@article {pmid41412637,
year = {2026},
author = {Ferrocino, I and Biolcati, F and Giordano, M and Bertolino, M and Zeppa, G and Cocolin, L},
title = {Dairy environment and seasons affect the microbiome of a traditional artisanal cheese.},
journal = {Food research international (Ottawa, Ont.)},
volume = {224},
number = {},
pages = {117927},
doi = {10.1016/j.foodres.2025.117927},
pmid = {41412637},
issn = {1873-7145},
mesh = {*Cheese/microbiology/analysis ; *Seasons ; *Microbiota ; Animals ; *Food Microbiology ; Italy ; Fungi/classification/genetics/isolation & purification ; *Dairying/methods ; Bacteria/classification/genetics ; Milk/microbiology ; Food Handling/methods ; Cattle ; Metagenomics ; },
abstract = {Cheese microbiome is a complex community shaped by raw ingredients and by the production environment that significantly influences final product characteristics. While environmental microbiome can establish stable resident populations, their composition remains susceptible to seasonal shifts, hygienic practices and other external factors. In this study we investigate the interplay of these factors on the bacterial and fungal communities throughout the production of a full-fat semi cooked semi-hard cow's milk cheese produced in the Piedmont region, North-West of Italy, named Maccagno. Amplicon based sequencing was used to characterize bacterial and fungal diversity across environmental surfaces (contact and non-contact) and during the manufacturing and ripening of Maccagno cheeses over three seasons (autumn, winter and summer). Metabolomic profiling and texture analysis of the ripened cheeses allowed for direct correlation with microbial community shifts. The facility environment maintained a remarkably stable core microbiota, including Staphylococcus, Streptococcus thermophilus, Lactococcus lactis, Debaryomyces, Penicillium and Cladosporium. Among the monitored processing plant sampling sites, the metal stirring tool, milk inlet pipe and the ripening room ventilation system emerged as critical points for microbial transfer and persistence. During ripening, core microbial taxa including Lc. lactis, S. thermophilus and Debaryomyces were observed. Shotgun metagenomics was then performed on final cheeses and genome reconstruction highlighted that Lc. lactis genomes showed impressive seasonal genomic adaptability, particularly in autumn, where it contributed to favorable texture and flavor through proteolytic activity and production of aroma-associated metabolites like acetoin and linear ketons. Conversely, summer production exhibiting the highest prevalence of spoilage-associated microbes such as Acinetobacter and Enterobacteriaceae, mainly of facility origin that led to off-flavor profiles inconsistent with the typical Maccagno sensory identity. The fungal communities, mainly composed by Debaryomyces and Penicillium, also varied seasonally, influenced significantly by the ventilation system in the ripening room. Maccagno cheese quality is a direct reflection of these complex microbial dynamics. Seasonal variations in raw milk microbiome and microbial populations established in specific environmental niches significantly affected the final product's sensory and textural attributes. To this end, understanding seasonal influences and the role of resident environmental populations is crucial for optimizing production protocols, mitigating spoilage risks, and ensuring the consistent quality of traditional cheeses.},
}

*Cheese/microbiology/analysis
*Seasons
*Microbiota
Animals
*Food Microbiology
Italy
Fungi/classification/genetics/isolation & purification
*Dairying/methods
Bacteria/classification/genetics
Milk/microbiology
Food Handling/methods
Cattle
Metagenomics

@article {pmid41412214,
year = {2025},
author = {Babalola, KT and Ganugula, R and Arora, M and Anderson, D and Agarwal, SK and Mohan, C and Mehrara, BJ and Kumar, MNVR},
title = {Dose optimization of lymph node-targeted cyclosporine-A for lupus-driven vasculopathy.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {114553},
doi = {10.1016/j.jconrel.2025.114553},
pmid = {41412214},
issn = {1873-4995},
abstract = {Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by immune dysregulation, systemic inflammation, and vascular complications. Cyclosporine A (CsA) is a potent immunosuppressant, but its systemic toxicity often limits its clinical use. To address this, we developed a lymph node-targeting nanoparticle formulation of CsA (P2Ns-GA-CsA) designed for CD71-mediated uptake to improve therapeutic efficacy while minimizing off-target effects. We conducted a preclinical dose optimization study in the MRL-lpr mouse model of lupus to define the effective therapeutic window of P2Ns-GA-CsA. Our preclinical dose optimization revealed a complex, biphasic immunological response. While all doses (5, 10, and 15 mg/kg) reduced inflammatory cytokines and kidney injury markers, a nuanced effect on immune activation was observed. The 5 mg/kg and 10 mg/kg doses successfully suppressed lymphocyte proliferation and immune activation, which was evident from reduced splenomegaly, lymphadenopathy, and plasma levels of anti-dsDNA and total IgG. Conversely, the 15 mg/kg dose paradoxically triggered immune hyperactivation, leading to aggressive lymphadenopathy, splenomegaly, and elevated autoantibodies. Mechanistically, the optimal 10 mg/kg dose downregulated key mediators of inflammation-induced lymphangiogenesis, corrected gut microbial dysbiosis, and restored microbiome-mediated tryptophan catabolism, contributing to systemic immunomodulation. These findings highlight the critical importance of non-regulatory dose optimization for nanomedicines, revealing complex pharmacodynamic responses often missed in conventional single-dose studies. Our results not only establish the targeted delivery of CsA as a viable therapeutic strategy for managing the vascular complications of SLE but also provide a crucial framework for ensuring the safety and efficacy of other repurposed immunomodulatory drugs in autoimmune diseases.},
}

@article {pmid41412203,
year = {2025},
author = {Rosales-Islas, V and Montes-García, JF and Ramírez-Paz-Y-Puente, GA and Paniagua-Contreras, GL and Gutiérrez-Pabello, JA and Zenteno, E and Vázquez-Cruz, C and Negrete-Abascal, E},
title = {Epinephrine and norepinephrine increase the growth and expression of adhesins and proteases in Mannheimia haemolytica.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108250},
doi = {10.1016/j.micpath.2025.108250},
pmid = {41412203},
issn = {1096-1208},
abstract = {Mannheimia haemolytica (Mh) is an opportunistic pathogen that causes pneumonic infections in different ruminants. It is also part of the respiratory tract microbiome, but it descends into the lower respiratory tract under stress, causing shipping fever. The stress hormones epinephrine and norepinephrine have been suggested to induce Mh biofilm dispersion, but their roles in virulence have not been shown. In this study, the effects of these two hormones on Mh growth and on the expression of adhesins, proteases, and biofilm formation are evaluated. Physiological concentrations (1-5 ng/mL) of epinephrine and norepinephrine increase the growth of Mh and the expression of 42- and 75-kDa gelatin proteases, induce biofilm dispersion, and decrease biofilm protein and carbohydrate concentrations. At 50 or 500 ng/mL concentrations of epinephrine and norepinephrine, the expression of OmpA and OmpH adhesins and 42- and 100-kDa casein proteases increases. Bacterial adhesion to bovine monocytes or oral epithelial cells also increases, but antibodies against OmpH and OmpA diminish adhesion. Our results strongly suggest that epinephrine and norepinephrine modulate the expression of Mh virulence factors.},
}

@article {pmid41412124,
year = {2025},
author = {Deng, L and Fehr, K and Toe, LC and Allen, LH and Bode, L and Hampel, D and Manus, MB and Mertens, A and Robertson, B and Yonemitsu, C and Meulenaer, B and Lachat, C and Sonnenburg, JL and Azad, MB and Dailey-Chwalibóg, T},
title = {Time-specific bidirectional links between the maternal microbiome, milk composition, and infant gut microbiota.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.11.014},
pmid = {41412124},
issn = {1934-6069},
abstract = {Early-life gut microbiome development is shaped by complex maternal and nutritional influences, yet the temporal and directional structure of these interactions remains unclear. In a longitudinal study of 152 mother-infant dyads in rural Burkina Faso, we examine how maternal gut and milk microbiomes, alongside milk components, influence infant gut microbiome development during the first 6 months. At 1-2 months, the infant gut microbiome clusters into three types: Escherichia-dominated, Bifidobacterium-dominated, and a diverse, pathogen-prevalent profile, which become less distinct by 5-6 months. Early infant gut microbiomes associate with maternal prenatal gut microbiota and early milk microbiome and oligosaccharides, while later variation links to other milk nutrients. Furthermore, early infant gut profiles predict subsequent milk composition, suggesting potential bidirectional communication between infant needs and maternal lactational physiology. These findings offer insights into early-life microbial development and inform future mechanistic studies and microbiome-targeted interventions, particularly in low-resource settings.},
}

@article {pmid41412116,
year = {2025},
author = {Collins, MK and Darch, H and Olavarría-Ramírez, L and McCafferty, C and O'Riordan, KJ and Cryan, JF},
title = {Robust Hippocampal Synaptic Plasticity Despite Gut Microbiota Depletion in Adult Mice.},
journal = {The European journal of neuroscience},
volume = {62},
number = {12},
pages = {e70346},
doi = {10.1111/ejn.70346},
pmid = {41412116},
issn = {1460-9568},
support = {754535//H2020 Marie Skłodowska-Curie Actions, Marie Sklodowska-Curie/ ; IRC GOIPG/2021/942//H2020 Marie Skłodowska-Curie Actions, Marie Sklodowska-Curie/ ; //Irish Research Council/ ; SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; *Hippocampus/physiology/drug effects ; Male ; *Neuronal Plasticity/physiology/drug effects ; Female ; Mice ; Anti-Bacterial Agents/pharmacology ; Mice, Inbred C57BL ; Long-Term Potentiation/drug effects ; },
abstract = {The microbiota-gut-brain axis describes the bidirectional communication between the brain and the trillions of microorganisms living in the gut. Moreover, current evidence suggests that this axis can influence host behaviour and brain physiology. Previously we have shown that adult mice that have not been exposed to microbes throughout their lives display sex-specific deficits in hippocampal synaptic plasticity. However, it is not known whether this phenomenon originates during neurodevelopment or whether similar effects could be recreated with microbiome depletion in adulthood. Therefore, we explored the vulnerability of hippocampal synaptic function to altered microbiome signals, depleting the microbiome of male and female mice for 2 weeks with either an antibiotic cocktail or a single antibiotic added to drinking water. The antibiotic cocktail contained a variety of antibiotics including broad-spectrum antibiotics to ensure widescale microbiota depletion (ampicillin, vancomycin and imipenem). In addition, a more targeted depletion of Gram-positive gut bacteria was conducted using the gut-restricted antibiotic vancomycin. Ex vivo hippocampal electrophysiology measures of basal synaptic efficacy, short-term plasticity, and long-term potentiation (LTP) were then examined. We found that there was no effect of antibiotic administration on any of these measures, demonstrating the robustness of these hippocampal circuits to microbiome depletion during early adulthood. Taken together, this shows the ability of adult hippocampal plasticity to withstand a gut microbiome insult.},
}

Animals
*Gastrointestinal Microbiome/drug effects/physiology
*Hippocampus/physiology/drug effects
Male
*Neuronal Plasticity/physiology/drug effects
Female
Mice
Anti-Bacterial Agents/pharmacology
Mice, Inbred C57BL
Long-Term Potentiation/drug effects

@article {pmid41412053,
year = {2025},
author = {Xu, Y and Han, Y and Dong, X and Feng, Y and Wu, F and Xing, F and He, J and Rogers, MJ and Luan, X and Liu, R and He, J and Dang, H and Zhang, D},
title = {Temperature shapes the biogeography of rdhA and reductive dehalogenators in sediment across northwestern Pacific marginal seas.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140847},
doi = {10.1016/j.jhazmat.2025.140847},
pmid = {41412053},
issn = {1873-3336},
abstract = {Dehalogenating microorganisms are crucial in organohalide detoxification in marine sediments. However, the large-scale biogeography and potential environmental adaptability of reductive dehalogenators (RDGs) in marginal sea sediments remain poorly understood. Here, dehalogenating cultures enriched from different marginal sea sediments across northwestern Pacific showed varied dehalogenation patterns, suggesting diverse reductive dehalogenase genes (rdhA). Genome-resolved metagenomic analysis of in situ marginal sea sediments revealed the presence of rdhA-like genes belonging to six distinct categories, with two novel clades more abundant in hypothermal deep-sea sediments (p<0.05). The results of canonical correspondence analysis and distance decay relationship revealed that temperature outweighed geographical contiguity in determining rdhA biogeography and phylogenetic diversity in sediments. A total of 64 putative RDGs were identified across 13 phyla. Low ratios of non-synonymous and synonymous polymorphisms and nucleotide diversity at gene and genome levels indicated the conservation of dehalogenation metabolism in sediment microbiome. RDGs at higher abundance (p<0.05) in mesothermal (≥17.40 ℃) sediments may rely more on sulfate reduction, whereas those with higher abundance (p<0.05) in hypothermal (≤5.5 ℃) sediments (hyp-RDGs) may rely on nitrate utilization. Additionally, hyp-RDGs were prone to external cobalamin acquisition, possibly as an efficient energy-saving strategy. These findings provide insights into the ecological roles of RDGs in marine sediments.},
}

@article {pmid41411975,
year = {2025},
author = {Dai, J and Cao, X and Xu, H and Wang, C and Hao, L and Xie, B and Li, S and Zhao, K and Cui, L and Yin, Z and Yao, B and Chen, T and Haderlein, SB and Wang, R and Xu, F},
title = {Anodic microbiota reassembly via cell-cell interactions confers oxygen resilience in microbial fuel cells.},
journal = {Bioresource technology},
volume = {443},
number = {},
pages = {133815},
doi = {10.1016/j.biortech.2025.133815},
pmid = {41411975},
issn = {1873-2976},
abstract = {An anaerobic environment is typically optimal for electrochemically active microorganisms to generate current. Previous studies have created an integrated chamber-free microbial fuel cell (iMFC) that enables anaerobic sludge-sourced EAMs to function under high dissolved oxygen (DO) for the first time, although the mechanism remained unclear. This study examined the power output and anode microbiome dynamics under DO exposure in the iMFC. Multi-omics revealed a three-phase microbiome reassembly during aeration. Indole-3-acetic acid (IAA) and its precursors from anaerobes, together with streptozocin, phenazine, and rhamnolipid produced sequentially by aerobes, drove the anaerobic-aerobic transition. Initially, DO suppressed anaerobes, alleviating their IAA-mediated inhibition of facultative aerobes. Subsequent cell-cell signaling guided anodic microbiome succession from Acinetobacter to Stenotrophomonas, and finally to Pseudomonas. These findings elucidate the anode microbiome transformation mechanism and confirm with a reassembled synthetic consortium that iMFCs can operate aerobically, providing key insights for scaling the technology.},
}

@article {pmid41411934,
year = {2025},
author = {Paul, SS and Dey, A and Chanu, YM and Paul, J and Andonissamy, J and Dahiya, SS and Punia, BS},
title = {Altered rumen microbiome of water buffalo (Bubalus bubalis) by dietary composite feed additive enhances growth and nutrient utilization with reduced enteric methane and nitrogen emissions.},
journal = {Journal of environmental management},
volume = {397},
number = {},
pages = {128347},
doi = {10.1016/j.jenvman.2025.128347},
pmid = {41411934},
issn = {1095-8630},
abstract = {Environmental pollution through animal agriculture is a great concern in recent days owing to enhanced demand of animal products. In view of reduced greenhouse gas emissions from ruminants, this study investigated the effects of a novel composite feed additive (RESMI) having an optimum combination of methane inhibitors and alternate hydrogen sinks on rumen microbial community, methanogenesis, digestibility of feed, rumen fermentation, and performance of water buffaloes. The feed additive, RESMI was fed to fourteen Murrah buffalo calves divided into two groups (control and treatment) in a completely randomized design along with basal feed wheat straw, green fodder and concentrate mixture for a period of six months to study growth rate, nutrient utilization and methane emissions. Another four rumen fistulated adult buffaloes were selected to investigate the abundance and dynamics of rumen microbiota including potential adaptation of rumen microbes over five months of feeding experimentation. The treatment significantly (p < 0.05) decreased methane emission by up to 75 %, increased (p < 0.05) body weight gain by 9.7 %, feed efficiency by 15.2 % and also increased (p < 0.05) feed digestibility, resulting reduced faecal N excretion. The ruminal ammonia concentration was decreased (p < 0.05) and the abundances of total archaea at 1month as well as 5 months post dosing were decreased (p < 0.05) as compared to pre-dosing level but did not adversely (p > 0.05) affect the abundances of total bacteria and anaerobic fungi. A substantial difference (p < 0.05) in the relative abundance of different phylotypes of archaea, bacteria, and anaerobic fungi and unclassified bacteria were demonstrated indicating possible microbial community reorientation over time. The study revealed that supplementing the novel composite feed additive (RESMI) comprising of a combination of adequate electron acceptors or alternate hydrogen sinks with multiple inhibitors of methanogens can be an effective approach to decrease environmental pollution from ruminants and enhance production performance without development of substantial methanogenic archaeal resistance over long-term usage.},
}

@article {pmid41411657,
year = {2025},
author = {Chitre, S and Gharaibeh, RZ and Jobin, C},
title = {A defined bacterial consortium and spatial transcriptomics highlight the complex interaction between Campylobacter jejuni and the murine intestine.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2600053},
doi = {10.1080/19490976.2025.2600053},
pmid = {41411657},
issn = {1949-0984},
mesh = {Animals ; *Campylobacter jejuni/genetics/physiology/isolation & purification ; *Gastrointestinal Microbiome ; Mice ; *Campylobacter Infections/microbiology/immunology/genetics ; *Transcriptome ; Mice, Inbred C57BL ; Mice, Knockout ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; Interleukin-10/genetics/deficiency ; Germ-Free Life ; *Intestines/microbiology/immunology ; Gene Expression Profiling ; },
abstract = {The intestinal microbiota influences host susceptibility to Campylobacter jejuni (C. jejuni) infection. However, the interaction between specific intestinal bacteria and the C. jejuni-mediated host response is unclear. We established a defined consortium of bacteria to delineate C. jejuni-induced host responses. Three groups of germ-free (GF) Il10[-/-] mice were used in this study: 1) mice colonized with a defined consortium of 13 bacterial isolates (C13) representing the four most prominent phyla in the mouse gut. 2) C13 plus C. jejuni 81-176 and 3) GF alone. The C13 + C. jejuni group induced significant intestinal inflammation and inflammatory mRNA gene expression compared to mice colonized with C13. 16S rRNA gene sequencing revealed an increased relative abundance of Escherichia and Paraclostridium in C13 + C. jejuni. Fluorescence in situ hybridization (FISH) and RNAscope integrated with spatial transcriptomics provided a high-resolution map of infection-induced gene expression, revealing localized immune responses and epithelial remodeling in defined colonic regions. Region-specific analysis further demonstrated that tissue-associated C. jejuni differentially modulates host gene expression compared to tissue-associated Enterobacteriaceae. Collectively, these findings demonstrate the potential of defined microbial consortia and spatially resolved transcriptomics to dissect the complex interplay between host, microbiota, and pathogens during enteric infection.},
}

Animals
*Campylobacter jejuni/genetics/physiology/isolation & purification
*Gastrointestinal Microbiome
Mice
*Campylobacter Infections/microbiology/immunology/genetics
*Transcriptome
Mice, Inbred C57BL
Mice, Knockout
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
Interleukin-10/genetics/deficiency
Germ-Free Life
*Intestines/microbiology/immunology
Gene Expression Profiling

@article {pmid41411654,
year = {2025},
author = {Zhang, L and Xu, W and Meng, HYH and Ching, JYL and Liu, Y and Wang, S and Yan, S and Lin, L and Cheong, PK and Ip, KL and Peng, Y and Zhu, J and Cheung, CP and Leung, TF and Leung, ASY and Tam, WH and Leung, TY and Chan, PKS and Chang, EB and Rubin, DT and Claud, EC and Wu, WKK and Tun, HM and Chan, FKL and Ng, SC},
title = {Impacts of COVID-19 pandemic on early life gut microbiome.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2443117},
doi = {10.1080/19490976.2024.2443117},
pmid = {41411654},
issn = {1949-0984},
mesh = {Humans ; *COVID-19/epidemiology ; *Gastrointestinal Microbiome/genetics ; Infant ; Female ; SARS-CoV-2 ; Infant, Newborn ; China/epidemiology ; Pandemics ; Male ; Bacteria/genetics/classification/isolation & purification/drug effects ; Cohort Studies ; Hygiene ; Anti-Bacterial Agents/pharmacology ; Feces/microbiology ; Drug Resistance, Bacterial/genetics ; },
abstract = {Increased hygiene and sanitation are theorized to predispose to developing atopic diseases, a process potentially mediated by the gut microbiome. We hypothesized that the gut microbiome maturation has been altered by COVID-19 lockdown measures during the first year of life, a critical period when environmental exposure shapes human microbiome development. The two large pre- and during-COVID-19 mother-baby pairs cohorts in the Greater Bay Area of China provided the unique opportunity to assess the effect of increased hygiene standards on early gut microbiome maturation. Our results showed that the gut microbiome diversity, composition, and developmental trajectory were significantly altered between pre- and during-COVID-19 cohorts. Functionally, there was decreased richness in both antimicrobial peptide resistance genes and antibiotic resistance genes in the during-COVID cohort. Specially, Staphylococcus epidermidis carried a lower copy number of fluoroquinolone and beta-lactam antibiotics resistance genes while Klebsiella pneumoniae possessed a higher copy number of fluoroquinolone antibiotic resistance genes in gut microbiota of infants born during the COVID-19 pandemic. Our study underscores the importance of considering the microbiome when evaluating hygiene measures and the need for future research to ascertain the role of the gut microbiome in disease development.},
}

Humans
*COVID-19/epidemiology
*Gastrointestinal Microbiome/genetics
Infant
Female
SARS-CoV-2
Infant, Newborn
China/epidemiology
Pandemics
Male
Bacteria/genetics/classification/isolation & purification/drug effects
Cohort Studies
Hygiene
Anti-Bacterial Agents/pharmacology
Feces/microbiology
Drug Resistance, Bacterial/genetics

@article {pmid41410816,
year = {2025},
author = {He, JH and Wang, H and Qiu, E and Qi, Q and Wang, Z},
title = {Gut Microbiota and Atherosclerosis: Integrative Multi-Omics and Mechanistic Insights.},
journal = {Current atherosclerosis reports},
volume = {28},
number = {1},
pages = {1},
pmid = {41410816},
issn = {1534-6242},
support = {R01HL170904/HL/NHLBI NIH HHS/United States ; K01HL169019/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Atherosclerosis/microbiology/metabolism ; Metabolomics/methods ; Metagenomics ; Dysbiosis ; Proteomics ; Multiomics ; },
abstract = {PURPOSE OF REVIEW: This review synthesizes and discusses evidence from metagenomics, metabolomics, and proteomics on gut microbiome alterations in atherosclerotic cardiovascular disease (ACVD), with carotid atherosclerosis (CAS) serving as an example.

RECENT FINDINGS: Evidence on gut microbial α-diversity and β-diversity was mixed and differs by disease status. Pro-inflammatory/pathogenic gut bacterial taxa (e.g., Escherichia coli, Klebsiella spp., Streptococcus spp., and Ruminococcus gnavus) were often enriched in patients with ACVD or CAS, whereas short-chain fatty acid (SCFA) producers (e.g., Faecalibacterium prausnitzii, Roseburia spp., Bacteroides spp., and Eubacterium eligens) were depleted. Targeted and untargeted metabolomics implicated multiple microbial-derived metabolites in relation to ACVD and CAS, including trimethylamine N-oxide, short-chain fatty acids, bile acids, lipopolysaccharides, phenylacetylglutamine, indole-3-propionate and imidazole propionate. Gut dysbiosis contributes to ACVD or CAS possibly via metabolite-mediated effects on endothelial function, inflammation, and lipid metabolism. Future research prioritizing longitudinal and interventional studies integrating microbial metagenomics with host multi-omics are needed to elucidate causal pathways and identify clinically actionable targets.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Atherosclerosis/microbiology/metabolism
Metabolomics/methods
Metagenomics
Dysbiosis
Proteomics
Multiomics

@article {pmid41410755,
year = {2025},
author = {Rath, T and Neurath, MF},
title = {[Chronic inflammatory bowel diseases : What contribution can endoscopy make?].},
journal = {Innere Medizin (Heidelberg, Germany)},
volume = {},
number = {},
pages = {},
pmid = {41410755},
issn = {2731-7099},
abstract = {Chronic inflammatory bowel diseases (IBD), primarily ulcerative colitis and Crohn's disease, are chronic relapsing-remitting inflammations of the gastrointestinal tract. The pathogenesis involves a dysregulation of the intestinal immune system in response to commensal components of the intestinal microbiome. A genetic predisposition forms the foundation for the sustained inflammatory reaction. While treatment approaches in the past focused mainly on the control of clinical symptoms through medication, the results of recent studies indicate that an endoscopically detected remission is superior to mere clinical symptom control in terms of disease progression and prognosis. This review article highlights the importance of endoscopy in the management of IBD, presents established scoring systems for the endoscopic grading of inflammatory activity and outlines in which situations and according to which guidelines endoscopic diagnostics are indicated. Finally, yet importantly applications and algorithms of artificial intelligence as well as advanced technologies in microscopy are increasingly being integrated into endoscopic procedures for patients with IBD and are also discussed in this article.},
}

@article {pmid41410660,
year = {2025},
author = {Tulone, G and Pavan, N and Fasciana, TM and Martorana, A and Minasola, C and Tricoli, MR and Claps, F and Mariyam, L and Marmo, D and Serra, N and Giammanco, A and Simonato, A},
title = {Exploring the influence of the bladder microbiome on BCG immunotherapy outcomes for high-risk non muscle invasive bladder cancer.},
journal = {Minerva urology and nephrology},
volume = {77},
number = {6},
pages = {820-827},
doi = {10.23736/S2724-6051.25.06431-6},
pmid = {41410660},
issn = {2724-6442},
mesh = {Humans ; *Urinary Bladder Neoplasms/microbiology/drug therapy/pathology/therapy ; *BCG Vaccine/therapeutic use/administration & dosage ; Retrospective Studies ; Female ; Male ; *Microbiota ; Aged ; *Urinary Bladder/microbiology ; *Adjuvants, Immunologic/therapeutic use/administration & dosage ; Treatment Outcome ; Middle Aged ; Immunotherapy/methods ; Administration, Intravesical ; },
abstract = {BACKGROUND: Intravesical Bacillus Calmette-Guérin (BCG) is an established adjuvant therapy for high-risk superficial bladder cancer, though its efficacy varies among patients. Recent interest in the urinary microbiome comprising microorganisms inhabiting the urinary tract stems from its potential impact on various urological conditions, including bladder cancer. Our study investigates the possible relationship between the bladder microbiome and BCG therapy outcomes in a preliminary and explorative analysis.

METHODS: We conducted a retrospective, descriptive study involving 31 high-risk bladder cancer (BC) patients treated with BCG. BC tissues were collected pre-treatment, and formalin-fixed paraffin-embedded (FFPE) samples were analyzed. DNA extracted from these samples underwent high-throughput 16S rRNA amplicon sequencing targeting the V1-V3 regions.

RESULTS: Our cohort consisted of 15 BCG-resistant patients and 16 responders. Median instillation numbers were six (IQR: 6-9) for resistant patients and twelve (IQR: 14-15) for responders, with a median follow-up length of six months (IQR: 3.3-9.5) and 43 months (IQR: 24-55), respectively. Significant differences were observed in the microbiome: BCG responders showed higher median percentages of Firmicutes (1.1 vs. 0.3, P=0.0293) and Verrucomicrobiota (0.9 vs. 0.1, P=0.0285). Additionally, Fusobacteriota was more prevalent among responders (75% vs. 33.3%, P=0.0198), while Cyanobacteria were more common in resistant patients (73.3% vs. 31.3%, P=0.0191).

CONCLUSIONS: Our preliminary findings illuminate the bladder microbiome's role in influencing BCG therapy outcomes, underscoring the complex microbial interplay affecting treatment efficacy in urological diseases. This explorative study sets the groundwork for ongoing data collection and future research pathways aimed at further delineating these relationships.},
}

Humans
*Urinary Bladder Neoplasms/microbiology/drug therapy/pathology/therapy
*BCG Vaccine/therapeutic use/administration & dosage
Retrospective Studies
Female
Male
*Microbiota
Aged
*Urinary Bladder/microbiology
*Adjuvants, Immunologic/therapeutic use/administration & dosage
Treatment Outcome
Middle Aged
Immunotherapy/methods
Administration, Intravesical

@article {pmid41410609,
year = {2025},
author = {Drost, M and Fuhrmann, G},
title = {Pseudomonas aeruginosa and Its Unsuspected Ally Lactiplantibacillus plantarum: Enhanced Pathogenicity in A Combined Cystic Fibrosis Sputum - Epithelial Cell Model.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.5c00759},
pmid = {41410609},
issn = {2373-8227},
abstract = {Pseudomonas aeruginosa is a notorious bacterial pathogen causing chronic pulmonary infections in people with cystic fibrosis (CF) due to its high tolerance to antibiotics and ability to form recalcitrant biofilms. A newer approach to attenuate the virulence of P. aeruginosa in CF could be the local reinforcement of a resilient community of competing bacteria in the lung. Lactobacilli can mediate antagonistic effects against P. aeruginosa by production of organic acids, but it is not entirely clear if they can exert this beneficial effect locally at the site of infection. While the nutritional environment of the airways in CF promotes P. aeruginosa, it does not support robust growth of lactic acid bacteria, thus attenuating their probiotic potential. To overcome this obstacle, we hypothesized that prebiotic fructooligosaccharides (FOS) could selectively stimulate Lactiplantibacillus plantarum during culture in synthetic cystic fibrosis sputum medium (SCFM2). Indeed, FOS supported the growth of L. plantarum and led to increased acid production. Co-cultivation of L. plantarum and P. aeruginosa reduced biofilm formation and FOS enabled L. plantarum to grow to higher densities in dual-species biofilms. However, this came at the cost of an increased production of the cytotoxic metabolite pyocyanin by P. aeruginosa. To examine whether L. plantarum would influence the pathogenicity of P. aeruginosa, we developed a dual-bacterial species infection model using a CF - relevant airway cell line exposed to the nutritional environment of SCFM2. L. plantarum, grown in SCFM2 or SCFM-FOS, did not inhibit the adhesion of P. aeruginosa. In contrast, the presence of live as well as heat-inactivated L. plantarum, or sterile L. plantarum supernatants drastically enhanced the cell damage during coinfection with P. aeruginosa. This effect was not exclusively dependent on differences in the proliferation of P. aeruginosa or addition of SCFM2 to the cell culture medium. Our data indicate that a potential benefit of bacteriotherapy is determined by the nutritional environment of the diseased body site and that the use of L. plantarum in the context of chronic pulmonary infections must be carefully evaluated.},
}

@article {pmid41410536,
year = {2025},
author = {Berruto, C and Grillo, E and Esturi, S and Demirer, GS},
title = {A 3D-printed capillary tube holder for high-throughput chemotaxis assays.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0038425},
doi = {10.1128/jb.00384-25},
pmid = {41410536},
issn = {1098-5530},
abstract = {Bacterial chemotaxis is an important behavior to study to understand spatial segregation of species in mixed communities and the assembly of host microbiomes. This is particularly relevant in the rhizosphere, where chemoattraction toward root exudates is an important determinant of plant colonization. However, current methods to screen chemoeffectors are limited in their throughput, creating a barrier to generating comprehensive data sets describing chemotactic profiles for species of interest. Here, we describe a novel 3D-printed capillary tube holder approach, which facilitates up to 384 simultaneous capillary tube chemotaxis assays. We optimized and benchmarked our assay using Escherichia coli K12 and Bacillus subtilis 3610 with known chemoattractants: serine and aspartate. We then tested the threshold concentration of these chemoattractants using our assay and found that we could detect chemoattraction toward concentrations spanning multiple orders of magnitude. In this paper, we describe our high-throughput chemotaxis assay in detail and provide the necessary files for 3D printing the capillary tube holder.IMPORTANCEChemotaxis is an important behavior to study to understand how microbial communities assemble and respond to their environment. Identifying chemoattractants may uncover key targets for microbiome engineering. However, the generation of large data sets describing chemotactic profiles has been limited by a lack of high-throughput tools to quantitatively screen chemotaxis. We designed a 3D-printed assay allowing for up to 384 simultaneous capillary tube chemotaxis assays and validated our method with two different bacterial species. The throughput of our approach is greatly increased by the ability to use lag time as a proxy for cell count. Our approach is easy to use and low cost, effectively lowering the barrier to expanding more comprehensive data sets describing the chemotactic profiles of different bacterial species.},
}

@article {pmid41410463,
year = {2025},
author = {Xie, Y and Cidan, Y and Cisang, Z and Ciwang, R and Liu, G and Wu, D and Cideng, D and Chilie, J and Kang, J and Zhu, Y and Basang, W},
title = {Effect of altitudes on serum parameters, metabolome, and gut microbiota in yaks on the Qinghai-Tibet Plateau.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0254925},
doi = {10.1128/spectrum.02549-25},
pmid = {41410463},
issn = {2165-0497},
abstract = {Yaks (Bos grunniens), native to the Qinghai-Tibet Plateau, have evolved extraordinary physiological resilience to chronic hypoxia, cold, and nutritional scarcity. However, the integrated metabolic and microbial mechanisms underlying these adaptations remain poorly defined. Here, a comprehensive multi-omics analysis was performed on thirty grazing heifer yaks (2.5 years old) from three altitudes-3,600 m (low altitude [LA]), 4,000 m (middle altitude [MA]), and 4,500 m (high altitude [HA])-to investigate how altitude affects host physiology, metabolism, and gut microbial ecology. Increasing altitude significantly reduced serum total protein, globulin, blood urea nitrogen, and alkaline phosphatase, indicating suppressed anabolic metabolism and nitrogen-sparing strategies. Antioxidant capacity (total superoxide dismutase, total antioxidant capacity) and pro-inflammatory cytokines (interleukin-2 [IL-2], IL-6, tumor necrosis factor-α, interferon-γ) increased (P < 0.05), while glutathione peroxidase, IL-4, IL-10, growth hormone, insulin-like growth factor-1, and growth hormone-releasing hormone declined (P < 0.05), reflecting energy reallocation from growth toward antioxidation and immune maintenance under hypoxia. Plasma metabolomics revealed distinct altitude-dependent reprogramming, with enrichment of retinol metabolism at 4,000 m and α-linolenic acid metabolism, tricarboxylic acid (TCA) cycle, and branched-chain amino acid biosynthesis at 4,500 m. These pathways link lipid remodeling, oxidative balance, and oxygen utilization. The gut microbiota displayed altitude-specific shifts, characterized by enrichment of Christensenellaceae_R-7_group and Monoglobus and reduced UCG-005 and Rikenellaceae_RC9_gut_group, accompanied by lower fecal volatile fatty acids (P < 0.05). Correlation analyses confirmed tight associations between fermentative taxa and volatile fatty acids production. Collectively, our results establish a serum-metabolome-microbiota axis as a central mechanism supporting yak adaptation to high altitude.IMPORTANCEThis study demonstrates that the gut microbiota plays a crucial role in how yaks adapt to high-altitude hypoxia. Rising altitude not only alters the composition of gut microbes but also shifts their metabolic activity toward improving fermentation efficiency and antioxidant capacity. These microbial changes are closely linked with host metabolism, forming a coordinated serum-metabolome-microbiota network that helps maintain energy balance and immune stability when oxygen is limited. The enrichment of retinol and α-linolenic acid metabolism as altitude-responsive pathways further highlights the metabolic interplay between host and microbes in supporting physiological resilience. Overall, our findings show that microbial flexibility and metabolic cooperation are key factors enabling ruminants to survive in extreme environments, providing a scientific basis for microbiome-informed strategies to enhance yak health and productivity on the Qinghai-Tibet Plateau.},
}

@article {pmid41410445,
year = {2025},
author = {Shin, R and Han, S and Ro, J and Lee, S and Ryu, S-H and Hur, H-G and Shin, H},
title = {Quantitative microbial risk assessment of antibiotic resistance genes and mobile genetic elements in orchard soils across South Korea.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0226025},
doi = {10.1128/aem.02260-25},
pmid = {41410445},
issn = {1098-5336},
abstract = {Antibiotic resistance is a global health crisis, but environmental pathways of resistance dissemination to farm workers remain poorly understood. Agricultural soils represent critical but underexplored reservoirs of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), particularly in orchards where antibiotics such as streptomycin and oxytetracycline are widely used for fire blight control. Here, we conducted a nationwide investigation of orchard soils in South Korea, integrating high-throughput qPCR, 16S rRNA gene sequencing, and quantitative microbial risk assessment (QMRA). We detected 297 ARGs and 52 MGEs, with eight core genes [aac(3)-VIa, tetL, aadE, sul1, qacH_351, tnpA-1, IS6100, and intI1] significantly enriched in orchard soils but absent in non-orchard soils, such as national parks or mountain soils. Aminoglycoside- and tetracycline-resistance genes were dominant, directly reflecting the application of streptomycin and oxytetracycline. QMRA estimated that orchard farmers ingest resistance genes through soil contact, with aac(3)-VIa posing the highest risk (~29 ingestion events per farmer annually), followed by qacH_351, tetL, and tnpA-1. These results demonstrate the quantifiable occupational risks of ARG exposure in orchard environments. By combining resistome profiling, microbial networks, and QMRA, this study establishes a framework for assessing the public health implications. Although the ingestion of ARGs may not immediately cause impacts on human health, such exposure has the potential to enrich antibiotic resistance within the gut microbiome of farm workers, thereby increasing the probability of treatment complications if infections occur.IMPORTANCEAntibiotic resistance is widely recognized as one of the most concerning threats to public health, yet the pathways through which resistance emerges and spreads remain underexplored. Orchard soils, where antibiotics are sprayed to control plant diseases, represent an overlooked environment where resistance may develop and circulate to people who work the land. By examining soils from orchards at a nationwide scale, we found resistance genes that mirror the antibiotics used in these settings and showed that farm workers are regularly exposed to them through routine contact with soil. This study provides the direct evidence that orchard farming can contribute to human exposure to resistance, heralding the need to include agricultural environments in efforts to prevent the spread of resistance. Our work offers a way to measure these risks and can guide protective strategies for workers and communities.},
}

@article {pmid41410441,
year = {2025},
author = {Chen, X and Olimi, E and Lobato, C and Berg, G and Cernava, T},
title = {The tomato seed microbiome is mainly shaped by host genotype and production site.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0144125},
doi = {10.1128/msystems.01441-25},
pmid = {41410441},
issn = {2379-5077},
abstract = {UNLABELLED: The seed microbiome plays a crucial role in plant health and productivity, yet the extent to which the plant genotype influences its composition remains unclear. We conducted a large-scale study using 100 tomato (Solanum lycopersicum L.) genotypes from 12 geographical locations in China, subjecting all seeds to the same processing to assess seed microbiome plasticity. The plant genotype was identified as the primary factor shaping microbiome structure (R[2] = 0.56, P = 0.001), followed by geographic location (R[2] = 0.11, P = 0.001), and insect resistance of the cultivar (R[2] = 0.07, P = 0.001). A rather small core microbiome of 21 amplicon sequence variants (ASVs) was shared across all tomato genotypes. Ubiquitous seed microbiome members found in 90% of the samples included Pseudomonas, Lactobacillus, Leuconostoc, and Ralstonia. A Random Forest modeling approach showed that tomato traits and their production environment can be predicted via seed microbiome features; core microbiome members, including Lactobacillus and Pseudomonas, were connected to specific tomato traits. This study unveils key factors influencing seed microbiome assembly and emphasizes the crucial role of host traits that can enable new venues for seed microbiomes in plant breeding and sustainable crop production.

IMPORTANCE: Seeds not only carry the plant's genetic material but also host distinct microbial communities that can influence early plant growth and performance. In a large-scale study involving 100 tomato genotypes collected from 12 geographical locations in China, we examine how plant genotype shapes the seed microbiome. The research findings reveal that plant genotype, more than location or parents' geography, primarily influences microbial community structure (R² = 0.56 vs 0.11). These findings highlight the strong association between host genetics and seed microbiome assembly. Understanding these interactions provides valuable opportunities for integrating microbiome-based strategies into plant breeding and crop improvement programs, ultimately supporting more resilient and sustainable agricultural systems.},
}

@article {pmid41410353,
year = {2025},
author = {Martínez-Lara, A and De Tena-Sanz, A and Durán-González, E and Reyes-Conde, ML and Díaz-López, C and Pérez-Sánchez, M and Ramírez-Tejero, JA and Cotán, D and Almansa, JAH},
title = {Gut Microbiota Alterations in Endometriosis: An Observational Study in a Spanish Female Cohort.},
journal = {Biology of reproduction},
volume = {},
number = {},
pages = {},
doi = {10.1093/biolre/ioaf272},
pmid = {41410353},
issn = {1529-7268},
abstract = {PURPOSE: Identifying potential gut biomarkers linked to endometriosis for diagnosis and treatment.

METHODS: The recruitment of this case-control study was done through the Endometriosis Health Profile-5 questionnaire, validated for endometriosis assessment. A total of 243 women completed the questionnaire and 73 women met the eligibility criteria of the study. Stool samples from the control group (n = 43) and patients with a positive diagnosis of endometriosis (n = 30) were collected and subjected to 16S rRNA gene sequencing using the V3-V4 regions. Various multivariate analysis approaches were used to assess diversity, composition and abundance of intestinal microbiota.

RESULTS: Among the 18 significantly different taxa (p < 0.05) between healthy controls and EMs patients, 3 families, 3 genera and 12 species were identified. Endometriosis patients exhibited slightly higher diversity at the family and genus levels compared to controls (p > 0.05). This could indicate endometriosis is characterized by dominance of few species across diverse families and genera, associated with inflammation and estrogen signaling. Finally, several significant correlations (p < 0.05) were found between questionnaire variables related to "pain" and "infertility" items and certain families, genus and species found in the endometriosis group.

CONCLUSION: The differential presence of estrobolome-presenting gut taxa between endometriosis patients and controls endorses the possible role of the gut microbiome in female reproductive health, offering potential microbial markers for endometriosis diagnosis, monitoring and treatment. Identified taxa may serve as future prognostic, diagnostic, and therapeutic targets for diagnosis and personalized, preventive or palliative/curative treatment of endometriosis.},
}

@article {pmid41410321,
year = {2025},
author = {Güralp, G and Acet, SN and Al-Khodor, J and Akkaya, Ö and Şeker, MG and Süzerer, V and Çiftçi, YÖ and Lucas, SJ},
title = {Taxonomic diversity and functional adaptations indicated by the rhizospheric soil microbiome derived from Turkish wheat fields.},
journal = {Biology open},
volume = {14},
number = {12},
pages = {},
doi = {10.1242/bio.062230},
pmid = {41410321},
issn = {2046-6390},
support = {121O649//Science and Technology Council of Türkiye/ ; //Sabanci University/ ; },
mesh = {*Triticum/microbiology/growth & development ; *Soil Microbiology ; *Microbiota ; *Rhizosphere ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Biodiversity ; Turkey ; Bacteria/classification/genetics ; Soil/chemistry ; },
abstract = {Optimization of the soil microbiome is a promising strategy to support sustainable crop production. With the goal of developing novel bio-fertilizers for wheat cultivation, we collected fresh soil samples from ten different fields representing wheat production regions in Türkiye. Wheat seedlings (Triticum turgidum ssp. durum) were cultivated in each soil and at the three-leaf stage, DNA was isolated from the rhizospheric soil associated with each plant and the bacterial microbiome composition determined by 16S metabarcoding. Long-read sequencing was used to maximize resolution, and 1269 high-quality operational taxonomic units (OTUs) were identified. Comparisons of wheat and non-wheat rhizospheric soil identified 77 OTUs that were enriched in the wheat rhizosphere, several belonging to taxa that have previously been described as plant growth-promoting rhizobacteria. Furthermore, 209 OTUs were present in all ten wheat fields sampled, indicating that they may be ubiquitous in wheat-growing regions of Türkiye; a subset of these were also reported in wheat rhizospheric soil from other countries. Additional taxa were shown to be enriched based on local soil conditions such as pH and macronutrient content. These findings shed light onto the essential composition of the wheat rhizospheric microbiome, which provides a foundation for the development of locally adapted bio-fertilizers.},
}

*Triticum/microbiology/growth & development
*Soil Microbiology
*Microbiota
*Rhizosphere
Phylogeny
RNA, Ribosomal, 16S/genetics
*Biodiversity
Turkey
Bacteria/classification/genetics
Soil/chemistry

@article {pmid41410162,
year = {2025},
author = {Sharma, P and Srivastava, S},
title = {The sticky situation of human skin.},
journal = {Journal of biosciences},
volume = {50},
number = {},
pages = {},
pmid = {41410162},
issn = {0973-7138},
mesh = {Humans ; *Skin/microbiology/immunology ; *Microbiota/genetics ; Epidermis/microbiology ; },
abstract = {The largest organ of the body, namely the skin, is a three-layer system composed of the epidermis, dermis, and subcutaneous tissue (Venus et al. 2010; Yousef et al. 2025). The outermost epidermis maintains the skin barrier and produces new skin cells and melanin. The middle layer, the dermis, contains glands, nerves, and blood vessels, providing strength and flexibility to the skin. The deepest fatty layer acts as the bridge between skin and underlying tissues. As with the gut microbiome, there is a plethora of microbes including bacteria, fungi, and viruses residing in the different layers of the skin, making up the skin microbiome (Chen and Tsao 2013; Swaney and Kalan 2021; Khan and Koh 2024). Skin microbiome composition varies by body site (Perez Perez et al. 2016; Bjerre et al. 2021) and factors such as age (Luna 2020), genetics (Si et al. 2015), and immunity (Belkaid and Segre 2014; Peroni et al. 2020). This diverse microbial ecosystem faces off challenges from invasive pathogens (Nakatsuji et al. 2021) and environmental aggressors such as some soaps (Mijaljica et al. 2022), UV radiation (D'Orazio et al. 2013; Tang et al. 2024), pollutants (Bocheva et al. 2023), and changes in temperature and humidity (Engebretsen et al. 2016).},
}

Humans
*Skin/microbiology/immunology
*Microbiota/genetics
Epidermis/microbiology

@article {pmid41410042,
year = {2025},
author = {Li, S and Huang, X and McNeil, R and Malmstrom, H and Ren, Y},
title = {Systemic health implications of dental prescribing in general practices.},
journal = {Quintessence international (Berlin, Germany : 1985)},
volume = {0},
number = {0},
pages = {0},
doi = {10.3290/j.qi.b6762787},
pmid = {41410042},
issn = {1936-7163},
abstract = {Dental prescribing is a crucial component of general dental practices, enabling the management of pain, control of infection, and promotion of postoperative recovery. Analgesics, antibiotics, and antiseptic mouthwashes are frequently prescribed as short-term adjuncts to definitive dental treatments, such as extractions, endodontic, and periodontal therapies. These medications can significantly affect cardiovascular, renal, hepatic, metabolic, and the microbiome beyond the oral cavity. In this review, we aim to summarize the systemic health effects of three medication classes frequently prescribed by general dentists and discusses their mechanisms, clinical implications, and stewardship opportunities. Nonsteroidal anti-inflammatory drugs (NSAIDs) are the first-line treatment for dental pain, but even a brief course can affect renal function, blood pressure, and gastrointestinal integrity in susceptible patients. Acetaminophen is an important analgesic for mild to moderate dental pain though its cumulative dosing may increase the risk of hepatotoxicity. Opioids are historically prescribed after tooth extractions, endodontic and periodontal surgeries, but they offer no advantage over non-opioid analgesics and contribute to opioid misuse in the community. Gabapentinoids are emerging as lower-risk opioid alternatives in patients who cannot use NSAIDs or acetaminophen, but their use also requires caution. Antibiotics continue to be prescribed for conditions that are not clinically indicated but may increase the risks of antimicrobial resistance, gut microbiome dysbiosis, and Clostridioides difficile infection. Mislabeling of penicillin allergies is widespread and may promote the use of higher-risk alternatives such as clindamycin. Antiseptic mouth rinses, particularly chlorhexidine, can effectively reduce oral microbial load but may disrupt nitrate-reducing oral bacteria and alter nitric oxide-mediated vascular function. General dental practitioners should integrate systemic health awareness when prescribing these medications to ensure safety and advance antimicrobial and pharmacologic stewardship in daily practices.},
}

@article {pmid41409986,
year = {2025},
author = {Bilesky-Jose, N and Lima, R},
title = {Biogenic nanoparticles from bacteria: a perspective on integrated applications in sustainable agriculture.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1724288},
pmid = {41409986},
issn = {1664-302X},
abstract = {The growing demand for sustainable agricultural solutions has driven the development of technologies that contribute to modern agriculture, which aims to achieve greater productivity while maintaining environmental responsibility. Biogenic nanoparticles (BNPs) synthesized using bacteria are emerging as a promising alternative to conventional methods, offering a green approach for producing nanomaterials with agricultural applications. This Perspective highlights the mechanistic basis of bacterial nanoparticle biosynthesis and strategies for genetic and metabolic optimization to enhance yield and functionality, accentuating their potential applications as phytosanitary agents and controlled-release fertilizers. We further propose an integrative "BNP-Plant-Microbiome" framework, in which microbial consortia and multi-nanoparticle formulations could synergistically deliver nutrients, boost stress resilience, and suppress pathogens. Future progress will depend on addressing key challenges in biosafety, regulatory compliance, and large-scale bioprocessing, as well as integrating BNPs with precision agriculture and data-driven monitoring tools. Ultimately, bacterial BNPs have the potential to redefine agricultural sustainability by coupling microbial innovation with circular, resource-efficient crop management systems.},
}

@article {pmid41409978,
year = {2025},
author = {Di Pierro, F and Fornaini, C and Palazzi, CM and Bertuccioli, A and Tagg, J and Zerbinati, N},
title = {From periodontal infection to oral-systemic dysbiosis: re-framing the oral microbiome's role in systemic health and the prophylactic potential of Streptococcus salivarius probiotics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1685071},
pmid = {41409978},
issn = {1664-302X},
abstract = {Since the late 19th century, the relationship between oral infections and systemic health has been widely debated. Recent advances in microbiome research suggest that oral microbial imbalance-dysbiosis-can contribute to systemic inflammatory and metabolic disorders. We propose that the term "oral-systemic dysbiosis" more accurately captures the complex interactions linking oral microbial disruption to systemic disease risk. This conceptual reframing moves beyond a purely infectious model toward a systems-based understanding of oral-body health connections. Furthermore, we hypothesize that oral administration of Generally Recognized as Safe (GRAS)-grade probiotic Streptococcus salivarius, such as strain K12, may help restore oral eubiosis and potentially reduce systemic inflammatory burden. While the hypothesis that oral probiotic maintenance may reduce the risk of systemic disorders remains to be clinically verified, defining oral-systemic dysbiosis provides a useful conceptual foundation for the exploration of integrated preventive strategies linking oral and general health.},
}

@article {pmid41409595,
year = {2025},
author = {Chen, L and Yang, M and Wang, Q and Tang, Y and Yu, H and Luo, X and Du, X and Hu, H},
title = {Airway microbial and metabolic features associated with ICS therapy in COPD.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1714879},
pmid = {41409595},
issn = {1663-9812},
abstract = {BACKGROUND: Inhaled corticosteroids (ICS) are a cornerstone of therapy for selected phenotypes of chronic obstructive pulmonary disease (COPD), yet the underlying mechanisms remain incompletely understood. Increasing evidence suggests that airway microbiome and their metabolites play crucial roles in shaping host immune responses and disease progression.

OBJECTIVE: This study used multi-omics technology to explore the differences in sputum microbiome, metabolites and the systematic connections in patients with stable COPD who use or not ICS.

METHODS: We performed an integrated microbiome-metabolome analysis of induced sputum samples from 53 stable COPD patients (40 ICS users and 13 non-users). Microbial communities were profiled using 16S rRNA sequencing, while metabolic signatures were assessed via liquid chromatography-mass spectrometry. Correlation analyses were conducted to explore microbe-metabolite interactions.

RESULTS: The microbial alpha diversity (Simpson, Shannon, Pielou indices; P < 0.05) was significantly reduced in the ICS group, and the beta diversity was distincted between the two groups. The relative abundance of Firmicutes, Streptococcus was significantly reduced, and the relative abundance of Veillonella was significantly increased in the ICS group (P < 0.05). Metabolomic profiling identified 70 differential metabolites enriched in pathways including caffeine metabolism, cobalamin transport and metabolism, and cysteine/methionine metabolism. Notably, Streptococcus abundance was negatively correlated with methylxanthine intermediates (caffeine, theobromine, 1,7-dimethylxanthine, 1-methylxanthine), while Veillonella abundance showed positive correlations with these metabolites (P < 0.05).

CONCLUSION: Our findings suggest that ICS therapy not only reshapes the airway microbial ecosystem but also alters host-microbe co-metabolic pathways, particularly caffeine metabolism. By reducing microbial degradation of methylxanthines, ICS may enhance the bioavailability of bronchodilatory compounds, providing a potential microbiome-mediated adjunctive mechanism of action. These insights advance our understanding of ICS pharmacology in COPD and highlight the therapeutic potential of targeting microbiome-metabolite interactions.},
}

@article {pmid41409546,
year = {2025},
author = {Zhao, L and Peng, S and Ge, M and Xing, B and Zhao, X and Yang, T and Yu, S and Zhang, C and Liu, J and Miao, Z and Ma, H},
title = {Gut-to-tumor translocation of multidrug-resistant Klebsiella pneumoniae shapes the microbiome and chemoresistance in pancreatic cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1694479},
pmid = {41409546},
issn = {2235-2988},
mesh = {Humans ; *Pancreatic Neoplasms/microbiology/drug therapy/pathology ; *Klebsiella pneumoniae/drug effects/genetics/isolation & purification ; *Gastrointestinal Microbiome ; Feces/microbiology ; Male ; Female ; Middle Aged ; Aged ; *Drug Resistance, Multiple, Bacterial ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Klebsiella Infections/microbiology ; },
abstract = {BACKGROUND: Despite advances and successes in precision oncology, pancreatic cancer (PC) remains a tumor with extremely low survival rates, and many of these cases experienced postoperative recurrence and metastasis. Alterations in the gut microbiota have been linked to the survival rates of PC patients. Nevertheless, the complexity of gut microbiota composition poses significant challenges in identifying definitive clinical biomarkers for PC.

METHODS: Fecal samples were collected from PC patients, half of whom had metastasis, and their matched healthy controls (HCs). A metagenomic analysis was employed to further investigate the functional features of gut microbiota with both PC and metastatic PC. The clinical correlations, microbial metabolic pathways and antibiotic resistome were further assessed. In a follow-up validation, intraoperative tumor tissue and pancreatic fluid were sampled from PC patients and underwent comprehensive microbiological analysis, including bacterial culture, mass spectrometry-based identification, and third-generation whole-genome sequencing of Klebsiella pneumoniae isolates.

RESULTS: We observed a significant alteration of the gut microbiota in PC patients, highlighted by an overall increase in microbial diversity compared to healthy controls (p < 0.05). Comparative abundance analysis identified 59 differentially abundant microbial species in non-metastatic pancreatic cancer (NMPC) (56 increased, 3 decreased) and 21 in metastatic pancreatic cancer (MPC) (19 increased, 2 decreased), alongside 18 significantly altered microbial metabolic pathways (FDR-adjusted p < 0.05). Notably, Klebsiella pneumoniae, Klebsiella oxytoca, and Akkermansia muciniphila were identified as prominent antibiotic resistance gene (ARG) carriers in the gut microbiota of PC patients, with 653 ARG subtypes detected across fecal samples, 38-47% of which were shared among groups. Strong co-occurrence patterns between ARGs (e.g., acrB, mdtC, cpxA, emr, pmrF) and the above species were observed predominantly in MPC samples (p < 0.05). Whole-genome sequencing of 14 isolates obtained from tumor tissue and pancreatic fluid revealed consistent ARG profiles and virulence genes, corroborating the metagenomic findings and supporting the hypothesis of gut-to-tumor translocation and potential intratumoral colonization.

CONCLUSION: This study provides a comprehensive microbiome-based insight into PC and its metastatic subtypes. By integrating microbiome analysis with microbial culture, this study provides direct evidence of gut-derived multidrug-resistant (MDR) K. pneumoniae colonization in PC tissues.},
}

Humans
*Pancreatic Neoplasms/microbiology/drug therapy/pathology
*Klebsiella pneumoniae/drug effects/genetics/isolation & purification
*Gastrointestinal Microbiome
Feces/microbiology
Male
Female
Middle Aged
Aged
*Drug Resistance, Multiple, Bacterial
Metagenomics
Anti-Bacterial Agents/pharmacology
Whole Genome Sequencing
Klebsiella Infections/microbiology

@article {pmid41409498,
year = {2025},
author = {Lage, A and Berrendero Gómez, E and García-Abad, L and Martínez-Gutiérrez, C and Garcia, J and Gonzalez-Flo, E},
title = {Assessment of Polyhydroxybutyrate Production by Cyanobacteria Strains Isolated from Environmental Water Sources Using a Secondary Effluent.},
journal = {ACS ES&T water},
volume = {5},
number = {12},
pages = {7267-7278},
pmid = {41409498},
issn = {2690-0637},
abstract = {Growing concern over plastic pollution has intensified research on biodegradable alternatives, such as polyhydroxybutyrate (PHB), a biopolymer produced by cyanobacteria. Despite their sustainability advantages, photoautotrophic PHB production remains limited, and cultivation strategies need optimization. In this study, five cyanobacterial strains were isolated from environmental microbiome cultures to evaluate their PHB production potential. The goal was to identify the most productive strains and optimal conditions for polymer synthesis. Cultures were grown in modified BG11 media (without nitrogen, phosphorus, or inorganic carbon) and in a secondary effluent from treated urban wastewater, both supplemented with acetate (0, 0.6, or 4 g/L) and incubated for 7 days in darkness. The biomass remained stable in most strains but declined to 0.28 g/L in the secondary effluent, except for one Leptolyngbya sp. strain that increased the biomass with acetate. The highest PHB yield per acetate consumed was achieved by Synechocystis sp. from an agricultural pond, reaching 3.1% dry cell weight in modified BG11 with 0.6 g/L acetate. In the secondary effluent, the maximum PHB content reached 2.9% in another Leptolyngbya sp. strain with 4 g/L acetate. These findings highlight strain-specific responses and the potential of wastewater-based cultivation for sustainable bioplastic production.},
}

@article {pmid41409473,
year = {2025},
author = {Inchingolo, AD and Inchingolo, AM and Palumbo, I and Guglielmo, M and Riccaldo, L and Morolla, R and Inchingolo, F and Palermo, A and Dipalma, G},
title = {The role of probiotics in preventing dental caries: a systematic review of clinical evidence.},
journal = {Frontiers in oral health},
volume = {6},
number = {},
pages = {1720036},
pmid = {41409473},
issn = {2673-4842},
abstract = {BACKGROUND: Probiotics have emerged as a promising adjunctive strategy for oral health, particularly in the prevention of dental caries, a multifactorial disease driven by ecological imbalances in the oral microbiome.

METHODS: A systematic search of PubMed, Scopus, and Web of Science was conducted for studies published between January 2014 and January 2025, focusing on the use of probiotics for caries prevention in children and young adults. Clinical trials and observational studies were included, and a qualitative synthesis was performed based on the extracted outcomes.

RESULTS: Twenty-one studies met the inclusion criteria. Most clinical trials reported a significant reduction in Streptococcus mutans levels following administration of probiotic strains, particularly Lactobacillus paracasei, Lactobacillus rhamnosus, and Bifidobacterium lactis. Several studies also demonstrated a decreased incidence of new carious lesions and an improvement in salivary immune markers. However, a minority of studies found no significant effect, highlighting potential variability due to strain type, dosage, delivery method, and population characteristics.

CONCLUSION: The current evidence supports the potential of specific probiotic strains to reduce cariogenic bacterial loads and contribute to caries prevention. Further standardized, long-term trials are needed to clarify the most effective formulations and regimens for clinical application.

PROSPERO CRD42025646287.},
}

@article {pmid41409448,
year = {2025},
author = {Julkunen, L and Manzoor, M and Hiltunen, K and Saarela, RK and Pitkälä, K and Pussinen, PJ and Mäntylä, P},
title = {Tooth-surface plaque microbiome and different levels of oral disease burden among dentate older adults living in long-term care.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2602387},
pmid = {41409448},
issn = {2000-2297},
abstract = {AIM: This study aimed to explore the composition of the tooth-surface plaque (subgingival with marginal supragingival) microbiome in dentate older adults residing in long-term care (LTC) facilities, stratified by clinically assessed oral disease burden (ODB). A total of 196 LTC residents aged ≥62 years underwent oral examinations and microbial sampling from each dentate quadrant. Microbial profiling was performed using 16S rRNA gene sequencing.

RESULTS: Participants were more frequently categorized into Moderate (n = 95, 48%) than Low (n = 32, 16%) or High (n = 69, 35%) ODB groups. Those with High ODB were oldest and had lowest number of remaining teeth. Alpha diversity did not differ between the ODB groups, whereas beta diversity analysis revealed significant differences between groups (Bray-Curtis: P = 0.005; weighted Unifrac: P = 0.025). The Low and Moderate ODB groups were enriched with both commensals and disease-associated genera, such as Ottowia, Lactococcus, Pseudoramibacter, and Anaeroglobus. High ODB group exhibited an increased abundance of genera linked to both oral and systemic diseases, including Cardiobacterium, Leptotrichia, Stomatobaculum, and Pseudopropionibacterium. Among ODB groups, periodontitis was a stronger determinant of oral microbiome composition than caries, whereas caries had a stronger effect on bacterial diversity.

CONCLUSION: These findings indicate a progressive shift toward a dysbiotic oral microbiome with increasing ODB.},
}

@article {pmid41409368,
year = {2025},
author = {Bhardwaj, M and Singhal, A and Bhardwaj, G and Dukic, I},
title = {Probiotic and Synbiotic Interventions Targeting Oxalate-Degrading Gut Bacteria for the Prevention of Kidney Stones: A Systematic Review.},
journal = {Cureus},
volume = {17},
number = {12},
pages = {e98728},
pmid = {41409368},
issn = {2168-8184},
abstract = {Kidney stone disease (KSD) is a common and recurrent healthcare problem. Calcium oxalate stones are the most common type of stones, influenced by urinary oxalate levels. Increasingly, the role of the gut microbiome is being studied, particularly oxalate-degrading bacteria such as Oxalobacter formigenes, Lactobacillus, and Bifidobacterium, as potential therapeutic targets. Probiotic and synbiotic interventions aimed at enhancing intestinal oxalate degradation have, therefore, been proposed as strategies to reduce urinary oxalate excretion and mitigate stone recurrence. A comprehensive search of PUBMED, Cochrane Library, Scopus, and Embase databases was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. A total of nine studies, published between January 1, 2000, and September 3, 2025, met the inclusion criteria, comprising five randomized controlled trials and four observational studies. Interventions included O. formigenes preparations, lactic acid bacteria mixtures, and multi-strain probiotics or synbiotics. Urinary oxalate excretion was the most consistently reported outcome, while assessment of kidney stone recurrence was limited due to short study durations and follow-ups. Across trials, probiotic or synbiotic therapy did not consistently reduce urinary oxalate levels compared with placebo or standard care. Although several studies demonstrated successful gastrointestinal colonization with O. formigenes, this did not translate into meaningful biochemical improvements. One randomized trial reported a reduction in the incidence of hyperoxaluria compared with an active comparator; however, this finding was not replicated elsewhere, and no included study demonstrated a significant reduction in clinically confirmed stone recurrence. Overall, the quality of evidence was limited by small sample sizes, heterogeneity in probiotic strains, dosing regimens, and short intervention periods. Current evidence does not support the use of probiotics or synbiotics targeting oxalate-degrading bacteria as effective therapies for reducing urinary oxalate excretion or preventing kidney stone recurrence. Despite their biological plausibility and favourable safety profile, their clinical utility remains unproven. Future research should prioritize long-term, randomized trials using standardized microbial formulations and incorporating imaging-confirmed recurrence outcomes to more definitively establish the role of microbiome-based interventions in KSD prevention.},
}

@article {pmid41409195,
year = {2025},
author = {Fu, T and Zhou, X and Chen, Z and Huang, Z and Li, J and Li, Q and Wu, W and Tang, Y},
title = {Chrono-Synergistic Nutrition: Gut Microbiota-Targeted Diets and Circadian-Aligned First Meal Timing Confer Robust Protection Against Kidney Stone Formation.},
journal = {Food science & nutrition},
volume = {13},
number = {12},
pages = {e71297},
pmid = {41409195},
issn = {2048-7177},
abstract = {The emerging gut-kidney axis paradigm suggests that dietary modulation of gut microbiota may influence nephrolithiasis pathogenesis, while the specific dietary components and the temporal dimension of nutritional intake remain unexplored. This study introduces a novel framework integrating gut microbiota-targeted dietary quality with circadian-aligned meal timing to elucidate their synergistic role in kidney stone prevention. We conducted a comprehensive analysis of 21,840 adults from the NHANES cohort (2007-2016), investigating the independent and combined associations of the Dietary Index for Gut Microbiota (DI-GM) and First Meal Timing (FMT) with kidney stone prevalence. Multivariable logistic regression models and restricted cubic spline analyses elucidated dose-response relationships, while stratified analyses explored population heterogeneity. Our investigation unveiled a compelling narrative of dietary protection: elevated DI-GM scores conferred significant nephroprotection, with the most pronounced benefits observed in participants consuming microbiota-supportive diets. Early meal initiation during the breakfast window (00:00-09:00) independently reduced stone risk compared to delayed feeding patterns. Remarkably, the convergence of optimal dietary quality with circadian-aligned meal timing created a synergistic protective shield, yielding the most substantial risk reduction and suggesting that temporal nutrition strategies may amplify the benefits of gut microbiome modulation. This pioneering investigation establishes the foundational evidence for precision chrono-nutritional interventions in kidney stone prevention. By harmonizing microbiome-targeted dietary optimization with circadian meal timing, our findings illuminate a transformative pathway toward personalized therapeutic strategies that transcend conventional nutritional paradigms, offering new hope for millions affected by recurrent nephrolithiasis.},
}

@article {pmid41409175,
year = {2025},
author = {Ng, DZW and Low, A and Khairul Sani, KRB and Liu, L and Zhang, Z and Koh, XQ and Zhu, M and Mitra, K and Muthiah, M and Dan, YY and Lee, JWJ and Chan, ECY},
title = {Dysbiosis-Driven Reprogramming of Secondary Bile Acid Metabolism in Metabolic Dysfunction-Associated Steatotic Liver Disease: Insights from an Ex Vivo Human Fecal Microbiota Model.},
journal = {ACS pharmacology & translational science},
volume = {8},
number = {12},
pages = {4335-4344},
pmid = {41409175},
issn = {2575-9108},
abstract = {Gut microbial dysbiosis-induced perturbations in bile acid (BA) metabolism are implicated in metabolic dysfunction-associated steatotic liver disease (MASLD), yet evidence remains largely associative. Using an optimized ex vivo fecal microbiota model, we modeled the metabolism kinetics of conjugated- and primary-BA between MASLD and healthy donors. Enzymes for known BA metabolic reactions were inferred using functional metagenomics. MASLD cultures exhibited impaired deconjugation capacity but preserved downstream primary-BA clearance and demonstrated a substrate-independent shift that favored oxidative metabolism over 7α-dehydroxylation. This was marked by increased formation clearance of 7-keto-deoxycholic acid (175%) and 3-oxo-cholic acid (51.7%) from cholic acid (CA) and 7-keto-lithocholic acid (77.9%) from chenodeoxycholic acid (CDCA). C7-oxidized BA constituted the major proportion of total BA clearance (CA = 56.0%, CDCA = 72.3%) in MASLD cultures. Enrichment of C3- and C7-hydroxysteroid dehydrogenases in MASLD compared to control corroborated the differential secondary BA profiles. Together, microbes catalyzing C7-oxidation warrants further investigation as potential pharmacological targets of MASLD.},
}

@article {pmid41409155,
year = {2025},
author = {Korth, N and Borrero, I and Rumley, K and Woodley, AL and Choudoir, MJ and Gage, JL},
title = {Investigating GERMs: How Genotype, Environment, and Rhizosphere Microbiome interactions underlie heat response in maize and sorghum.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.10.693489},
pmid = {41409155},
issn = {2692-8205},
abstract = {Plant resistance to heat stress can be modelled by variation attributable to the genotype, environment, the rhizosphere microbiome, and their interactions. Using this Genotype × Environment × Rhizosphere Microbiome (GERMs) model, we studied three cereal genotypes: two inbred maize lines with contrasting heat sensitivity, and a sorghum inbred that displayed moderate heat tolerance. Plants were grown under optimal and heat stressed conditions across two soil treatments. We developed a systems-level metatranscriptomics approach to examine both plant and microbial transcriptomic profiles and integrated them with microbiome compositional data and plant phenotypes. We compared our strategy to amplicon profiling and found that our metatranscriptomic strategy offers greater functional and taxonomic resolution, allowing us to characterize active microbial pathways and analyze them jointly with plant gene expression profiles within a single system. We show that the microbiome functional profile is driven by host genotype and environmental factors and can enhance plant resilience. Our analyses identified plant genes and microbial pathways consistently associated with heat tolerance and key host-microbe interactions. Specifically, we identified D-amino acid metabolism as a plausible mechanism underlying a synergistic response to heat stress. These results demonstrate that the rhizosphere microbiome is not a passive component but an active participant in plant responses to abiotic stress. This work offers a new perspective on cereal adaptation to high temperatures and underscores the utility of the GERMs framework for dissecting functional relationships among plant genotype, environment, and the rhizosphere microbiome.},
}

@article {pmid41408754,
year = {2025},
author = {Zhang, Q and Zhao, R and Zhang, W and Liu, S and Gan, X},
title = {Interspecific allelopathy suppresses potato cyst nematodes by 1-Decanol produced from Houttuynia cordata.},
journal = {Plant communications},
volume = {},
number = {},
pages = {101679},
doi = {10.1016/j.xplc.2025.101679},
pmid = {41408754},
issn = {2590-3462},
abstract = {Potato cyst nematodes (PCNs), Globodera rostochiensis, are one type of important quarantine plant parasitic nematode and seriously threaten the potato industry and food security due to the lack of effective control measures. In this work, intercropping of Houttuynia cordata was demonstrated to be effective in reducing PCNs as well as stimulating the yield of potato, and it released a key allelopathic volatile compound 1-decanol exhibiting significant nematicidal activity (LC50 = 31.5 μg/mL), which was notably superior to that of nematicide avermectin (LC50 = 63.8 μg/mL). Meanwhile, the root irrigation with 1-decanol could significantly reduce PCN infection in potato. Furthermore, 1-decanol could not only directly damage surface structure, induce cell apoptosis, and disrupt balance of oxidative stress of nematodes, but also downregulate defense-related metabolic pathways, driving the redistribution of metabolic resources from defense to growth pathways in potato. In addition, 1-decanol did not alter the overall diversity of the rhizosphere soil microbial community, however specifically reduced the abundance of pathogens such as Fusarium, while recruiting beneficial microbiota to the potato rhizosphere, thereby resisting the synergistic infection of pathogens and nematodes. These data suggest that intercropping with H. cordata can control PCNs and promote potato yield through the antimicrobial actions of its allelochemicals and their impacts on nematodes. Ultimately, the effects of 1-decanol reshape the rhizosphere microbiome, regulating the physiological processes of the host to provide a sustainable management strategy against PCNs.},
}

@article {pmid41408749,
year = {2025},
author = {Zuccaro, A},
title = {Effector biology and immunometabolic (re)programming: microbial strategies for compatibility.},
journal = {Molecular plant},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molp.2025.12.016},
pmid = {41408749},
issn = {1752-9867},
abstract = {Root immunometabolism: balancing defense and accommodation Plant health depends on balanced immune defense and microbial accommodation. As constant contact zones, roots must exclude pathogens while fostering beneficial symbionts. Classical, leaf-based immunity models fail to capture the spatial and metabolic complexity of roots, which contain functionally distinct zones and cell types with diverse immune sensitivities and responses (Tsai et al., 2023). Unlike broad immune responses in leaves, root defense is often confined to a few neighboring cells where cellular damage signals coincide with microbial cues. This localized activation likely prevents excessive immunity that could disrupt root development or beneficial colonization (Tsai et al., 2023), shaping microbiome assembly by determining which taxa persist in specific root niches. Beyond immunity, metabolic cues also influence niche formation, collectively defining the physicochemical landscape that selects specific microbial consortia (Loo et al., 2024). Microbial effector proteins from both pathogens and mutualists act individually or cooperatively to reprogram host immune and metabolic pathways, modulating compatibility and plant health. This integrated regulation, known as immunometabolism, is well established in animals, where defined metabolic pathways govern immune cell fate and function. In plants, immunometabolic control is emerging as a conceptual frontier, with host transporters, receptors, and microbial effectors increasingly recognized as key modulators along the mutualism-pathogenesis continuum. Central to this molecular dialogue are extracellular and intracellular signaling metabolites, or infochemicals, produced by both plants and microbes. These small molecules coordinate immune-metabolic states and shape community composition, with purine-derived signals and iron-mediated redox exchanges representing conserved regulatory axes across plant and animal systems (Dangol et al., 2019; Dunken et al., 2024). Together, these cross-kingdom principles offer conceptual and practical leverage for predictive microbiome engineering. Because this opinion piece spans immunity, metabolism, and microbial ecology, INFOBOX 1 defines key terms to establish a shared conceptual framework.},
}

@article {pmid41408736,
year = {2025},
author = {Adriouch, S and Belda, E and Swartz, TD and Forslund, S and Prifti, E and Aron-Wisnewsky, J and Chakaroun, R and Nielsen, T and Poitou, C and Bel-Lassen, P and Rouault, C and Le Roy, T and Andrikopoulos, P and Chechi, K and Puig-Castellví, F and Dionicio, IC and Froguel, P and Holmes, B and Alili, R and Andreelli, F and Soula, H and Salem, JE and Falony, G and Vieira-Silva, S and , and Raes, J and Bork, P and Stumvoll, M and Pedersen, O and Ehrlich, SD and Dumas, ME and Oppert, JM and Dao, MC and Zucker, JD and Clément, K},
title = {Prominent mediatory role of gut microbiome in the effect of lifestyle on host metabolic phenotypes.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2599565},
doi = {10.1080/19490976.2025.2599565},
pmid = {41408736},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Life Style ; Male ; Female ; Middle Aged ; Insulin Resistance ; Phenotype ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Diet ; Adult ; Exercise ; },
abstract = {Lifestyle factors influence both gut microbiome composition and host metabolism, yet their combined and mediating effects on host phenotypes remain poorly characterized in cardiometabolic populations. In 1,643 participants from the MetaCardis study, we developed a composite lifestyle score (QASD: dietary quality, physical activity, smoking, and diet diversity) that outperformed individual lifestyle variables in explaining microbial gene richness and exhibited a significant impact on the gut microbiome composition. While bidirectional pathways linking the QASD score, host phenotypes, and microbiome composition were assessed, causal inference-based mediation analyses indicated stronger effects when the microbiome was modeled as the mediator variable, particularly in relation to the insulin resistance-associated profile. Microbiome gene richness emerged as a key mediator explaining 27.8% of QASD score's effect on the insulin resistance marker (HOMA-IR), while no significant mediation was observed on BMI. Extended mediation analyses on microbial species and serum metabolomics deconfounded for drug use and clinical profiles identified 47 mediations where microbial taxa mediated more than 20% of the effect of the QASD score on serum metabolites associated with insulin resistance. Notably, several Faecalibacterium lineages enriched in individuals with high QASD score played a significant mediatory role in increasing the serum biomarkers of microbiome diversity (as cinnamoylglycine or 3-phenylpropionate). Conversely, elevated levels of secondary bile acids in individuals with low QASD scores were strongly mediated by high levels of Clostridium bolteae. These findings highlight distinct and clinically relevant microbiome pathways linking lifestyle behaviors to cardiometabolic risks.One sentence summary:The gut microbiome mediates the impact of diet quality and diversity, physical activity and smoking status - combined in a composite lifestyle score - on cardiometabolic phenotypes.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Life Style
Male
Female
Middle Aged
Insulin Resistance
Phenotype
*Bacteria/classification/genetics/isolation & purification/metabolism
Diet
Adult
Exercise

@article {pmid41408693,
year = {2025},
author = {Esener, N},
title = {Omics technologies in mastitis: text mining and topic modelling analysis of global research trends.},
journal = {The Journal of dairy research},
volume = {},
number = {},
pages = {1-11},
doi = {10.1017/S0022029925101830},
pmid = {41408693},
issn = {1469-7629},
abstract = {Mastitis, an inflammation of the mammary gland, is a disease of significant clinical and economic importance. In recent years, advances in omics technologies have provided powerful tools to unravel the complex biological mechanisms underlying mastitis. These approaches encompass diverse fields such as genomics, proteomics, transcriptomics, metagenomics, metabolomics, epigenomics, lipidomics, glycomics, pharmacogenomics, foodomics, interactomics and exposomics. However, despite the rapid growth of omics research, the thematic structure of this literature has not been systematically examined. In this study, latent dirichlet allocation (LDA) was employed to perform topic modelling on publications related to omics and mastitis retrieved from Scopus and Web of Science. The LDA analysis revealed ten distinct topics, labelled according to the most frequent terms within each cluster: 'proteomics', 'pathogen genomics', 'differential expression', 'metabolism', 'genetic selection', 'disease economy', 'molecular diagnostics', 'microbiome', 'antimicrobial resistance' and 'genetic variation.' Among these, the topics of 'genomics', 'differential expression' and 'antimicrobial resistance' accounted for the highest number of publications, while 'metabolism' emerged more recently. All topics exhibited an increasing trend in publication volume over time, likely driven by the declining costs and greater accessibility of high-throughput omics technologies. This study provides a comprehensive thematic overview of omics research on mastitis, identifies key areas of emphasis and emerging directions, and highlights knowledge gaps that may inform future investigations and the development of targeted strategies for disease control and prevention.},
}

@article {pmid41408680,
year = {2025},
author = {Zhao, Y and Shen, W and Zhao, A and Mavrodi, OV and Cui, C and Wen, S and Yang, M},
title = {Domestication-Driven Changes in Plant Traits Are Associated With the Assemblage of the Rhizosphere Microbiome.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70338},
pmid = {41408680},
issn = {1365-3040},
support = {2023YFF1000604//National Key R&D Program of China/ ; KF2024-1//Laboratory of Nutrient Use and Management/ ; 32372199//National Natural Science Foundation of China/ ; },
abstract = {Plant domestication involved prolonged artificial selection that progressively adapted plants to human agricultural practices. This process significantly modified both the genetic diversity and the phenotypic and genotypic characteristics of the domesticated plants, resulting in traits that markedly differ from those of their wild ancestors. At the same time, rhizosphere microorganisms, the second largest gene pool of plants, were also inadvertently altered by domestication through changes in root secretions, nutrient uptake or plant defence responses. In this review, we discuss the effects of domestication on plant rhizosphere microbiota and how plants and microbes interact and co-evolve during domestication. The effects of these changes are poorly understood and the subject of active ongoing research. The expected knowledge will help to exploit specific microbial communities for the improvement of plant traits and develop microbial-based management strategies that can be used instead of chemicals to increase plant productivity, reduce environmental pollution and promote the sustainable development of agriculture as a part of the second Green Revolution.},
}

@article {pmid41408433,
year = {2025},
author = {Triadafilopoulos, G},
title = {Ninety-Six-Hour Ambulatory Esophageal pH Monitoring in Patients with Refractory Acid Reflux Symptoms Off- and On-Proton Pump Inhibition Therapy and Their Response to Anti-reflux Diet.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {41408433},
issn = {1573-2568},
abstract = {BACKGROUND: The proton pump inhibitors (PPIs) are widely prescribed for the treatment of dyspepsia and heartburn. However, their use carries the long-term potential for drug-drug interactions, osteopenia, opportunistic infections, adverse cardiovascular outcomes, and altered gut microbiome. Proper indication for and PPI dose optimization would be clinically beneficial.

AIMS: Examine the use of endoscopy with esophageal 96-h ambulatory pH monitoring with patients off- and on-PPI, to guide clinicians in prescribing PPI, thereby minimizing inappropriate use, or adverse effects. Specifically, examine (1) the prevalence of normal and abnormal acid exposure time (AET) in PPI users and non-users; (2) the degree, if any, of restrictive diet on AET in the presence or absence of PPI use. We hypothesized that such patients would have inadequate esophageal pH control and that restrictive diet would be beneficial.

PATIENTS AND METHODS: Retrospective cohort study of consecutive patients presenting with PPI-refractory symptoms of gastroesophageal reflux disease (GERD). All patients underwent an endoscopy with wireless esophageal ambulatory pH monitoring performed either off-PPI or on-PPI therapy for 96 h, following a "liberal diet" for the first 48 h and a "restricted diet" for the latter 48 h of the study. AET was defined as the % time the pH in the distal esophagus was < 4.0; values ≥ 6% per 24 h defined an abnormal AET off-PPI. Control of AET on-PPI was defined as distal esophageal pH < 4 < 1.6% total time. For each patient, the average from the first 2 days (on liberal diet) was considered as the baseline AET and was compared with the average from the latter 2 days (on restricted diet). Depending on the baseline (first 48 h) AET, patients were further divided into 2 groups: those with normal and those with abnormal AET.

RESULTS: We studied 54 consecutive patients with PPI-refractory GERD symptoms. There were 2 groups: those who underwent pH monitoring off-PPI (n = 32) and those who were studied on-PPI (n = 22). In the off-PPI group, there were 26 women (81%) and 6 men (19%), median age 59 years (range 43-76). In the on-PPI group, there were 16 women (73%) and 6 men (27%), median age 66 years, (range 44-78). Of the 32 patients studied off-PPI, 12 (38%) exhibited abnormal AET (% > 6), while the remaining 20 (62%) had normal AET. Of the 22 patients studied on-PPI, 7 (32%) exhibited abnormal AET (% > 1.6), while 15 (68%) had normal AET. The dietary restriction had a statistically significant impact on reducing and (often normalizing) AET in both PPI users and non-users.

CONCLUSIONS: Together with endoscopy, ambulatory 96-h pH monitoring, is feasible and well-tolerated. Most patients (62-68%) with symptomatically PPI-refractory GERD studied either off- or on-PPI, exhibit normal AET. Restrictive diet has a favorable impact on AET in most such patients, but its long-term impact remains unknown.},
}

@article {pmid41408356,
year = {2025},
author = {Yao, QC and Zhang, DY and Du, YP and Chen, C and Lv, YT and Li, D and Xing, YX and Xu, XY and Lin, QQ and Tan, WF and Bai, FH},
title = {Gut microbiome-metabolome dysregulation in systemic sclerosis: a multi-omics study.},
journal = {Rheumatology (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/rheumatology/keaf668},
pmid = {41408356},
issn = {1462-0332},
abstract = {OBJECTIVES: The interplay between the gut microbiome (GM), plasma metabolites, and systemic sclerosis (SSc) has not been systematically studied. We hypothesized that disruption at the GM-metabolome interface contributes to the pathogenesis of SSc. This study aims to investigate the faecal microbiome composition and plasma metabolite profiles in SSc patients.

METHODS: To evaluate the interactions, deep shotgun metagenomic sequencing was conducted on faecal samples from 15 SSc patients and 33 healthy controls. Simultaneously, untargeted Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) metabolomic profiling was performed on plasma samples from 14 SSc patients and 30 controls.

RESULTS: The analysis revealed significant alterations in 11 microbial species and 266 MS2-identified metabolites in SSc patients vs controls. In SSc, elevated levels of Escherichia coli, Lactobacillus mucosae, and Parabacteroides distasonis were noticed. Conversely, P. plebeius, B. hansenii, and Agathobaculum butyriciproducens were enriched in the control group. Functional predictions indicated a depletion of amino acid biosynthesis pathways, including L-isoleucine and L-methionine, in SSc patients. The metabolomic analysis demonstrated a significant reduction in lipid-like molecules and amino acid levels in SSc patients. Dysregulated pathways, such as alanine, aspartate, and glutamate metabolism, arginine and proline metabolism, and glycine, serine, and threonine metabolism, were associated with the development of SSc. Striking microbiota-metabolite correlations (168 significant associations) were identified, with disease-enriched species showing specific metabolic linkages.

CONCLUSIONS: This study offers a comprehensive characterization of the disrupted GM-metabolite interface in SSc patients, providing new perspectives on SSc pathogenesis and potential therapeutic targets.},
}

@article {pmid41408259,
year = {2025},
author = {Guo, Y and Yu, R and Wang, Z and Chang, J and Han, L},
title = {The application of AI-driven and engineered intratumoral microbes in cancer therapy.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-025-07546-4},
pmid = {41408259},
issn = {1479-5876},
support = {TJYGZ51//Tianjin Municipal Education Commission/ ; TJWJ2024XK001//Tianjin Municipal Health Commission/ ; TJWJ2023ZD001//Tianjin Municipal Health Commission/ ; 2022YFF1202500//Key Technologies Research and Development Program/ ; 2024YFA1210100//Key Technologies Research and Development Program/ ; 81773187//National Natural Science Foundation of China/ ; 32471442//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Although investigations of the intratumoral microbiota date back thousands of years, breakthrough transformations have only recently been achieved through high-throughput sequencing and multiomic technologies. These advances have revealed diverse and tumor type-specific microbial communities that drive carcinogenesis via immunomodulation, metabolic reprogramming, and genomic instability. Current cornerstones of cancer therapies-including chemotherapy, radiotherapy, immunotherapy, and targeted therapy-are limited by systemic toxicity, localized tissue damage, drug resistance, and low patient response rates. These constraints underscore the urgent need for more effective and precise therapeutic strategies.

MAIN BODY: This review comprehensively integrates artificial intelligence (AI) technologies into the characterization of the intratumoral microbiota, facilitating the development of novel computational pipelines for mapping microbe-host crosstalk. We systematically summarize recent advances in engineered microbial therapeutics, including bacteria designed for targeted antitumor activity and engineered microorganisms that enable the localized delivery of therapeutic agents. Furthermore, this review critically evaluates the safety profiles of microbiota-based interventions and discusses key challenges in clinical translation.

CONCLUSIONS: By combining cutting-edge computational technologies, biological research, and clinical insights, this review aims to bridge the gap between microbiome science and oncological practice, pioneering innovative strategies for microbiota-guided diagnostics and personalized cancer therapy.},
}

@article {pmid41408188,
year = {2025},
author = {Halimi, H and Hesami, Z and Asri, N and Khorsand, B and Rostami-Nejad, M and Houri, H},
title = {Exploring the biliary microbiome in hepatopancreatobiliary disorders: a comprehensive systematic review of microbial signatures and diagnostic potential.},
journal = {BMC gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12876-025-04551-1},
pmid = {41408188},
issn = {1471-230X},
support = {NO. IR.SBMU.RIGLD.REC.1404.036//Shahid Beheshti University of Medical Sciences/ ; },
abstract = {BACKGROUND: Hepatopancreatobiliary (HPB) diseases, encompassing hepatobiliary and pancreatic disorders, pose substantial global health challenges due to their high morbidity and mortality rates. Recent research highlights the crucial role of the biliary microbiome in the development of these diseases.

METHODS: This study provides a comprehensive systematic review of the biliary microbiome's characteristics across various HPB disorders, including cholangiocarcinoma (CCA), pancreatic cancer (PC), primary sclerosing cholangitis (PSC), and gallstone disease (GSD). Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we screened articles from multiple databases, focusing on original research utilizing 16 S rRNA gene sequencing or metagenomics.

RESULTS: Our review included 24 studies that met stringent inclusion criteria. The results indicate distinct alterations in bacterial diversity and composition associated with different HPB conditions, highlighting potential pathogenic mechanisms and candidate taxa as potential microbial indicators. In lithiasis conditions, elevated levels of Pyramidobacter and Citrobacter were associated with recurrent and giant common bile duct (CBD) stones. Proteobacteria were prevalent in PSC and CCA, potentially contributing to these diseases by promoting chronic inflammation. Sphingomonas was associated with both CCA and PSC, with potential implications for lymph node metastasis in PC.

CONCLUSIONS: These findings suggest the potential of the biliary microbiome as a diagnostic tool, offering insights into the pathophysiology and possible therapeutic targets for HPB diseases. However, given the heterogeneity in methodologies and the limited number of studies including healthy controls, these observations remain preliminary; further prospective validation is required before clinical translation.},
}

@article {pmid41408023,
year = {2025},
author = {Wang, H and Zhang, M and Hua, B and He, J and Yang, Y and Wu, W and Zhang, Y and Wei, F and Cai, Y and Wang, Q},
title = {Exploring the gut microbiome in systemic lupus erythematosus: metagenomic and metabolomic insights into a new pro-inflammatory bacteria Clostridium scindens.},
journal = {Clinical rheumatology},
volume = {},
number = {},
pages = {},
pmid = {41408023},
issn = {1434-9949},
support = {C2301008，C2404002//Shenzhen Medical Research Fund/ ; 2023B1515230002//Guangdong Basic and Applied Basic Research Foundation/ ; 2023A1515010294//Guangdong Basic and Applied Basic Research Foundation/ ; 0102018-2019-YBXM-1499-01-0414//Treatment and Prevention Integration Project of Shenzhen Municipal Health Commission/ ; SZSM202311030//Sanming Project of Medicine in Shenzhen/ ; No. NSFC 82302037//The National Natural Science Foundation of China/ ; KYQD2024355//Shenzhen High-level Hospital Construction Fund and Peking University Shenzhen Hospital Scientific Research Fund/ ; },
abstract = {OBJECTIVES: Systemic lupus erythematosus (SLE) is a complex autoimmune disease with unclear pathogenesis. Emerging evidence indicates that the gut microbiome may play a critical role in immune regulation. This study aimed to investigate gut microbiome and metabolome alterations in SLE patients, with a focus on the pro-inflammatory bacterium Clostridium scindens (C. scindens), and explore its potential contribution to disease pathogenesis.

METHOD: We performed metagenomic sequencing to analyze gut microbial composition in SLE patients and healthy controls, alongside untargeted metabolomic profiling of peripheral blood to assess systemic metabolic changes. We examined species diversity, taxonomic differences at both phylum and species levels, and metabolic alterations. Statistical analyses identified significant associations and potential diagnostic markers.

RESULTS: SLE patients did not show a consistent reduction in species diversity, but exhibited significant microbial compositional differences compared to healthy controls. These patterns suggest potential diagnostic utility. Metabolomic analysis revealed systemic metabolic disturbances linked to gut dysbiosis. Ruminococcus gnavus was associated with altered amino acid, lactose, and sphingolipid metabolism, potentially affecting host immunity. Notably, C. scindens appeared to contribute to immune dysregulation via bile acid metabolism.

CONCLUSIONS: This study reveals distinct microbial and metabolic profiles in SLE, identifying C. scindens as a potential driver of immune imbalance. The findings suggest that targeting the gut microbiome could offer novel strategies for diagnosis and therapeutic intervention in SLE. Key Points • Gut microbial composition is significantly altered in SLE patients compared to healthy controls. • Metabolomic profiling reveals systemic disturbances linked to gut dysbiosis. • Clostridium scindens is associated with bile acid metabolism and immune dysregulation in SLE. • The gut microbiome may serve as a potential target for diagnosis and treatment in SLE.},
}

@article {pmid41408007,
year = {2025},
author = {Abrishami, M and Sabouri, M and Joneidi, F and Haghshenas, Z and Khalili-Tanha, G and Nazari, E},
title = {The role of gut microbiota in breast cancer: biomarker identification and therapeutic applications.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {1},
pages = {14},
pmid = {41408007},
issn = {1572-9699},
support = {1403-1121//Student Research Committee, Shahid Beheshti University of Medical Sciences, Tehran, Iran/ ; },
mesh = {Humans ; *Breast Neoplasms/therapy/microbiology/diagnosis ; *Gastrointestinal Microbiome/physiology ; Female ; *Biomarkers, Tumor ; Dysbiosis/microbiology ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; },
abstract = {Recent studies have established the gut microbiome as a crucial player in breast cancer diagnosis, progression, and treatment. Distinct microbial patterns have shown promise as non-invasive diagnostic and prognostic biomarkers, supporting patient stratification and risk assessment based on microbiota composition. The gut microbiome also modulates estrogen metabolism, influencing the risk of hormone receptor-positive breast cancer, while dysbiosis can promote chronic inflammation and tumor expansion. Moreover, accumulating evidence demonstrates that gut bacteria can alter responses to chemotherapy and immunotherapy, suggesting that microbiota modulation may enhance treatment efficacy. With the advent of omics technologies and machine learning, intricate host-microbe interactions are being decoded, revealing new molecular targets and therapeutic opportunities. Importantly, early clinical and interventional studies using probiotics, prebiotics, and fecal microbiota transplantation (FMT) are being explored to restore microbial balance, mitigate therapy-related side effects, and improve antitumor immunity in breast cancer patients. Together, these advances underscore the translational potential of microbiome research, paving the way for microbiota-guided diagnostic, prognostic, and therapeutic strategies in personalized breast cancer management.},
}

Humans
*Breast Neoplasms/therapy/microbiology/diagnosis
*Gastrointestinal Microbiome/physiology
Female
*Biomarkers, Tumor
Dysbiosis/microbiology
Probiotics/therapeutic use
Fecal Microbiota Transplantation

@article {pmid41407853,
year = {2025},
author = {Wolff, R and Garud, NR},
title = {Gene-specific selective sweeps are pervasive across human gut microbiomes.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41407853},
issn = {1476-4687},
abstract = {The human gut microbiome is composed of a highly diverse consortia of species that are continually evolving within and across hosts[1,2]. The ability to identify adaptations common to many human gut microbiomes would show not only shared selection pressures across hosts but also key drivers of functional differentiation of the microbiome that may affect community structure and host traits. However, the extent to which adaptations have spread across human gut microbiomes is relatively unknown. Here we develop a new selection scan statistic named the integrated linkage disequilibrium score (iLDS) that can detect sweeps of adaptive alleles spreading across host microbiomes by migration and horizontal gene transfer. Specifically, iLDS leverages signals of hitchhiking of deleterious variants with a beneficial variant. Application of the statistic to around 30 of the most prevalent commensal gut species from 24 human populations around the world showed more than 300 selective sweeps across species. We find an enrichment for selective sweeps at loci involved in carbohydrate metabolism, indicative of adaptation to host diet, and we find that the targets of selection differ significantly between industrialized populations and non-industrialized populations. One of these sweeps is at a locus known to be involved in the metabolism of maltodextrin-a synthetic starch that has recently become a widespread component of industrialized diets. In summary, our results indicate that recombination between strains fuels pervasive adaptive evolution among human gut commensal bacteria, and strongly implicate host diet and lifestyle as critical selection pressures.},
}

@article {pmid41407782,
year = {2025},
author = {Su, S and Li, G and Ge, S and Wang, HH and Pan, XF and Yao, Q and Cao, X and Zhang, M and Hong, AJ and Fang, L and Zhai, D and Bai, XH},
title = {Analysing fungal microbiome differences between the roots of healthy and diseased Chinese hickory (Carya cathayensis) trees.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {44018},
pmid = {41407782},
issn = {2045-2322},
support = {hsxyssd007, 2021xkjg009, and 2022xzx005//the Scientific Research Project of Huangshan University/ ; hsxyssd007, 2021xkjg009, and 2022xzx005//the Scientific Research Project of Huangshan University/ ; 2023AH040173//the Major Project of Anhui Department of Education/ ; ylxk202101//the First-class Discipline at Huangshan University/ ; AHLYCX-2023-04 and AHLYCX-2018-29//the Anhui Forestry Science and Technology Innovation project/ ; gxgwfx2020060//the Excellent top-notch Talent Project of Anhui Province/ ; 202310375022, 202410375035, S202410375081, and S202410375082//the College Student´ Innovation and Entrepreneurship Training Program/ ; },
mesh = {*Plant Roots/microbiology ; *Plant Diseases/microbiology ; Soil Microbiology ; *Carya/microbiology ; *Mycobiome ; Rhizosphere ; Basidiomycota/genetics/isolation & purification ; *Fungi/genetics/classification/isolation & purification ; China ; *Microbiota ; Ascomycota/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; },
abstract = {Chinese hickory (Carya cathayensis), an important economic nut species in China, has recently suffered significant losses due to root rot. Previous 16S rRNA amplicon sequencing suggested that the bacterial dysbiosis may contribute to root rot, but the specific pathogens remained unclear. In this study, fungal community analysis revealed that Ascomycota and Basidiomycota dominated the rhizosphere soil, bulk soil, and root tissues, accounting for approximately 93.63% of total fungal communities. The relative abundance of Basidiomycota were more abundant in healthy root tissues, whereas the relative abundance of Ascomycota were enriched in diseased and dead roots. Interestingly, at the genus level, the dominant fungi Xylaria and Ilyonectria were detected exclusively in diseased and dead trees, while Condinaea and Gliocladiopsis were primarily found in dead trees. These genera have been previously reported as root rot pathogens in various plants, suggesting their association with C. cathayensis root rot. Notably, two biocontrol fungi, Chaetomium and Trichoderma, were also present in diseased and dead trees, highlighting potential strategies for disease management. Overall, this study identifies for the first time the potential pathogenic fungi responsible for C. cathayensis root rot and highlights candidate biocontrol agents, providing a foundation for future disease verification and control efforts.},
}

*Plant Roots/microbiology
*Plant Diseases/microbiology
Soil Microbiology
*Carya/microbiology
*Mycobiome
Rhizosphere
Basidiomycota/genetics/isolation & purification
*Fungi/genetics/classification/isolation & purification
China
*Microbiota
Ascomycota/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Phylogeny

@article {pmid41407526,
year = {2025},
author = {Fidelle, M and Zitvogel, L},
title = {Tryptophan metabolite indole-3-acetate: a new culprit in irinotecan-induced gut epithelial injury.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336758},
pmid = {41407526},
issn = {1468-3288},
}

@article {pmid41407501,
year = {2025},
author = {Zhu, W and Li, L and Wang, Y and Wang, Y and Cui, Z and Wang, T and Zhang, L and Wang, C},
title = {Exploring the relationship between gut microbiota and spinal canal stenosis: a bidirectional Mendelian randomization and hub gene study across East Asian and European populations.},
journal = {Asian spine journal},
volume = {},
number = {},
pages = {},
doi = {10.31616/asj.2025.0235},
pmid = {41407501},
issn = {1976-1902},
abstract = {STUDY DESIGN: Mendelian randomization (MR) and gene-level analysis.

PURPOSE: To investigate the relationship between gut microbiota (GM) and spinal canal stenosis (SCS).

OVERVIEW OF LITERATURE: To date, no studies have demonstrated the relationship between GM and SCS or explored its racial differences.

METHODS: This study utilized summary data from publicly available, large-scale genome-wide association studies to investigate the causal relationship between GM and SCS in interracial, European, and East Asian populations using a bidirectional two-sample MR approach. Reverse MR analysis was conducted to estimate the effect of SCS on GM taxa with significant associations. Additionally, genelevel analyses-including Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and protein-protein interaction network analysis-were performed to elucidate key biological processes and hub genes involved in both GM and SCS.

RESULTS: In the interracial population, five bacterial taxa were identified as risk factors and four as protective factors for SCS. Among Europeans, three bacterial taxa were associated with increased risk and three with reduced risk. In the East Asian population, seven bacterial taxa demonstrated protective effects, while one taxon was associated with increased risk. Sensitivity analyses revealed no evidence of heterogeneity or horizontal pleiotropy. Cross-comparisons indicated significant differences in GM profiles between European and East Asian populations. Gene-level analysis identified key GO terms, enriched KEGG pathways, and hub genes potentially mediating the relationship between GM and SCS.

CONCLUSION: This study identified a potential causal relationship between GM and SCS, highlighting distinct microbial and genetic mechanisms in European and East Asian populations. The findings provide novel insights into the pathogenesis, prevention, and treatment of SCS. Gene-level analyses suggest potential molecular pathways underlying the GM-SCS association, providing a foundation for future mechanistic research.},
}

@article {pmid41407319,
year = {2025},
author = {Park, SH and Jung, CH and Ahn, J},
title = {Precision Geronutrition: Personalized Nutritional Strategies to Extend Healthy Lifespan.},
journal = {BMB reports},
volume = {},
number = {},
pages = {},
pmid = {41407319},
issn = {1976-670X},
abstract = {Aging is a multifactorial and heterogeneous biological process, where chronological age alone does not accurately reflect an individual's functional or physiological state. The emerging discipline of precision geronutrition integrates the principles of geroscience with precision nutrition, aiming to delay the onset of age-related functional decline by modulating fundamental molecular mechanisms, such as nutrient-sensing pathways (mTOR, AMPK, and sirtuins), inflammaging, and oxidative stress. A major barrier to progress has been the absence of validated biomarkers that can quantify biological aging and assess intervention efficacy. Recent advances in biological aging clocks, in particular DNA methylation-based epigenetic clocks, provide powerful tools to objectively measure biological age, and evaluate the impact of nutritional interventions. This review discusses how personalized dietary strategies, guided by multi-omics data (genomic, metabolomic, and microbiome profiles), can decelerate aging trajectories. We propose that individualized daily nutrition, aligned with an individual's unique biological characteristics, represents a targeted and actionable approach to extend healthspan. The integration of dynamic aging clocks into nutritional intervention frameworks will be essential to transition from a disease-oriented model to a preventive, healthspan-centered paradigm. Future challenges include large-scale clinical validation, standardization of aging biomarkers, cost reduction, and translation into public health and clinical applications.},
}

@article {pmid41407317,
year = {2025},
author = {Masutani, K and Brune, JE and Duclos, D and Rich, N},
title = {Topical ethyl alcohol as a novel treatment for superficial bacterial pyoderma in dogs.},
journal = {The Journal of small animal practice},
volume = {},
number = {},
pages = {},
doi = {10.1111/jsap.70068},
pmid = {41407317},
issn = {1748-5827},
abstract = {OBJECTIVES: To assess topical ethyl alcohol as a novel treatment for canine superficial pyoderma and compare its effects with chlorhexidine digluconate on the relative abundance of Staphylococcus pseudintermedius and Staphylococcus schleiferi within the skin microbiome.

MATERIALS AND METHODS: In this prospective, randomised, blinded study, 15 client-owned dogs with bilaterally symmetric bacterial skin lesions received twice-daily topical chlorhexidine digluconate 3% (Douxo™ S3 Pyo mousse, CEVA; Libourne, France) or 70% ethyl alcohol (Purell™ Gel, GOJO Industries; Wooster, OH, USA) for 28 days. Lesions were clinically and cytologically scored at days 0, 14 and 28 using a modified split-body system to generate a global score. Next-generation DNA sequencing characterised the S. pseudintermedius and S. schleiferi loads at day 0 and 28.

RESULTS: Both treatments significant improved global scores from baseline (chlorhexidine 18.22 ± 3.54; ethyl alcohol 17.95 ± 3.78) at 14-days (chlorhexidine 12.80 ± 2.74, p ≤ 0.001; ethyl alcohol 12.40 ± 3.06, p ≤ 0.001) and 28-days (chlorhexidine 9.24 ± 3.57, p ≤ 0.001 and ethyl alcohol 8.40 ± 4.06, p ≤ 0.001). Global scores were not significantly different between treatment groups at any time point. Both treatments also reduced the relative abundance of S. pseudintermedius (chlorhexidine -28.73% ± 42.86%; ethyl alcohol -25.66% ± 38.74%) and S. schleiferi (chlorhexidine -65.93% ± 13.03%; ethyl alcohol -79.82% ± 8.37%). No statistically significant differences were observed in the relative abundance of either species between the topical treatments (p=0.95 S. pseudintermedius; p=0.38 S. schleiferi).

CLINICAL SIGNIFICANCE: This study suggests topical 70% ethyl alcohol may be an effective treatment for canine superficial pyoderma.},
}

@article {pmid41407286,
year = {2025},
author = {Herbst, R and Ibrahim, A and Hübner, A and Knüpfer, U and Regestein, L and Wiedemann, C and Hellmich, UA and Warinner, C and Stallforth, P},
title = {Actifensin Evolution in the Human Oral Cavity over the Past 100,000 Years.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.5c14335},
pmid = {41407286},
issn = {1520-5126},
abstract = {Bacterially produced antimicrobial peptides (AMPs), or bacteriocins, play key roles in shaping microbial communities via interspecies competition. Unlike the more temporally dynamic gut microbiome, the oral microbiome exhibits long-term stability and is preserved into deep time in dental calculus, enabling evolutionary analysis across time. Here, we combine metagenomics, structural modeling, and experimental validation to investigate AMP diversity in ancient and modern dental biofilms from humans, Neanderthals, and nonhuman primates spanning 100,000 years. Using our newly developed platform, AMPcombi, we uncover evolutionary trajectories of bacteriocins and elucidate their ecological functions. Among these, we identify a conserved family of Actinomyces-derived defensin-like peptides, termed actifensins, present across all time periods. Phylogenetic, structural, and functional analyses revealed shared ancestry and adaptive diversification between ancient (paleo-) and modern actifensins, with evidence of positive selection and maintained antimicrobial activity. Our findings position the oral microbiome as a valuable reservoir for natural product discovery. In the face of rising antimicrobial resistance, evolutionary insights into AMP function open a door to next-generation therapeutics. AMPcombi streamlines this process, linking ancient biomolecules with biotechnology.},
}

@article {pmid41407129,
year = {2025},
author = {Knobloch, S and Mace, S and Skirnisdóttir, S and Lagirarde, J and Klonowski, AM and Kolypczuk, L and Passerini, D and Marteinsson, VÞ and Leroi, F},
title = {Administering a bioprotective strain to live fish in aquaculture prevents growth of Listeria and spoilage bacteria on the processed fillets.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100679},
doi = {10.1016/j.jfp.2025.100679},
pmid = {41407129},
issn = {1944-9097},
abstract = {Seafood is prone to rapid spoilage and transmission of foodborne diseases. Here we investigate the effect of the bioprotective strain Carnobacterium divergens V41 on the health of on-growing Atlantic salmon (Salmo salar) and spoilage of its fillets throughout storage. The strain was administered throughout a three-month growth period and applied to the water in the fish tanks prior to harvest to assess its impact on animal health, shelf-life properties of the processed fillets, and growth inhibition of Listeria. Administering the strain through feed for three months had no adverse effect on the farmed fish, and no significant differences were detected in growth or mortality between the treatment and control groups. However, adding C. divergens V41 to the tank water prior to harvesting markedly changed the fillet microbiome, suppressing the growth of spoilage organisms and thereby possibly extending the shelf-life period. A Listeria challenge test demonstrated that exposure of the fish to C. divergens V41 prior to harvesting and processing resulted in over 99.9 % inhibition of Listeria growth on the fillets over a 21-day period, compared with the control group. This is the first study to show that administering a bioprotective strain to live farmed fish can have a bioprotective effect on fish fillets after processing. This is a simple method to modify the food microbiome of a rapidly perishable product without specialised equipment, thereby increasing food safety and reducing food waste.},
}

@article {pmid41406967,
year = {2025},
author = {Liu, J and Glukhov, E and De Clerck, O and Gerwick, WH and Donia, MS},
title = {Environmentally controlled production of pagoamide A in marine macroalgae by an intracellular bacterial symbiont.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.11.023},
pmid = {41406967},
issn = {1879-0445},
abstract = {Marine algae are a rich source of diverse molecules, most of which are thought to be produced by the alga itself. We recently reported the discovery of pagoamide A from a cultured marine macroalga collected from American Samoa. Here, we found that the production of pagoamide A is conditional upon environmental temperature. Using comparative metagenomic, metatranscriptomic, and metabolomic analyses of algal cultures, we identified a nonribosomal peptide synthetase biosynthetic gene cluster (NRPS BGC) in the algal microbiome that varies in abundance between producing and non-producing conditions and whose architecture and biosynthetic logic match pagoamide A (named pag). pag belongs to a bacterium that we named "Candidatus Bryopsidiphilus pagoamidifaciens BP1," a new genus in the family Amoebophilaceae and a relative of amoeba, arthropod, and nematode endosymbionts. Ca. B. pagoamidifaciens lives intracellularly in its Bryopsis sp. algal host, harbors a reduced genome (1.7 Mbp), has lost most genes essential for free living, and is enriched in genes containing eukaryotic domains. By quantitatively monitoring longitudinal algal cultures under varying conditions for 9 weeks, we found that the abundance of both Ca. B. pagoamidifaciens and pagoamide A undergoes dramatic fluctuations in response to temperature changes. Finally, we discovered three additional strains of Ca. B. pagoamidifaciens that vary in their NRPS BGCs and eukaryotic domain-containing genes from algal samples of diverse geographical origins. Our findings suggest that symbiont-derived production of algal molecules is more common than previously anticipated and provide a unique case of environmental control of both symbiont and chemical levels in marine algae.},
}

@article {pmid41406907,
year = {2025},
author = {Chen, C and Chen, Q and Zou, H and Zhao, C and Wang, X},
title = {Research Trends in Periodontitis and Alzheimer's Disease: A Bibliometric Analysis Based on Web of Science and Scopus.},
journal = {International dental journal},
volume = {76},
number = {1},
pages = {109327},
doi = {10.1016/j.identj.2025.109327},
pmid = {41406907},
issn = {1875-595X},
abstract = {INTRODUCTION AND AIMS: This study aimed to conduct a comprehensive bibliometric analysis to identify global research trends, key contributors and emerging hot spots in the field investigating the association between periodontitis and Alzheimer's disease (AD).

METHODS: Scientific publications from 2002 to 2025 were retrieved from the Web of Science Core Collection (WoSCC) and Scopus databases. The data were analysed using VOSviewer, CiteSpace and the R package 'bibliometrix' to perform co-authorship, co-occurrence and citation analyses.

RESULTS: A total of 262 articles from WoSCC and 272 from Scopus were included in the analysis. China was the leading contributing country, and Shanghai Jiao Tong University was the most productive institution. The Journal of Alzheimer's Disease was identified as the most influential journal in this domain. Keyword co-occurrence analysis identified central research themes, including 'dementia', 'tooth loss', and 'Porphyromonas gingivalis'. Citation burst analysis indicated that 'oral microbiome' and 'oral health' are currently emerging research frontiers.

CONCLUSION: This is the first bibliometric study to systematically map the intellectual structure and evolution of research linking periodontitis and AD. The findings underscore the strengthening link between oral inflammatory conditions and neurodegeneration.

CLINICAL RELEVANCE: The analysis highlights a shifting focus towards mechanisms such as the oral microbiome and systemic inflammation, pointing to promising directions for future research aimed at novel preventive strategies and therapeutic interventions for AD.},
}

@article {pmid41406905,
year = {2025},
author = {Li, X and Liu, M and Xiang, H and Gui, L and Ma, Y and Dan, X},
title = {Integrated microbiome and metabolome revealing new insight into the combination of lactic acid bacteria in preventing postpartum metritis of dairy cows.},
journal = {Animal reproduction science},
volume = {285},
number = {},
pages = {108078},
doi = {10.1016/j.anireprosci.2025.108078},
pmid = {41406905},
issn = {1873-2232},
abstract = {Probiotics, particularly composite lactic acid bacteria (CLAB), are emerging as a potential alternative to antibiotics for managing bovine metritis. While prior studies have highlighted CLAB's anti-inflammatory effects, limited data exist on its impact on vaginal and uterine microbiomes and systemic metabolism. In this study, Holstein cows received deep vaginal infusions of CLAB (a blend of Lactobacillus rhamnosus, Pediococcus acidilactici and Lactobacillus reuteri; at a standardized 4.5 × 10[10] CFU/dose and a proportion of 25/25/2, respectively) at 20 and 10 days prepartum. We analyzed changes in vaginal and uterine microbiota, plasma metabolomes, and assessed the incidence of metritis, conception rate, and lactation performance postpartum. CLAB administration significantly altered the vaginal microbiota by reducing opportunistic pathogens (Prevotella heparinolytica, Bacteroides and Fusobacteria) and promoting beneficial taxa (Akkermansia and Prevotellaceae). In the uterus, CLAB enriched Rikenellaceae, Christensenellaceae and Lachnospiraceae, while suppressing pathogenic genera such as Cutibacterium and Fournierella. Metabolomic analysis identified pyruvic acid, L-glutamine and L-valine as hub metabolites, with KEGG enrichment revealing involvement in amino acid metabolism and immunomodulatory pathways. Although CLAB infusion did not significantly reduce metritis incidence (5.00 % vs. 5.52 %) or improve conception rate (47.50 % vs. 45.00 %), it showed promising trends without affecting milk production. These findings suggest that prepartum vaginal CLAB infusion modulates reproductive tract microbiota and systemic metabolism, potentially contributing to uterine health maintenance in dairy cows. A key limitation of this study was the absence of significant reductions in metritis incidence and improvements in conception rates, likely attributable to the small sample size and limited study period. Further large-scale studies are warranted to validate its efficacy during high-risk seasons.},
}

@article {pmid41406883,
year = {2025},
author = {Veilleux, C and Erenben, ED and Ismail, N},
title = {Autism and hormones: A perspective from the immune system and the gut microbiome.},
journal = {Hormones and behavior},
volume = {177},
number = {},
pages = {105867},
doi = {10.1016/j.yhbeh.2025.105867},
pmid = {41406883},
issn = {1095-6867},
abstract = {Autism Spectrum Disorder (ASD) affects 2.7 % of individuals worldwide, and it is characterized by abnormal social interactions, communication deficits, restricted interactions, and repetitive behaviors. This disorder appears early in life, and it has been diagnosed more frequently in males than in females. Several factors have been shown to be associated with the onset of ASD. However, the mechanisms underlying the onset of this neurodevelopmental disorder and the higher prevalence in males remain unclear. This review discusses the role of hormonal imbalances, immune system activation during the prenatal (maternal immune activation) and the neonatal periods (neonatal immune activation), immune dysregulation and gut dysbiosis in the development of ASD. It also highlights the many interactions between these systems and demonstrates the true complexity of this disorder.},
}

@article {pmid41406735,
year = {2025},
author = {López-Dávalos, PC and Requena, T and Pozo-Bayón, MÁ and Muñoz-González, C},
title = {In vivo metabolism of fruity carboxylic esters in the human oral cavity is partly driven by microbial enzymes.},
journal = {Food chemistry},
volume = {501},
number = {},
pages = {147554},
doi = {10.1016/j.foodchem.2025.147554},
pmid = {41406735},
issn = {1873-7072},
abstract = {Food flavor perception is shaped by biochemical events during oral processing, with oral metabolism remaining poorly understood. This study investigated the oral fate of fruity carboxylic esters and its relationship with salivary and microbiological parameters. Participants (n = 101) rinsed their mouths with either water (control) or an ester-containing solution for 30 s. Esters and their corresponding acids were analyzed by gas chromatography-mass spectrometry before and after rinsing. Results showed a significant decrease in ester and a marked increase in acid levels, indicating rapid metabolic conversion. Ester recovery was associated with the physicochemical properties of the compounds, participants' body mass index, and salivary esterase activity (SEAC). SEAC also correlated with oral microbiota composition and the abundance of microbial genes encoding carboxylic ester hydrolases, as assessed by shotgun metagenomics. These findings provide the first evidence of rapid ester metabolism in the human mouth and its relationship with the salivary microbiome.},
}

@article {pmid41406635,
year = {2025},
author = {Maeng, LS and Yoon, JH and Chung, BY and Seo, KJ and Lee, HK and Chung, MG and Park, WS and Chae, HS},
title = {Refined photobiomodulation therapy ameliorates inflammatory bowel disease via modulation of immune pathways and gut microbiota.},
journal = {Journal of photochemistry and photobiology. B, Biology},
volume = {274},
number = {},
pages = {113330},
doi = {10.1016/j.jphotobiol.2025.113330},
pmid = {41406635},
issn = {1873-2682},
abstract = {BACKGROUND: Inflammatory bowel diseases (IBD), such as ulcerative colitis and Crohn's disease, are chronic conditions influenced by genetic and environmental factors. Current treatments are costly and not universally effective. This study aimed to evaluate the therapeutic potential of refined photobiomodulation (PBM) therapy by addressing limitations in light delivery and its impact on gut microbiota using a dextran sodium sulfate (DSS)-induced colitis mouse model.

METHODS: PBM therapy was administered using an 830 nm infrared LED with optimized light delivery protocols, including abdominal hair removal and a four-directional irradiation approach. DSS-induced colitis was established in mice, and therapeutic efficacy was assessed through histological analysis, transcriptomic profiling, immune marker expression, and gut microbiota diversity using 16S rRNA sequencing.

RESULTS: PBM therapy significantly ameliorated DSS-induced colitis by reducing inflammatory cell infiltration, crypt damage, and ulceration (p < 0.05). Colon length was restored, and disease activity index scores were reduced (p < 0.001). Transcriptomic profiling revealed modulation of inflammatory pathways, including downregulation of NF-κB signaling and apoptosis-related genes. PBM decreased neutrophil activity (MPO levels) and immune cell marker expression while promoting gut microbiota richness (Chao1 index, p < 0.05). PBM-treated mice exhibited altered microbial composition with increased abundance of protective taxa such as Bacteroides.

CONCLUSIONS: Refined PBM therapy effectively alleviates DSS-induced colitis by modulating immune responses and gut microbiota composition. These findings highlight PBM as a promising non-invasive strategy for IBD management, warranting further translational studies.},
}

@article {pmid41406626,
year = {2025},
author = {Habich, D and Horvath, A and Feldbacher, N and Rebol, L and Nepel, M and Madl, T and Habisch, HJ and Baumann-Durchschein, F and Fürst, S and Plank, J and Rainer, F and Spindelböck, W and Stauber, RE and Tatscher, E and Wagner, M and Zollner, G and Stadlbauer, V},
title = {An observational study on the effect of l-ornithine-l-aspartate (LOLA) on the gut microbiome in liver cirrhosis. A single center phase 4 study.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {56},
number = {},
pages = {106522},
doi = {10.1016/j.clnu.2025.11.007},
pmid = {41406626},
issn = {1532-1983},
abstract = {BACKGROUND & AIMS: Liver cirrhosis is associated with gut microbiome dysbiosis, intestinal inflammation and gut barrier dysfunction, contributing to reduced quality of life and the development of complications. We showed in a retrospective study that l-ornithine-l-aspartate (LOLA) was associated with improvement in taxonomic composition of the microbiome. Here we prospectively studied the influence of LOLA on the gut microbiome, quality of life, sarcopenia and the gut barrier.

METHODS: In this phase 4 study, patients with liver cirrhosis and hepatic encephalopathy grade 0-2 received LOLA 18 g/day orally for 3 months. We studied faecal microbiome composition (primary endpoint abundance of the genus Flavonifractor), microbiome function, quality of life, serum ammonia levels, sarcopenia and frailty, biomarkers of the gut liver axis and the stool, serum and urine metabolome.

RESULTS: We screened 258 patients with liver cirrhosis, included 65, of whom 52 patients (40 % female, age 62 (58; 65)) completed the study. LOLA intake decreased the abundance of the genus Romboutsia, increased the abundance of the genus Enterococcus, but did not alter other microbiome parameters. LOLA improved one out of 8 dimension of quality of life (vitality) and decreased serum ammonia concentrations. The subgroup of patients with improved ammonia concentrations responded with a halt in further muscle mass declined over the study period. Diamine oxidase, a marker of intestinal mucosal condition, decreased and LPS binding protein increased. Metabolomic analysis indicated an increase in alanine concentration.

CONCLUSIONS: LOLA improved one quality of life dimension (vitality) and biomarker of the gut-liver axis, altered innate immune response, faecal microbiome and metabolome. LOLA prevented muscle loss only in patients with elevated ammonia concentrations at baseline. LOLA may therefore be a useful adjunct treatment to improve quality of life in cirrhosis and a promising intervention for muscle loss prevention in hyperammonemic patients.

clinicaltrials.gov NCT05737030.

IMPACT AND IMPLICATION: We conducted a 12-week prospective cohort study to test the effect of the ammonia lowering drug l-ornithine-l-aspartate (LOLA) on the gut microbiome, biomarkers along the gut-liver-axis, muscle health and quality of life in patients with liver cirrhosis and hepatic encephalopathy. Although our primary endpoint was not reached, LOLA slightly altered microbiome composition and function and improved vitality, a clinically relevant patient reported outcome parameter. LOLA also improved biomarkers for the gut-liver-axis, innate immune response and prevented muscle loss in patients with elevated ammonia levels at baseline. LOLA may therefore be a useful adjunct treatment to improve quality of life in cirrhosis and to prevent muscle loss in hyperammonemic patients.},
}

@article {pmid41406001,
year = {2025},
author = {Thornton, CS and Bouzek, DC and Caverly, LJ},
title = {Microbiota, Mucus, and Modulators: CF Infection Pathogenesis in the CFTR Modulator Era.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf626},
pmid = {41406001},
issn = {1537-6613},
abstract = {Cystic fibrosis (CF) lung disease is a result of defective CFTR-mediated ion transport, producing dehydrated mucus, impaired mucociliary clearance and an opportune environment for chronic airway infection. CF airway infections are polymicrobial airway ecosystems often dominated by CF pathogens such as Pseudomonas aeruginosa, Staphylococcus aureus, Burkholderia, Stenotrophomonas, Achromobacter, and nontuberculous mycobacteria that drive cycles of infection, inflammation, and bronchiectasis. Highly effective CFTR modulators, including elexacaftor/tezacaftor/ivacaftor, improve airway hydration and mucociliary clearance and reduce pathogen CF acquisition and density. However, even with CFTR modulator treatment, most individuals with established infection remain chronically infected, and long-term impacts of CFTR modulators on airway infection dynamics and associated clinical outcomes remain unclear. In this review, we address key gaps in understanding chronic infection in the CFTR modulator era, including changes in infection-related lung disease pathogenesis, airway-gut microbiome interactions, approaches to airway infection sampling, and implications for infection management.},
}

@article {pmid41405666,
year = {2025},
author = {Wenbin, T and Feng, D and Jing, L},
title = {The interplay between insect gut microbiota and host immunity in the development and dissemination of antibiotic resistance.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {41405666},
issn = {1874-9356},
support = {25DF0314//China Higher Education Society Higher Education Science Research Planning Project/ ; },
abstract = {The escalating crisis of antibiotic resistance presents a formidable challenge to global public health and food security. Insects are increasingly recognized as significant reservoirs and vectors for antibiotic resistance genes (ARGs) which inhabit diverse ecosystems. This review explores how the insect gut microbiota contributes to the development and spread of antibiotic resistance, focusing on the mediating role of the host immune system. We outline the structural and functional dynamics of the insect gut microbiome and elaborate on direct mechanisms through which microbiota contribute to resistance, including ARG carriage, enzymatic inactivation of antibiotics, and modulation of host detoxification pathways. Special emphasis is placed on the bidirectional crosstalk between gut microbes and the host immune system: we discuss how immune effectors, particularly antimicrobial peptides (AMPs), exert selective pressures that may enrich resistant taxa, and how microbial metabolites reciprocally regulate immune activity. Key immune signaling pathways-Toll, Immune Deficiency(Imd), and Janus kinase-signal transducer and activator of transcription (JAK-STAT)-are explored for their roles in maintaining microbial homeostasis and modulating resistance phenotypes. We also highlight cutting-edge experimental approaches, including gnotobiotic models and multi-omics technologies, that are essential for elucidating causal relationships. We conclude by highlighting outstanding questions and outlining future research priorities that integrate microbiology, immunology, and computational biology. This review aims to establish a holistic framework for understanding the insect gut as a hotspot for antibiotic resistance evolution and to inspire innovative microbiome-based interventions.},
}

@article {pmid41405552,
year = {2025},
author = {Smith, ML and Rillaer, TV and Willmott, T and Lebeer, S and Souza, A and O'Neill, CA and McBain, AJ},
title = {The human skin microbiome remains unchanged after 24 h of sunscreen application.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0147625},
doi = {10.1128/aem.01476-25},
pmid = {41405552},
issn = {1098-5336},
abstract = {UNLABELLED: To ensure safe, long-term use, topical products should be investigated to understand how they interact with the resident skin microbiota to mitigate potential risk. Sunscreens are essential for protecting skin from UV damage, but their effects on skin-resident microbes have not been well characterized. We examined the impact of two sunscreen formulations (containing titanium dioxide or zinc oxide) on both cultured skin bacteria and the skin microbiomes of human volunteers. No loss of viability was observed after a 2 h exposure to either sunscreen in cultures of Staphylococcus epidermidis, Staphylococcus capitis, Staphylococcus hominis, Micrococcus luteus, and Corynebacterium tuberculostearicum. The effects of the sunscreens were then studied across the skin microbiomes of 20 human participants. Skin swabs were collected before application and at 1, 6, and 24 h afterward. DNA was extracted and sequenced at the 16S rRNA V4 region, and sequences were denoised and taxonomically assigned using the nf-core/ampliseq pipeline. Across all time points, alpha diversity (Shannon index, Friedman test) and beta diversity (permutational multivariate analysis of variance) remained stable, with no significant differences in beta dispersion. Differential abundance analysis revealed minor fluctuations in some low-abundance genera, identified as likely transient due to their low prevalence, but overall resident community composition was not significantly altered. These findings suggest that short-term sunscreen application does not disrupt the skin microbiome, supporting their safe use from a microbial standpoint. Outcomes from both in vitro and in vivo experimentation point to the compositional resilience of the skin microbiota to sunscreens.

IMPORTANCE: Understanding how sunscreens affect the skin microbiome is important, given their widespread use and the role of the microbiome in skin health. This study demonstrates that common sunscreens do not significantly alter skin microbiome diversity or viability, including that of the core skin microbiome genera, Staphylococcus, Micrococcus, Kocuria, Cutibacterium, and Corynebacterium. This highlights the resilience of the skin microbiota and supports the microbiome-safe profile of these products.},
}

@article {pmid41405456,
year = {2025},
author = {Pervaiz, K and Tabassum, R and Steidele, C and Brender, N and John, E and Djamei, A},
title = {Transcriptional Response of Magnaporthe oryzae Towards Barley-Microbiome Derived Bacteria.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {},
number = {},
pages = {},
doi = {10.1094/MPMI-11-25-0158-FI},
pmid = {41405456},
issn = {0894-0282},
abstract = {The composition of the plant microbiome is shaped not only by the host plant and abiotic environmental factors, but also by inter-microbial cooperation and competition. Plant pathogens, therefore must remain competitive within the microbiome in order to establish themselves within their host niche. Magnaporthe oryzae, the blast-disease causing ascomycete fungus, is able to infect economically important hosts including rice, barley and wheat. We sought to identify barley associated bacteria able to antagonize M. oryzae and to characterize the fungal transcriptional responses following confrontation to reveal antimicrobial self-defence mechanisms. From a library of 25 barley-associated bacteria, two strains were identified as moderate and strong antagonists. Through RNA-seq, we demonstrate large-scale transcriptional changes in M. oryzae during their confrontation. Common responses to both strains included an over-representation of genes encoding drug efflux transporters, hydrolases, signalling components, DNA repair and oxidative stress responses. This indicates M. oryzae prioritizes stress adaptation and detoxification. We did not observe a significant increase in secreted proteins of M. oryzae as part of the common response. However, significant strain-specific changes were observed, indicating that independent of host plant, specific microbial antagonists are perceived by M. oryzae leading to altered secretome profiles. Understanding these adaptive strategies provides insight into antimicrobial resistance mechanisms with respective parallels to drug- and fungicide resistance mechanisms in the medical and agricultural context. Additionally, our study provides potential targets on the plant pathogen side to weaken its fitness within the plant microbiome.},
}

@article {pmid41405404,
year = {2025},
author = {Levy, S and McCauley, KE and Strength, R and Robbins, ES and Chen, Q and Namasivyam, S and Maxwell, G and Hourigan, SK},
title = {Colibactin genes are highly prevalent in the developing infant gut microbiome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2604874},
doi = {10.1080/19490976.2025.2604874},
pmid = {41405404},
issn = {1949-0984},
mesh = {Humans ; *Polyketides/metabolism ; *Gastrointestinal Microbiome/genetics ; *Peptides/genetics/metabolism ; Infant ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Infant, Newborn ; Female ; Male ; },
abstract = {Early-life exposure to colibactin-producing pks+ gut bacteria is hypothesized to imprint mutations on the colorectal epithelium, increasing the risk of colorectal cancer later in life. We demonstrate an extremely high prevalence of pks+ bacteria (>50% of infants) during the first 2 y of life, suggesting carriage is likely normal during early-life microbiome development. Further investigation is required to understand the circumstances in which carriage can lead to mutagenesis.},
}

Humans
*Polyketides/metabolism
*Gastrointestinal Microbiome/genetics
*Peptides/genetics/metabolism
Infant
*Bacteria/genetics/classification/isolation & purification/metabolism
Infant, Newborn
Female
Male

@article {pmid41405322,
year = {2025},
author = {Wang, W and Wu, J},
title = {Global clinical landscape of microbiome modulation therapies for non-alcoholic fatty liver disease exploring the role of the gut-liver Axis.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000004431},
pmid = {41405322},
issn = {1743-9159},
}

@article {pmid41405260,
year = {2025},
author = {Liu, H and Song, H and Pu, L and Zhao, J and Yin, X and Liu, B and Zheng, X and Zhu, Y and Yang, J},
title = {Multi-omics analysis reveals microbiome-associated subtypes of esophageal cancer with distinct immune profiles and therapeutic responses.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000004503},
pmid = {41405260},
issn = {1743-9159},
abstract = {BACKGROUND: Esophageal cancer is an aggressive malignancy with poor prognosis. Comprehensive molecular characterization is crucial for identifying novel therapeutic targets and improving outcomes.

METHODS: We performed an integrative multi-omics analysis of esophageal tumors, profiling the microbiome, transcriptome, epigenome, and clinical data. Unsupervised consensus clustering using ten different algorithms identified robust molecular subtypes, which were further characterized by functional enrichment analyses and experimental validation to uncover subtype-specific features and therapeutic vulnerabilities.

RESULTS: Microbiome profiling revealed distinct taxonomic differences between normal and tumor tissues, with Proteobacteria and Pseudomonas being more abundant in tumors. Two molecular subtypes, C1 (n = 92) and C2 (n = 57), were identified, exhibiting unique clinical, prognostic, and molecular features. Subtype C2 showed higher mutation burden, increased abundance of Pseudomonas species, and an immunologically active microenvironment, with greater infiltration of effector memory CD4 + T cells, regulatory T cells, and M2 macrophages. Subtype C2 also exhibited higher predicted immunotherapy response rates and lower T cell exclusion scores. In contrast, subtype C1 was characterized by elevated expression of specific RNAs and DNA methylation, as well as higher sensitivity to chemotherapy agents and EGFR inhibitors, which was experimentally validated using representative cell lines. Notably, STAT3 inhibitors potentiated the efficacy of PD-L1 blockade in subtype C2 cells by enhancing apoptosis, downregulating PD-L1 expression, suppressing EMT, and attenuating invasion and migration.

CONCLUSION: This multi-omics analysis reveals esophageal cancer's molecular heterogeneity and identifies microbiome and immune signatures associated with prognosis and therapeutic response, providing a framework for developing personalized treatments targeting specific subtypes.},
}

@article {pmid41405224,
year = {2025},
author = {Kok, CR and Morrison, MD and Thissen, JB and Mabery, S and Carson, ML and Kimbrel, JA and Bennett, JW and Tribble, DR and Millar, EV and Mende, K and Be, NA},
title = {Microbiome dynamics in the congregate environment of U.S. Army Infantry training.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0047425},
doi = {10.1128/spectrum.00474-25},
pmid = {41405224},
issn = {2165-0497},
abstract = {Within military training and operational environments, individuals from diverse backgrounds share common spaces, follow structured routines and diets, and engage in physically demanding tasks. While there has been interest in leveraging microbiome features to predict and improve military health and performance, the longitudinal convergence of microbiomes in such constrained environments has not been established. To assess the degree of microbiome convergence, we performed shotgun metagenomic sequencing on swab samples from a military trainee cohort. Samples were taken across four different body sites, three timepoints, and two spatially distinct platoons. We observed evidence of convergence in one platoon, whereby similarity in microbiome composition increased over time, with numerous differentially abundant species. We found no indication of strain transfer between individuals, suggesting that convergence was influenced by external environmental factors, diet, and lifestyle. Microbial shifts observed in the convergence process included a decrease in fungal species, such as Malassezia restricta in nasal cavities, and a decrease in Prevotella species at inguinal regions across time. Shifts in multiple Corynebacterium species were also observed with varying magnitudes depending on the body site. Overall, we provide preliminary evidence of convergence of host microbial communities in military-associated environments that were distinguishable using shotgun metagenomic sequencing approaches. The data presented here on microbiome convergence, dynamics, and stability may inform risk-based mitigation in congregate military settings facilitating development of targeted microbial, dietary, or other interventions to optimize health and performance of military populations.IMPORTANCEMicrobiome convergence in deployed environments could impact the health and readiness of the warfighter, with potential implications for susceptibility to biothreats. This study describes a shotgun metagenomic approach used to study the microbiomes of swab samples collected at different body sites in a military trainee cohort. The results presented here provide a foundation for developing future microbiome-based interventions and protocols to enhance operational readiness.},
}

@article {pmid41405172,
year = {2026},
author = {Molina-Viramontes, JP and Gómez-Acata, ES and Hereira-Pacheco, S and Estrada-Torres, A and Navarro-Noya, YE},
title = {Comparison of Methods to Characterize the Microbiota of Myxomycete Plasmodia.},
journal = {The Journal of eukaryotic microbiology},
volume = {73},
number = {1},
pages = {e70058},
doi = {10.1111/jeu.70058},
pmid = {41405172},
issn = {1550-7408},
support = {CBF2023-2024-1480//Secretaría de Ciencia, Humanidades, Tecnología e Innovación/ ; },
mesh = {*Microbiota ; *Myxomycetes/microbiology/genetics/classification ; *Bacteria/genetics/classification/isolation & purification ; DNA, Bacterial/genetics/isolation & purification ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Myxomycetes are valuable models for studying interactions between single-celled eukaryotes and bacteria; however, little is known about their microbiota or optimal DNA extraction methods. We analyzed the bacterial community of Claustria didermoides plasmodia using commercial and noncommercial DNA extraction methods. A total of 218 amplicon sequence variants (ASVs) were identified, dominated by Pseudomonadota (78%), Bacillota (10%), and Actinomycetota (9%). Achromobacter denitrificans was the most abundant species, with 3-7 codominant ASVs, including opportunistic pathogens. The commercial kit captured higher diversity, while the noncommercial method favored Gram-negatives and preserved DNA integrity longer when phenol was added.},
}

*Microbiota
*Myxomycetes/microbiology/genetics/classification
*Bacteria/genetics/classification/isolation & purification
DNA, Bacterial/genetics/isolation & purification
Phylogeny
Sequence Analysis, DNA

@article {pmid41404904,
year = {2025},
author = {Jensen, EEB and Jespersen, ML and Svendsen, CA and Sonda, T and Otani, S and Aarestrup, FM},
title = {Tanzanian goat gut microbiomes adapt to roadside pollutants and environmental stressors.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0203625},
doi = {10.1128/spectrum.02036-25},
pmid = {41404904},
issn = {2165-0497},
abstract = {The impact of environmental pollution reaching and affecting the gut microbiome is rising. Pollution from vehicle emissions can release compounds harmful to both animal and environmental health, and their effect on the host microbiome is yet to be determined, particularly in understudied locations. Here, we have investigated the potential effect of environmental pollution on the gut microbiome of Tanzanian goats grazing near a heavily trafficked road compared to goats living in a more rural setting. We identified 1,468 metagenome-assembled genomes (MAGs), of which 768 were unidentified species, and created a genomic database to which 52% of the bacterial community could be assigned. We find significant differences in the composition of the bacterial communities and resistomes between rural and road-exposed goats, but not a major difference in antimicrobial resistance (AMR) abundance. Genes involved in pollutant biodegradation were significantly more abundant in the microbiome of goats grazing along the road. This includes genes involved in degradation of naphthalene and toluene (both present in motor vehicle exhaust), as well as the detoxification enzyme, glutathione S-transferase. These findings suggest living near a heavily trafficked road selects for xenobiotic degrading functions within the goat gut microbiome, which might aid the host in detoxification of these compounds.IMPORTANCETo the best of our knowledge, this is the first study on the potential effect of environmental pollution on the gut microbiome of Tanzanian goats. Using shotgun metagenomics, we compare the gut microbiome of goats living near a heavily-trafficked road in Kigoma, Tanzania, with the gut microbiome of goats living in a rural area. We find that genes involved in pollutant biodegradation were significantly more abundant in the gut microbiome of the road-exposed goats, which potentially aids pollutant detoxification in the host. The effect of environmental pollution on the gut microbiome remains poorly understood; however, with this study, we link a potential effect of environmental pollution to changes in the gut microbiome of Tanzanian goats.},
}

@article {pmid41404876,
year = {2025},
author = {Van Beeck, W and Eilers, T and Smets, W and Delanghe, L and Vandenheuvel, D and Tuyaerts, I and Van Malderen, J and Ahannach, S and Michiels, K and Dricot, C and Van de Vliet, N and Huys, AJ and De Boever, P and Lebeer, S},
title = {Sonmat, a citizen-science enabled Kimjang kimchi case study on associations between hand and kimchi microbiota.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0036825},
doi = {10.1128/spectrum.00368-25},
pmid = {41404876},
issn = {2165-0497},
abstract = {UNLABELLED: Kimjang kimchi is traditionally made in Korea in autumn to preserve vegetables during colder winter times after the harvest. Kimjang is an important societal tradition in which families and communities come together to process vegetables, such as cabbage, into kimchi. The origin of the microorganisms that contribute to the flavor and safety during fermentation is still unclear. Although bacteria present on the raw ingredients are considered to be important colonizers of the fermentation, in Korean culture, the term "Sonmat" is often used, which literally translates into "hand flavor," suggesting a role for hand microbiota in the kimchi fermentation. In this citizen-science project, we investigate the impact of the hand microbiome on kimchi fermentation during the Sonmat festival organized in Belgium. The kimchi fermentations contained mainly lactic acid bacteria belonging to the genera Leuconostoc, Weissella, and Latilactobacillus. The hand microbiota was characterized by the presence of Staphylococcus, Corynebacterium, Micrococcus, and Enhydrobacter. Associations were found between the relative abundance of Staphylococcus on the hand and the relative abundance of Latilactobacillus and Leuconostoc found in kimchi, despite limited overlap between the hand and the kimchi microbiome. In addition, different microbiota were found to dominate the kimchi made following the traditional group Kimjang practices compared with individually prepared kimchi. These findings pave the way for future research into how traditional practices and the skin microbiome influence the unique qualities of kimchi, offering exciting possibilities for enhancing fermentation processes and cultural food heritage through citizen science.

IMPORTANCE: Vegetable fermentation has been a staple of human culture for centuries, with deeply rooted traditions behind it. However, the effects of these traditional practices on the microbes in the final fermented product, and their origin, are often not understood. By using participatory citizen-science approaches, it is possible to study these important foods while preserving the authenticity and integrity of the traditional fermentation practices that define them. The results obtained from our citizen-science case study support the importance of exploring traditional fermentation practices and their effect on microbial and sensory properties of fermented foods. Additionally, our case study found associations between microbiota present on the hand and microbiota important in the early successional stage of kimchi fermentation.},
}

@article {pmid41404617,
year = {2025},
author = {Coleman, I and Mametyarova, N and Zaznaev, A and Cai, P and Yu, L and Meydan, Y and Litman, A and Sharma, A and He, L and Simkhovich, A and Seeram, D and Park, H and Nobel, YR and Kav, AB and Pe'er, I and Uhlemann, AC and Korem, T},
title = {Comparative metagenomics using pan-metagenomic graphs.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.24.690211},
pmid = {41404617},
issn = {2692-8205},
abstract = {Identifying microbial genomic factors underlying human phenotypes is a key goal of microbiome research. Sequence graphs are a highly effective tool for genome comparisons because they enable high-resolution de novo analyses that capture and contextualize complex genomic variation. However, applying sequence graphs to complex microbial communities remains challenging due to the scale and complexity of metagenomic data. Existing multi-sample sequence graphs used in these settings are highly complex, computationally expensive, less accurate than single-sample alternatives, and often involve arbitrary coarse-graining. Here, we present copangraph, a multi-sample sequence-graph-based analysis framework for comprehensive comparisons of genomic variation across metagenomes. Copangraph uses a novel homology-based graph, which provides both non-arbitrary, evolutionary-motivated grouping of sequences into the same node as well as flexibility in the scale of variation represented by the graph. Its construction relies on hybrid coassembly, a new coassembly approach in which single-sample graphs are first constructed separately and are then merged to create a multi-sample graph. We also present an algorithm that uses paired-end reads to improve detection of contiguous genomic regions, increasing accuracy. Our results demonstrate that copangraph captures sequence and variant information more accurately than alternative methods, provides graphs that are more suitable for comparative analysis than de Bruijn graphs, and is computationally tractable. We show that copangraph reflects meaningful metagenomic variation across diverse scenarios. Importantly, it enables significantly better performance than other metagenomic representations when predicting the gut colonization trajectories of Vancomycin-resistant Enterococcus. Our results underscore the value of our multi-sample, graph-based framework for comparative metagenomic analyses.},
}

@article {pmid41404442,
year = {2025},
author = {Lee, M and Hwang, SY and Wi, K and Kim, J and Lee, MH and Hwang, IH},
title = {Pharmacological evaluation of 1-acetyl-β-carboline, a naturally occurring compound with anti-skin cancer potential.},
journal = {Molecular therapy. Oncology},
volume = {33},
number = {4},
pages = {201093},
pmid = {41404442},
issn = {2950-3299},
abstract = {The human microbiome comprises microbial communities that reside in the human body and contribute to host health through molecular mediators. Lactobacillus spp. are frequently used as probiotics to restore microbial balance, and L. gasseri has been reported to exert a wide range of beneficial effects. In this study, 1-acetyl-β-carboline (ABC) was identified in L. gasseri cultures and subsequently synthesized via the Pictet-Spengler reaction followed by palladium-catalyzed oxidation. ABC exhibited significant anticancer activity by reducing colony formation and growth of epidermal growth factor-induced JB6 cells and by inhibiting the proliferation of SK-MEL-5 and SK-MEL-28 melanoma cells. Mechanistic studies revealed that ABC induced G2/M phase cell-cycle arrest and promoted apoptosis by regulating related markers, including p27 and caspases-3 and -7. Additionally, ABC significantly inhibited the mitogen-activated protein kinase kinase (MEK)-extracellular signal-regulated kinase (ERK) signaling pathway by reducing phosphorylated MEK and phosphorylated ERK levels. ABC also downregulated cyclooxygenase-2 expression, targeting inflammation-related pathways in melanoma cells. In a mouse model, ABC effectively mitigated 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced epidermal hyperplasia and reduced inflammation. These findings highlight the pharmacological significance of ABC, independent of its origin, and suggest that this naturally occurring compound possesses preventive and therapeutic potential against skin cancer.},
}

@article {pmid41404370,
year = {2025},
author = {Liu, M and Wu, M and Tang, Y and Lin, Z and Ye, C and Huang, X and Zhou, L and Lin, Q and Zheng, D and Lu, Y},
title = {Correlation between oral microbial characteristics and overall bone density of Postmenopausal women based on macrogenomic analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1663645},
pmid = {41404370},
issn = {2235-2988},
mesh = {Humans ; Female ; *Bone Density ; Middle Aged ; Saliva/microbiology ; *Osteoporosis, Postmenopausal/microbiology ; *Postmenopause ; *Microbiota ; Dental Plaque/microbiology ; *Mouth/microbiology ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; Absorptiometry, Photon ; },
abstract = {BACKGROUND: Postmenopausal osteoporosis (PMO), a prevalent bone disease triggered by estrogen deficiency - induced bone mass reduction and deterioration of bone tissue microarchitecture, escalates the risk of fragility fractures. Recent research has highlighted the pivotal role of oral and gut microbiota in PMO development, giving rise to the "oral - gut - bone axis" concept.

METHODS: A total of 21 postmenopausal women, aged 50 - 60, were recruited for the study. Based on bone mineral density (BMD) measurements from dual - energy X - ray absorptiometry (DXA), participants were divided into osteopenia, osteoporosis, and healthy groups. Saliva and dental plaque samples were collected for metagenomic sequencing to analyze microbial diversity and community composition, with differences identified via LEfSe analysis. KEGG pathway analysis was used to reveal variations in microbial functions. Based on these analyses, predictive models for bone density status were constructed using LASSO regression and random forest algorithms.

RESULTS: Significant differences in salivary microbial community structures were found between the osteoporosis and healthy groups (P = 0.041). LEfSe analysis revealed higher abundance of Aggregatibacter, Haemophilus haemolyticus, Haemophilus sputorum, Pasteurellaceae, Neisseria elongata, Aggregatibacter segnis, and Aggregatibacter aphrophilus in the osteopenia group, and higher abundance of Streptococcus pneumoniae and Haemophilus paraphrohaemolyticus in the osteoporosis group compared to the healthy group. The random forest models for osteopenia vs. healthy and osteoporosis vs. healthy yielded AUC values of 0.82 and 0.74, respectively, suggesting potential predictive capability, though further validation in larger cohorts is needed to confirm their generalizability. Functional analysis using LEfSe identified differential KEGG pathways, including glycan biosynthesis and metabolism in cancer, choline metabolism in cancer, and the cGMP-PKG signaling pathway.

CONCLUSION: This exploratory study utilized metagenomic sequencing to analyze the relationship between oral microbiota and PMO while controlling for key confounders. We identified significant compositional and functional alterations in the oral microbiome associated with bone mineral density status, including specific bacterial species showing marked intergroup differences. A model based on differential microbial features exhibited preliminary discriminative capacity, and functional analysis suggested involvement of inflammatory and metabolic pathways. These findings provide initial evidence linking oral microbiota to PMO.},
}

Humans
Female
*Bone Density
Middle Aged
Saliva/microbiology
*Osteoporosis, Postmenopausal/microbiology
*Postmenopause
*Microbiota
Dental Plaque/microbiology
*Mouth/microbiology
Metagenomics
*Bacteria/classification/genetics/isolation & purification
Absorptiometry, Photon

@article {pmid41404120,
year = {2025},
author = {Kim, RY and Kuraji, R and Kapila, YL},
title = {Systemic Health Implications of the Leaky Barriers within the Oral-Gut-Brain Axis and its Pathways of Communication.},
journal = {European Medical Journal (Chelmsford, England)},
volume = {10},
number = {1},
pages = {47-50},
pmid = {41404120},
issn = {2397-6764},
}

@article {pmid41403940,
year = {2025},
author = {Riebelmann, J and Kienzle, N and Sauer, B and Schittek, B},
title = {Commensal Staphylococci attenuate Staphylococcus aureus skin colonization and inflammation via AHR-dependent signaling.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1726557},
pmid = {41403940},
issn = {1664-3224},
mesh = {Humans ; *Receptors, Aryl Hydrocarbon/metabolism/immunology ; Signal Transduction ; *Staphylococcus aureus/immunology ; *Skin/microbiology/immunology/metabolism ; Keratinocytes/immunology/microbiology/metabolism ; Dermatitis, Atopic/immunology/microbiology ; Inflammation/immunology ; *Staphylococcal Skin Infections/immunology/microbiology/metabolism ; Culture Media, Conditioned/pharmacology ; *Staphylococcus/immunology ; Staphylococcus epidermidis ; Microbiota ; *Basic Helix-Loop-Helix Transcription Factors/metabolism ; },
abstract = {INTRODUCTION: Staphylococcus aureus is the leading cause of bacterial skin infections in several inflammatory skin diseases, however, is rarely detected on healthy skin. Skin barrier defects, such as in atopic dermatitis, promote S. aureus colonization by yet unknown mechanism. In our previous work we found that in healthy skin commensal staphylococci including Staphylococcus epidermidis and Staphylococcus lugdunensis (SL) protect against S. aureus skin colonization, however, the microbiome-mediated protection is lost in inflammatory skin. Here, we investigated how microbiome-derived factors contribute to skin defense under homeostatic and inflammatory conditions.

METHODS: We examined how bacterial conditioned media (BCM) from S. epidermidis and S. lugdunensis influence immune responses in primary human keratinocytes, human skin explants, and 3D skin reconstructs. Immune signaling was assessed using LEGENDplex cytokine profiling, RT2 Profiler PCR arrays, and western blotting. To investigate how BCM pretreatment limits S. aureus colonization, we performed inhibitor studies with a focus on aryl hydrocarbon receptor (AHR) signaling. The effects of BCM under inflammatory conditions were analyzed in tape-stripped human skin explants and 3D skin models with an atopic dermatitis-like phenotype.

RESULTS: We show that released factors from SE and SL reduce S. aureus skin colonization by inducing antimicrobial peptides (AMPs) and suppressing inflammatory responses in the skin. Both, factors released by SE and SL, limit S. aureus-induced immune activation in the skin by dampening inflammatory signaling, reducing reactive oxygen species, and suppressing expression of danger-associated molecular patterns (DAMPs). We show that this anti-inflammatory effect is mediated by activation of aryl hydrocarbon receptor (AHR) signaling in keratinocytes. Mechanistically, SE and SL membrane vesicles are involved in activating AHR signaling in keratinocytes via direct vesicle-cell contact as well as by bacterial tryptophan metabolites. This protective effect is lost in inflamed skin, where it instead exacerbated inflammation due to impaired AHR activity in inflamed skin. Interestingly, co-treatment of human AD-like skin equivalents with released SE factors together with an AHR ligand effectively reduces S. aureus colonization pointing out a potential novel AHR- and microbiome-based therapeutic strategy in AD.

DISCUSSION: Together, these findings highlight a context-dependent role of microbiome-derived factors in shaping cutaneous immunity and underscore the therapeutic potential of restoring AHR signaling to enhance the skin's defense against S. aureus, particularly in inflammatory disorders such as AD.},
}

Humans
*Receptors, Aryl Hydrocarbon/metabolism/immunology
Signal Transduction
*Staphylococcus aureus/immunology
*Skin/microbiology/immunology/metabolism
Keratinocytes/immunology/microbiology/metabolism
Dermatitis, Atopic/immunology/microbiology
Inflammation/immunology
*Staphylococcal Skin Infections/immunology/microbiology/metabolism
Culture Media, Conditioned/pharmacology
*Staphylococcus/immunology
Staphylococcus epidermidis
Microbiota
*Basic Helix-Loop-Helix Transcription Factors/metabolism

@article {pmid41403899,
year = {2025},
author = {Shi, W and Wu, L and Qin, Q and Li, Y and Chen, W},
title = {Research progress on the role of microbiome-immune-neurotransmitter network in post-stroke sleep disorders.},
journal = {Frontiers in aging neuroscience},
volume = {17},
number = {},
pages = {1694709},
pmid = {41403899},
issn = {1663-4365},
abstract = {Post-stroke sleep disorders, as a significant complication affecting patient rehabilitation, are closely associated with dysregulation of the microbiome-immune-neurotransmitter network. Following stroke, activation of the hypothalamic-pituitary-adrenal axis and sympathetic nervous system triggers intestinal barrier disruption (reduced tight junction proteins and intestinal permeability) along with microbial imbalance (decreased Bifidobacterium and increased Enterobacteriaceae). Reduced short-chain fatty acids and lipopolysaccharide (LPS) translocation exacerbate systemic inflammatory responses and neurotransmitter imbalances (inhibited serotonin synthesis and excitotoxic glutamate production). These changes further disrupt circadian regulation by the hypothalamic suprachiasmatic nucleus, leading to reduced REM sleep and disrupted slow-wave sleep architecture. Future research should prioritize interventional strategies targeting the gut microbiota, such as probiotics, prebiotics, and fecal microbiota transplantation, integrated with multi-omics technologies and neural circuit modulation approaches, to elucidate the spatiotemporal dynamics of the microbiome-immune-neurotransmitter network and provide a theoretical basis for clinical translation. Restoring brain-gut axis homeostasis is expected to improve post-stroke sleep disorders and neurological functional outcomes in patients.},
}

@article {pmid41403886,
year = {2025},
author = {Tarracchini, C and Bottacini, F and Mancabelli, L and Lugli, GA and Turroni, F and van Sinderen, D and Ventura, M and Milani, C},
title = {Approaches to dissect the vitamin biosynthetic network of the gut microbiota.},
journal = {Microbiome research reports},
volume = {4},
number = {4},
pages = {37},
pmid = {41403886},
issn = {2771-5965},
abstract = {B-group vitamins and vitamin K are essential micronutrients required for numerous cellular processes in both microbial and human physiology. While traditionally considered to originate predominantly from dietary sources, the biosynthetic capacity of the human gut microbiota has recently been recognized as a valuable, though historically underappreciated, endogenous source of these vitamins. In particular, the microbial contribution to the host vitamin pool is increasingly acknowledged as a functionally relevant aspect of vitamin homeostasis, especially in the colon, where microbiota-derived vitamins may be absorbed via specific transport mechanisms. This review provides a comprehensive overview of our current understanding of the biosynthesis of B-group vitamins and vitamin K by human gut-associated bacteria, with particular emphasis on key methodologies employed to assess if, how and to what extent members of the gut microbiota supply their host with such micronutrients. Through an integrated overview of available evidence, we highlight both the progress made and the outstanding challenges in elucidating the microbial contribution to the host vitamin metabolism.},
}

@article {pmid41403881,
year = {2025},
author = {Sun, Y and Huang, Y and Li, R and Zhang, J and Fan, X and Su, X},
title = {Benchmarking and optimizing microbiome-based bioinformatics workflow for non-invasive detection of intestinal tumors.},
journal = {Microbiome research reports},
volume = {4},
number = {4},
pages = {43},
pmid = {41403881},
issn = {2771-5965},
abstract = {Background: The human gut microbiome is closely linked to disease states, offering substantial potential for novel disease detection tools based on machine learning (ML). However, variations in feature types, data preprocessing strategies, feature selection strategies, and classification algorithms can all influence the model's predictive performance and robustness. Methods: To develop an optimized and systematically evaluated workflow, we conducted a comprehensive evaluation of ML methods for classifying colorectal cancer and adenoma using 4,217 fecal samples from diverse global regions. The area under the receiver operating characteristic curve was used to quantify model performance. We benchmarked 6,468 unique analytical pipelines, defined by distinct tools, parameters, and algorithms, utilizing a dual validation strategy that included both cross-validation and leave-one-dataset-out validation. Results: Our findings revealed that shotgun metagenomic (WGS) data generally outperformed 16S ribosomal RNA gene (16S) sequencing data, with features at the species-level genome bin, species, and genus levels demonstrating the greatest discriminatory power. For 16S data, Amplicon Sequence Variant-based features yielded the best disease classification performance. Furthermore, the application of specific feature selection tools, such as the Wilcoxon rank-sum test method, combined with appropriate data normalization, also optimized model performance. Finally, in the algorithm selection phase, we identified ensemble learning models (eXtreme Gradient Boosting and Random Forest) as the best-performing classifiers. Conclusion: Based on the comprehensive evaluation results, we developed an optimized Microbiome-based Detection Framework (MiDx) and validated its robust generalizability on an independent dataset, offering a systematic and practical framework for future 16S and WGS-based intestinal disease detection.},
}

@article {pmid41403880,
year = {2025},
author = {Gargari, G and Meroño, T and Peron, G and Del Bo', C and Marino, M and Cherubini, A and Andres-Lacueva, C and Kroon, PA and Riso, P and Guglielmetti, S},
title = {Effect of a polyphenol-rich dietary pattern on subjects aged ≥ 60 years with higher levels of inflammatory markers: insights into microbiome and metabolome.},
journal = {Microbiome research reports},
volume = {4},
number = {4},
pages = {38},
pmid = {41403880},
issn = {2771-5965},
abstract = {Background: Aging may be associated with low-grade chronic inflammation ("inflammaging") and gut microbiome alterations. Dietary polyphenols have been proposed as modulators of these processes. This study aimed to explore the effects of a polyphenol-rich diet (PR-diet) on inflammatory markers, gut microbiota, and metabolomic profiles in subjects aged ≥ 60 years stratified by baseline inflammation levels. Methods: In this post-hoc analysis of the MaPLE (Microbiome mAnipulation through Polyphenols for managing Leakiness in the Elderly) randomized crossover trial, 50 subjects aged ≥ 60 years were categorized into two subgroups: high inflammation (cH) and low inflammation (cL). Participants received a PR-diet or a control diet for 8 weeks, with a washout period in between. Fecal, blood, and urine samples were analyzed using shallow shotgun metagenomics and untargeted metabolomics. Results: The PR-diet was associated with a significant reduction in key inflammatory markers [e.g., interleukin-6 (IL-6), C-reactive protein] in the cH group. Distinct microbial shifts were observed, including an increase in Blautia and Dorea and a modest improvement in microbial diversity in cH subjects. Metabolomic analysis revealed group-specific changes, notably in polyphenol-derived metabolites. Conclusion: These findings suggest that PR-diets may beneficially modulate inflammation and the gut microbial ecosystem in subjects aged ≥ 60 years with elevated baseline inflammation. Stratification by inflammatory status may improve the targeting and personalization of dietary interventions to support healthy aging.},
}

@article {pmid41403706,
year = {2025},
author = {Ghisleni, G and Armanni, A and Fumagalli, S and Rosatelli, A and Bacchi, YM and Barillari, C and Battista, DA and Benocci, M and Brunelli, A and Cammarano, F and Bovolini, G and Capuano, F and Bulla, N and Colombo, A and Colombo, L and Corneo, L and Evangelista, D and Giorgetti, P and Marin, G and Meziu, A and Riva, M and Rizzo, D and Romano, S and Ronchi, S and Rossi, R and Volpi, R and Zanotti, M and Zenaro, M and Franzetti, A and Casiraghi, M and Bruno, A},
title = {The Bicocca sampling days model: a participatory citizen science approach to environmental microbiome research and education.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf220},
pmid = {41403706},
issn = {2730-6151},
abstract = {Environmental microbiota are essential yet often overlooked, with urbanization driving microbial diversity loss and diseases of civilization. Public misconceptions, exacerbated by COVID-19, have widened the gap between microbiologists and society, highlighting the need for science-society integration. The Bicocca Sampling Days (BSDs) model offers a reproducible "citizen science" framework integrating research, education, and public engagement through large-scale microbiome sampling. Tested while assessing environmental microbiomes in different urbanized outdoors, 76 undergraduates participated in four sampling events, collecting 2429 samples in 8 h of effective sampling, achieving over than 303 samples/hour in 29 288.74 m[2]. Manual metadata curation revealed only 0.58% critical errors and no data loss, emphasizing the effectiveness of structured submission forms in ensuring data quality. Educational outcomes, assessed through a validated survey, significant gains in participants' perceived skills, understanding, and knowledge of microbiome sampling compared to non-participants. The BSDs model, including a step-by-step guide, illustrated protocol, and templates, is freely available for replication. Our findings demonstrate that citizen science can rival or complement traditional microbiome research in efficiency, scale, and data quality while broadening accessibility. BSDs offers a scalable tool to advance educational and societal, empower participation, and support informed decision-making.},
}

@article {pmid41403704,
year = {2025},
author = {Yu, QY and Liu, X and Yao, H and Lü, PP and Yang, GJ and Lü, XT and Han, XG and Guo, LD and Huang, Y},
title = {The adaptability of grassland soil microbiomes to resource and stress shifts is mainly accomplished by niche conservatism under nitrogen deposition.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf215},
pmid = {41403704},
issn = {2730-6151},
abstract = {Atmospheric nitrogen (N) deposition usually alters the ratio of resources to stress in terrestrial ecosystems and has important impacts on soil microbiomes. To elucidate the adaptability of soil microbiomes under N deposition scenarios, we conducted a 6-year N addition experiment in a temperate grassland in Inner Mongolia, applying different levels of ammonium nitrate (AN) and urea (AU) to form different resource-to-stress ratio. Our results reveal that the inborn high yield (Y)-resource acquisition (A)-stress tolerance (S) life history strategies of soil microbiomes collectively drive their adaptability to resources and stress under N deposition. Enriched taxa under AN treatment mainly belonged to Actinomycetota and Chloroflexota with Y and S strategies, while those under AU mainly belonged to Pseudomonadota with A and S strategies. Functional preference analysis indicated that bacterial phyla maintained consistent Y-A-S life history strategies across AN and AU treatments. Moreover, strong purifying selection restricted the pace of adaptive evolution, and horizontal gene transfer expanded the functional repertoire in a complementary rather than essential manner. Thus, the adaptation of microbiomes to shifting resources and stress under N deposition scenarios is mainly accomplished by niche conservatism ("move") rather than niche evolution ("evolve"). Our results support the point that it may be easier for microbial species to move into a befitting niche than to evolve to acclimate a new environment.},
}

@article {pmid41403646,
year = {2025},
author = {Pagano, F and Bemis, DH and Rehman, R and Shapiro, JM and Belenky, P},
title = {Differential impacts of hemin and free iron on amoxicillin susceptibility in ex vivo gut microbial communities.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1629464},
pmid = {41403646},
issn = {1664-302X},
abstract = {INTRODUCTION: The rise of antibiotic-resistant infections worldwide has created a need to enhance the efficacy of existing antibiotics. Modification of metabolism has been shown to potentiate antibiotic lethality. In this study, we employed a novel ex vivo microbiome culture approach to study the effects of different forms of iron on amoxicillin susceptibility.

METHODS: Synthetic and human stool-derived microbiota were cultured and treated with amoxicillin, with growth monitored by optical density. These samples were sequenced using an Oxford nanopore long-read 16S rRNA V4-V9 approach and computationally defined using the Emu algorithm. The validity of this pipeline was confirmed with consortia, murine cecal content, and a human stool sample. The stool-derived community was then cultured for 24 h with ranging concentrations of either hemin, FeSO4, or FeCl3 and concurrent amoxicillin dosage, then profiled to identify the effects of different forms of iron on amoxicillin susceptibility.

RESULTS: Alpha diversity, beta diversity, and normalized relative abundances confirmed the efficacy of the selected ex vivo pipeline, allowing for ~77% species retention over 24 h. Treatment of communities with hemin protected Bacteroides, Escherichia-Shigella, Parabacteroides, and Parasutterella against amoxicillin, while two forms of free iron did not.

DISCUSSION: This ex vivo pipeline enables reproducible assessment of how metabolic modulators like hemin alter amoxicillin susceptibility, highlighting a link between iron-sequestering genera and antibiotic-protection. Future mechanistic insights may support hemin-based strategies to boost antibiotic efficacy.},
}

@article {pmid41403645,
year = {2025},
author = {Lei, H and Li, Z and Deng, J and Lei, H and Li, H and Ding, Z},
title = {Electroacupuncture pretreatment ameliorates anesthesia and surgery-induced cognitive dysfunction in aged rats: insights from gut microbiota modulation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1642337},
pmid = {41403645},
issn = {1664-302X},
abstract = {OBJECTIVE: This study aimed to investigate the effects of electroacupuncture (EA) on postoperative cognitive dysfunction (POCD) and gut microbiota in aged rats anesthetized with propofol.

METHODS: Forty 18-months-old male SD rats were randomly divided into four groups: Sham, Model (MD), Sham Electroacupuncture (JE), and Electroacupuncture (EA), with 10 rats in each group. The Sham group underwent a skin incision without surgery, while the MD, JE, and EA groups received propofol anesthesia followed by right tibial surgery. The EA group received electroacupuncture at Baihui, Shenmen, and bilateral Zusanli points for 5 days prior to surgery, while the JE group received acupuncture without electrical stimulation. Behavioral tests, including the Morris water maze and open field tests, were conducted at 1-, 2-, and 3-weeks post-surgery to assess cognitive function. Gut microbiota composition was analyzed using second-generation sequencing.

RESULTS: At 1-week post-surgery, the MD, JE, and EA groups showed longer latencies and fewer crossings in the behavioral tests. However, at 3- and 4-weeks post-surgery, the EA group exhibited significantly reduced latency and increased crossing times compared to the MD and JE groups. Gut microbiome analysis revealed that the EA group had a higher relative abundance of Bacteroidetes and Proteobacteria, and a reduced relative abundance of Unclassified Lactobacillaceae compared to the MD and JE groups.

CONCLUSION: Electroacupuncture was associated with improved postoperative cognitive function in aged rats after propofol anesthesia and tibial surgery. These effects were accompanied by alterations in gut microbiota composition, suggesting a possible link with the gut-brain axis, although causality remains to be established.},
}

@article {pmid41403643,
year = {2025},
author = {Wang, B and Zhang, Y and Li, J and Wu, M and Shi, Y and Sun, X and Xiao, X and Zhang, P and Shi, Y and Li, Y and Tian, H},
title = {Revealing dietary habits and intestinal microbiome composition of the Beijing swift (Apus apus pekinensis) through regurgitated pellets and fecal samples.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1693396},
pmid = {41403643},
issn = {1664-302X},
abstract = {INTRODUCTION: The Beijing swift, an important insectivorous bird, is a key protected wild animal in Beijing. Current research on this species primarily focuses on distribution surveys and population dynamics, while systematic studies on its diet and intestinal microbiome composition remain lacking, a knowledge gap that constrains in-depth understanding of its ecological adaptability.

METHODS: This study integrated DNA barcoding and high-throughput 16S rRNA gene sequencing to systematically analyze regurgitated pellets and fecal samples from ringed and rescued individuals, revealing the following findings.

RESULTS: The dietary composition primarily encompasses insects from five orders, Diptera, Coleoptera, Hemiptera, Hymenoptera and Lepidoptera, with significant differences observed between adults and nestlings. Dominant intestinal bacterial phyla included Proteobacteria, Firmicutes, Bacteroidota, and Actinobacteriota. Correlation network analysis indicated that Stenotrophomonas, Aminobacter, etc., exhibit extensive mutually promotive interactions with other bacteria, suggesting their potential roles as core functional bacterial communities in the intestine.

DISCUSSION: This research provides the first evidence of dietary differentiation patterns and intestinal microbial composition characteristics of Beijing swifts, providing key foundational data for assessing its survival and adaptation mechanisms. It is highly significant for developing scientific rescue strategies and conservation initiatives.},
}

@article {pmid41403581,
year = {2025},
author = {Alikamali, M and Mohammad-Alizadeh-Charandabi, S and Ahmadi, S and Memar, MY and Shahnazi, M},
title = {The Role of the Vaginal Microbiome in Preterm Premature Rupture of Membranes: A Comprehensive Review of Mechanisms and Clinical Implications.},
journal = {Health science reports},
volume = {8},
number = {12},
pages = {e71484},
pmid = {41403581},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: Preterm premature rupture of membranes (PPROM), a complication in approximately 4.5% of pregnancies, is a leading cause of preterm birth and significant perinatal morbidity. A substantial body of evidence implicates vaginal dysbiosis a departure from a healthy, Lactobacillus-dominant microbiome in the pathogenesis of PPROM. This review synthesizes the current understanding of the mechanistic links between the vaginal microbiome and PPROM and discusses the clinical implications for future therapeutic strategies.

METHODS: A comprehensive literature search was conducted in the PubMed, Scopus, and Google Scholar databases. The selection focused on peer-reviewed articles including systematic reviews, meta-analyses, clinical trials, and influential observational studies (e.g., cohort and case-control), as well as key preclinical studies investigating the vaginal microbiome, PPROM pathogenesis, and relevant therapies.

RESULTS: The synthesized evidence supports a multi-step mechanistic framework wherein ascending pathobionts, characteristic of dysbiosis, trigger a host inflammatory cascade via Toll-like receptors. This inflammatory milieu orchestrates a synergistic attack on fetal membrane integrity through three primary pathways: (1) enzymatic degradation of the extracellular matrix by matrix metalloproteinases (MMPs), (2) programmed cell death (apoptosis) of membrane cells, and (3) damage from oxidative stress. Although conventional therapies such as antibiotics have limitations, emerging strategies, including probiotics, immunomodulators, and antioxidants, are being developed to target these specific mechanistic pathways.

CONCLUSION: This review positions the vaginal microbiome as a central player in the pathophysiology of PPROM, rather than merely a risk factor. This mechanistic understanding shifts the therapeutic focus from broad-spectrum antibiotics toward targeted therapies designed to prevent dysbiosis or neutralize specific downstream inflammatory and degradative pathways. Translating this knowledge into effective clinical practice through rigorous randomized controlled trials remains a critical priority for improving perinatal outcomes.},
}

@article {pmid41403505,
year = {2025},
author = {Sanjrambam, B and Sharma, D and Bakshi, RK and Deka, MB and Agarwala, S and Kalita, A},
title = {Gut microbe's consortium in pregnant women influenced by diet of North-east India: A metagenomic study.},
journal = {Journal of family medicine and primary care},
volume = {14},
number = {11},
pages = {4705-4711},
pmid = {41403505},
issn = {2249-4863},
abstract = {INTRODUCTION: Recent research highlights that the gut microbiota of pregnant women undergoes significant changes throughout pregnancy, influenced by factors such as diet, environment, and sociocultural practices. A diverse gut microbiome during pregnancy is linked to improved metabolic health and the lower risk of complications like gestational diabetes and pre-eclampsia.

OBJECTIVE: This study aimed to investigate the relationship between dietary practices of different communities of Assam and Manipur with the composition of gut microbes during pregnancy.

METHODS: A total of 18 pregnant women completed a survey assessing macronutrient consumption during the first and third trimesters. Dietary data, obtained through questionnaires, were subjected to PCoA (Principal Co-ordinate Analysis) to find similarities and dissimilarities in dietary patterns. Metagenomics analysis of stool samples was done to study the consortium of gut bacteria for the participants.

RESULTS: This study has demonstrated that higher intake of carbohydrates and fats during pregnancy results in a decrease in phylum such as Firmicutes and Actinobacteria. Phylum such as Gemmatimonadetes, Crenarchaeote, Fibrobacteres, and Fusobacteria dominated the gut of most participants.

CONCLUSION: The relationship between gut microbiota composition and dietary habits among pregnant women in Northeast India is essential for designing effective nutritional interventions aimed at improving both maternal and infant health. Future studies should prioritize longitudinal research to better understand these connections and their impact on public health in the region, with a particular focus on identifying the specific foods and dietary patterns responsible for the observed similarities.},
}

@article {pmid41403411,
year = {2025},
author = {García-Ortega, A and Del-Campo-Moreno, R and Sánchez, V and Hervás-Marín, D and Avendaño-Ortiz, J and Rivas-Guerrero, A and Muriel, A and Pedro-Tudela, A and Taberner-Lino, L and De-Juana, C and Barreiro, E and Lobo-Beristain, JL and Jiménez, D and Otero Candelera, R},
title = {Evaluation of microbial-derived metabolites in patients with acute pulmonary embolism: findings from the MICTEP study.},
journal = {ERJ open research},
volume = {11},
number = {6},
pages = {},
pmid = {41403411},
issn = {2312-0541},
abstract = {INTRODUCTION: Functional analysis of microbiome with microbial-derived metabolites (MDMs) has emerged as key for several inflammatory and cardiovascular diseases. However, the data on the relationship of pulmonary embolism (PE) to microbiome are scarce. This study aimed to compare MDM levels between acute PE patients and healthy controls, and to investigate their associations with predisposing factors (i.e. unprovoked, provoked and cancer-associated thrombosis).

METHODS: We collected serum samples from a multicentric cohort, including 96 patients with acute PE at hospital admission and 30 healthy controls. Serum concentrations of MDMs and inflammation/coagulation-related markers were quantified by liquid chromatography-mass spectrometry and flow cytometry, respectively.

RESULTS: Compared with healthy controls, patients with acute PE showed significantly higher serum levels of trimethylamine N-oxide (TMAO) (11.5 μM versus 6.7 μM; p=0.02) and acetate (48.3 μM versus 33.0 μM; p=0.04); and lower levels of propionate (3.8 μM versus 5.3 μM; p=0.007), butyrate (4.03 µM versus 7.68 µM; p=0.009), isobutyrate (5.0 μM versus 7.32 μM; p=0.002) and valerate (0.4 μM versus 0.63 μM; p<0.001). Valerate showed the best discrimination between PE and controls (area under the receiver operating characteristic curve 0.758, 95% CI 0.66-0.86). In the multinomial analysis, higher values of TMAO and acetate were associated with a higher probability of unprovoked PE. MDM levels exhibited different correlation with inflammation-related markers highlighting TGF-β1, CCL2 and CXCL10.

CONCLUSION: These findings reveal imbalances in the serological concentrations of MDMs in patients with acute PE and highlight the potential role of the microbiome and its functional metabolites as novel predisposing risk factors for PE.},
}

@article {pmid41403286,
year = {2025},
author = {Yoshinami, Y and Yamaguchi, S and Shoji, H and Okita, N and Takamaru, H and Hirose, T and Hirano, H and Takashima, A and Imazeki, H and Yamamoto, S and Koyama, S and Ishikawa, D and Terauchi, J and Tanaka, K and Ogawa, K and Watanabe, H and Kato, K},
title = {Feasibility of antibiotic-assisted fecal microbiota transplantation with immunotherapy for esophageal and gastric cancer.},
journal = {Future oncology (London, England)},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/14796694.2025.2599371},
pmid = {41403286},
issn = {1744-8301},
abstract = {AIMS: Immune checkpoint inhibitors (ICIs) have improved outcomes in several malignancies, but survival remains poor for patients with unresectable advanced or recurrent esophageal or gastric cancer. Recent evidence suggests that modulation of the intestinal microbiota may influence the therapeutic response to ICIs. This study aims to evaluate the safety and preliminary efficacy of fecal microbiota transplantation following antibiotic pretreatment (A-FMT) in patients scheduled to receive ICI-containing regimens.

METHODS: This phase I - II, single-institution clinical trial enrolls patients with unresectable advanced or recurrent esophageal or gastric cancer. Participants receive a 1-week course of oral antibiotics (amoxicillin, fosfomycin, and metronidazole) prior to transplantation. A single dose of donor-derived intestinal microbiota solution is administered via colonoscopy, followed by initiation of ICI-based therapy on the next day. The primary endpoint is the incidence of dose-limiting toxicity. Secondary endpoints include response rate, disease control rate, progression-free survival, overall survival, and adverse events. Comprehensive translational research is conducted using stool, blood, and tissue samples to characterize immune responses and identify biomarkers associated with A-FMT and ICI efficacy.Trial registration: jRCTs031240170.The study is ongoing, and patients are currently being enrolled. Enrollment started in June 2024. A total of 7 patients have been enrolled as of August 2025. This protocol is version 3.2.},
}

@article {pmid41403078,
year = {2025},
author = {Moosburner, A and Bilc, M and Anheyer, D and Schleinzer, A and Rahmdel, S and Vitinius, F and Cramer, H},
title = {The effect of MEditerranean DIet and MINdfulness eating on Depression severity in people with major depressive disorder and obesity (MEDIMIND) - a study protocol of a randomized controlled clinical trial with multifactorial design.},
journal = {The British journal of nutrition},
volume = {},
number = {},
pages = {1-25},
doi = {10.1017/S0007114525105849},
pmid = {41403078},
issn = {1475-2662},
abstract = {Obesity and depression are highly prevalent diseases that are strongly correlated. At the same time, there is a growing gap in care, and treatment options should be improved and extended. Positive effects of a mediterranean diet on mental health have already been shown in various studies. Additionally to physiological effects of nutrients, the way how food is eaten, such as mindful eating, seems to play a role. The present study investigates the effect of a mediterranean diet and mindful eating on depression severity in people with clinically diagnosed major depressive disorder and obesity. Participants will be randomized to one of the four intervention groups (mediterranean diet, mindful eating, their combination and a befriending control group). The factorial design allows investigating individual effects as well as potential synergistic effects of the interventions. The study consists of a 12-week intervention period, where five individual appointments will take place, followed by a 12-week follow up. The primary outcome is depression severity. Secondary outcomes are remission of depression, assessor-rated depression severity, quality of life, self-efficacy, BMI, waist-to-hip ratio and body composition, also adherence to mediterranean diet and mindful eating will be assessed. Alongside, mediator and moderator analysis, a microbiome analysis, a qualitative evaluation and an economic analysis will be conducted. The study investigates an important health issue in a vulnerable target group. It allows to draw valuable conclusions regarding effectiveness of different interventions, and therefore contributes to improving available care options for people suffering from depression and obesity.},
}

@article {pmid41402934,
year = {2025},
author = {Liu, B and Li, X and Yang, J and Lu, W and Tang, G and Shi, Y and Li, J and Ding, A and Wang, H and Song, X and Liu, Q and Jiang, X},
title = {Synthetic microbial community in pristine environment promotes the growth of the endangered plant Lilium tsingtauense.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02281-w},
pmid = {41402934},
issn = {2049-2618},
support = {2025CXPT149//Key R&D Program of Shandong Province，China/ ; },
abstract = {BACKGROUND: Habitat fragmentation and degradation have led to the critical endangerment of numerous wild plant species. Although significant achievements in the conservation of endangered wild plants in various regions worldwide, the interaction mechanisms between these plants and their associated rhizosphere microorganisms have yet to be fully elucidated.

RESULTS: Here, we present a communication model between the endangered wild plant Qingdao lily (Lilium tsingtauense) and its associated rhizosphere microorganisms. We isolated a rhizosphere fungus, Trichoderma longibrachiatum QDAU 0920, which effectively colonizes the roots of Qingdao lily and significantly promotes root growth. This growth enhancement is mediated by multiple plant hormones, with auxin playing a particularly prominent role. Further investigation revealed that a non-canonical AUX/IAA protein of the LtIAA16 may augment the transcriptional activation activity of LtARF22 by competitively interacting with LtIAA6, LtIAA17, and LtIAA11, thereby facilitating root growth in Qingdao lily. The growth-promoting effects of this interaction were subsequently validated in several other plant species, including tomato, pepper, corn, pumpkin, and cucumber. Notably, T. longibrachiatum QDAU 0920 forms synthetic microbial consortia (SynComs) in conjunction with other Trichoderma and Penicillium species. These SynComs consistently enhance the growth of Qingdao lily as well as other lily species such as L. lancifolium, Lilium 'Avalon Sunset', and Lilium 'Deliana'.

CONCLUSION: Collectively, these findings underscore the considerable potential of native microorganisms in the development of plant growth-promoting agents and the conservation of endangered plant species. Video Abstract.},
}

@article {pmid41402920,
year = {2025},
author = {Jinato, T and Khamjerm, J and Manprasong, S and Iadsee, N and Tangkijvanich, P and Nookaew, I and Chuaypen, N},
title = {Gut microbiota and host transcriptome interactions reveal diagnostic biomarkers in MASLD-associated hepatocellular carcinoma.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-025-00782-5},
pmid = {41402920},
issn = {1757-4749},
support = {P20GM125503/NH/NIH HHS/United States ; PMU-B-B36G660004//the NSRF via the Program Management Unit for Human Resources & Institutional Development, Research and Innovation/ ; HEAF67300060//Thailand Science research and Innovation Fund Chulalongkorn University/ ; FF67//Fundamental Fund 2024/ ; RA65/039//Ratchadapiseksompotch Fund, Faculty of Medicine Chulalongkorn University/ ; },
abstract = {BACKGROUND: Alterations in the gut microbiome via the gut-liver axis are closely linked to metabolic dysfunction-associated steatotic liver disease (MASLD) and may contribute to hepatocellular carcinoma (HCC) development. However, the interplay between the gut microbiome and host gene expression in MASLD and HCC remains poorly understood.

METHODS: We analyzed the gut microbiome from fecal samples and host transcriptomic profiles from peripheral blood mononuclear cells (PBMCs) in healthy controls and MASLD patients without HCC (mild fibrosis F01 and significant fibrosis F234) and with HCC.

RESULTS: Integrated analysis identified 260 differentially expressed genes (DEGs) and 29 bacterial taxa differentiating MASLD without HCC from MASLD-HCC. Subgroup analysis revealed seven bacterial genera associated with 84 host genes. Notably, Veillonella correlated with regulating synaptic membrane exocytosis 3 (RIMS3), collagen type X alpha 1 (COL10A1), and enabled homolog (ENAH). Real-time PCR validation confirmed COL10A1 as a significant diagnostic biomarker for distinguishing MASLD from MASLD-HCC (AUC = 0.835). Combining COL10A1, and AFP, or Veillonella with AFP, significantly improved differentiation between MASLD and MASLD-HCC, particularly in early-stage fibrosis (F01) (AUC = 0.941 and 0.996, respectively).

CONCLUSIONS: Gut microbiome-host gene interactions appear to play a significant role in MASLD-related HCC progression. Specific bacterial genera and host gene expression profiles may serve as early diagnostic markers for MASLD-HCC.},
}

@article {pmid41402861,
year = {2025},
author = {Chen, Q and Wang, L and Wei, Y and Xu, X and Wei, Z and Peng, Y and Pang, J and Peng, B and Shi, Q and Qudsi, AI and Liang, Q},
title = {Sodium butyrate modulates ocular surface microbiome and attenuates inflammation of meibomian gland dysfunction in ApoE[-/-] mice.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02294-5},
pmid = {41402861},
issn = {2049-2618},
support = {81970765//National Natural Science Foundation of China/ ; 2021YFC2301000//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: The ocular surface microbiome (OSM) in patients with meibomian gland dysfunction (MGD) differs from that of healthy individuals. However, the precise role of OSM in MGD remains unknown. Therefore, we aimed to investigate the mechanism of OSM in the inflammation of MGD and the effects of topical sodium butyrate (SB) treatment in ApoE[-/-] mice.

METHODS: ApoE[-/-] (n = 36) and wild-type C57BL/6J (n = 16) mice served as MGD models and healthy controls, respectively. MGD mice were treated with safety-confirmed concentrations of SB (1, 5, and 10 mM) and PBS for 3 weeks. OSM was analyzed by 16S rRNA gene sequencing (V3-V4). The slit-lamp biomicroscopy, tear cytokines, histopathology (oil red O/PAS/TUNEL staining), and TLR4/MyD88/NF-κB signaling (RT-qPCR, immunohistochemistry, and Western blotting) were evaluated.

RESULTS: Five-month-old ApoE[-/-] mice exhibited typical clinical and histological features of MGD. These mice exhibited elevated tear levels of inflammatory cytokines and activation of the TLR4/NF-κB signaling pathway in the MGs and conjunctivae. Treatment with SB improved the corneal fluorescein staining score of MGD. The ApoE[-/-] mice demonstrated dysbiosis of OSM, characterized by an increase in Proteobacteria and a decrease in Bacteroidota. Additionally, the relative abundance of Muribacter and Muribacter muris increased in ApoE[-/-] mice, while that of Staphylococcus and Staphylococcus lentus decreased, and these alterations were restored by SB treatment. SB also reduced the expression of the TLR4/NF-κB p65 signaling pathway, inflammatory cytokines, and apoptosis in MGs and conjunctival tissues.

CONCLUSION: ApoE[-/-] mice exhibited characteristic features of MGD, accompanied by dysbiosis of OSM. Topical administration of SB modulated the OSM and reduced MGD-associated inflammation. Video Abstract.},
}

@article {pmid41402854,
year = {2025},
author = {Dong, W and Guo, X and Lu, H and Liu, Z and Xie, L and Liu, Y and Wan, Q and Chen, R and Liu, S},
title = {Therapeutic mechanisms of Zi Chong granules against hydroxyurea-induced diminished ovarian reserve based on integrated multi-omics analyses.},
journal = {Journal of ovarian research},
volume = {18},
number = {1},
pages = {295},
pmid = {41402854},
issn = {1757-2215},
support = {2018YFC1704305//Ministry of Science and Technology of the People's Republic of China/ ; },
mesh = {Female ; Animals ; *Hydroxyurea/adverse effects ; *Ovarian Reserve/drug effects ; Mice ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Ovary/drug effects ; Gastrointestinal Microbiome/drug effects ; Metabolomics ; Multiomics ; Animals, Outbred Strains ; },
abstract = {BACKGROUND: Hydroxyurea (HU) is an antitumor drug. However, HU exposure is associated with diminished ovarian reserve (DOR). Zi Chong granules, a Chinese Medicine, can protect against DOR, but little is known regarding its underlying mechanisms of DOR treatment, and thus the target of the present study.

METHODS: Seventy-two female Kunming (KM) mice (4-6 weeks old) were randomly divided into three groups: the control group (Con), the hydroxyurea group (HU), and the Zi Chong group (ZC). The Con group received saline, while the HU and ZC groups were administered hydroxyurea (400 mg/kg/d) by gavage for 21 days to induce diminished ovarian reserve (DOR). Subsequently, the Con and HU groups were given saline, while the ZC group was treated with Zi Chong granules (2.72 g/kg/d) for 15 days. Ovaries and uterus of mice were examined histologically by H&E. The levels of anti-Mullerian hormone (AMH), estradiol (E2), and progesterone (P) were quantified using ELISA kits. The number and quality of oocytes were assessed, and endometrial receptivity was evaluated by immunohistochemistry. 16 S rDNA gene sequencing was used to analyze the composition and abundance of gut microbiome in feces, and non-targeted metabolomics was performed to detect serum metabolite profiles. Correlation analysis was performed to explore the relationships between different gut microbiota and differential metabolites.

RESULTS: ZC granules increased the number of primordial follicles in the ovaries, reduced excessive follicular atresia, restored low AMH, upregulated estrogen and progesterone secretion, and increased the number of mature oocytes after ovulation promotion. It also increased thickness of uterine endometrium and the number of glands, resulting in increased endometrial microvessel density (MVD), enhanced endometrial blood supply, reduced CD138 expression levels and endometrial inflammation. HU decreased the abundance of Lactobacillus spp. in mouse intestines and decreased arachidonic acid metabolism, tryptophan metabolism, spermidine and spermine biosynthesis, steroidogenesis, and nicotinate and nicotinamide metabolism. Correlation analysis revealed that HU exerted its side effects by altering the gut microbiome and bacteria-derived metabolites, while ZC granules could reverse DOR partly depends on regulating gut microbiota and metabolites.

CONCLUSIONS: ZC granules may be a potential therapy for alleviating HU-induced DOR.},
}

Female
Animals
*Hydroxyurea/adverse effects
*Ovarian Reserve/drug effects
Mice
*Drugs, Chinese Herbal/pharmacology/therapeutic use
Ovary/drug effects
Gastrointestinal Microbiome/drug effects
Metabolomics
Multiomics
Animals, Outbred Strains

@article {pmid41402846,
year = {2025},
author = {Huang, YX and Deng, ZC and Cao, KX and Yang, JC and Liu, M and Zhao, L and Zheng, JS and Sun, LH},
title = {Gut microbiome-derived indole-3-carboxaldehyde promotes intestinal development via AHR-NRF2 signaling in the early-life of chicks.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02289-2},
pmid = {41402846},
issn = {2049-2618},
abstract = {BACKGROUND: The development of the small intestine is crucial during early life, with the gut microbiota and microbe-derived metabolites playing key roles in regulating intestinal epithelial barrier function and overall development. However, the underlying mechanism remains unclear. Here, chicks were used to investigate the influences of early-life crosstalk among bacteria, metabolites, and the host on small intestinal development.

RESULTS: We investigated bacterial succession in the small intestine of broiler chicks at four time points during early development. After 3 days post-hatch, Bacillota became the dominant phylum. At the genus level, Lactobacillus and Ligilactobacillus emerged as the two dominant genera, and their abundance was significantly positively correlated with small intestine weight. Metabolome analysis revealed that indole-3-carboxaldehyde (IAld) is derived from both L. gallinarum C2-16-2 (LG) and L. salivarius D7-21 (LS). Moreover, we found that IAld can be converted into bioactive indole-3-carboxylic acid (ICA) in animals, which exhibited greater biological activity than IAld in vitro. Further chick feeding trials revealed that both bacteria (LG and LS) and metabolites (IAld and ICA) promoted epithelial barrier function and enhanced antioxidant capacity during early life in chicks. Moreover, both IAld and ICA promoted tight junction protein expression and enhanced antioxidant capacity by activating AHR-NRF2 signaling.

CONCLUSIONS: These findings suggest that specific bacterial strains (L. gallinarum C2-16-2 and L. salivarius D7-21) and metabolites (IAld and ICA) serve as effective promoters of intestinal epithelial barrier function and antioxidant capacity during early intestinal development in chicks Video Abstract.},
}

@article {pmid41402662,
year = {2025},
author = {Gupta, P and Debnath, B and Ashique, S and Ramzan, M and Yasmin, S and Shorog, E and Mantry, S and Tariq, M and Sridhar, SB and Panigrahy, UP and Sharma, H and Iqbal, A and Prabhakar, PK and Ansari, MY},
title = {The melatonin-microbiome axis: a new frontier in gut health for the immunomodulatory, antioxidant and anti-inflammatory properties.},
journal = {Inflammopharmacology},
volume = {},
number = {},
pages = {},
pmid = {41402662},
issn = {1568-5608},
support = {RGP. 2/8/46//Deanship of Scientific Research, King Khalid University/ ; },
abstract = {Melatonin, primarily produced by the pineal gland, is also synthesized in significant amounts within the gastrointestinal (GI) tract, where its presence surpasses that in the brain. While the pineal gland secretes melatonin to regulate circadian rhythms and promote sleep, gut-derived melatonin plays a crucial role in regulating motility, protecting the mucosa from oxidative stress, and modulating immune function. The interaction between melatonin and gut microbiota is gaining significant attention, as melatonin can influence specific gut microbes and functions, potentially altering the intestinal microbiota, which is essential for maintaining overall health. This review explores the bidirectional relationship between melatonin and gut microbiota, highlighting its influence on microbial composition, intestinal barrier function, microbial metabolism, and immune modulation. Additionally, melatonin indirectly affects the gut microbiota through circadian regulation, further reinforcing its critical role in gut homeostasis. The presence of melatonin receptors in the gut and its interaction with microbial biofilms underline its importance in maintaining a balanced gut environment. Given these multifaceted roles, melatonin emerges as a promising therapeutic candidate for managing gut-related disorders such as irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), and metabolic dysregulation. Despite its promising therapeutic potential, several aspects of melatonin-gut microbiome interactions remain unexplored, necessitating further research into its molecular mechanisms and clinical applications. This review provides an in-depth exploration of melatonin's role in gut microbiome regulation, its therapeutic implications, and future research directions.},
}

@article {pmid41402190,
year = {2025},
author = {Vickers, D and Martynchyk, A and Henden, A and Smibert, OC and Hawkes, EA and Chong, G},
title = {The gut microbiome in B cell lymphoma.},
journal = {Blood reviews},
volume = {},
number = {},
pages = {101357},
doi = {10.1016/j.blre.2025.101357},
pmid = {41402190},
issn = {1532-1681},
abstract = {The gut microbiome (GMB) describes the commensal bacteria which reside in the gastrointestinal tract. Mounting evidence suggests a major role of the GMB in several key aspects of lymphoma development and care. The GMB is implicated in lymphomagenesis, response to therapy and lymphoma-specific outcomes. Moreover, certain gut bacteria can also specifically influence the course of the disease and therapeutic response. In this review we provide an overview of sampling techniques and analytical methodologies for characterising the GMB, a brief outline pertaining to the "healthy" GMB and detailed description of existing literature regarding differences in GMB composition in lymphoma patients, prognostic indicators and the impact of different treatment modalities on the GMB in different lymphoma histologies. Additionally, we describe the relationship of the GMB and treatment of infections in lymphoma patients as well as early-stage research results in GMB manipulation to improve outcomes in patients with B cell lymphomas.},
}

@article {pmid41402129,
year = {2025},
author = {Wang, J and Li, J and Li, Y and Huang, W and Huang, C and Xu, Q and Sun, J and Gong, J and Ma, X and Wang, G and Meng, Y and Li, X},
title = {Angiotensin-(1-7) alleviates intestinal barrier dysfunction and dysbiosis in mice with polymicrobial sepsis.},
journal = {British journal of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bph.70248},
pmid = {41402129},
issn = {1476-5381},
support = {82170641//National Natural Science Foundation of China/ ; 82470663//National Natural Science Foundation of China/ ; 82270089//National Natural Science Foundation of China/ ; 81873583//National Natural Science Foundation of China/ ; 2021A1515012595//Guangdong Provincial Science and Technology Projects under Grant/ ; 2024A1515220136//Guangdong Provincial Science and Technology Projects under Grant/ ; 202312121006//National College Students' Innovation and Entrepreneurship Training Program/ ; S202012121056//Guangdong Provincial Innovation Training Projects under Grant/ ; 2017B020209003//Guangdong Science and Technology Project under Grant/ ; JCYJ20210324112807021//Technical Research and Development Project of Shenzhen/ ; },
abstract = {BACKGROUND AND PURPOSE: The intestine plays a key role in the initiation of sepsis. The gut barrier impedes the translocation of commensal bacteria to the liver in sepsis. Previous studies have reported that angiotensin-(1-7) [Ang-(1-7)] attenuated sepsis-induced organ injury and mortality. However, its role in sepsis-induced intestinal barrier dysfunction remains unclear. Here we have investigated therapeutic effects of Ang-(1-7) on the intestinal barrier dysfunction and dysbiosis in a murine model of sepsis.

EXPERIMENTAL APPROACH: We used a model of sepsis in C57BL/6 mice with caecal ligation and puncture (CLP), to assess mortality and histological and biochemical changes in the gut and liver tissues. Faecal microbiota transplantation (FMT) was used to assess the role of the gut microbiome. 16-s rDNA and metabolomics analyses were performed to characterize differences in the gut microbiome signatures and metabolic profiles.

KEY RESULTS: Plasma Ang-(1-7) was decreased in patients with sepsis. In CLP mice, exogenous Ang-(1-7) attenuated intestinal barrier dysfunction and liver damage. FMT experiments showed that the protective effects of Ang-(1-7) on the gut depended on the gut microbiota. Furthermore, 16-s ribosomal DNA analysis revealed that Ang-(1-7) treatment increased the abundance of Lactobacillus gasseri (L. gasseri) among commensal bacteria. Mechanistically, L. gasseri regulated the production of antimicrobial peptides in intestinal epithelia by activating NLRP6 inflammation.

CONCLUSION AND IMPLICATIONS: Ang-(1-7) protected against sepsis-induced intestine barrier dysfunction and liver injury in mice by modulating gut homeostasis and NLRP6 inflammasome. Ang-(1-7) is a promising candidate drug for protecting intestinal homeostasis in sepsis, offering new insights for clinical treatment.},
}

@article {pmid41401934,
year = {2025},
author = {Chen, W and Peters, DL and Lam, S and Kettal, M},
title = {Bacteriophages as vaccine platforms: Opportunities and challenges in translation.},
journal = {Human vaccines & immunotherapeutics},
volume = {21},
number = {1},
pages = {2599632},
doi = {10.1080/21645515.2025.2599632},
pmid = {41401934},
issn = {2164-554X},
mesh = {Humans ; *Vaccine Development/methods ; *Bacteriophages/immunology/genetics ; Phage Therapy/methods ; Animals ; *Bacterial Vaccines/immunology ; *Viral Vaccines/immunology ; },
abstract = {Bacteriophages (phages) have recently received increased interest as versatile candidates for vaccine development. Their inherent characteristics, such as ease of genetic manipulation, high-density antigen display, intrinsic immunostimulatory properties, demonstrated human safety, and scalability in bacterial hosts, make them attractive as next-generation vaccine platforms. Additionally, their cost-effective production, stability, and existing regulatory approval for food and compassionate phage therapy provide a strong foundation for further development of phage-based vaccines. This commentary summarizes the types of phages, the strategies used, and current advances in phage-based vaccine development for viral and bacterial targets, and discusses the promises and challenges of this platform for novel vaccine development. Phage-based vaccines represent an innovative and promising platform for vaccine development to address significant medical and public health challenges, particularly in antimicrobial resistance, pandemic preparedness, and One Health. Accumulative experimental data have demonstrated that phage-based vaccines induce specific cellular, humoral, and mucosal immune responses at magnitudes comparable to those induced by other vaccine platforms. However, a better understanding of phage biology (interactions with the human immune system and microbiome), more carefully designed preclinical studies, Good Manufacturing Practice production development, the regulatory framework, and ultimately clinical trials are needed before the full potential of this platform is realized.},
}

Humans
*Vaccine Development/methods
*Bacteriophages/immunology/genetics
Phage Therapy/methods
Animals
*Bacterial Vaccines/immunology
*Viral Vaccines/immunology

@article {pmid41401858,
year = {2025},
author = {Memon, FU and Xu, J and Xie, X and Shu, C and Li, Y and Li, K and Xiao, Y and Tian, L},
title = {Strain-specific gut microbiota modulation is linked to resistance to BmNPV infection in silkworms.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108518},
doi = {10.1016/j.jip.2025.108518},
pmid = {41401858},
issn = {1096-0805},
abstract = {Bombyx mori nucleopolyhedrovirus (BmNPV) is a major pathogen threatening sericulture, yet the role of gut microbiota in strain-specific resistance remains poorly understood. This study compared three silkworm strains with high (Xinjiu, XJ), intermediate (AN3, A3), and low (Zhenchixian, ZCX) resistance to BmNPV. Protein assays showed that the resistant XJ strain exhibited the lowest viral EGFP and VP39 expression, minimal weight loss, and highest survival, whereas the susceptible ZCX strain displayed the opposite trend. Shotgun metagenomics revealed strain-specific microbial responses to infection. XJ and A3 maintained significantly higher alpha diversity and more dynamic beta diversity clustering than ZCX, with infection inducing increased microbial gene abundance and emergence of unique taxa in XJ. Taxonomic profiling showed XJ enriched in Firmicutes and beneficial fungal taxa such as Mucoromycota, Ascomycota, Basidiomycota, and Zoopagomycota, alongside reductions in Actinobacteria and Proteobacteria following infection. At finer resolution, resistant strains were enriched in beneficial bacterial classes (Bacilli, Alphaproteobacteria, Opitutae) and fungal classes (Agaricomycetes, Saccharomycetes), with cooperative co-occurrence networks linking these taxa and antagonizing pathogens. In contrast, ZCX was dominated by Gammaproteobacteria, Actinomycetia, and Hydrogenophilalia, consistent with dysbiosis and susceptibility. Functional analysis demonstrated pronounced metabolic reprogramming in resistant strains, especially XJ, with coordinated activation of carbohydrate, amino acid, nucleotide, and lipid metabolism, forming tightly integrated functional networks. Together, these findings reveal that silkworm resistance to BmNPV is associated with microbiome diversity, restructuring toward beneficial taxa, and synergistic metabolic pathways, offering new insights for probiotic-based antiviral strategies.},
}

@article {pmid41401777,
year = {2025},
author = {Bertolini, F and Bovo, S and Bolner, M and Schiavo, G and Ribani, A and Zambonelli, P and Dall'Olio, S and Gallo, M and Fontanesi, L},
title = {Identification of biomarkers for feed efficiency and growth rate by exploring the plasma metabolome of divergent heavy pigs.},
journal = {Animal : an international journal of animal bioscience},
volume = {20},
number = {1},
pages = {101725},
doi = {10.1016/j.animal.2025.101725},
pmid = {41401777},
issn = {1751-732X},
abstract = {Feed represents the largest expense in pig farming and significantly affects the sustainability of the production system. Therefore, enhancing feed efficiency is a key strategy to mitigate these costs and environmental impacts. This is particularly relevant in the context of the heavy pig system in which animals are slaughtered at a heavier live weight than in many other production systems to follow the rules of Protected Designation of Origin (PDO) value chains. Since growth rate is correlated with feed efficiency, and under PDO rules, pigs cannot reach the slaughter weight earlier than a set age limit, the daily gain of the pigs needs to be controlled. In this study, we used untargeted metabolomics to identify plasma metabolites in Italian Large White heavy pigs that may differentiate between animals with divergent feed efficiency and growth rate, and that may constitute biomarkers for one or the other trait. From a starting cohort of 672 performance-tested pigs, two partially overlapping datasets of 200 pigs each, extreme and divergent for feed conversion ratio (FCR) and average daily gain (ADG), were selected. Approximately 700 metabolites were analysed in the plasma of these pigs. Metabolomic data were analysed with the Boruta machine learning algorithm. Discriminant metabolites were further evaluated through univariate and multivariate analyses. Boruta identified 10 and 7 metabolites that differentiate between FCR and ADG extreme pigs, respectively, with an additional metabolite shared by the two datasets. Most metabolites selected in the FCR dataset still show significant abilities to discriminate among high and low ADG pigs, even if they have not been selected in the Boruta analysis, showing medium to high values of Area Under the Curve, and highly significant Mann-Whitney test U P-values, while the opposite was not true. Among the metabolites detected, L-carnitine and O-adipoylcarnitine, both involved in fatty acid metabolism, were significantly higher in pigs with high FCR. Isoleucylhydroxyproline and prolylhydroxyproline, linked to collagen turnover, were higher in low FCR pigs, potentially reflecting more efficient protein metabolism. Other metabolites linked to gut microbiome activity significantly differentiate between high and low FCR and ADG pigs, suggesting a potential role of the microbiota in nutrient utilisation. The identified metabolomic profiles confirm that feed efficiency and growth rate are related yet distinct traits, whose independent consideration will enhance the accuracy of biomarker discovery and genetic selection in Italian heavy pigs.},
}