp._TF1113AC,Clostridium_sp._OF134,Clostridium_disporicum, Butyrivibrio_sp._CB08,Butyrivibrio_sp._INlla14, Roseburia_sp._CAG:50 (p < 0.05). Pearson correlation analysis revealed that Gemmiger_sp._An120 was positively correlated with Skindex-16 and negatively correlated with ECLA score (P < 0.05). Clostridium_sp._CAG:299 was negatively correlated with HADS scores and positive correlation with ECLA score (P < 0.05). KEGG pathway analysis found KO05034, KO04024 and KO00920 pathways exhibited increased activity in the Rosacea group (P < 0.05).

CONCLUSIONS: The gut microbiota in individuals with rosacea displayed changed from that of healthy control. These microbial alterations may contribute to the pathogenesis of rosacea through multiple mechanisms, including impairment of the intestinal barrier function, induction of pro-inflammatory cytokine release, and modulation of neurotransmitter synthesis. By integrating taxonomic shifts with functional alterations, this study provides deeper insights into the gut ecosystem changes associated with systemic inflammation in rosacea.},
}

@article {pmid41332831,
year = {2025},
author = {Armet, AM and Li, F and Deehan, EC and Nikolaeva, DD and Delannoy-Bruno, O and Siegwald, L and Berger, B and Castelli, KM and Rodionov, DA and Arzamasov, AA and Liu, J and Seethaler, B and Cole, JL and Nguyen, KN and Jin, M and Zhao, YY and Sharma, AM and Curtis, JM and Proctor, SD and Bischoff, SC and Wismer, WV and Osterman, AL and Bakal, JA and Greiner, R and Field, CJ and Knights, D and Prado, CM and Walter, J},
title = {Mechanistic insights into microbiome-dependent and personalized responses to dietary fibre in a randomized controlled trial.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.20.25340625},
pmid = {41332831},
abstract = {Dietary fiber supplementation can reduce cardiometabolic risk, but its effective use is limited by incomplete understanding of fibre-microbiome interactions and highly individualized responses. We tested acacia gum (AG; fermentable fibre), resistant starch type 4 (RS4; fermentable fibre), and microcrystalline cellulose (MCC; non-fermentable control fibre) in a six-week randomized trial in adults with excess body weight. Multi-omics profiling revealed distinct, structure-specific microbiota and short-chain fatty acid shifts with AG and RS4, which were not directly linked to physiological outcomes. Improvements in inflammation, gut barrier function, and satiety occurred across all arms, indicating fermentation-independent effects. AG reduced plasma ghrelin, linked to microbial carbohydrate-active enzyme genes targeting its structures. Machine-learning models predicted individualized, fiber-specific effects on blood pressure (AG) and C-reactive protein (RS4) from microbial pathways and fecal bile acids. These findings delineate fermentation-dependent and independent mechanisms of fibre action and provide a mechanistic basis for personalized fibre supplementation. Trial registration: ClinicalTrials.gov NCT02322112.},
}

@article {pmid41332770,
year = {2025},
author = {Anton, L and Kholod, O and Phatate, R and Ferguson, B and Klohonatz, K and Goods, BA and Gerson, KD},
title = {Multiomic analysis reveals that polyamines alter G. vaginalis -induced cervicovaginal epithelial cell dysfunction.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.20.689523},
pmid = {41332770},
issn = {2692-8205},
abstract = {An anaerobe-dominant, Lactobacillus -deplete cervicovaginal microbiome is associated with adverse reproductive outcomes. Gardnerella vaginalis , a common cervicovaginal anaerobe, alters cervicovaginal epithelial cell function, resulting in inflammatory immune responses and epithelial barrier breakdown. Specific host-microbial mechanisms inducing this epithelial dysfunction remain unknown. Here we show microbe-specific alterations in cervicovaginal epithelial cell metabolite profiles where G. vaginalis , but not Lactobacillus crispatus , increases polyamine biosynthesis. Pretreatment with polyamines (putrescine, spermidine and spermine) globally shifts G. vaginalis -induced transcriptomic profiles. Alterations in transcripts encoding enzymes responsible for polyamine synthesis and catabolism provides further evidence that G. vaginalis modifies polyamine biosynthesis. Additionally, polyamine-mediated transcriptomic changes include genes related to bacterial defense, inflammation, and epigenetic processes. Polyamines mitigate G. vaginalis -induced inflammatory responses through reduction of cytokines, chemokines, and matrix metalloproteinases. The ability of cervicovaginal metabolites to alter microbe-mediated changes in epithelial cell function suggests that metabolite-microbe interactions are critical mediators of epithelial defense against a Lactobacillus -deplete microbiota.},
}

@article {pmid41332743,
year = {2025},
author = {Patan, A and Xing, S and Charron-Lamoureux, V and Hu, Z and Deleray, V and Agongo, J and El Abiead, Y and Mannochio-Russo, H and Mohanty, I and Gouda, H and Zemlin, J and Rajkumar, P and Lee, C and Leanos, D and Weimann, N and Tsuda, W and Giddings, S and Bui, T and Kvitne, KE and Zhao, HN and Zuffa, S and Nguyen, V and Andrade, A and Gonçalves Nunes, WD and Caraballo-Rodríguez, AM and Caetano David, L and Carver, J and Bandeira, N and Wang, M and Burnett, LA and Siegel, D and Dorrestein, PC},
title = {Charting the Undiscovered Metabolome with Synthetic Multiplexing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.18.689170},
pmid = {41332743},
issn = {2692-8205},
abstract = {In untargeted metabolomics, reference MS/MS libraries are essential for structural annotation, yet currently explain only 6.9% of the more than 1.7 billion MS/MS spectra in public repositories. We hypothesized that many unannotated features arise from simple, biologically plausible transformations of endogenous and exposure-derived compounds. To test this, we created a reference resource by synthesizing over 100,000 compounds using multiplexed reactions that mimic such biochemical transformations. 91% of the compounds synthesized are absent from existing structural databases. Through improvements in the construction of the computational infrastructure that enables pan repository-scale MS/MS comparisons, searching this biologically inspired MS/MS library increased the overall reference-based match rate by 17.4%, yielding over 60 million new matches and raising the global pan-repository MS/MS annotation rate to 8.1%. By facilitating structural hypotheses for previously uncharacterized MS/MS data, this framework expands the accessible detectable biochemical landscape across human, animal, plant, and microbial systems, revealing previously undescribed metabolites such as ibuprofen-carnitine and 5-ASA-phenylpropionic acid conjugates arising from drug-host and host-microbiome co-metabolism.},
}

@article {pmid41332636,
year = {2025},
author = {Donado, CEP and Liu, S and Seravalli, J and Auchtung, JM and Rose, DJ},
title = {Cadmium toxicity to the human gut microbiome varies depending on composition.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.19.689308},
pmid = {41332636},
issn = {2692-8205},
abstract = {UNLABELLED: Cadmium (Cd) is a toxic heavy metal with detrimental impacts on the gut microbiota. We investigated the compositional and functional effects of acute Cd exposure on human fecal microbiotas using 24-hour in vitro cultures from 21 healthy adult donors. Regression analysis of butyrate production in the absence (Cd-) versus presence (Cd+) of Cd identified three categories of microbial responses: sensitive, intermediate, and resilient. Under Cd stress, sensitive microbiomes exhibited significant decreases in butyrate [-3.22±0.96 log 2 (Cd+/Cd-), p=0.001] coupled with elevated acetate [1.53±1.83 log 2 (Cd+/Cd-), p=0.003] and lactate [1.86±0.95 log 2 (Cd+/Cd-), p=0.001] production. In contrast, resilient microbiomes did not show significant changes in butyrate [0.22±0.43 log 2 (Cd+/Cd-), p=0.59] or acetate [-0.18±0.35 log 2 (Cd+/Cd-), p=0.26] and exhibited attenuated increases in lactate compared with sensitive microbiomes [0.45±0.43 versus 1.86±0.95 log 2 (Cd+/Cd-), p=0.002]. Sensitive microbiomes had a larger shift in global microbiota composition under Cd stress than resilient microbiomes (weighted UniFrac distance: 0.098±0.026 versus 0.073±0.035, p=0.04). Several genera were significantly different between sensitive and resilient communities after exposure to Cd, but the most striking was Anaerostipes (7.15 centered-log-ratio difference, Cd+/Cd-, q<0.001). Network analysis revealed a significantly greater disruption of microbial interactions in sensitive communities compared with resilient (χ [2] = 9.21, p = 0.002). Multivariable Association with Linear Models revealed that, in resilient communities, butyrate production was primarily associated with Faecalibacterium in the absence of Cd (q<0.001) and Anaerostipes in the presence of Cd (q=0.005). These findings highlight distinct gut microbial responses to acute Cd exposure and provide a foundation to investigate microbiota features underlying Cd sensitivity or resilience.

IMPORTANCE: Cadmium is a widespread environmental contaminant that reaches the human intestine, where it can disrupt the gut microbial community and negatively impact digestive and systemic health. However, this study demonstrates that human gut microbiomes vary in their responses to cadmium exposure: sensitive communities exhibit losses of beneficial organisms, particularly butyrate-producing taxa that contribute to intestinal integrity and metabolic balance, whereas resilient communities retain microorganisms with this key functional capacity. This work advances our understanding of how gut microbial functions may mitigate the adverse effects of cadmium exposure by identifying the compositional features that distinguish sensitive from resilient microbiomes. These findings highlight the importance of elucidating microbiome-mediated mechanisms that help sustain host health and lay the groundwork for deeper mechanistic studies aimed at mitigating cadmium toxicity.},
}

@article {pmid41332528,
year = {2025},
author = {Aufiero, MA and Hohl, TM},
title = {Antibiotic-induced microbiota disruption impairs neutrophil-mediated immunity to respiratory Aspergillus fumigatus infection in mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.18.689104},
pmid = {41332528},
issn = {2692-8205},
abstract = {UNLABELLED: Aspergillus fumigatus is an environmental mold that forms ubiquitous airborne conidia and can cause life-threatening infections in immunocompromised individuals. Invasive aspergillosis occurs in patients with quantitative or qualitative neutrophil defects, who often receive systemic antibiotics to prevent or manage bacterial infections. Antibiotic-induced bacterial dysbiosis has been linked to impaired neutrophil bactericidal activity and to intestinal commensal bacteria escape during systemic candidiasis, though it remains unclear whether receipt of antibacterial antibiotics impairs neutrophil-dependent defenses against inhaled mold pathogens in the lung. Herein, we measured the outcome of Aspergillus challenge in C57BL/6J mice that were treated with different antibiotics in the drinking water for three weeks prior to experimental infection. We found that ampicillin but not neomycin or vancomycin treatment significantly increased murine mortality and lung fungal burden. The heightened susceptibility was associated with impaired fungal killing by lung-infiltrating neutrophils and monocytes, as well as reduced neutrophil production of NADPH oxidase 2 (NOX2)-dependent reactive oxygen species (ROS). These findings demonstrate that systemic antibiotic treatment can compromise pulmonary anti- Aspergillus immunity and suggest that the host microbiota can enhance neutrophil fungicidal activity by promoting NOX2-mediated ROS production.

IMPORTANCE: Aspergillus fumigatus is an environmental mold that causes invasive pulmonary disease in immunocompromised individuals. Owing to limited diagnostic tools, a narrow arsenal of effective treatments, and rising antifungal resistance, the World Health Organization (WHO) has designated Aspergillus as a critical priority fungal pathogen, highlighting the urgent need for further research. Patients with compromised immunity often receive broad-spectrum antibiotics to prevent or treat opportunistic infections, leading to significant disruption of the resident commensal microbiota. This antibiotic-induced dysbiosis has been linked to Clostridium difficile colitis and to intestinal overgrowth of vancomycin-resistant Enterococcus and Candida parapsilosis , preceding bloodstream infection. However, the impact of antibiotic treatment on susceptibility to invasive pulmonary aspergillosis remains undefined. In this study, we found that oral treatment with ampicillin, but not neomycin or vancomycin, significantly increased mortality in mice following Aspergillus infection. Neutrophils from the lungs of ampicillin-treated mice also showed markedly impaired fungal killing. These findings raise the possibility that preserving microbiome integrity during antibiotic treatment could enhance immune protection against invasive aspergillosis in at-risk patient groups.},
}

@article {pmid41332522,
year = {2025},
author = {Salman, T and Luo, Z and Johnson, D and Noorani, AA and Wan, Z and Bordieanu, B and Ye, ZW and Penrod, RD and Xian, H and Fitting, S and Kalivas, PW and Jiang, W},
title = {Cannabis-enriched oral Actinomyces induces anxiety-like behavior via impairing mitochondria and GABA signaling.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.21.689724},
pmid = {41332522},
issn = {2692-8205},
abstract = {UNLABELLED: The human oral microbiome is increasingly recognized as a contributor to brain health, yet its mechanisms remain unclear. Our previous work revealed that oral Actinomyces species was enriched in chronic cannabis smokers. Here, we show oral inoculation of cannabis use-associated Actinomyces species, especially A. meyeri , to wild-type C57BL/6 mice leads to anxiety-like behaviors, non-region-specific microglia activation, mitochondrial dysfunction, and reduced GABAergic neurotransmission, without evidence of bacterial translocation to the brain, neuroinflammation, and memory decline. Notably, Actinomyces species-producing metabolites, i.e., arginine and argininosuccinate, were increased in both oral swabs and brain following inoculation in vivo . These Actinomyces species-producing metabolites induced mitochondrial dysfunction and oxidative stress in neurons in vitro , indicating a neuropathogenic role and aligning with reduced GABAergic neurotransmission in vivo. Together, these results suggest that oral cannabis-associated dysbiosis impacts behavior through mitochondrial stress and impaired inhibitory signaling, indicating the oral-brain metabolic axis is potentially consequential in neuropsychiatric disorders.

TEASER: Chronic heavy cannabis use-enriched oral bacteria can drive anxiety and neuropathogenesis in mice.

HIGHLIGHTS: Cannabis-associated oral Actinomyces enrichment induces anxiety-like behavior in miceMicroglial activation occurs without neuroinflammation (IL-1β, TNF-α, and IL-6)Mitochondrial hyperactivation and reduced inhibitory GABAergic signaling.},
}

@article {pmid41332499,
year = {2025},
author = {Feng, X and Gan, X and Ren, B and Wan, Z and Wang, Y and Gao, X and Zhu, Z},
title = {Spatial and temporal dynamic changes of oral microbiome in removable partial denture wearers: a longitudinal study using full-length 16S rRNA sequencing.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2589655},
pmid = {41332499},
issn = {2000-2297},
abstract = {OBJECTIVE: This longitudinal study aimed to characterize the spatial and temporal dynamics of oral microbiome colonization on removable partial dentures (RPDs) and corresponding dental surfaces at species-level resolution, to elucidate ecological succession patterns and identify potential pathogenic colonizers.

METHODS: We conducted a longitudinal study of 10 participants requiring RPDs. Plaque samples were collected from four sites at five time points. The microbial communities were profiled using PacBio full-length 16S rRNA sequencing, enabling high accuracy taxonomic assignment to the species level. Bioinformatic analyses included alpha/beta diversity, LEfSe, and PICRUSt2 functional prediction.

RESULTS: Significant differences in microbial composition were observed between RPD and dental plaques, despite similar alpha diversity. Temporal analysis revealed a progressive decrease in RPD plaque diversity. Notably, the potential respiratory pathogen Klebsiella pneumoniae was detected in early RPD biofilms. A three-stage ecological succession model for RPD biofilm was proposed, initiating with acidogenic pioneers, followed by functional amplification of taxa involved in extracellular polysaccharide production, and culminating in a stable, acid-tolerant community.

CONCLUSION: This study provides a species-level understanding of microbiome changes associated with RPDs, confirms differences between RPD plaque and dental plaque, proposes a succession model for RPD-associated bacteria, and determines key turning points and potential pathogens.},
}

@article {pmid41332420,
year = {2025},
author = {Wang, X and Wang, Q and Guo, X and Tong, P and Li, C and Zhou, D and Yin, F},
title = {Regulating effects of hydroxytyrosol acyl esters with different acyl chain lengths and isomers on gut microbiota: insights from in vitro gastrointestinal digestion, fecal fermentation and Lactobacillus fermentation.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70360},
pmid = {41332420},
issn = {1097-0010},
support = {//Dalian Outstanding Youth Science and Technology Talent Project (2023RY018)/ ; //The National Natural Science Foundation of China (32472260)/ ; },
abstract = {BACKGROUND: Phenolic compounds are increasingly recognized for their diverse health benefits, particularly their potent antioxidant capacities. To enhance its lipophilicity, stability and bioavailability, hydroxytyrosol has been successfully esterified with various alkyl chains lengths and different isomers (branched-chain and straight-chain), forming hydroxytyrosol-fatty acid acyl esters (Hty-Es). These synthesized Hty-Es, have garnered significant interest and are widely explored in fields such as food preservation because of their superior antioxidant properties. However, little is known about the digestion, fermentation characteristics and the effects on the intestinal microbiota in vitro.

RESULTS: This study evaluated the influence of hydroxytyrosol (HTy) esterified with fatty acids of varying chain lengths (C2:0, C3:0, C4:0n, C4:0i, C6:0, C8:0, C12:0, C14:0 and C16:0) on polyphenol sustained-release properties and gut microbiota modulation during simulated in vitro digestion, fecal fermentation and Lactobacillus fermentation. The findings demonstrated partial hydrolysis of HTy-Es in both simulated gastric fluid and intestinal fluid to slowly release a small amount of polyphenols, suggesting their potential to reach the colon and cecum. Analysis of fermented fecal samples revealed that HTy-Es supplementation modulated microbiota composition, elevating the diversity of Actinobacteriota, Firmicutes and Bacteroidetes, whereas it decreased the diversity of Desulfobacterota, Actinobacteriota, Chloroflexi and Verrucomicrobiota. At the genus level, the growth of detrimental genera (Escherichia shigella) was successfully suppressed. Notably, HTy-Es with distinct acyl chain lengths and isomer configurations exhibited divergent effects on polyphenol bioaccessibility and gut microbiome diversity, underscoring their structure-dependent functional potential for health applications.

CONCLUSION: Conclusively, the slow release of fatty acids and HTy clearly demonstrated that HTy-Es would be an effective approach for enhancing the beneficial health effects of fatty acids and HTy. © 2025 Society of Chemical Industry.},
}

@article {pmid41332240,
year = {2025},
author = {Chua, W and Hei, Y and Koh, LF and Yap, BLH and Saw, HL and Fernandes, THM and da Silva, EB and Goh, S and Dawson, TL and O'Donoghue, AJ and Common, JE and Li, H},
title = {Aspartyl protease MfSAP2 is a key virulence factor in mycelial form of skin fungi Malassezia furfur.},
journal = {The Biochemical journal},
volume = {},
number = {},
pages = {},
doi = {10.1042/BCJ20253109},
pmid = {41332240},
issn = {1470-8728},
support = {H18/01/a0/016//Agency for Science, Technology and Research/ ; MOH-000612-00//Ministry of Health -Singapore/ ; },
abstract = {Malassezia is the dominant genus of fungi residing on human skin and is associated with both healthy skin and many dermatological conditions. Among these skin diseases, pityriasis versicolor (PV) has strong etiological connections with Malassezia. In the hyper or hypo-pigmented scales of PV patients, Malassezia is enriched in its mycelial form which is rarely present on healthy skin. How these Malassezia hyphae contribute to disease pathology in PV is unknown. In this study, we observed a distinct shift in the extracellular proteolytic activity when Malassezia furfur transitions from yeast to hyphae. We identified that the expression of the aspartyl protease MfSAP2 is dramatically upregulated at both the mRNA and protein level when M. furfur is in the mycelial form. We determined the protease substrate specificity and observed that MfSAP2 can degrade corneodesmosome proteins, which are intercellular adhesive proteins between corneocytes in the stratum corneum. In a 3D human skin model with MfSAP2 treatment, we observed clear degradation of corneodesmosin, a component of the corneodesmosome. Taken together, our study demonstrates that a secreted protease is a key virulence factor associated with M. furfur mycelium and is potentially involved in the disease pathogenesis of PV.},
}

@article {pmid41331985,
year = {2025},
author = {Lopez-Oliva, I and Chapple, IL and Paropkari, A and Saraswat, S and Sharma, P and Serban, S and de Pablo, P and Raza, K and Filer, A and Dietrich, T and Grant, M and Kumar, PS},
title = {Dysbiosis-Mediated Inflammation: A Pathophysiological Link Between Rheumatoid Arthritis and Periodontitis.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.70063},
pmid = {41331985},
issn = {1600-051X},
support = {R01 DE022579/DE/NIDCR NIH HHS/United States ; U01 CA188250/CA/NCI NIH HHS/United States ; PB-PG-0609-19100//Department of Health, Social Services and Public Safety, UK Government/ ; DRF-2014-07-109//Department of Health, Social Services and Public Safety, UK Government/ ; PDF-2014-07-055//Department of Health, Social Services and Public Safety, UK Government/ ; //Department of Health, Social Services and Public Safety, UK Government/ ; },
abstract = {AIM: To explore mechanistic links between rheumatoid arthritis (RA) and periodontitis (PD) through the lens of subgingival microbial dysbiosis-mediated inflammation.

METHODS: Subgingival plaque from 100 volunteers with RA and PD (RAPD), 22 with RA (RAnoPD), 18 with PD (PDnoRA) and 19 healthy controls (noRAnoPD) was analysed using 16S-amplicon sequencing, semi-quantitative bead-based flow cytometry to measure crevicular fluid cytokines and ELISA to quantify antibodies to oral pathogens and systemic inflammatory markers in serum. The RAPD group had been randomised to receive intensive non-surgical periodontal therapy (PMPR) or oral hygiene alone and reviewed at 3 and 6 months in our previously reported study.

RESULTS: Subgingival microbial dysbiosis, as evidenced by higher species richness, alpha-diversity and higher levels of known and putative periodontal pathobionts, was evident at baseline in RAnoPD, RAPD and PDnoRA. Higher serum antibodies to oral pathogens were recorded in RAPD. PMPR restored host-microbial homeostasis in RAPD within 3 months. Significant decreases in serum antibodies to microbial antigens and clinical measures of RA activity were seen after 3 and 6 months in the PMPR group but not controls.

CONCLUSIONS: We demonstrate a mutualistic influence of RA and PD, beginning with RA-induced dysbiosis of the periodontal microbiome, progressing to periodontal inflammation and culminating in PD-driven exacerbation of systemic inflammation.},
}

@article {pmid41331872,
year = {2025},
author = {Zhu, L and Hu, J and Li, J and Qu, X and Zhou, X and Gan, G and Liu, Y and Liu, S and Chen, X},
title = {Sini San ameliorates symptoms of depression by modulating gut microbiota structure, Tryptophan metabolism, and short-chain fatty acid levels.},
journal = {BMC complementary medicine and therapies},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12906-025-05190-5},
pmid = {41331872},
issn = {2662-7671},
support = {82004253//National Natural Science Foundation of China/ ; 82004253//National Natural Science Foundation of China/ ; 82004253//National Natural Science Foundation of China/ ; 82004253//National Natural Science Foundation of China/ ; 82004253//National Natural Science Foundation of China/ ; [2023] No.2//Key Discipline Construction Project of Traditional Chinese Medicine in Hubei Province-Febrile Diseases/ ; 2023AFD146//Natural Science Foundation of Hubei Province/ ; 2023AFD146//Natural Science Foundation of Hubei Province/ ; 2023AFD146//Natural Science Foundation of Hubei Province/ ; WJ2023Z002//the Key Scientific Research Project of Hubei Provincial Health and Wellness Commission/ ; },
abstract = {BACKGROUND: Sini San (SNS) is a traditional Chinese medicinal formulation originating from the "Treatise on Febrile Diseases", an ancient text that has been historically employed for treating depression. However, the underlying mechanisms by which SNS potentially ameliorates symptoms of depression remain unclear. This study aimed to elucidate the role of gut microbiota in tryptophan metabolism and examine the involvement of short-chain fatty acids (SCFAs) in the putative antidepressant effects of SNS.

METHODS: A rat model of depression using chronic unpredictable mild stress (CUMS) was established through simultaneous modeling and treatment for six consecutive weeks. The possible therapeutic effect of SNS on CUMS-induced rats was thoroughly assessed using body weight measurements, open-field tests, and sucrose preference tests. Alterations in rat gut microbiota were analyzed using full-length 16 S rRNA third-generation sequencing. Furthermore, metabolomic analysis was performed on fecal samples. An enzyme-linked immunosorbent assay (ELISA) was used to quantify tryptophan (Trp), serotonin (5-HT), and kynurenine (Kyn) in the hippocampal and colonic tissues. Reverse transcription quantitative PCR (RT-qPCR) was used to measure the mRNA levels of TPH-1 and TPH-2 in hippocampal and colonic tissues. Immunofluorescence was used to assess hippocampal IDO-1 and IBA-1 expression. Finally, gas chromatography-mass spectrometry (GC-MS) was used to analyze the SCFAs content in fecal samples.

RESULTS: Administration of SNS significantly alleviated depressive symptoms induced by CUMS, as demonstrated by increased body weight, improved sucrose preference, and a statistically significant decrease in immobility time during the forced swim test (P < 0.05). The Shannon and Simpson indices were elevated following SNS treatment, signifying an enhancement in both the quantity and variety of the gut microbiota. Analysis using 16 S rRNA gene sequencing revealed that SNS influenced the composition of the gut microbiome, favorably increasing the presence of beneficial bacteria, such as Firmicutes, Lactobacillaceae, Ruminococcaceae, and Oscillospiraceae, while simultaneously decreasing the levels of potentially detrimental bacteria, such as Muribaculaceae, Prevotellaceae, Lachnospiraceae, and Alloprevotella. Fecal metabolomic studies identified 87 metabolites, of which 57 were differentially expressed, most notably l-tryptophan and phenylalanine. These metabolites were primarily linked to 15 metabolic pathways, with notable enrichment in the biosynthetic pathways of phenylalanine, tyrosine, and tryptophan, as well as the metabolic pathways of arachidonic acid and phenylalanine. Metabolomic profiling indicated that SNS stimulated the kynurenine pathway, leading to increased levels of metabolites with antidepressant properties, such as Trp, 5-HT, and Kyn, in both hippocampal and colonic tissues. In addition, SNS promoted the synthesis of SCFAs, particularly butyrate and propionate, which are known for their neuroprotective properties.

CONCLUSIONS: The present study suggests that the antidepressant effects of SNS can be attributed to its ability to modulate the structure of the gut microbiota, consequently regulating tryptophan metabolism and SCFA levels, which ultimately ameliorate symptoms of depression. These findings provide experimental evidence supporting the concept of the brain-gut axis in depression treatment and lay a foundation for further investigation of the underlying antidepressant mechanisms of the SNS.},
}

@article {pmid41331870,
year = {2025},
author = {Chen, M and Wang, J and Yang, Y and He, Y and Li, L},
title = {The interplay of estrogen, gut microbiome, and bone immunity in osteoporosis.},
journal = {Cell communication and signaling : CCS},
volume = {23},
number = {1},
pages = {516},
pmid = {41331870},
issn = {1478-811X},
support = {CSTB2023NSCQ-MSX0956//Natural Science Foundation of Chongqing/ ; 2023B23//Teaching Research Proiect of Army Medical University/ ; 2022YQB033//Xingiao hospital Young DoctIncubation Program/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Osteoporosis/immunology/microbiology/metabolism/pathology ; *Estrogens/metabolism ; *Bone and Bones/immunology ; Animals ; },
abstract = {Osteoporosis is a global health concern arising from estrogen deficiency, intestinal dysbiosis, and dysregulation of the bone immune system. The absence of estrogen after menopause created environmental changes within the gut, where the microbial growth of the body was disturbed by the endocrine hormone, and inflammation increases due to the gut-bone axis, which leads to heightened bone loss. The gut microbiota, composed of bacteria and their metabolites such as short-chain fatty acids, play a crucial role in bone immune regulation by modulating immune cell function, influencing bone cell activity, and mediating epigenetic modifications. Malfunction of this system, characterized by the activation of immune cells and the imbalance of cytokines, also leads to the development of osteoporosis. Treatment strategies involved the regulation of the dysbiosis of the gut microbiota, reposition estrogen to the body, and immune modulation. The future direction should be the clarification of these interactions between estrogen and intestinal microflora, identification of new therapeutic targets, and personalization of osteoporosis management.},
}

Humans
*Gastrointestinal Microbiome
*Osteoporosis/immunology/microbiology/metabolism/pathology
*Estrogens/metabolism
*Bone and Bones/immunology
Animals

@article {pmid41331711,
year = {2025},
author = {Lee, SH and Ha, NG and Jang, YH},
title = {Unraveling the Pathogenesis of Asian Atopic Dermatitis: Key Characteristics and Insights.},
journal = {Annals of dermatology},
volume = {37},
number = {6},
pages = {317-326},
doi = {10.5021/ad.25.008},
pmid = {41331711},
issn = {2005-3894},
support = {20023929/MOTIE/Ministry of Trade, Industry and Energy/Korea ; /SCH/Soonchunhyang University/Korea ; },
abstract = {Atopic dermatitis (AD) is a chronic skin condition influenced by genetic, environmental, and immune factors, with notable ethnic variations in its prevalence and mechanisms. In Asian populations, distinct immunopathogenic features include the significant roles of helper (Th) 17 and Th22 cytokine pathways, differing from other ethnic groups. Key genetic variations related to immune regulation and skin barrier function are more prevalent in Asians. Microbiome studies reveal the role of Staphylococcus aureus in AD skin and emerging microbial species linked to microbiome dysbiosis and the gut-skin axis. Environmental factors like pollution and fine dust further exacerbate symptoms in Asia. This study consolidates findings to highlight the genetic, immunological, microbiome, and environmental factors contributing to AD's unique characteristics in Asians. Tailored treatment approaches are essential for improving outcomes and management of AD in diverse populations.},
}

@article {pmid41331700,
year = {2025},
author = {Borum, LS and Bartolomaeus, TUP and Lamont, RF and Bagge, JR and Markó, L and Vinter, CA and Löber, U and Dechend, R and Forslund-Startceva, SK and Joergensen, JS},
title = {Probiotic ice cream influences gut and vaginal microbiota in women at high risk of preterm birth: a randomized controlled study.},
journal = {Maternal health, neonatology and perinatology},
volume = {11},
number = {1},
pages = {43},
pmid = {41331700},
issn = {2054-958X},
abstract = {BACKGROUND: Research into probiotic use in pregnancy typically focuses on general probiotic strains. We instead investigated the relation between intake of ice cream with vaginal commensal probiotics (L. crispatus, L. gasseri, L. jensenii, L. rhamnosus GR-1; these may govern a stable microbiota and may carry beneficial functions in the vagina), throughout pregnancy, and the impact on gut and vaginal microbiomes, in women at high risk of preterm birth.

METHODS: This was a randomised controlled feasibility trial where the impact on gut and vaginal microbiomes was assessed by using 16 S rRNA gene sequencing and qPCR. In total 43 pregnant women were randomized, with 29 assigned to the intervention group and 14 to the control group. Both groups provided vaginal and rectal swabs by self-sampling at gestational time points. Pregnancy outcomes were registered through hospital records, and ice cream adherence and study experience was recorded.

RESULTS: We observed statistically significant gut and vaginal Lactobacillus increase during first half of pregnancy in all women with a continued increase in the second half in women compliant with the intervention. L. crispatus was found more often in the intervention group, and L. gasseri, L. jensenii and L. rhamnosus GR-1 in the ice cream could be recovered in both rectal and vaginal samples. Finally, vaginal Prevotella spp, as well as gut Gardnerella and Atopobium spp, significantly decreased upon intervention. Adherence to the intervention varied but gradually decreased throughout the study with 30.4% displaying excellent adherence in the first time period.

CONCLUSIONS: We conclude that vaginal commensal probiotics administered in ice cream can be an effective method of optimizing the vaginal and intestinal health in pregnant women at high risk of preterm birth when administered regularly. We give recommendations for future studies.

TRIAL REGISTRATION: Clinicaltrials.gov registration number 18/27209. Date of registration 03/25/2019. Date of first enrolment 04/08/2019.},
}

@article {pmid41331687,
year = {2025},
author = {Abedi, Z and Sheikh Beig Goharrizi, MA and Abbasi, A and Sadat Soleimani Zakeri, N and Jangi, H},
title = {Metagenomic insights into microbial community alterations and co-occurrence networks in infective endocarditis.},
journal = {Genomics & informatics},
volume = {23},
number = {1},
pages = {25},
pmid = {41331687},
issn = {1598-866X},
abstract = {BACKGROUND: Infective endocarditis (IE) is a serious infection of the heart valves, and standard culture methods often miss the bacteria responsible, especially in culture-negative cases. To address this, we used 16S rRNA gene-based next-generation sequencing (NGS) on heart valve tissue. This approach allowed us to map out the bacterial communities present and evaluate their potential role in IE.

RESULT: We identified six key bacterial genera-Enterococcus, Streptococcus, Coxiella, Staphylococcus, Haemophilus, and Cutibacterium-plus three specific species: Streptococcus troglodytae, Haemophilus parainfluenzae, and Coxiella burnetii. Our co-occurrence analysis showed that these bacteria tend to exist independently within infected valve tissue, with no significant correlations between them.

CONCLUSION: We detected bacterial taxa, including Cutibacterium and Streptococcus troglodytae. Although S. troglodytae is rarely associated with IE, and Cutibacterium comprises low-abundance bacteria not typically linked to this condition. These findings demonstrate the value of NGS in identifying pathogens that standard culture methods may overlook. As these results are based on computational analyses, further laboratory validation is required. Incorporating NGS into diagnostic protocols may enhance pathogen detection in culture-negative IE and support more targeted treatment and prevention strategies.},
}

@article {pmid41331684,
year = {2025},
author = {Núñez-Pons, L and Cusano, LM and Chiarore, A and Mirasole, A and Teixidó, N and Efremova, J and Mazzella, V},
title = {Too hot for my bugs: mediterranean heatwave disrupts associated microbiomes in the sponge Petrosia ficiformis.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00830-2},
pmid = {41331684},
issn = {2524-6372},
support = {CN_00000033//National Biodiversity Future Center - NBFC/ ; CN_00000033//National Biodiversity Future Center - NBFC/ ; P05//EuroMarine-EMBRC 2020 call/ ; },
abstract = {BACKGROUND: Global climate change exacerbates the incidence of marine heatwaves (MHWs), which have increased in intensity and frequency over the past years, causing severe impacts on marine coastal ecosystems. MHWs have already triggered mass mortalities of habitat-forming species, including corals, sponges and gorgonians, in temperate, tropical and polar seas. In the Mediterranean, these high peaks of temperature have been shown to affect several sponge species, and likely, their symbiotic microbial communities. During the summer of 2022, populations of the sponge Petrosia ficiformis (Poiret, 1789) were conspicuously observed with signs of thermal stress linked to a MHW around the Gulf of Naples (Tyrrhenian Sea, Italy). These included depigmentation spots and tissue texture alterations, which often evolved in necrotic processes and eventual death. At the peak of the MHW, however, apparently thermoresistant sponges co-occurred with sensitive unhealthy specimens. In order to explore potential microbial drivers correlated with these divergent thermal-stress tolerances, Healthy and Unhealthy individuals were sampled along the coast of Ischia Island in early September 2022.

RESULTS: Prokaryotic community characterization based on the 16 S rRNA gene revealed dissimilar compositions in Unhealthy versus apparently Healthy sponges. Increased alpha diversity richness and low evenness in thermosensitive sponges were due to an extensive presence of rare taxa, and to the introduction of potentially pathogenic groups (e.g., Vibrio spp.). Major microbial families regularly associated with P. ficiformis - SAR202, Caldilineaceae, Poribacteria or TK17, were replaced in thermosensitive specimens by professed opportunistic groups within Lentimicrobiaceae, Rhodobacteraceae or Flavobacteriaceae. In turn, conservancy of hub microbes and thermotolerant symbionts (e.g., Rhodothermaceae, Thermoanaerobaculaceae) in Healthy sponges were observed during this disrupting event. Unhealthy microbiomes reflected lower network stability with respect to Healthy holobionts, due to the inconsistency of functional keystone taxa and prevalence of transient microbes.

CONCLUSIONS: Dysbiotic shifts due to colonization of scavenger groups and opportunistic microbes, and interconnectivity loss characterized thermally stressed sponges. In contrast, resistant specimens retained keystone symbionts that could have ensured functional cooperation, and maintenance of prokaryotic community cohesion under thermal stress. The existence of stress-resistant phenotypes in sponge holobionts offers a glimmer of hope for species persistence, and their study may identify potential source populations for ecosystem recovery.},
}

@article {pmid41331251,
year = {2025},
author = {Zhao, Y and Chen, H and Huang, J and Chistoserdova, L and Yu, Z},
title = {The gut methanotroph Methylocystis intestini modulates intestinal peristalsis and fat metabolism via reducing methane levels.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66596-w},
pmid = {41331251},
issn = {2041-1723},
support = {32300051//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Methane, a predominant component of human intestinal gas, has been reported to be associated with a reduction in intestinal transit speed, as well as correlations with elevated body mass index. While the gut methanogenic archaea that produce this gas have been studied, the countervailing role of methane-consuming bacteria (methanotrophs) within the human gut ecosystem remains a critical, under-explored area. The potential for these bacteria to act as a built-in sink for intestinal methane and thereby mitigate its negative physiological effects is unknown. Here, we isolate an unreported methanotroph from human fecal samples, classified as Methylocystis intestini. Using a mouse model, we observe that methane challenge is associated with gastrointestinal motility and fat metabolism. We then demonstrate that the administration of Methylocystis intestini effectively reverses these dysfunctional processes, restoring motility and metabolic parameters. Additional analysis of methane-oxidation genes abundance in 1207 public metagenomic sequences from individuals with varying health statuses, including obesity and constipation, provides consistent correlative support for our experimental conclusions. Expanding this view to a global scale, we conducted a metagenomic survey of 550 human fecal samples from populations across five continents. This broader analysis reveals that methane-oxidizing genes are not a rarity but a common feature of the human gut microbiome, being detectable in over 91% of samples. This ubiquity underscores their fundamental role in human biology. Collectively, our findings establish gut methanotrophs as key mediators of intestinal methane level. Their presence is widespread across global populations, and their functional capacity can balance the effects of methane on host physiology. This work elucidates a crucial component of gut homeostasis and opens a promising avenue for developing microbiome-based therapeutic strategies aimed at managing methane-related gastrointestinal disorders by harnessing the power of these native methane-consuming bacteria.},
}

@article {pmid41331216,
year = {2025},
author = {Wang, ZM and He, CJ and Hou, J and Zhang, SQ and Zhang, HB and Wu, LP},
title = {The Role of Roux-en-Y Gastric Bypass and Sleeve Gastrectomy in Improving Type 2 Diabetes Through Modulation of Gut Microbiota and Metabolites.},
journal = {Obesity surgery},
volume = {},
number = {},
pages = {},
pmid = {41331216},
issn = {1708-0428},
abstract = {With the rising incidence of type 2 diabetes mellitus (T2DM) worldwide, the search for effective treatments has become an important direction of contemporary medical research. Bariatric metabolic surgery, as a new therapeutic approach, has made remarkable progress in improving T2DM in recent years. In this paper, we collected studies on the mechanisms by which metabolic surgery improves T2DM by altering the intestinal flora and its metabolites in the last 5 years, and systematically analysed the effects of different weight loss surgeries, such as gastric bypass and sleeve gastrectomy, on the composition of the intestinal flora. Then, the changes in the metabolites of the flora triggered by these surgeries and the possible downstream molecular mechanisms were explored. Although it has been revealed that the intestinal flora is altered by bacterial genera after metabolic surgery, the downstream mechanisms remain unclear. The aim of this review is to provide a new perspective for a deeper understanding of the microbiological mechanisms of metabolic surgery for T2DM and to provide a theoretical basis for future microbiome-based therapeutic strategies.},
}

@article {pmid41331190,
year = {2025},
author = {Guo, A and Wang, C and Chen, Y and Zhang, W and Yan, J and Wang, X},
title = {Comparative analysis of prokaryotic and fungal communities dynamics in Fusarium wilt-infected and healthy tomato rhizospheres at different growth stages.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {12},
pages = {495},
pmid = {41331190},
issn = {1573-0972},
support = {JKTD2025002//Outstanding Scientist Project of Beijing Academy of Agriculture and Forestry Sciences/ ; },
mesh = {*Solanum lycopersicum/microbiology/growth & development ; *Rhizosphere ; *Fusarium/pathogenicity/genetics ; *Plant Diseases/microbiology ; Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology ; *Fungi/classification/genetics/isolation & purification ; Microbiota ; },
abstract = {Tomato is severely affected by Fusarium wilt, yet the dynamics of root-associated microbial communities linked to disease across growth stages remain unclear. This study used 16S rDNA and ITS amplicon sequencing to compare the trends in prokaryotic and fungal communities in rhizosphere of healthy and diseased tomato plants at the young and peak fruiting stages. At the young fruiting stage, healthy samples showed higher prokaryotic diversity than diseased ones, but this advantage diminished by the peak fruiting stage; in contrast, fungal diversity remained consistently higher in healthy samples across both stages. LEfSe analysis indicated that the biomarkers in prokaryotic and fungal communities vary between growth stages in healthy samples, whereas diseased samples exhibit a degree of consistency in fungal biomarkers-particularly the pathogens Plectosphaerella, Neocosmospora and Fusarium. Co-occurrence networks revealed that these three pathogens have lower abundance and strong positive correlations during the young fruiting stage, but as their abundance increases at the peak fruiting stage, the positive correlation lost, suggesting altered interactions during disease advancement. These findings uncover growth stage-dependent shifts in rhizosphere microbiome structure and pathogen dynamics during Fusarium wilt development, offering novel insights for designing stage-specific, precision-based disease management strategies in tomato cultivation systems.},
}

*Solanum lycopersicum/microbiology/growth & development
*Rhizosphere
*Fusarium/pathogenicity/genetics
*Plant Diseases/microbiology
Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Plant Roots/microbiology
*Fungi/classification/genetics/isolation & purification
Microbiota

@article {pmid41330943,
year = {2025},
author = {Aggarwal, D and Bellis, KL and Blane, B and de Goffau, MC and Wagner, J and Ng, DYK and Raven, KE and Naydenova, P and Kaptoge, S and Burton, S and Henry, R and Perry, C and Walker, MR and Moore, C and Churcher, C and Girgis, ST and de Sousa, CR and Sarkane, L and Brennan, J and Akram, A and Duthie, S and Johnson, E and Juhasz, M and Anderson, D and Irvine, S and McMahon, A and Lay, L and Salter, SJ and Raisen, C and Ba, X and Holmes, M and van Tonder, AJ and Di Angelantonio, E and Butterworth, AS and Geoghegan, JA and Danesh, J and Parkhill, J and Peacock, SJ and Harrison, EM},
title = {Large-scale characterisation of the nasal microbiome redefines Staphylococcus aureus colonisation status.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10415},
pmid = {41330943},
issn = {2041-1723},
support = {211864/Z/18/Z//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 222903/Z/21/Z//Wellcome Trust (Wellcome)/ ; 17.07(1)//Isaac Newton Trust/ ; NIHR203312, NIHR203337,//DH | National Institute for Health Research (NIHR)/ ; CH/12/2/29428//British Heart Foundation (BHF)/ ; },
mesh = {Humans ; *Staphylococcus aureus/isolation & purification/genetics ; Female ; *Microbiota/genetics ; *Staphylococcal Infections/microbiology ; Male ; *Nose/microbiology ; *Carrier State/microbiology ; Adult ; Middle Aged ; Young Adult ; Nasal Cavity/microbiology ; Staphylococcus epidermidis/isolation & purification ; },
abstract = {Staphylococcus aureus colonises the nose in humans, with individuals defined as persistent, intermittent or non-carriers. Unlike the gut microbiome, the nasal microbiome has not been studied in large numbers of people. Here, we define the nasal microbiome in ~1100 individuals from the CARRIAGE study (ISRCTN: ISRCTN10474633) and combine with S. aureus culture data. We identify seven community state types (CST), including two CSTs more common in females. Approximately 70% of those who are persistently colonised with S. aureus have a CST dominated by S. aureus, while non-carriers are distributed across the other six CSTs. Intermittent carriers are not a unique state but have microbiomes that resemble non- or persistent carriers. Persistent carriage is positively associated with S. aureus abundance, and negatively associated with three Corynebacterium species, Dolosigranulum pigrum, Staphylococcus epidermidis, and Moraxella catarrhalis; the microbiome can be exploited with machine learning to accurately predict the persistence of S. aureus colonisation. Finally, we find that certain S. aureus lineages are better adapted to colonisation than others. Our data provides a comprehensive view of the nasal microbiome with respect to S. aureus colonisation, describing two key states: a S. aureus dominated CST in which S. aureus shapes the microbiome, and CSTs in which S. aureus is rare or absent.},
}

Humans
*Staphylococcus aureus/isolation & purification/genetics
Female
*Microbiota/genetics
*Staphylococcal Infections/microbiology
Male
*Nose/microbiology
*Carrier State/microbiology
Adult
Middle Aged
Young Adult
Nasal Cavity/microbiology
Staphylococcus epidermidis/isolation & purification

@article {pmid41330371,
year = {2025},
author = {Zagieboylo, AP and Mo, R and Lim, B and Goodman, AL},
title = {A commensal bacterium secretes effector proteins to establish population heterogeneity in the gut.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.11.009},
pmid = {41330371},
issn = {1934-6069},
abstract = {The gut microbiome, comprising hundreds of individual species, is a complex and dynamic host-associated microbial community. However, how microbes interact within populations of the same species is largely unexplored. Using single-cell approaches, we discover that the human gut microbe Bacteroides thetaiotaomicron forms distinct sub-populations in the gut environment, which can be distinguished using N-hydroxysuccinimide (NHS) ester probes. This heterogeneity results from a locus encoding two secreted effector proteins and a cognate immunity factor. At the population level, this locus is among the most significantly upregulated across the B. thetaiotaomicron transcriptome in response to gut colonization; at the single-cell level, its variable expression leads to heterogeneity within the population. Sub-populations form in response to these effectors, exhibit distinct gene expression programs, and remain stable over time. Together, these findings demonstrate that prominent gut commensals establish population heterogeneity by producing and responding to secreted effector proteins.},
}

@article {pmid41330369,
year = {2025},
author = {Cole, CG and Zhang, ZJ and Dommaraju, SR and Dong, Q and Pope, RL and Son, SS and McSpadden, EJ and Woodson, CK and Lin, H and Dylla, NP and Sidebottom, AM and Sundararajan, A and Mitchell, DA and Pamer, EG},
title = {Lantibiotic-producing bacteria impact microbiome resilience and colonization resistance.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.11.007},
pmid = {41330369},
issn = {1934-6069},
abstract = {A subset of commensal bacterial strains secretes bacteriocins, such as lantibiotics, to inhibit or kill neighboring bacteria, thereby protecting their niche in the gut. The antimicrobial spectrum of lantibiotics includes pathogens, offering a potential therapeutic approach for antibiotic-resistant infections. However, the impact of lantibiotic-producing bacteria on the microbiome remains poorly defined. We find that bacterial species encoding lanthipeptide genes in hospitalized patients are present in greater abundance than lantibiotic-deficient strains of the same species. Among the lanthipeptide sequences, some overlapped with the lantibiotic genes of Blautia pseudococcoides SCSK (BpSCSK). In mice, BpSCSK administration prevents intestinal recolonization by a wide range of commensal species following antibiotic-induced dysbiosis and markedly reduces fecal concentrations of microbiota-derived metabolites. Lantibiotic-mediated dysbiosis results in sustained loss of colonization resistance against Klebsiella pneumoniae and Clostridioides difficile infection. Our findings reveal the impact of lantibiotic-producing bacterial species on microbiome resilience and susceptibility to infection following antibiotic treatment.},
}

@article {pmid41330368,
year = {2025},
author = {Liu, R and Zhang, Y and Ge, S and Cho, JY and Esteves, NC and Zhu, J and Hsiao, A},
title = {Diet modulates Vibrio cholerae colonization and competitive outcomes with the gut microbiota.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.11.004},
pmid = {41330368},
issn = {1934-6069},
abstract = {The amount or type of dietary macronutrients dramatically changes the microbiota and physicochemical environment of the gut. Because the microbiota plays key roles in pathogen susceptibility, macronutrients could impact infection outcomes. We show that dietary protein sources differentially restrict colonization of Vibrio cholerae (V. cholerae) as well as impact pathogen-dependent changes in microbiota composition. Specifically, dietary proteins, notably casein, alter levels of the V. cholerae central flagellar regulator, FlrA, which controls expression of the type VI secretion system (T6SS), a key mediator of intra-bacterial competition. Resultant decreases in T6SS lead to a competitive disadvantage for V. cholerae against human commensal Escherichia coli, as well as changes in the abundance and composition of a model human gut microbiota. Mutations in FlrA restore V. cholerae T6SS expression and abrogate diet-dependent impacts on V. cholerae infection. These findings suggest dietary interventions for restricting V. cholerae and highlight the importance of diet in pathogen-commensal interactions.},
}

@article {pmid41330292,
year = {2025},
author = {Sarfraz, W and Hussain, M and Chan, CM and Chen, C and Khalid, N and Razavi, BS and Rezaei Rashti, M},
title = {Microplastics and anammox: Unravelling the hidden threats to nitrogen cycling and microbial resilience.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140654},
doi = {10.1016/j.jhazmat.2025.140654},
pmid = {41330292},
issn = {1873-3336},
abstract = {Microplastics (MPs) are emerging contaminants that significantly alter soil ecosystems, particularly by disrupting nitrogen (N) cycling processes. This review assessed the impact of MPs on anaerobic ammonia oxidation (AnAOB) in soil, with a focus on their interactions with key soil parameters such as soil texture, pH, organic matter, heavy metals, and biofilm formation. Microplastics influence N removal efficiency (NRE) by modifying microbial habitats, destabilizing biofilms, and altering enzymatic activities. Their hydrophobic and electrostatic properties facilitate the adsorption of heavy metals, which further inhibit activity of anammox bacteria. The anammox bacteria perform optimally in neutral to slightly alkaline conditions (pH 7.5-8.5), where enzymatic activities remain stable, supporting efficient N removal. In acidic soils (pH < 6.5), MPs undergo increased chemical leaching, releasing toxic additives and heavy metals that impair microbial function. However, in alkaline conditions (pH > 8.5), heavy metals remain bound to MPs, reducing their bioavailability and limiting microbial accessibility to essential nutrients. Organic matter-rich soils enhance microbial resilience but can also shift competition toward denitrifies, potentially increasing nitrate accumulation and nitrous oxide emissions. Biofilms formed on MPs can act as microbial hotspots, stabilizing bacterial populations while reducing anammox efficiency by promoting non-anammox N transformations. The presence of MPs not only enhance anammox activity but also increase the abundance of denitrification genes, contributing to enhanced N reduction processes. These findings indicate that MPs not only alter soil microbial dynamics but also disrupt the delicate balance of the N cycle, leading to reduced NRE and increased greenhouse gas emissions, raising concerns about their long-term impact on soil fertility and ecosystem sustainability.},
}

@article {pmid41330219,
year = {2025},
author = {Guo, J and Xu, Y and Chen, Q and Zhang, H},
title = {Integrative analysis of transcriptomics and gut microbiome in grass carp under alkalinity stress.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {57},
number = {},
pages = {101698},
doi = {10.1016/j.cbd.2025.101698},
pmid = {41330219},
issn = {1878-0407},
abstract = {Alkalinity, a key environmental stressor in saline-alkali ecosystems, adversely affects the growth and survival of aquatic organisms. Genetic improvement of alkali-tolerant fish strains offers a promising strategy for utilizing saline-alkaline water resources; however, the molecular mechanisms underlying the response to alkalinity stress remain inadequately understood. This study aimed to identify novel molecular signatures of alkaline exposure in grass carp by integrating gut microbiome profiling with host transcriptome data. Histological analysis revealed significant alterations in the height of intestinal folds, muscle layer thickness, and fold width in response to NaHCO3 exposure, along with an increased number of goblet cells under alkalinity stress. Differential gene expression (DEGs) analysis identified 1620, 6564, and 3190 genes with significant expression changes at 24, 48, and 72 h of NaHCO3 treatment, respectively, compared to controls. Several known alkalinity-responsive genes, such as aquaporin 1a (aqp1a), carbonic anhydrase 6 (ca6), heat shock protein 30 (hsp30), prostaglandin-endoperoxide synthase 2b (ptgs2b), caspase 23 (casp23), solute carrier family 7a (slc7a), toll-like receptor 5 (tlr5), and toll-like receptor 13 (tlr13), were identified and validated through real-time quantitative PCR. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that immune- and disease-related signaling pathways played critical roles in mitigating acute alkaline stress. Furthermore, a total of 1,521,323 quality-filtered sequences with an average of 416 bp in length were generated through 16S rRNA sequencing. Bioinformatics analysis indicated that NaHCO3 exposure reduced microbial diversity and altered the gut microbiota composition in grass carp. Notably, Fusobacteriota abundance significantly increased, while Firmicutes and Proteobacteria decreased substantially at 48 h post-alkalinity stress. Integrative analysis further highlighted strong correlations between specific bacterial taxa and alkalinity-responsive differentially expressed genes (DEGs). These findings provided valuable insights into the molecular mechanisms underlying alkalinity stress and identified potential targets for molecular breeding to enhance alkaline tolerance in grass carp.},
}

@article {pmid41330099,
year = {2025},
author = {Barman, P and Paul, A and Sinha, S and Saha, T and Mondal, N and Dutta, S and Chatterjee, S and Ghosh, W and Chakraborty, R},
title = {Microbial-viral synergy in Eisenia fetida gut supports earthworm survival, detoxification, and functional resilience.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181101},
doi = {10.1016/j.scitotenv.2025.181101},
pmid = {41330099},
issn = {1879-1026},
abstract = {The ecological success of Eisenia fetida within decomposer food webs is closely linked to the functional diversity of its gut microbiome. This study integrates 16S rRNA gene profiling, whole-metagenome sequencing, and virome analysis to elucidate how microbial and viral communities within the earthworm gut contribute to nutrient biosynthesis, xenobiotic degradation, and environmental adaptation. Earthworms reared on compost feed enriched with Quisqualis indica plant matter showed selective enrichment of bacterial genera such as Ohtaekwangia, Nocardioides, and Steroidobacter, which are associated with hydrocarbon degradation and aromatic compound detoxification. Functional annotation of the gut metagenome revealed complete biosynthetic pathways for riboflavin, lysine, and methionine, and degradation routes for 3-nitropropionic acid (3-NPA) and aromatic pollutants. The gut virome, dominated by Siphoviridae and Myoviridae, carried auxiliary metabolic genes (AMGs) related to redox and xenobiotic metabolism, highlighting viral contributions to microbial adaptability. Reconstruction of metagenome-assembled genomes (MAGs), including a high-quality Flavobacterium MAG encoding both riboflavin biosynthesis and denitrification genes, underscored metabolic specialization within the gut. Collectively, these findings demonstrate that bacterial-viral metabolic synergy underpins E. fetida survival and ecological resilience, suggesting new microbiome-informed strategies for biowaste valorization and soil health restoration through vermicomposting.},
}

@article {pmid41329990,
year = {2025},
author = {Choi, HI and Cha, JM},
title = {Non-invasive colorectal cancer screening: emerging tools and clinical evidence.},
journal = {Clinical endoscopy},
volume = {},
number = {},
pages = {},
doi = {10.5946/ce.2025.246},
pmid = {41329990},
issn = {2234-2400},
abstract = {The fecal immunochemical test (FIT) is a widely used non-invasive screening method for colorectal cancer (CRC) in many countries, valued for its simplicity, affordability, and reasonable sensitivity. Typically recommended on an annual or biennial basis, the FIT is effective in reducing CRC incidence and mortality by facilitating early detection. Stool DNA tests, including multitarget DNA tests and DNA methylation assays, demonstrate higher sensitivity than FIT for CRC and advanced adenomas, although they have slightly lower specificity and higher cost. These tests are generally performed at longer intervals, such as every 3 years, and are useful alternatives for individuals who are unwilling or unable to undergo a colonoscopy. Emerging non-invasive CRC screening tools, such as liquid biopsy, microRNA, microbiome tests, and urine-based tests, are being developed to improve patient compliance and test convenience. In particular, liquid biopsy offers a minimally invasive option that may be more acceptable to populations hesitant to undergo stool-based tests. Furthermore, the integration of machine learning with metagenomic sequencing data has shown promise in distinguishing patients with CRC from healthy individuals. As CRC screening evolves, these novel approaches may enable the development of more personalized, accessible, and effective screening strategies, ultimately improving adherence and reducing CRC-related mortality.},
}

@article {pmid41329940,
year = {2025},
author = {Aguilar-Fuentes, AN and Montes García, JF and Salcedo-Álvarez, MO and Sanchez Alonso, P and Vazquez-Cruz, C and Rojas, L and Meneses-Romero, EP and Erasmo, NA},
title = {Epinephrine and norepinephrine affect the cellular morphology, composition, and structure of Gallibacterium anatis biofilm.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2025-0135},
pmid = {41329940},
issn = {1480-3275},
abstract = {Gallibacterium anatis is a Gram-negative bacterium that is a pathogen and part of the microbiome of both domestic and wild birds. It is also the cause of reproductive infections, primarily when birds are stressed. Its pathogenicity has been associated with the expression of virulence factors. The effect of Epinephrine (Epi) and Norepinephrine (NEpi) hormones on the composition and structure of G. anatis biofilms is evaluated here. Catecholamines induced compaction and fragmentation of biofilms at 24h. Biofilm amount diminishes (50%) by NEpi. At 48h, biofilm fragments are immersed in exopolymer material, and the control biofilm shows a high quantity of filamentous cells, not observed with hormones. Enzymatic digestion of biofilm polymers showed increased protein levels in the presence of Epi at 24 or 48h and NEpi at 24 or 72h. Epi increased carbohydrate quantity, but NEpi diminished, and DNA quantities diminished at 48h by Epi. Epi diminishes the expression of proteins in the 70 to 200 kDa range but increases the expression of secreted proteins. NEpi induces proteolytic activity in the range of 20 to 110 kDa. A 55 kDa protease was induced at 72h by both hormones. G. anatis biofilm changes could be significant in its dispersion and pathogenesis.},
}

@article {pmid41329729,
year = {2025},
author = {Zhou, C and Hibberd, MC and Lee, EM and Pilgaard, B and Vuillemin, M and Kiehn, E and Henrissat, S and Crane, MA and Cheng, J and Pfaff, L and Meyer, AS and Holck, J and Terrapon, N and Castillo, JJ and Couture, G and Lebrilla, CB and Rodionov, DA and Barratt, MJ and Henrissat, B and Gordon, JI},
title = {Glycoside hydrolase-mediated glucomannan catabolism in Segatella copri, a target of microbiota-directed foods for malnourished children.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {49},
pages = {e2521522122},
doi = {10.1073/pnas.2521522122},
pmid = {41329729},
issn = {1091-6490},
support = {DK30292//HHS | NIH (NIH)/ ; INV016367//Bill and Melinda Gates Foundation (GF)/ ; F30DK131866//HHS | NIH (NIH)/ ; NNF20SA0067193 NNF22OC0077058//KU | Novo Nordisk Foundation Center for Protein Research, University of Copenhagen (CPR)/ ; T32HG000045//HHS | NIH (NIH)/ ; },
mesh = {*Mannans/metabolism ; Animals ; Mice ; *Gastrointestinal Microbiome ; *Glycoside Hydrolases/metabolism/genetics ; Humans ; Prebiotics ; *Malnutrition/diet therapy/microbiology ; Polysaccharides/metabolism ; Child ; },
abstract = {Evidence is emerging that perturbed postnatal gut microbiota development is causally related to childhood undernutrition. Clinical trials in undernourished Bangladeshi children found that a polysaccharide-rich, microbiota-directed complementary food (MDCF-2) designed to repair this perturbation produced superior ponderal and linear growth compared to a standard ready-to-use supplementary food. Subsequent analyses disclosed several candidate bioactive polysaccharides in the MDCF and their bacterial targets, notably strains of Segatella copri that possess carbohydrate-active enzymes (CAZymes) organized into polysaccharide utilization loci (PULs) targeting these glycans. A Bangladeshi S. copri isolate (BgF5_2) containing these PULs metabolized MDCF-2 glycans and promoted MDCF-dependent weight gain in a gnotobiotic mouse model emulating the clinical trials. Identifying prebiotic mixtures that mimic the effects of MDCF-2 would offer new options for treatment and prevention. Here, we describe a CAZyme-based approach to characterize the effects of glucomannan, a component of MDCF obtainable from sustainable sources, on growth and gene expression in S. copri BgF5_2 in vitro and in gnotobiotic mice. Biochemical characterization of purified CAZymes expressed by two of its MDCF-2 and glucomannan-targeted PULs disclosed a multifunctional GH26|GH5_4 CAZyme, inducible by glucomannan, that degrades several bioactive MDCF-2 glycans; glucomannan, arabinoxylan, xyloglucan, and mixed-linkage β-glucan. Our data suggest that this CAZyme functions as a multisubstrate "sentinel" that can produce diverse oligosaccharides from a variety of β-linked glycans, with each oligosaccharide able to induce corresponding PULs and non-PUL enzymes. This observation, plus the restricted distribution of the multifunctional CAZyme among S. copri strains, may partially explain strain responsiveness to MDCF-2.},
}

*Mannans/metabolism
Animals
Mice
*Gastrointestinal Microbiome
*Glycoside Hydrolases/metabolism/genetics
Humans
Prebiotics
*Malnutrition/diet therapy/microbiology
Polysaccharides/metabolism
Child

@article {pmid41329536,
year = {2025},
author = {Hojná, S and Mráziková, L and Shánělová, A and Pelantová, H and Montezano, A and Touyz, RM and Maletínská, L and Kuneš, J},
title = {Oxidative Stress, Metabolic Impairment and Neuroinflammation are Associated With Target Organ Damage in SHRSP.},
journal = {Physiological research},
volume = {74},
number = {5},
pages = {779-795},
pmid = {41329536},
issn = {1802-9973},
mesh = {Animals ; *Oxidative Stress/physiology ; Rats, Inbred SHR ; Rats, Inbred WKY ; Rats ; Male ; *Hypertension/metabolism/pathology ; *Neuroinflammatory Diseases/metabolism/pathology ; *Stroke/metabolism/pathology ; Gastrointestinal Microbiome ; },
abstract = {Stroke-prone spontaneously hypertensive rats (SHRSP) are widely used as a model to study cerebral small vessel disease (CSVD) and its association with chronic hypertension. This study investigated the relationship between metabolic, cardiovascular, and neuronal comorbidities in 32-week-old SHRSP rats versus Wistar-Kyoto (WKY) controls, with a focus on oxidative stress, inflammation, and metabolic alterations. Despite hypertension and cardiac and renal hypertrophy, no significant cerebral vascular changes or microbleeds and no cerebral edema were detected in SHRSP. NMR-based urinary metabolomics revealed reduced gut microbiome-derived metabolites, such as p-cresylglucuronide, hippurate, and phenylacetylglycine, alongside increases in methylamine and dimethylamine. These findings reflect gut dysbiosis and altered microbial composition in hypertensive conditions. Elevated markers of oxidative stress, including thiobarbituric acid-reactive substances, and increased expression of NADPH oxidase (NOX) 2 and NOX4 in peripheral tissues suggested oxidative damage in SHRSP rats. Astrocytic hyperreactivity, indicated by increased expression of glial fibrillary acidic protein in brain cortex and hippocampus, was suggestive of neuroinflammatory responses. Our findings highlight complex interplay between hypertension, metabolism, and neuroinflammation while underscoring the variability in SHRSP models. Key words SHRSP " Neuroinflammation " Oxidative stress " Metabolomics.},
}

Animals
*Oxidative Stress/physiology
Rats, Inbred SHR
Rats, Inbred WKY
Rats
Male
*Hypertension/metabolism/pathology
*Neuroinflammatory Diseases/metabolism/pathology
*Stroke/metabolism/pathology
Gastrointestinal Microbiome

@article {pmid41329386,
year = {2025},
author = {Pandupuspitasari, NS and Sugiharto, S and Khan, FA and Raza, MA and Lestari, DA and Setiaji, A and Agusetyaningsih, I},
title = {Gut microbiota profile, potential engineering techniques and its genetic and epigenetic implications in poultry health.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {12},
pages = {488},
pmid = {41329386},
issn = {1573-0972},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Poultry/microbiology/genetics ; *Epigenesis, Genetic ; Meat ; Fatty Acids, Volatile/metabolism ; Bacteria/genetics/metabolism/classification ; Genetic Engineering ; },
abstract = {Poultry-derived meat and eggs represent economically viable and nutritionally rich resources for the burgeoning global population. The engineering of the gut microbiota has demonstrated potential in enhancing poultry health by establishing a homeostatic milieu and refining immune responses, optimizing metabolic pathways, and augmenting the physiological responses and structural integrity of the involved organs. The processes of fermentation, nutrient uptake, and absorption, alongside their optimized utilization by the host, are governed by complex interactions within the functional population of the gut microbiota. Microbiota influences these responses through the synthesis of distinct microbial metabolites, especially in the form of short-chain fatty acids (SCFAs) which affect host gene expression through both genetic and epigenetic mechanisms. The widespread use of antibiotic growth promoters disrupts the composition and function of the gut microbiota, resulting in adverse effects on host health and long-term sustainability. These concerns underscore the urgent need to develop alternative, safer, and more organic methodologies for sustainable poultry production. In addition, we examine the bidirectional influence of the host on the modulation of the gut microbiota in hope of future personalized treatments. The engineering of gut microbiota by various means is a viable alternative to antibiotic growth promoters, having been shown to significantly enhance both the quality and quantity of eggs and meat within the poultry industry.},
}

*Gastrointestinal Microbiome/genetics
Animals
*Poultry/microbiology/genetics
*Epigenesis, Genetic
Meat
Fatty Acids, Volatile/metabolism
Bacteria/genetics/metabolism/classification
Genetic Engineering

@article {pmid41329359,
year = {2025},
author = {Feng, L and Yi, H and Xie, Z and Zhou, P and Zhang, Y and Cheng, L and Chen, S and Chen, L and Jiang, C and Diao, H and Yan, H},
title = {Dietary Houttuynia cordata Thunb attenuates redox imbalance and inflammation possibly induced by heat stress in dairy cows associated with altered fecal microbiota and metabolomics profile.},
journal = {Tropical animal health and production},
volume = {57},
number = {9},
pages = {523},
pmid = {41329359},
issn = {1573-7438},
support = {2022ZYDF081//the Local Science and Technology Development/ ; 2022YFH0063//Sichuan Science and Technology Program/ ; },
}

@article {pmid41329233,
year = {2025},
author = {Guarino, M and Di Ciaula, A and Portincasa, P and De Giorgio, R},
title = {Narrative review on microbiota and sepsis: the host's betrayal?.},
journal = {Internal and emergency medicine},
volume = {},
number = {},
pages = {},
pmid = {41329233},
issn = {1970-9366},
abstract = {Sepsis remains a leading cause of morbidity and mortality worldwide. Increasing evidence suggests that the gut microbiota, long considered a "less relevant" to human body health, it plays a crucial role in the pathophysiology of sepsis. Disruption of the host-microbe balance contributes to impaired barrier integrity, microbial translocation, and dysregulated immune responses. This perspective raises the possibility that dysbiosis is not merely a consequence of critical illness, rather an active driver of septic progression. This narrative review explores the relationship between sepsis and gut microbiome. PubMed, Scopus, and EMBASE were searched from inception to September 2025. Recent studies have highlighted the triangular interplay between the intestinal barrier, gut microbiota, and immune system. Altered microbial composition and increased permeability foster systemic inflammation and immune dysfunction. Biomarkers such as diamine oxidase and intestinal fatty acid-binding protein are emerging as promising indicators of gut injury. Experimental therapies (i.e., faecal microbiota transplantation, targeted probiotics, prebiotics, postbiotics, and personalized antibiotic regimens guided by microbial profiling) provide potential to modulate host-microbe interactions. Integration of microbiome analysis with multi-omics and advanced bioinformatics may enable stratification of septic patients by microbial signatures, paving the way for precision medicine approaches. Modulation of gut microbiota represents a novel therapeutic frontier in sepsis. Conceptualizing sepsis as a disease of disrupted host-microbe symbiosis may unravel new diagnostic and therapeutic strategies. Future research should aim at prioritizing high-quality trials, innovative designs, and equitable implementation to target microbiota to improve survival and recovery in patients with sepsis.},
}

@article {pmid41329062,
year = {2025},
author = {Yun, Y and Xu, GQ and Jiang, XJ and Ren, XY and Lu, MF and Chen, JW and Zhang, SX},
title = {Gut Microbiota in Rheumatoid Arthritis: Unraveling Pathogenic Mechanisms and Therapeutic Opportunities.},
journal = {Comprehensive Physiology},
volume = {15},
number = {6},
pages = {e70078},
doi = {10.1002/cph4.70078},
pmid = {41329062},
issn = {2040-4603},
support = {202203021221269//Natural Science Foundation of Shanxi Province/ ; 82001740//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Arthritis, Rheumatoid/microbiology/immunology/therapy ; *Gastrointestinal Microbiome/physiology/immunology ; Animals ; Dysbiosis/immunology ; Antirheumatic Agents/therapeutic use ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; },
abstract = {Rheumatoid arthritis (RA), a chronic autoimmune disorder driven by genetic-environmental interplay, manifests as progressive synovitis and irreversible joint damage. Despite mechanistic advances in disease-modifying antirheumatic drugs (DMARDs) and biologics, upstream mucosal triggers of autoimmunity remain elusive. Mounting evidence implicates gut microbiota dysbiosis as a pivotal environmental factor in RA pathogenesis through multifaceted mechanisms: (1) compromising intestinal barrier integrity, (2) facilitating molecular mimicry via cross-reactive microbial antigens, (3) skewing mucosal immunity toward pro-inflammatory T helper 17 (Th17)/T follicular helper (Tfh) cell responses, and (4) generating bioactive metabolites with dual roles in regulating osteoclastogenesis and synovial inflammation. This review synthesizes recent advances in gut microbiome profiling, mechanistic studies, and preclinical models, elucidating microbial-host crosstalk in autoimmune cascades. Furthermore, we critically evaluate microbiota-directed strategies, including dietary and probiotic modulation, microbiome-informed optimization of conventional DMARDs and biologics, and investigational approaches like fecal microbiota transplantation and Chinese herbal medicine, that may offer promising adjunctive approaches to complement conventional RA management.},
}

Humans
*Arthritis, Rheumatoid/microbiology/immunology/therapy
*Gastrointestinal Microbiome/physiology/immunology
Animals
Dysbiosis/immunology
Antirheumatic Agents/therapeutic use
Probiotics/therapeutic use
Fecal Microbiota Transplantation

@article {pmid41328989,
year = {2025},
author = {Charbel, N and Masri, A and Rammal, F and Aramouni, K and Jabbour, K and Hodroj, MH and Rizkallah, J and Kabbara, F and Kreidieh, F},
title = {Unveiling the interplay between gut and skin microbiomes and their influence on skin cancer.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0027024},
doi = {10.1128/cmr.00270-24},
pmid = {41328989},
issn = {1098-6618},
abstract = {SUMMARYThe interplay between the gut and skin microbiomes and their influence on skin cancer development has garnered significant attention. The gut and skin microbiomes, composed of bacteria, fungi, and viruses, play vital roles in immune modulation, inflammation regulation, and maintaining skin health. Dysbiosis in either microbiome may contribute to inflammatory skin conditions and cancer development through the gut-skin axis. The gut microbiota influences immune responses, skin barrier function, and carcinogenesis via microbial metabolites, such as short-chain fatty acids. These compounds impact systemic inflammation, immune cell activity, and response to immunotherapy, particularly in melanoma and non-melanoma skin cancers. Emerging evidence links distinct microbial profiles to skin cancer progression, with specific taxa associated with advanced stages. Conversely, certain skin commensals exhibit potential anti-tumor effects. In addition, microbial imbalances correlate with tumorigenesis via inflammatory and metabolic pathways. Advancements in microbiome profiling have further elucidated these associations, offering diagnostic and therapeutic opportunities. Potential interventions include probiotic therapies to restore microbial balance and enhance immunotherapy efficacy. However, the intricate dynamics of the gut-skin axis necessitate further investigation into causal mechanisms, microbial metabolite impacts, and personalized therapeutic strategies. This review highlights the dualistic role of the gut and skin microbiomes in skin cancer, emphasizing their diagnostic and therapeutic potential while proposing future research directions to unravel their complexities and clinical implications.},
}

@article {pmid41328924,
year = {2025},
author = {Arnadottir, AT and Skirnisdottir, S and Knobloch, S and Corral-Jara, KF and Klonowski, AM and Gunnarsdottir, I and Marteinsson, VT},
title = {Results from the IceGut study: tracking the gut microbiome development from mothers and infants up to five years of age.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0074525},
doi = {10.1128/msphere.00745-25},
pmid = {41328924},
issn = {2379-5042},
abstract = {UNLABELLED: The infant gut microbiome plays a critical role in the early development of the immune system, brain function, metabolism, and defense against pathogens. However, data from underrepresented populations, like Iceland, with its distinct dietary and lifestyle habits, remain limited. This paper presents the initial findings from the Icelandic Diet and the Infant Gut Microbiome Development (IceGut) study. Fecal samples were collected at multiple time points, representing 328 unique study identifiers, with one to five samples per child, from before the introduction of solid foods up to 5 years of age, and postpartum samples from 214 mothers. Microbial composition and predicted functional potential were assessed using 16S rRNA gene sequencing. Children in the cohort followed typical gut microbiome maturation, but at 1 year of age, they showed a notably higher relative abundance of Blautia than reported in comparable cohorts. This time point marked a transition in both taxonomic composition and predicted functional gene counts. By 5 years, the children had higher observed richness than their mothers but lower Shannon and Simpson diversities. At 2 and 5 years, and in the mothers, samples positive for archaea had significantly higher alpha diversity than samples that tested negative for archaea. Mothers with gestational diabetes mellitus (GDM) exhibited a higher relative abundance of Blautia but a lower alpha diversity. The variance in offspring gut microbiome explained by maternal GDM became progressively stronger over time, being significant at the age of 5 and explaining 2.5% of the variance.

IMPORTANCE: This study provides the first comprehensive analysis of gut microbiome development in Icelandic children, covering the time from before the introduction of solid foods to 5 years of age. Although the overall developmental patterns of the gut microbiome in Icelandic children were similar to what has been seen in other studies, interesting differences were observed, such as a higher abundance of Blautia at an earlier age compared to other study populations. Higher alpha diversity in archaeal-positive samples, both in mothers and in children at the ages of 2 and 5, compared with archaeal-negative samples seen in the present study, is worth further investigation. Additionally, the study suggests a potential role of maternal and perinatal factors, particularly GDM, which was not evident until the age of 5 years, emphasizing the necessity of long-term studies.},
}

@article {pmid41328917,
year = {2025},
author = {Ghorbani, M and Kvedaraite, A and Al-Manei, K and Too, CB and Cederberg, S and Johannessen, A and Reikvam, DH and Valentini, D and Maucourant, C and Björkström, NK and Aleman, S and Sällberg Chen, M},
title = {Oral Microbiome Diversity Matters on Nucleos(t)ide Analogue Cessation in Chronic Hepatitis B.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf591},
pmid = {41328917},
issn = {1537-6613},
abstract = {BACKGROUND: Withdrawal of nucleos(t)ide analog (NUC) therapy in HBeAg-negative chronic hepatitis B (CHB) may lead to functional cure in a subset of patients. Although gut microbiota is known to influence both CHB-progression and treatment outcomes, the oral microbiome in NUC-cessation remains unexplored.

METHODS: This long-term longitudinal study aimed to explore the oral microbiome in CHB patients who have been on NUC therapy >2 years having a planned NUC cessation. Oral microbiome composition was analyzed in 110 saliva samples across seven timepoints from 18 HBeAg-negative patients with 36 months of follow-up. Favorable outcome was defined as either HBsAg loss or decline of >1 log10 or sustained off-therapy HBV DNA level <2000 IU/ml during year 3. Hepatic flare was defined as ALT >80 U/L or 2x baseline level.

RESULTS: The overall microbial composition remained stable during the study period. Patients with favorable outcome (n=8) showed consistently higher alpha diversities (Shannon and Simpson indices, p<0.001) from baseline, with lower inter-sample variations across all timepoints (Bray-Curtis and Jaccard distances, p<0.05), compared to unfavorable (n=10). HBsAg, ALT and AST correlated inversely with several Prevotella taxa with specific pathways (Spearman´s rho>-0.5, p<0.01). Unfavorable outcome and high HBsAg level correlated with opportunistic taxa Haemophilus parainfluenzae and Porphyromonas catoniae at multiple timepoints. Random forest model incorporating ANCOM-validated microbial markers predicting favorable vs unfavorable outcome achieved higher predictive performance than clinical markers alone (AUC 0.78 vs. 0.66).

CONCLUSION: Our exploratory study suggests that oral microbiome profiling at NUC cessation in HBeAg-negative CHB could support prognostication of virological outcome.},
}

@article {pmid41328870,
year = {2025},
author = {Cihan, E and Penney, JL and Humphreys, GJ and Ledder, RG and Sreenivasan, PK and Willmott, T and Wu, Y and McBain, AJ},
title = {Exploring Intra-individual Oral Microbiome diversity and Streptococcal Colonisation Patterns.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf296},
pmid = {41328870},
issn = {1365-2672},
abstract = {AIMS: We have investigated bacterial colonisation and site-specific distribution across hard and soft oral tissues focusing on both intra- and inter-individual patterns of Streptococcus clonality and overall microbial composition.

METHODS AND RESULTS: Thirty samples were collected from five healthy adults, covering six oral sites (buccal mucosa, tongue dorsum, maxillary central incisors, mandibular molar fissure, and saliva). Repetitive sequence-based PCR (rep-PCR) assessed Streptococcus clonality, while 16S rRNA gene sequencing characterised broader microbial communities. Among 98 Streptococcus isolates, 67.3% were clonal and frequently recovered from multiple sites within individuals. Identical S. vestibularis clones were detected across all sampled sites in one participant and across several sites in others, indicating shared intra-oral reservoirs. Amplicon sequencing revealed distinct microbial compositions across oral sites, with saliva displaying the highest alpha diversity (Shannon index) and significant beta-diversity differences between most sites, except saliva and tongue. Firmicutes predominated overall, and Streptococcus was the most abundant genus. Differential-abundance testing (ANCOM-BC2) identified 26 genera varying significantly across sites, with lower abundance generally observed on soft tissues.

CONCLUSIONS: These findings suggest that while microbial communities vary by oral site, certain streptococcal clones, including S. vestibularis, occur across multiple habitats. This suggests potential intra-oral reservoirs that may contribute to microbiome stability.},
}

@article {pmid41328492,
year = {2025},
author = {Knoll, RL and Podlesny, D and Fortmann, I and Göpel, W and Zemlin, M and Lynch, S and Bork, P and Gehring, S and Härtel, C},
title = {Staphylococcus aureus colonization and bloodstream infection in very preterm infants.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2592423},
doi = {10.1080/19490976.2025.2592423},
pmid = {41328492},
issn = {1949-0984},
mesh = {Humans ; *Staphylococcal Infections/epidemiology/microbiology ; Infant, Newborn ; Feces/microbiology ; *Staphylococcus aureus/isolation & purification/genetics/growth & development/classification ; Female ; Male ; Infant, Premature ; *Bacteremia/microbiology/epidemiology ; Gastrointestinal Microbiome ; Germany/epidemiology ; Infant ; Cohort Studies ; Infant, Very Low Birth Weight ; Metagenomics ; Incidence ; Gestational Age ; },
abstract = {BACKGROUND: Staphylococcus (S.) aureus remains a frequent pathogen for neonatal late-onset bloodstream infections (BSIs). The impact of colonization screening on BSI incidence is less understood.

METHODS: We assessed the epidemiology of late-onset S. aureus BSI in two independent multicenter cohorts of preterm infants born at < 33 weeks' gestation, the German Neonatal Network (GNN, very low birth weight infants) and PRIMAL (infants with a gestational age 28-32 weeks). In the PRIMAL cohort, we determined S. aureus colonization in fecal samples by culture and shotgun metagenomic sequencing (metaG) during the first year of life. In addition, we integrated publicly available metaG data from preterm infant cohorts born at 23-34 weeks' gestation.

RESULTS: Late-onset S. aureus BSI was noted in 1.5% (336/21491) in preterm infants in the GNN cohort and 0.5% (3/638) in the PRIMAL cohort, respectively. At day 30 of life, 7.6% (42/553) of fecal samples were positive for S. aureus, while available metaG data of corresponding samples revealed S. aureus positivity in 36.6% (159/434). Every 10-fold increase in S. aureus relative abundance (metaG) was associated with a 2.9-fold higher odds of S. aureus detection in blood culture. We also confirmed S. aureus detection in 22% (393/1782) of samples across several published cohorts of preterm infants by metaG, while 95 samples carried at least one Staphylococcus-specific virulence gene (SVG).

CONCLUSION: Our study demonstrates that metagenomic quantification of pathobionts such as S. aureus in intestinal samples provides a stronger predictor of colonization than culture. Future prevention strategies should focus on promoting S. aureus colonization resistance through microbiome-informed approaches.},
}

Humans
*Staphylococcal Infections/epidemiology/microbiology
Infant, Newborn
Feces/microbiology
*Staphylococcus aureus/isolation & purification/genetics/growth & development/classification
Female
Male
Infant, Premature
*Bacteremia/microbiology/epidemiology
Gastrointestinal Microbiome
Germany/epidemiology
Infant
Cohort Studies
Infant, Very Low Birth Weight
Metagenomics
Incidence
Gestational Age

@article {pmid41328416,
year = {2025},
author = {Ueira-Vieira, C and Santos, ACC and Araújo, TN and Augusto, SC and de Avila, NB and Bonetti, AM and Dos Santos, AR},
title = {A Deep Metagenomic Snapshot as a Proof-of-Concept for Resource Generation: Simultaneous Assembly of Host, Food, and Microbiome Genomes From Stingless Bee Larval Food.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72546},
pmid = {41328416},
issn = {2045-7758},
abstract = {Characterizing the complex web of ecological interactions is a central challenge in molecular ecology. Shotgun metagenomics of environmental samples offers a powerful, high-resolution approach, yet its potential for simultaneously generating multiple genomic resources from different trophic levels remains underexplored. This study serves as a proof-of-concept, using deep sequencing of a single, complex sample-the larval food of the stingless bee Tetragonisca angustula-to demonstrate the method's capacity to recover genomic information across varying template abundances. We successfully assembled three genomes of different completeness levels: a near-complete bacterial genome (Acetilactobacillus jinshanensis, 2,097,977 bp with 0.002% ambiguous bases), a draft mitochondrial genome (T. angustula, 15,498-15,549 bp), and a fragmented chloroplast genome (Lactuca sativa, 130,532 bp with 23.47% ambiguous bases). The assembly quality gradient, observed from complete to fragmented, directly reflects the relative abundance of each DNA template in the environmental sample, demonstrating the method's sensitivity and ecological informativeness. Beyond these genomic resources, the data provided a comprehensive biodiversity profile, revealing DNA from seven major taxonomic groups, including 209 bacterial genera, 123 plant families, and 55 insect taxa. Additionally, genomic comparisons using Average Nucleotide Identity (ANI) and digital DNA-DNA Hybridization (dDDH) analyses suggest that the dominant bacterial strain represents a putative novel species within the genus Acetilactobacillus. This approach simultaneously provided insights into host genetics, food sources, and microbial communities, illustrating the potential of single metagenomic datasets to generate multiple valuable genomic resources for molecular ecology research.},
}

@article {pmid41328415,
year = {2025},
author = {Long, D and Zhao, W and Li, X and Sun, Q and Li, J and Lin, X},
title = {Rhizosphere Effect Enhances Belowground Competition of Coastal Invasive Spartina alterniflora With Mangroves.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72565},
pmid = {41328415},
issn = {2045-7758},
abstract = {Spartina alterniflora has severely invaded mangroves in China. In order to explore the possible belowground interspecific interaction along with its invasion, the rhizosphere effect enhancing the competition of S. alterniflora neighboring mangroves was hypothesized. Here, both rhizosphere soil of S. alterniflora and bulk soil were collected from the center of S. alterniflora marsh and border sites where S. alterniflora was adjacent to Kandelia obovata and Aegiceras corniculatum, respectively, in both vigorous growth and senescent periods. Soil nutrient properties, rhizospheric low-molecular-weight organic acids (LMWOAs), soil microbiomes, and microbial functional genes were analyzed. Soil total carbon and total nitrogen contents of S. alterniflora neighboring mangroves were increased, and its LMWOAs were altered when adjacent to mangroves in both vigorous growth and senescent periods. These changes were significantly correlated with variation in the composition of S. alterniflora rhizosphere microbiome. Microbial interkingdom co-occurrence networks were simplified when S. alterniflora neighbored mangroves, while network modularity significantly increased. Metagenomics indicated that genes involved in methanogenesis (ackA, mvhD, etc.) and nitrogen fixation (nifH, nifK, etc.) were significantly enriched in those S. alterniflora neighboring K. obovata, and genes related to phosphate transporter (pstA, pstB, etc.) were significantly enriched in those S. alterniflora neighboring A. corniculatum. These results demonstrated that the rhizosphere effect intensified the belowground interspecific competition of S. alterniflora adjacent to mangroves by altering root exudates, changing the soil microbial composition, and modulating strategies for core nutrient metabolism.},
}

@article {pmid41328252,
year = {2025},
author = {Ge, X and Pan, J and Mo, K and Chen, H and Sun, J and Huang, H and Zhang, Y and Mai, K and Gu, H and Hu, Y},
title = {The versatility of Bacillus tequilensis Bt-CO as an additive: Antagonizing pathogens, enhancing immunity, promoting intestinal health, and optimizing gut microbiota of tilapia.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {23},
number = {},
pages = {502-515},
pmid = {41328252},
issn = {2405-6383},
abstract = {Probiotics are gaining increasing attention as potential alternatives to antibiotics for enhancing the health and welfare of aquatic organisms. However, identifying and developing highly effective probiotic strains with superior intestinal colonization and antagonistic properties remains a significant challenge. This study identified a strain of Bacillus tequilensis, designated as Bt-CO, from coral in a tropical marine environment. Following an in vitro assessment of its antimicrobial activity and colonization properties, the potential of Bt-CO as an antibiotic alternative was evaluated through in vivo trials. A total of 720 fish (initial body weight 2.06 ± 0.01 g) were randomly distributed across four dietary treatments in triplicates, consisting of a basal diet (CON group), and the diet supplemented with 1 × 10[7] (T1 group), 1 × 10[8] (T2 group), or 1 × 10[9] colony-forming unit (CFU)/g (T3 group) of Bt-CO. After a feeding period of 4 weeks, fish were sampled or challenged with Aeromonas hydrophila. For the challenge, 30 fish in each tank were intramuscularly injected with 50 μL of A. hydrophila at a concentration of 5 × 10[6] CFU/mL. Tilapia survival was monitored for 20 d post-infection. The results demonstrated that Bt-CO possessed pronounced antagonistic effects against several important pathogenic bacteria affecting tilapia, particularly A. hydrophila. Bt-CO also demonstrated excellent physiological characteristics, including auto-aggregation, adhesion, biofilm formation, and exhibited remarkable tolerance to bile and gastrointestinal conditions. Notably, Bt-CO possessed colonization potential in the intestines of tilapia without negatively impacting the growth performance. Following a 4-week supplementation with Bt-CO at an optimal concentration of 1 × 10[8] CFU/g, tilapia displayed an increased resistance to A. hydrophila infection (P = 0.011), suggesting its potential to enhance disease resistance. Additionally, Bt-CO significantly augmented the hemocyte respiratory burst (P < 0.001), serum bactericidal activity (P = 0.002), complement C3 (P = 0.027), lysozyme (P < 0.001), alkaline phosphatase (P = 0.031), and superoxide dismutase (P = 0.003) levels in tilapia. In addition, Bt-CO supplementation modulated inflammatory responses by inhibiting pro-inflammatory cytokines such as interleukin-1β (P = 0.045) and tumor necrosis factor-α (P = 0.020) and promoting anti-inflammatory cytokines such as transforming growth factor-β (P = 0.013) and interleukin-10 (P = 0.021), concurrently enhancing the expressions of intestinal barrier related factors such as claudin-1 (P = 0.051) and claudin-3 (P = 0.014) thereby improving intestinal health. Microbiome analysis indicated that Bt-CO supplementation increased the diversity of gut microbiota, promoted beneficial microorganisms but suppressed pathogenic microorganisms within the intestines of tilapia. In conclusion, incorporating Bt-CO into the diet at 1 × 10[8] CFU/g shows significant probiotic potential and effectively enhances tilapia's disease resistance, which is likely attributed to its role in strengthening non-specific immunity and improving fish intestinal health and microecology.},
}

@article {pmid41328072,
year = {2025},
author = {Zheng, L and Wang, H and Zhang, Z and Gu, J and Yin, Y},
title = {Structure and diversity of microbial communities in the rhizosphere soil of Trichosanthes kirilowii from different cultivation patterns.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20459},
pmid = {41328072},
issn = {2167-8359},
mesh = {*Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Trichosanthes/growth & development/microbiology ; Bacteria/classification/genetics ; Soil/chemistry ; Fungi/classification/genetics/isolation & purification ; Biodiversity ; Nitrogen/analysis ; },
abstract = {BACKGROUND: To analyze the effects of different cultivation patterns on the structure and diversity of the microbial community in the rhizosphere soil of Trichosanthes kirilowii (T. kirilowii) arms to establish reasonable and effective strategies to mitigate the continuous cropping barriers and promote the high-quality cultivation of T. kirilowii.

METHODS: Three distinct cultivation patterns were investigated: open-field cultivation (TM1), film-mulched cultivation (TM2), and soybean intercropping cultivation (TM3). High-throughput sequencing and bioinformatic analyses were employed to evaluate the rhizosphere microbiome, and redundancy analysis was utilized to investigate the relationship between the microbial communities and soil nutrient indicators.

RESULTS: TM2 and TM3 increased soil bacterial community diversity, reduced fungal community diversity, elevated the relative abundance of beneficial bacterial genera, and reduced the abundance of detrimental fungal genera in the rhizosphere soil. The relative abundance of Pseudarthrobacter, unclassified_Steroidobacteraceae, and Nocardioides in TM2 and TM3 was markedly higher than in TM1. Conversely, the relative abundance of Fusarium, Rhizoctonia, Ceratobasidium, and Plectosphaerella in TM2 and TM3 was significantly reduced compared to TM1. The contents of available potassium (AK), total nitrogen (TN), total phosphorus (TP), and pH in the rhizosphere soil of TM2 and TM3 were significantly higher than those in TM1. The distribution of soil bacterial genera was significantly influenced by the contents of TN and AK, while the distribution of soil fungal genera was significantly or extremely significantly impacted by the contents of TP, total potassium (TK), soil organic matter (SOM), and pH. The content of AK was extremely significantly positively correlated with the relative abundance of Nocardioides, whereas the content of TK showed an extremely negative correlation with the relative abundance of Ceratobasidium. Similarly, pH demonstrated an extremely negative correlation with the relative abundance of Rhizoctonia and Ceratobasidium.

CONCLUSIONS: Film-mulched cultivation and soybean intercropping cultivation altered the soil nutrients, as well as the structure and diversity of soil microbial communities. Thus, in agricultural production, film-mulched cultivation and soybean intercropping cultivation can serve to regulate soil nutrients and microbial communities, thereby mitigating the barriers of continuous cropping of T. kirilowii.},
}

*Rhizosphere
*Soil Microbiology
*Microbiota
*Trichosanthes/growth & development/microbiology
Bacteria/classification/genetics
Soil/chemistry
Fungi/classification/genetics/isolation & purification
Biodiversity
Nitrogen/analysis

@article {pmid41328046,
year = {2025},
author = {Imbroane, M and Bussies, P and Schachter, C and Frankel, L and Bosch, A and Santarosa, J and Falcone, T and Richards, EG},
title = {The role of pharmacotherapy in the treatment of endometriosis: an update.},
journal = {Expert opinion on pharmacotherapy},
volume = {},
number = {},
pages = {},
doi = {10.1080/14656566.2025.2597272},
pmid = {41328046},
issn = {1744-7666},
abstract = {INTRODUCTION: Endometriosis is a chronic inflammatory condition affecting ~10% of reproductive-age individuals and contributing significantly to infertility, pain, and reduced quality of life. Since our 2020 review, new pharmacologic strategies, updated guidelines, and advances in clinical trial evidence have reshaped the therapeutic landscape. Effective, patient-centered management is essential to lessen the burden of disease.

AREAS COVERED: This review synthesizes current evidence-based pharmacotherapy for endometriosis, integrating 2022 European Society of Human Reproduction and Embryology recommendations and including a literature review of PubMed, with an emphasis on articles published after 2020. First-line therapies, including NSAIDs, combined oral contraceptives, and progestins such as dienogest, remain central, while GnRH agonists/antagonists and aromatase inhibitors are considered in refractory cases. Recent data highlight add-back therapy to reduce hypoestrogenic side effects. We also review postoperative regimens, fertility-preserving strategies, management in post-hysterectomy and postmenopausal populations, and therapies under investigation - including anti-inflammatory, antifibrotic, angiogenesis-modulating, and microbiome-targeting approaches.

EXPERT OPINION: Hormonal suppression remains the cornerstone of treatment, but novel nonhormonal strategies and advances in precision medicine hold promise for more durable and individualized care. Ongoing clinical trials, artificial intelligence - assisted diagnostics, and fertility-focused pharmacotherapies represent exciting frontiers. Multimodal, patient-tailored approaches will be key to optimizing long-term outcomes in endometriosis management.},
}

@article {pmid41328036,
year = {2025},
author = {Woo, J and Cheng, D and Long, EA and Whitney, KL and Shen, G and Reddivari, L and Jiang, Q and Simsek, S and Ju, T and Wang, W},
title = {Hemp seed mitigates colonic inflammation through macrophage polarization and microbiota-barrier axis restoration.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo04119h},
pmid = {41328036},
issn = {2042-650X},
abstract = {Hemp seed, historically considered a byproduct of the hemp fiber industry, has gained increasing attention for its nutritional and functional properties. Recent advances in hemp seed research have elucidated its benefits for gut health; however, its impact on colitis remains unclear. In this study, we demonstrate that hemp seed consumption reduced colonic inflammation and mitigated tissue injury in an experimental colitis mouse model. Notably, hemp seed reduced macrophage infiltration and promoted a phenotypic shift from pro-inflammatory M1 to anti-inflammatory M2 macrophages. It also enhanced intestinal barrier function by restoring goblet cells, upregulating tight junction proteins, and reducing systemic lipopolysaccharide translocation. Furthermore, hemp seed optimized gut microbiota composition by enriching beneficial taxa, particularly Bifidobacterium, while suppressing colitis-associated genera. Collectively, these findings indicate that hemp seed, as a whole-food dietary approach, confers protection against colitis by modulating immune responses, preserving barrier integrity, and reshaping gut microbiome. These results underscore the potential of hemp seed as a sustainable nutritional strategy for promoting gut health.},
}

@article {pmid41328031,
year = {2025},
author = {Delaroque, C and Desai, MS},
title = {Context-dependent roles of the gut microbiome in food allergy tolerance versus sensitization.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2590830},
doi = {10.1080/19490976.2025.2590830},
pmid = {41328031},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/immunology ; *Food Hypersensitivity/immunology/microbiology ; Humans ; Animals ; *Immune Tolerance ; Intestinal Mucosa/immunology/microbiology ; T-Lymphocytes, Regulatory/immunology ; Immunoglobulin E/immunology ; Host Microbial Interactions ; },
abstract = {Exposure to food antigens that can trigger aberrant type-2 immunity is ubiquitous. However, only a subset of individuals develops allergy, implicating environmental drivers of sensitization, among which diet- and antibiotic-induced changes in intestinal microbiome activity stand out for their ability to alter host-microbe interactions at the gut mucosa. While efforts seek microbial signatures and microbiome-based therapies, the same microbes or pathways may foster either tolerance or sensitization depending on host and environmental context, which must be considered when designing interventions. We synthesize recent molecular insights into mucosal host-microbiome crosstalk, focusing on regulatory T cells, the colonic mucus barrier, and host immunoglobulins (IgA and IgE). Using examples of microbiome functional duality in which diet-driven altered microbial activities and secreted molecules such as lipopolysaccharides and flagellins yield opposing effects, we discuss the context-dependent mechanisms by which microbes either protect against or promote food allergy.},
}

*Gastrointestinal Microbiome/immunology
*Food Hypersensitivity/immunology/microbiology
Humans
Animals
*Immune Tolerance
Intestinal Mucosa/immunology/microbiology
T-Lymphocytes, Regulatory/immunology
Immunoglobulin E/immunology
Host Microbial Interactions

@article {pmid41328024,
year = {2025},
author = {Abbas, R and Javaid, N},
title = {Role of Oral microbiome in modulating immune response in Oral cancer development. A systematic review.},
journal = {Expert review of molecular diagnostics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14737159.2025.2599227},
pmid = {41328024},
issn = {1744-8352},
abstract = {BACKGROUND: Oral squamous cell carcinoma, the most common head and neck cancer, is characterized by aggressive invasion, frequent lymph node metastasis, and high recurrence.

OBJECTIVE: This review explores the role of microbial dysbiosis in shaping the immune landscape of oral squamous cell carcinoma. It aims to identify key microbial taxa altered in Oral squamous cell carcinoma, examine the immunological pathways they influence, and assess their impact on tumor progression and immune evasion.

METHODS: A comprehensive literature search was conducted across three major databases: PubMed, Scopus, and Embase. A total of 300 records were initially identified (PubMed: n = 68; Scopus: n = 63; Embase: n = 169). After screening and eligibility assessment, 17 studies meeting inclusion criteria were selected for final analysis.

RESULTS: Fusobacterium was the most frequently enriched genus in Oral squamous cell carcinoma, followed by Peptostreptococcus, Prevotella, Porphyromonas, Campylobacter, Treponema, Capnocytophaga, and Dialister. Streptococcus was the most consistently depleted, along with Rothia, Veillonella, Leptotrichia, Capnocytophaga, and Neisseria.

CONCLUSION: Cancer remains a leading cause of death. Oral microbial dysbiosis, with loss of beneficial species and enrichment of pathogens, has been linked to oral cancer, but its mechanistic role remains hypothetical and requires validation.},
}

@article {pmid41327907,
year = {2025},
author = {Ranson, A and Vazquez Gomez, M and Alili, R and Durrafourd, J and Vitalis, O and Taillandier, P and Rebière, C and Merabtene, F and Belda, E and Crespo-Piazuelo, D and Gonzalez-Bulnes, A and Marcelin, G and Mardinoglu, A and Chikh, K and Le Roy, T and Clément, K},
title = {Moderate increase in dietary fat induces alterations of microbiota and metabolome along the digestive tract prior to systemic metabolic changes: insights from a pig model.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2587964},
doi = {10.1080/19490976.2025.2587964},
pmid = {41327907},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Swine ; *Metabolome ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Male ; Female ; *Dietary Fats/metabolism/administration & dosage ; *Gastrointestinal Tract/microbiology/metabolism ; Intestine, Small/microbiology/metabolism ; },
abstract = {The small intestine is a key site for nutrient sensing and host-microbiota interactions, yet how it functionally adapts to dietary changes remains poorly understood. Using a translational porcine model, we investigated the impact of moderate dietary fat increase on the gut microbiota and metabolome across five locations in the digestive tract. Pigs were fed either a low-fat (3%) or a medium-fat (12%) diet for 12 weeks without developing obesity. Multiomics profiling revealed significant dietary effects on bile and duodenojejunal metabolomic profiles, particularly lipid and stachydrine, with notable sex-specific responses. These metabolite shifts were accompanied by segment- and sex-specific changes in microbial communities, including the depletion of metabolically beneficial taxa (e.g., Limosilactobacillus reuteri and Lactobacillus johnsonii) and the enrichment of bacteria linked to metabolic dysfunction (e.g., Streptococcus alactolyticus). In the small intestine lumen, multiple bacterial-metabolite associations correlated with host metabolic markers, suggesting early diet-induced alterations with potential relevance for metabolic disease onset. Our findings position the small intestine as a critical site for early diet-induced microbial and metabolic remodeling, potentially influencing metabolic disease risk and shaping the downstream intestinal environment. This study also underscores the importance of considering both region- and sex-specific responses in diet-microbiota-metabolome research.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Swine
*Metabolome
*Bacteria/classification/genetics/metabolism/isolation & purification
Male
Female
*Dietary Fats/metabolism/administration & dosage
*Gastrointestinal Tract/microbiology/metabolism
Intestine, Small/microbiology/metabolism

@article {pmid41327880,
year = {2025},
author = {Jadhav, NK and Magdum, AB and Shinde, KV and Nimbalkar, MS},
title = {Next-Generation Probiotics: From Traditional Strains to Personalized Therapeutics.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70339},
doi = {10.1002/mnfr.70339},
pmid = {41327880},
issn = {1613-4133},
support = {//Council of Scientific and Industrial Research (CSIR), Government of India/ ; },
abstract = {Traditional probiotics such as Lactobacillus and Bifidobacterium have long supported gut health, but recent advances in microbiome research have introduced next-generation probiotics (NGPs) such as Akkermansia muciniphila and Faecalibacterium prausnitzii. These strains are associated with more specific functions, including mucin degradation, butyrate production, enhanced gut barrier integrity, immune regulation, and modulation of host metabolism and inflammation. Unlike conventional probiotics, which mainly promote general digestive balance, NGPs demonstrate targeted mechanisms that link them to metabolic, inflammatory, and even neurological conditions. This review provides a critical comparison of traditional and NGPs, highlighting mechanistic distinctions and functional advancements. It also explores recent innovations in synthetic biology, including programmable gene circuits, and examines how artificial intelligence and microbiome profiling are paving the way toward personalized probiotic therapies, though widespread clinical application remains in its early stages. Key safety, regulatory, and translational challenges are also addressed, outlining barriers to clinical adoption. By integrating omics technologies and precision medicine, NGPs represent a promising frontier with the potential to advance personalized nutrition and therapeutic strategies.},
}

@article {pmid41327627,
year = {2025},
author = {Ma, X and Ling, L and Wang, B and Nian, H and Ma, Q and Zhao, S and Lian, T},
title = {Chemical Communication Between Plant and Microbe in the Phyllosphere.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70314},
pmid = {41327627},
issn = {1365-3040},
support = {//This study was supported by the National Natural Science Foundation of China (grant no. 32470090), the Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops (grant no. FCBRCE-202506), the Natural Science Foundation of Xinjiang Province (grant no. 2025D01D47), the Guangdong Provincial Construction Project for Modern Agriculture Industry Technology System Innovation Teams (Oil Crop Industry Technology System) (grant no. 2024CXTD06), the Science and Technology Plan Project of Guangzhou (grant no. 2024A04J5487), the Double First-Class Discipline Promotion Project (grant no. 2021B10564001) and the Science and Technology Plan Project of Shanwei (grant no. 2024E005). Guangdong Basic and Applied Basic Research Foundation (grant no. 2023A1515030275)./ ; },
abstract = {The phyllosphere encompasses all above-ground plant parts, covering ~10[9] km[2] and hosting as many as 10[26] microbial cells, yet its chemical ecology remains understudied compared to the rhizosphere. This review synthesizes recent advances in metabolite-mediated communication orchestrating phyllosphere microbiome assembly, function and host feedback. Leaf structural traits, host immune genes, developmental stage, and fluctuating environmental drivers create spatiotemporal chemical niches that filter incoming microbes. We then examine four major classes of plant-derived signals, including primary metabolites, secondary metabolites and phytohormones, with an emphasis on their dual functionality. Microbial feedback occurs through phytohormone synthesis/catabolism, volatile and soluble effectors and antimicrobial metabolites that collectively modulate plant immunity, growth and stress tolerance while structuring inter-microbial competition. These bidirectional exchanges form a dynamic network where plants and microbes continuously negotiate cooperation and conflict under diurnal and seasonal oscillations. We outline translational prospects, including probiotic foliar applications, metabolite priming and breeding for beneficial consortia, while identifying key challenges in signal attribution, microbiota stabilization and deciphering community-level crosstalk dynamics for sustainable crop protection.},
}

@article {pmid41327409,
year = {2025},
author = {Jin, J and Wang, X and Zhang, X and Mei, J and Zheng, W and Guo, L and Sun, H and Zhang, L and Liu, C and Ye, W and Guo, L},
title = {Grapevine phyllosphere pan-metagenomics reveals pan-microbiome structure, diversity, and functional roles in downy mildew resistance.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02287-4},
pmid = {41327409},
issn = {2049-2618},
support = {ZR2024QC241//Shandong Provincial Natural Science Foundation Youth Project/ ; 2024CXPT031//Key R&D Program of Shandong Province/ ; ZR2023JQ010//Natural Science Foundation for Distinguished Young Scholars of Shandong Province/ ; },
abstract = {BACKGROUND: Grapevines are among the most economically important fruit crops, and the microbiome profoundly influences their health, yield, and quality. However, mechanistic insights into microbiome-orchestrated grapevine biology remain limited.

RESULTS: Here, we conduct large-scale pan-metagenomic and pan-metatranscriptomic analyses of the phyllosphere microbiome from 107 grapevine accessions spanning 34 Vitis species. We show that the grapevine core microbiome is dominated by phyla Bacillota and Pseudomonadota. Leveraging PacBio sequencing, we assembled 19 high-quality metagenome-assembled genomes (MAGs) from the grapevine pan-microbiome, representing the first MAG reconstruction in plant-associated microbial communities using PacBio reads. These MAGs encode genes associated with antibiotic resistance, secondary metabolism, and carbohydrate-active enzymes (CAZymes), which could potentially influence grapevine biology. During downy mildew (DM) infection, DM-resistant grapevines exhibit significantly higher microbial network complexity than susceptible counterparts. Among the key taxa contributing to this complexity, Bacillota emerged as the dominant phylum, displaying strong abundance correlations with phylum Euglenozoa and Cyanobacteriota, and an isolated Bacillota species from the grapevine leaves, Bacillus cereus, demonstrated potent biocontrol activity against DM infection. Pan-metatranscriptomic analysis further revealed significant upregulation of eukaryotic microbial genes involved in primary and secondary metabolism.

CONCLUSIONS: This pan-metagenomic study offers unprecedented insights into the complex structure, diversity, and functional roles of the grapevine phyllosphere microbiome and presents valuable genomic and microbial resources for microbiome research and engineering to enhance viticulture productivity and quality. Video Abstract.},
}

@article {pmid41327304,
year = {2025},
author = {Zhang, X and Li, Y and Xiong, Z and Zheng, N and Wang, J and Zhao, S},
title = {Biochanin A improves nitrogen utilization efficiency by regulating ruminal microbial community in dairy goats.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02275-8},
pmid = {41327304},
issn = {2049-2618},
support = {32402768//National Natural Science Foundation of China/ ; 2004DA125184G2108//State Key Laboratory of Animal Nutrition and Feeding/ ; CARS-36//Earmarked Fund for CARS/ ; 2022YFD1301000//National Key R&D Program of China/ ; CAAS-ZDRW202304//Agricultural Science and Technology Innovation Program/ ; },
abstract = {BACKGROUND: Rumen microbial nitrogen metabolism is crucial for animal health, productivity, and environmental sustainability in ruminants. Natural products like biochanin A are garnering interest as potential feed additives due to their beneficial effects and safety profiles. Here, we collected total mixed diet, plasma, milk, urine, and feces samples of dairy goats to evaluate the impact of biochanin A on nitrogen metabolism and elucidated regulatory mechanisms of nitrogen metabolism using multi-omics approaches by analyzing plasma metabolites and ruminal microbial communities.

RESULTS: Supplementation with biochanin A significantly enhanced nitrogen utilization efficiency of dairy goats. Plasma metabolomics revealed that biochanin A altered pathways related to amino acid biosynthesis/metabolism and glycolysis/gluconeogenesis. In the rumen, biochanin A enriched microbial strains from the families Selenomonadaceae and Aminobacteriaceae. Up-regulated proteins predominantly associated with glycolysis were identified by metaproteomics. Integrated metagenomic and metaproteomic analyses demonstrated that biochanin A positively influenced carbohydrate metabolism, amino acid metabolism, and energy metabolism pathways.

CONCLUSION: Biochanin A enhances nitrogen metabolism by regulating rumen microbial community function, supporting its potential as a natural feed additive to improve nitrogen utilization of ruminants. Video Abstract.},
}

@article {pmid41327300,
year = {2025},
author = {Ni, J and Hernández-Cacho, A and Nishi, SK and Babio, N and Belzer, C and Konstati, P and Vioque, J and Corella, D and Castañer, O and Vidal, J and Moreno-Indias, I and Torres-Collado, L and Coltell, O and Fitó, M and Ruiz-Canela, M and Wang, DD and Tinahones, FJ and Salas-Salvadó, J},
title = {Mediterranean diet, gut microbiota, and cognitive decline in older adults with obesity/overweight and metabolic syndrome: a prospective cohort study.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {669},
pmid = {41327300},
issn = {1741-7015},
support = {FPU 20/00385//Ministerio de Ciencia, Innovación y Universidades/ ; 2022PMF-INV-01//predoctoral grant from Martí Franquès - INVESTIGO research fellowship funded and supported by NextGenerationEU, Servicio Público de Empleo Estatal and Universitat Rovira i Virgili/ ; CIHR, MFE-171207/CAPMC/CIHR/Canada ; PI13/00233, PI13/00728, PI13/00462, PI14/01206, PI14/ 00696, PI16/00533, PI16/00366, PI16/00501, PI17/01441, PI17/00855, PI19/00017, PI19/00781, PI19/00576, PI20/ 00557, PI21/0046//Spanish Institutions for funding scientific biomedical research, CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN) and Instituto de Salud Carlos III (ISCIII), through the Fondo de Investigación para la Salud (FIS), which is co-funded by the European Regional Development Fund/ ; PI0458/2013, PS0358/2016, PI0137/2018//Consejería de Salud de la Junta de Andalucía/ ; PROMETEO/ 2017/017 and PROMETEO/2021/21//Conselleria de Innovación, Universidades, Ciencia y Sociedad Digital from the Generalitat Valenciana/ ; CPII21/00013//"Miguel Servet Type II" program of the ISCIII-Madrid (Spain) and cofounded by the European Union/ ; R01DK127601//NIH grant/ ; 2013ACUP00194//Recercaixa/ ; grant agreement #847879//Eat2beNICE/H2020-SFS-2016-2 EU- H2020 European grant, and the Horizon 2020 PRIME study/ ; },
mesh = {Humans ; *Diet, Mediterranean ; *Gastrointestinal Microbiome/physiology ; Aged ; Female ; Male ; Prospective Studies ; *Cognitive Dysfunction/microbiology ; *Obesity/complications/psychology/microbiology ; *Metabolic Syndrome/complications/microbiology/psychology ; *Overweight/complications/microbiology/psychology ; Middle Aged ; },
abstract = {BACKGROUND: Emerging evidence highlights that diet dynamically shapes the gut microbiome, which in turn influences cognitive function through bidirectional gut-brain communication, offering a promising target for mitigating cognitive decline and neurodegenerative disorders. While the Mediterranean diet (MedDiet) is a well-established dietary pattern with demonstrated neuroprotective benefits, the interplay between MedDiet adherence, gut microbiota, and longitudinal cognitive trajectories remains poorly understood. We aimed to identify a gut microbial signature of the MedDiet adherence and prospectively examine the associations of MedDiet adherence and MedDiet gut microbial signature (MedDiet-GMS) with cognitive changes over time in older adults at high risk of cognitive decline.

METHODS: This study included 746 participants (mean age 65 ± 5 years, 48% women) with overweight/obesity and metabolic syndrome. Adherence to the MedDiet was assessed using a validated 14-item Mediterranean Diet Adherence Screener (MEDAS). Baseline gut microbiota composition was profiled via 16S rRNA sequencing. Cognitive function was evaluated at baseline, 2, 4, and 6 years using a comprehensive neuropsychological battery. Elastic net regressions were applied to derive a MedDiet-GMS, and linear mixed models were used to assess associations of both MEDAS and MedDiet-GMS with trajectories of cognitive function, adjusting for potential confounders.

RESULTS: Higher adherence to the MedDiet was associated with greater gut microbial diversity (p < 0.05) and distinct microbial composition (PERMANOVA, p = 0.001). The MedDiet-GMS comprised 20 taxa, including short-chain fatty acid-producers (e.g., Barnesiella, Butyricicoccus) positively weighted and pro-inflammatory taxa (e.g., Eggerthella) negatively weighted. Both higher MEDAS scores (p = 0.007) and MedDiet-GMS (p = 0.036) were independently associated with slower global cognitive decline. The MedDiet-GMS was additionally linked to preserved executive function (p = 0.049), while MEDAS was associated with attenuated general cognitive decline (p = 0.028). Eggerthella, inversely associated with MedDiet adherence, was linked to greater executive function decline (FDR < 0.05).

CONCLUSIONS: Greater adherence to the MedDiet was associated with a favorable gut microbiota profile and slower cognitive decline over 6-year of follow-up. A microbiome-derived signature of MedDiet adherence was prospectively associated with favorable cognitive trajectories in older adults at risk of cognitive decline. External validation and experimental research are warranted to translate these findings into targeted microbiome-based dietary interventions for healthy cognitive aging.},
}

Humans
*Diet, Mediterranean
*Gastrointestinal Microbiome/physiology
Aged
Female
Male
Prospective Studies
*Cognitive Dysfunction/microbiology
*Obesity/complications/psychology/microbiology
*Metabolic Syndrome/complications/microbiology/psychology
*Overweight/complications/microbiology/psychology
Middle Aged

@article {pmid41327182,
year = {2025},
author = {Zhang, Y and Zheng, W and Yan, X and Zhang, Y and Peng, B and Wu, D and Zhang, L and Pang, H and Yang, R and Wang, Y and Li, G and Ma, X},
title = {Influence from the intestinal microbiota of neonate on early child development.},
journal = {BMC pediatrics},
volume = {25},
number = {1},
pages = {976},
pmid = {41327182},
issn = {1471-2431},
support = {2022GJM04//Central Public-interest Scientific Institution Basal Research Fund of China/ ; 2016YFC1000307//National Key Research and Development Program of China/ ; 2016YFC1000301//National Key Research and Development Program of China/ ; 2016YFC1000307//National Key Research and Development Program of China/ ; 2016YFC1000307//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant, Newborn ; Case-Control Studies ; Male ; *Child Development ; Female ; *Developmental Disabilities/microbiology ; Meconium/microbiology ; Infant ; Child, Preschool ; },
abstract = {OBJECTIVE: The early-life microbiome is gaining appreciation as a major influencer in human development and long-term health. The present study explored the influence from the intestinal microbiota of neonate on early child development.

METHODS: The first internal discharge was collected from the Beijing Birth Cohort Study (BBCS) located in Beijing, China. Then these children were followed up using the Ages & Stages Questionnaires (ASQ). 77 children were found with at least one domain of developmental delay, and 259 children with no delays were randomly selected as control group, as a nested case-control study. Their meconium microbiome were profiled using multi-barcode 16 S rRNA sequencing at V1-V9 hypervariable region.

RESULTS: There were significant difference in alpha-diversity and beta-diversity measures of intestinal microbiota between groups of children with or without developmental delays(P<0.05), as group of children with developmental delays had less diversity in intestinal microbiota. And there were significant differences on the species composition as well. On genus level, linear discriminant analysis effect size (LefSe) showed higher abundances of Serratia, Burkholderia-Caballeronia-Paraburkholderia, and Enterococcus in the group with developmental delays. It indicated that the lower diversity of intestinal microbiota, and higher abundances of certain intestinal microbiota might be related to developmental delays.

CONCLUSION: There were significant differences in the intestinal microbiota of neonate between children with or without developmental delays. Lower diversity of intestinal microbiota, and higher abundances of certain intestinal microbiota might be related to developmental delays.},
}

Humans
*Gastrointestinal Microbiome
Infant, Newborn
Case-Control Studies
Male
*Child Development
Female
*Developmental Disabilities/microbiology
Meconium/microbiology
Infant
Child, Preschool

@article {pmid41327157,
year = {2025},
author = {Zhang, XY and Li, YT and Guo, J and Feng, Y and Han, Q and Zhang, SH and Gao, Y and Yin, HT and Ding, XX and Li, XJ and Liang, BB},
title = {Saliva from oral squamous cell carcinoma patients promotes tumor progression via Inflammation, stromal remodeling, and metabolic reprogramming in a mouse model.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-025-07413-0},
pmid = {41327157},
issn = {1472-6831},
support = {ZF2025241//Hebei Provincial Government-Funded Clinical Medicine Talent Cultivation Program/ ; ZF2024151//Hebei Provincial Government-Funded Clinical Medicine Talent Cultivation Program/ ; 2025350//Research projects under the Hebei Provincial Administration of Traditional Chinese Medicine/ ; 2025350//Research projects under the Hebei Provincial Administration of Traditional Chinese Medicine/ ; 2025350//Research projects under the Hebei Provincial Administration of Traditional Chinese Medicine/ ; 2025350//Research projects under the Hebei Provincial Administration of Traditional Chinese Medicine/ ; 2025350//Research projects under the Hebei Provincial Administration of Traditional Chinese Medicine/ ; 20240101//Hebei Province Medical Science Research Project/ ; 25297704D//S&T Program of Hebei/ ; },
abstract = {BACKGROUND: Oral squamous cell carcinoma (OSCC) is a prevalent and aggressive malignancy with increasing evidence implicating the oral microbiome and tumor microenvironment in its progression. However, the mechanistic impact of OSCC patient-derived saliva on tumor development remains poorly understood.

METHODS: We established an orthotopic OSCC mouse model and topically applied saliva collected from OSCC patients to assess its effects on tumor progression. Multi-omics analyses, including 16 S rRNA sequencing, tumor transcriptomics (RNA-seq), and metabolomics (LC-MS), were performed to explore changes in the oral microbiota, gene expression profiles, and metabolic pathways.

RESULTS: Treatment with OSCC patient saliva significantly accelerated tumor growth compared to controls. Saliva application altered the oral microbiota, most notably causing a significant enrichment of the genus Staphylococcus. Tumor transcriptomics revealed upregulation of genes associated with chronic neutrophilic inflammation (Mpo), cancer-associated fibroblast (CAF) activation, and extracellular matrix (ECM) remodeling (Angptl4, Col2a1). Metabolomic analysis demonstrated profound metabolic reprogramming within the tumors, including enhanced amino acid metabolism (tryptophan, glutamate), fatty acid oxidation, and accumulation of the oncometabolite succinate. Integrated analysis showed that Staphylococcus abundance was strongly correlated with these inflammatory and metabolic signatures.

CONCLUSIONS: This study demonstrates that saliva from OSCC patients promotes tumor progression in vivo through a multifactorial mechanism involving inflammation, stromal remodeling, and metabolic rewiring. These findings highlight the tumor-promoting potential of salivary and microbial components, suggesting new avenues for diagnostic and therapeutic strategies targeting the oral microenvironment in OSCC.},
}

@article {pmid41326814,
year = {2025},
author = {Kelliher, JM and Mirzayi, C and Bordenstein, SR and Oliver, A and Kellogg, CA and Hatcher, EL and Berg, M and Baldrian, P and Aljumaah, M and Miller, CML and Mungall, C and Novak, V and Palucki, A and Smith, E and Tabassum, N and Bonito, G and Brister, JR and Chain, PSG and Chen, M and Degregori, S and Dundore-Arias, JP and Emerson, JB and Moreira C Fernandes, V and Flores, R and Gonzalez, A and Hansen, ZA and Jackson, SA and Moustafa, AM and Northen, TR and Pariente, N and Pett-Ridge, J and Record, S and Reji, L and Reysenbach, AL and Rich, VI and Richardson, L and Roux, S and Schriml, LM and Shabman, RS and Sierra, MA and Sullivan, MB and Sundaramurthy, P and Thibault, KM and Thompson, LR and Tighe, S and Vereen, E and , and Eloe-Fadrosh, EA},
title = {STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies.},
journal = {Nature microbiology},
volume = {10},
number = {12},
pages = {3059-3068},
pmid = {41326814},
issn = {2058-5276},
mesh = {Humans ; *Microbiota ; *Guidelines as Topic ; *Research Design/standards ; *Rivers/microbiology ; },
abstract = {The interdisciplinary nature of microbiome research, coupled with the generation of complex multi-omics data, makes knowledge sharing challenging. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines provide a checklist for the reporting of study information, experimental design and analytical methods within a scientific manuscript on human microbiome research. Here, in this Consensus Statement, we present the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines. The guidelines expand on STORMS and include 67 items to support the reporting and review of environmental (for example, terrestrial, aquatic, atmospheric and engineered), synthetic and non-human host-associated microbiome studies in a standardized and machine-actionable manner. Based on input from 248 researchers spanning 28 countries, we provide detailed guidance, including comparisons with STORMS, and case studies that demonstrate the usage of the STREAMS guidelines. STREAMS, like STORMS, will be a living community resource updated by the Consortium with consensus-building input of the broader community.},
}

Humans
*Microbiota
*Guidelines as Topic
*Research Design/standards
*Rivers/microbiology

@article {pmid41326813,
year = {2025},
author = {},
title = {STREAM-lining guidelines for microbiome research.},
journal = {Nature microbiology},
volume = {10},
number = {12},
pages = {3041-3042},
pmid = {41326813},
issn = {2058-5276},
}

@article {pmid41326768,
year = {2025},
author = {Polizel, GHG and Cánovas, Á and Diniz, WJS and Ramírez-Zamudio, GD and Cesar, ASM and Fukumasu, H and Fernandes, AC and Furlan, É and de Almeida Santana, MH},
title = {Unveiling long-term prenatal nutrition biomarkers in beef cattle via multi-tissue and multi-OMICs analysis.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {22},
number = {1},
pages = {8},
pmid = {41326768},
issn = {1573-3890},
support = {23/09113-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 17/12105-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 307593/2021-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Animals ; Cattle ; Female ; Pregnancy ; *Biomarkers/metabolism/analysis ; *Metabolomics/methods ; Male ; Liver/metabolism ; Transcriptome ; *Maternal Nutritional Physiological Phenomena ; *Prenatal Nutritional Physiological Phenomena ; Multiomics ; },
abstract = {INTRODUCTION: Maternal nutrition during gestation plays a crucial role in shaping offspring development, metabolism, and long-term health, yet the underlying molecular mechanisms remain poorly understood.

OBJECTIVES: This study investigated potential biomarkers through multi-OMICs and multi-tissue analyses in offspring of beef cows subjected to different gestational nutrition regimes.

METHODS: A total of 126 cows were allocated to three groups: NP (control, mineral supplementation only), PP (protein-energy supplementation in the last trimester), and FP (protein-energy supplementation throughout gestation). Post-finishing phase, samples (blood, feces, ruminal fluid, fat, liver, and longissimus muscle/meat) were collected from 63 male offspring. RNA sequencing was performed on muscle and liver, metabolomics on plasma, fat, liver, and meat, and 16S rRNA sequencing on feces and ruminal fluid. Data were analyzed via DIABLO (mixOmics, R).

RESULTS: The muscle transcriptome showed strong cross-block correlations (|r| > 0.7), highlighting its sensitivity to maternal nutrition. Plasma glycerophospholipids (PC ae C30:0, PC ae C38:1, lysoPC a C28:0) were key biomarkers, particularly for FP. The PP group exhibited liver-associated markers (IL4I1 gene, butyrylcarnitine), reflecting late-gestation effects, while NP had reduced ruminal Clostridia (ASV151, ASV241), suggesting impaired microbial energy metabolism.

CONCLUSIONS: This integrative multi-OMICs approach provided deeper insights than single-layer analyses, distinguishing nutritional groups and revealing tissue- and OMIC-specific patterns. These findings demonstrate the value of combining transcriptomic, metabolomic, and microbiome data to identify biomarkers linked to maternal nutrition in beef cattle.},
}

Animals
Cattle
Female
Pregnancy
*Biomarkers/metabolism/analysis
*Metabolomics/methods
Male
Liver/metabolism
Transcriptome
*Maternal Nutritional Physiological Phenomena
*Prenatal Nutritional Physiological Phenomena
Multiomics

@article {pmid41326607,
year = {2025},
author = {Tovar-Herrera, OE and Grinshpan, I and Sorek, G and Lybovits, I and Levin, L and Moraïs, S and Mizrahi, I},
title = {Core rumen microbes are functional generalists that sustain host metabolism and gut ecosystem function.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {41326607},
issn = {2397-334X},
support = {866530//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 101000213//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101000309//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
abstract = {Some microbes persist across diverse gut microbiomes, raising the question of what features define these core taxa and allow them to persist across hosts. Using the rumen microbiome as a model system, we show that core microbes exhibit distinct attributes of ecological generalists, including greater strain variability and broader functional capacity, linked to larger genome sizes. By analysing ~3,000 genomes of core and non-core microbes and metabolically measuring their functional attributes with both biochemical assays and untargeted/targeted metabolomics, we find that these traits enable core microbes to be metabolically independent while also supporting non-core microbes and the host. Core taxa produce essential metabolites, such as amino acids and vitamins, and encode fibre-degrading enzymes crucial for host nutrition. Additionally, they engage in cross-feeding, providing non-core microbes with vital nutrients. This independence positions core microbes as foundational pillars of gut ecosystem stability, and influencing these microbes could modulate microbiome functionality and ruminant host metabolism, with possible downstream consequences for food security and environmental sustainability.},
}

@article {pmid41326565,
year = {2025},
author = {Wiśniewska, K and Przemieniecki, SW and Krawczyk, K and Piwowarczyk, R},
title = {Diversity and functional traits of the flower stigma microbiome in heterotrophic and autotrophic plants: Phelipanche ramosa vs. its host Nicotiana tabacum.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30322-9},
pmid = {41326565},
issn = {2045-2322},
support = {2021/05/X/NZ8/01154//National Science Centre, Poland/ ; SUPB.RN.24.207, SUPB.RN.25.234 (2024, 2025)//Jan Kochanowski University/ ; },
abstract = {Phelipanche ramosa is a widespread parasitic weed of significant economic importance, particularly affecting tomatoes and tobacco. Despite its well-documented impact on agriculture, its microbial associations remain poorly understood. For the first time, we used Next-Generation Sequencing (NGS) to determine the composition of microorganisms (bacteria and fungi) on the flower stigma of P. ramosa and its host, Nicotiana tabacum, as well as to explore their potential functions. The stigma is a nutrient-rich environment that fosters a varied microbial community, encompassing both beneficial and pathogenic organisms affecting plant health and reproductive success. Unique bacterial populations were identified in P. ramosa stigmas, which were absent or less abundant in N. tabacum stigmas. We identified 49 bacterial OTUs in P. ramosa stigmas, primarily Proteobacteria (87.5%) with dominant genera like Pantoea and Pseudomonas. In contrast, N. tabacum stigmas (18 OTUs) were also rich in Proteobacteria (69.6%) but showed higher levels of Leuconostoc and Enterobacteriaceae. Phelipanche ramosa stigmas exhibited a higher abundance of Actinobacteria, while N. tabacum stigmas had a greater proportion of Firmicutes. Fungal communities differed significantly: P. ramosa stigmas (109 OTUs) were dominated by Basidiomycota, while N. tabacum (69 OTUs) was primarily colonised by Ascomycota, with the genus Candida common in the host but absent in the parasite. Specific genera such as Chalastospora, Ustilaginaceae, and Bensingtonia were more abundant or exclusive to P. ramosa stigmas. Nicotiana tabacum stigmas hosted a potentially functionally rich bacterial microbiome, while P. ramosa harbored a more limited one. In contrast, both the structural diversity and functional (metabolic) potential of the fungal communities were higher in P. ramosa compared to N. tabacum. Microbiome network analysis highlighted distinct physiological functions associated with autotrophic and heterotrophic lifestyles. Some identified microorganisms may play key roles in nutrient availability and pathogenicity, including potentially beneficial ones that could provide new opportunities for biological control. This study highlights the significant relationships between microbial diversity and functional traits, underscoring the importance of these dynamics in the structure and functioning of the stigma microbiome.},
}

@article {pmid41326564,
year = {2025},
author = {Daniels, S and Martin, S and Harris, P and Moore-Colyer, M},
title = {Using culture 'omics to explore the microbial structure and function in an equid in vitro digestion model.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-29936-w},
pmid = {41326564},
issn = {2045-2322},
abstract = {The in vitro gas production system (GPS), developed to estimate degradation of ruminant feedstuffs, has been adapted for equine use. This study aimed to characterise the bacterial community profile and metabolome of donor faeces and faecal inoculum within the GPS when fermenting the same diet as faecal donors. Six Welsh ponies on identical diets were faecal donors with samples collected for microbiome profiling and system inoculation. Gas production (manual pressure transducer technique) was performed for 156 h with 2 replicate bottles from each donor harvested at 8,20,28 and 36 h. Faecal and inoculum samples were subject to PMAxx for viability PCR, 16S rRNA sequencing and 1[H] NMR metabonomics. Time in the GPS effected bacterial community profile, metabolic phenotype and predicted metabolic pathways. Collectively a system dysbiosis was observed at 8 h. End point metabolic profile was similar to the donor faeces but GP fibre degrading microbiota better reflected previously reported literature on rumen microbiota, rather than those found in horses. The GPS estimates dry matter digestibility similar to in vivo digestibility, resulting in a similar metabolic profile to donor faeces. However, the GPS either favours rumen dwelling microbiota or demonstrates functional microbial redundancy compared to the donor faeces of equids.},
}

@article {pmid41326479,
year = {2025},
author = {Marawan, AE and Elmetwally, OA and Marwan, MM and El-Sokkary, MMA and Abass, SA and Eissa, LA},
title = {Diagnostic significance of gut Microbiome dysbiosis and biomarker expression in Egyptians with hepatocellular carcinoma.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {42932},
pmid = {41326479},
issn = {2045-2322},
mesh = {Humans ; *Carcinoma, Hepatocellular/diagnosis/microbiology ; *Gastrointestinal Microbiome ; *Liver Neoplasms/diagnosis/microbiology ; *Dysbiosis/microbiology/diagnosis/complications ; Male ; Female ; Middle Aged ; Egypt/epidemiology ; Liver Cirrhosis/microbiology/diagnosis ; Adult ; *Biomarkers, Tumor ; Matrix Metalloproteinase 9/blood/metabolism ; Vascular Endothelial Growth Factor A/blood ; Biomarkers ; Feces/microbiology ; Case-Control Studies ; Hepatitis C/complications ; North African People ; },
abstract = {Egypt has the greatest incidence of hepatitis C virus (HCV) infection globally, which is a considerable trigger of fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). The gut microbiome has been recognized for contributing to various hepatic conditions. Nevertheless, its correlation with HCV and HCC is not well understood. Our study is conducted to investigate the potential relevance of some biomarkers: matrix metalloproteinase 9 (MMP9), Signal transducer and activator of transcription 3 (STAT3), superoxide dismutase (SOD), vascular endothelial growth factor (VEGF), and nuclear factor-κB (NF-κB), along with gut microbial variations, for the differentiation between HCV-related cirrhosis and HCC. The 90 fecal and blood samples were collected from 30 healthy controls, 30 HCV-related cirrhosis, and 30 HCC for detecting gut microbial abundance and biochemical markers examination. Our findings displayed the existence of intestinal microbiome dysbiosis with marked enrichment of specific species, including Bifidobacterium, Fusobacterium, Providencia, E. faecium, and Pseudomonas aeruginosa in HCC patients. Furthermore, the most enriched genera in HCV-related cirrhosis patients were Bifidobacterium, Porphyromonas, and Bacteroides. MMP9 exhibited the highest diagnostic performance of the five measured biomarkers, discriminating against HCC vs. HCV-related cirrhosis with specificity and sensitivity of 100% and 90%, respectively, at a cut-off value > 166.8. Additionally, SOD and NF-κB were statistically significant discriminators of HCC from cirrhosis at cutoff values of ≤ 0.197 and > 166.8. A significant correlation between microbiome abundance and VEGF and MMP9 was observed. This study illustrated that gut microbiomes contribute to HCC and HCV-related cirrhosis pathogenesis, opening approaches for cancer management and prevention.},
}

Humans
*Carcinoma, Hepatocellular/diagnosis/microbiology
*Gastrointestinal Microbiome
*Liver Neoplasms/diagnosis/microbiology
*Dysbiosis/microbiology/diagnosis/complications
Male
Female
Middle Aged
Egypt/epidemiology
Liver Cirrhosis/microbiology/diagnosis
Adult
*Biomarkers, Tumor
Matrix Metalloproteinase 9/blood/metabolism
Vascular Endothelial Growth Factor A/blood
Biomarkers
Feces/microbiology
Case-Control Studies
Hepatitis C/complications
North African People

@article {pmid41326384,
year = {2025},
author = {Lu, K and Zhang, Z and Zhu, X and Ibánhez, JSP and Yang, B and Jiang, S},
title = {Coastal rest during the COVID-19 pandemic enhances microbial community stability and metabolic potential in a subterranean estuary.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00873-w},
pmid = {41326384},
issn = {2055-5008},
support = {41706081//the National Natural Science Foundation of China/ ; },
abstract = {This study examines a subterranean estuary seepage face in China's Sanggou Bay by comparing environmental parameters and microbiome data before and after the COVID-19 lockdown, in order to reveal the regulatory mechanisms of coastal resting on microbial community stability and biogeochemical functions. The results revealed that reduced human activities significantly decreased sediment nutrient loading and shifted organic matter sources from terrestrial- to marine-dominated. This environmental restructuring drove profound microbial community reorganization: while α-diversity indices declined, the relative abundance of core species increased, with marked enhancements in community stability and metabolic efficiency, particularly in pathways related to amino acid metabolism, carbohydrate metabolism, and biogeochemical cycling. The study confirms that a coastal rest period can enhance ecosystem resilience by reducing anthropogenic disturbance, optimizing resource allocation, and activating microbial functional plasticity. These findings suggest that rest periods may represent a potential strategy for supporting ecosystem resilience and sustainability.},
}

@article {pmid41326075,
year = {2026},
author = {Wang, R and Liu, B and Wu, Y and Wang, Y and Xia, X and Yan, X and Huang, L},
title = {Regulation of phenazine-1-carboxylic acid synthesis by hmgL in Pseudomonas chlororaphis and its role in restructuring plant microbiomes for disease resistance.},
journal = {Pesticide biochemistry and physiology},
volume = {216},
number = {Pt 1},
pages = {106762},
doi = {10.1016/j.pestbp.2025.106762},
pmid = {41326075},
issn = {1095-9939},
mesh = {*Pseudomonas chlororaphis/metabolism/genetics ; *Phenazines/metabolism ; *Malus/microbiology ; *Microbiota ; *Disease Resistance ; Plant Diseases/microbiology ; },
abstract = {The hmgL, encoding 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) lyase, is known for its metabolic role in cleaving HMG-CoA into acetyl-CoA and acetoacetate, but its involvement in antimicrobial activity remains unclear. In this study, we isolated Pseudomonas chlororaphis H2Q4, from vigorous and healthy apple branches, demonstrating strong biocontrol potential. Genetic analysis revealed that deletion of hmgL, significantly impaired the antimicrobial activity and colonization capacity of the H2Q4 strain in plant tissues. Notably, the deletion of hmgL led to a marked reduction in the production of phenazine-1-carboxylic acid (PCA). While phzD is recognized as essential for PCA synthesis in P. chlororaphis, our findings highlight a previously unrecognized role of hmgL in modulating PCA production. Furthermore, treatment with strain H2Q4 and PCA altered the bacterial community composition across various plant compartments in apple seedlings, with the leaf microbiome exhibiting enhanced resistance to plant pathogenic fungi. Interestingly, PCA treatment significantly increased the relative abundance of Bacillus species in the phyllosphere microbiome. These results underscore the dual role of hmgL in both secondary metabolism and microbial community dynamics, providing new insights into the biocontrol mechanisms of P. chlororaphis and its potential applications in sustainable agriculture.},
}

*Pseudomonas chlororaphis/metabolism/genetics
*Phenazines/metabolism
*Malus/microbiology
*Microbiota
*Disease Resistance
Plant Diseases/microbiology