@article {pmid41428895,
year = {2026},
author = {Vijayan, N and Briseño, J and Simakov, O and Nyholm, SV},
title = {Maintaining microbiota across diverse symbiotic organs in Euprymna scolopes: Insights into shared immune responses.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {1},
pages = {e2512903122},
doi = {10.1073/pnas.2512903122},
pmid = {41428895},
issn = {1091-6490},
support = {IOS2247195//NSF (NSF)/ ; 9349 and 12342//Gordon and Betty Moore Foundation (GBMF)/ ; 945026//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; },
mesh = {Animals ; *Symbiosis/immunology ; *Decapodiformes/microbiology/immunology/genetics ; Female ; *Microbiota/immunology ; Aliivibrio fischeri/physiology ; Transcriptome ; Carrier Proteins ; },
abstract = {Many animals have multiple organs or tissues that are colonized by diverse microbiota. The female Hawaiian bobtail squid, Euprymna scolopes, has two organs with distinct symbiotic communities: the accessory nidamental gland (ANG) and the light organ (LO). The ANG hosts a bacterial consortium, whereas the LO has a binary relationship with Vibrio fischeri, housed in extracellular crypt spaces as part of the central core (CC). To understand how the host maintains distinct symbiotic communities, we used transcriptomics to identify immune-related genes that are uniquely and similarly expressed in the ANG and LO-CC compared to organs without a known microbiota. Genes such as peptidoglycan recognition proteins EsPGRP2 and EsPGRP3, cathepsin-Z, alkaline phosphatase, and acidic phospholipase exhibited significant upregulation in the symbiotic organs compared to other tissues like gills, skin, mantle, optic lobe, ovaries, and brain. Moreover, EsPGRP2 displayed distinct localization patterns within the ANG, inversely correlating with bacterial presence, whereas the protein was colocalized with V. fischeri in the LO-CC. Notably, 10 different galaxins (EsGal) were uniquely highly expressed in both the ANG and LO-CC, with EsGal1 messenger RNA predominantly localized to the LO-CC epithelium, while EsGal2 and EsGal3 were primarily found in the epithelia of ANG tubules. Furthermore, antimicrobial assays using partial peptides derived from EsGal1 and EsGal2 showed varying and distinct patterns of inhibitory activity for these peptides. In summary, our findings identify similar immune gene families expressed across functionally distinct symbiotic organs in E. scolopes, suggesting that common immunomodulatory factors may maintain distinct symbiotic niches in the host.},
}

Animals
*Symbiosis/immunology
*Decapodiformes/microbiology/immunology/genetics
Female
*Microbiota/immunology
Aliivibrio fischeri/physiology
Transcriptome
Carrier Proteins

@article {pmid41428865,
year = {2025},
author = {Rutkowski, N and Yang, B and Gray-Gaillard, E and Ruta, A and Mejías, JC and Patatanian, M and Cherry, C and Celik, N and Stivers, KB and Ramanujam, S and Price, NL and Housseau, F and Pardoll, DM and Sears, CL and Elisseeff, JH},
title = {Antibiotic-induced microbiota depletion impairs the proregenerative response to a biological scaffold.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {52},
pages = {e2510841122},
doi = {10.1073/pnas.2510841122},
pmid = {41428865},
issn = {1091-6490},
support = {DGE2139757//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; DGE1746891//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; K99AG081564/GF/NIH HHS/United States ; },
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology/adverse effects ; *Gastrointestinal Microbiome/drug effects/immunology ; Mice ; Dysbiosis/immunology/chemically induced ; *Tissue Scaffolds ; Mice, Inbred C57BL ; Male ; Macrophages/immunology ; Female ; Interleukin-4/metabolism ; CD4-Positive T-Lymphocytes/immunology ; },
abstract = {Therapeutic biological scaffolds promote tissue repair primarily through the induction of type 2 immunity. However, systemic immunological factors, including aging, sex, and previous infections, can modulate this response. The gut microbiota is a well-established modulator of immune function across organ systems, yet its influence on type 2-mediated repair remains underexplored. Here, we establish a bidirectional relationship between the gut microbiota and biological scaffold-mediated tissue repair. Utilizing a conventionalized germ-free mouse, we demonstrate that scaffold implantation induces compositional and functional changes in the gut microbiome, particularly affecting amino acid biosynthesis. Additionally, in a model of antibiotic-induced microbiota depletion, we show that dysbiosis disrupts key immune regulators of type 2 immunity, including reductions in eosinophils, proregenerative macrophages, and interleukin-4 (IL-4)-producing CD4[+] T cells. At 6 wk post-scaffold implantation, we observed a significant decrease in myocytes with centrally located nuclei alongside an upregulation in profibrotic gene expression with antibiotic treatment. These findings provide insights into the influence of the gut microbiota on type 2-mediated tissue repair.},
}

Animals
*Anti-Bacterial Agents/pharmacology/adverse effects
*Gastrointestinal Microbiome/drug effects/immunology
Mice
Dysbiosis/immunology/chemically induced
*Tissue Scaffolds
Mice, Inbred C57BL
Male
Macrophages/immunology
Female
Interleukin-4/metabolism
CD4-Positive T-Lymphocytes/immunology

@article {pmid41428827,
year = {2025},
author = {De Sotto, R and Aggarwal, N and Tham, EH and Chang, MW},
title = {Machine Learning in Microbiome Research and Engineering.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00273},
pmid = {41428827},
issn = {2161-5063},
abstract = {Microbiomes, complex communities of microorganisms and their genetic material, hold immense potential for addressing global challenges in diverse sectors, including healthcare, agriculture, and bioproduction. Engineering these intricate ecosystems, however, necessitates a comprehensive understanding of the complex web of microbial interactions. The emergence of machine learning (ML) has revolutionized microbiome research, offering powerful tools to analyze massive data sets, uncover hidden patterns, and predict microbial behavior. ML algorithms have demonstrated remarkable success in identifying and characterizing microbial communities, predicting interactions between organisms and optimizing the design of microbial communities for specific functions. This Perspective examines the transformative applications of ML in the context of microbiome engineering, encompassing both microbiome data analysis and the targeted manipulation of microbial communities. These techniques employ a variety of strategies, including the manipulation of quorum sensing molecules, antimicrobial peptides, growth conditions, the introduction of probiotics, and the utilization of bacteriophages. By integrating ML with experimental approaches, researchers are pushing the boundaries of microbiome engineering, paving the way for novel applications in diverse fields. However, it is important to acknowledge the challenges that ML algorithms face, such as the limited availability of high-quality, large-scale data sets, the inherent complexity of biological systems, and the need for improved integration of experimental and computational methods. This perspective further discusses the future perspectives of the field, highlighting expected developments in data generation, algorithm development, and interdisciplinary collaboration. These advancements hold the key to unlocking the full potential of microbial communities for addressing pressing global challenges.},
}

@article {pmid41428801,
year = {2025},
author = {Sauša, S and Zodāne, A and Kumar, S and Plūme, J and Baranova, J and Kozlova, T and , and Saušs, H and Kloviņš, J and Pīrāgs, V and Mitravinda, KS and Kistkins, S and Brīvība, M},
title = {Rapid and Selective Gut Microbiome Modulation by Polyherbal Formulation in Type 2 Diabetes.},
journal = {Endocrine connections},
volume = {},
number = {},
pages = {},
doi = {10.1530/EC-25-0463},
pmid = {41428801},
issn = {2049-3614},
abstract = {BACKGROUND: Metformin, the first-line treatment for type 2 diabetes, often induces gastrointestinal side effects, affecting treatment adherence. Recent research suggests that the gut microbiome mediates both the efficacy and tolerability of metformin. This study evaluates the effect of a polyherbal formulation, used as an add-on to metformin, on the gut microbiota in patients with type 2 diabetes and metformin intolerance.

METHODS: We report preliminary findings from the first 7-day intervention phase of an ongoing randomized, placebo-controlled, crossover trial (NCT06846138) in 27 adults with type 2 diabetes. Participants received either polyherbal formulations or a placebo alongside metformin for 7 days. Stool samples were collected pre- and post-intervention for shotgun metagenomic sequencing. Microbial diversity, composition, and pathway functions were analyzed using Kraken2, Bracken, and HUMAnN3. Continuous glucose monitoring was used to assess glycemic metrics.

RESULTS: No significant alpha-diversity changes were observed; however, beta-diversity differed significantly between arms (PERMANOVA R2 = 0.04, p = 0.04). In the polyherbal formulation group, 17 species changed post-treatment (FDR < 0.25), with significant increases in six Bifidobacterium spp. (e.g., B. adolescentis, B. ruminantium). In contrast, the placebo group showed no major microbial shifts. Polyherbal formulation also altered 10 microbial pathways (FDR < 0.25). Continuous glucose monitoring revealed no short-term changes in glycemic levels.

CONCLUSION: Short-term polyherbal formulation co-administration significantly modulates gut microbiota, promoting beneficial taxa like Bifidobacterium in metformin-treated type 2 diabetes patients. This supports the potential role of the polyherbal formulation in microbiome-targeted strategies to improve metformin tolerability and effectiveness.},
}

@article {pmid41428602,
year = {2025},
author = {Zhang, Y and Chen, W and Wang, B and Rehman, KU and van Huis, A and Henawy, AR and Cai, M and Zheng, L and Ren, Z and Huang, F and Zhang, J},
title = {Enhancing Salmonella Inhibition in Black Soldier Fly Larvae (Hermetia illucens L.) Conversion by Bioaugmentation With Gut Microbiota.},
journal = {Microbial biotechnology},
volume = {18},
number = {12},
pages = {e70242},
doi = {10.1111/1751-7915.70242},
pmid = {41428602},
issn = {1751-7915},
support = {31770136//National Natural Science Foundation of China/ ; 2662022SKYJ006//Fundamental Research Funds for the Central Universities/ ; 2662023DKPY003//Fundamental Research Funds for the Central Universities/ ; 2022hszd013//Major Project of Hubei Hongshan Laboratory/ ; 2024BCA006//Hubei Province Technological Innovation Plan Project/ ; },
mesh = {Animals ; Larva/microbiology ; *Gastrointestinal Microbiome ; *Salmonella/growth & development ; Manure/microbiology ; *Diptera/microbiology ; Chickens ; Bacillus ; Metagenomics ; *Antibiosis ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Black soldier fly larvae (BSFL) can efficiently convert organic waste into biomass and reduce pathogenic bacteria in organic waste. The microbial composition of the substrate and the gut of BSFL is a pivotal factor in determining the efficacy of BSFL in pathogen elimination. However, there are insufficient data on the gut microbiology of BSFL in relation to pathogen inhibition. To address this gap, we investigated the dynamics of Salmonella during the conversion of chicken manure by BSFL and examined the role of intestinal bacterial communities and core bacteria in reducing Salmonella levels. The results indicate that BSFL treatment can reduce the amount of Salmonella in chicken manure, with the gut microbiome of the BSFL playing a crucial role in this reduction. Combining metagenomic analysis with culturomics methods, we isolated 158 strains from the larval gut, in which seven gut bacteria belonging to the genus Bacillus can promote BSFL to reduce Salmonella. In reinoculation and validation experiments, the combination of BSFL and Bacillus velezensis A2 enhanced the elimination of Salmonella from chicken manure and larvae. This study provides insight into how BSFL can reduce pathogenic bacteria in chicken manure and suggests that pairing BSFL with functional microorganisms can improve the biosafety of organic waste conversion by BSFL.},
}

Animals
Larva/microbiology
*Gastrointestinal Microbiome
*Salmonella/growth & development
Manure/microbiology
*Diptera/microbiology
Chickens
Bacillus
Metagenomics
*Antibiosis
Bacteria/classification/genetics/isolation & purification

@article {pmid41428567,
year = {2025},
author = {Khromova, AM and Timerzyanov, MI and Valeeva, YV and Khaertynova, IM and Endaltseva, KM and Siraeva, ZY},
title = {[The study of the meconial microbiota for the purposes of forensic science and practice].},
journal = {Sudebno-meditsinskaia ekspertiza},
volume = {68},
number = {6},
pages = {47-51},
doi = {10.17116/sudmed20256806147},
pmid = {41428567},
issn = {0039-4521},
mesh = {Humans ; *Meconium/microbiology ; Infant, Newborn ; *Gastrointestinal Microbiome/physiology ; *Forensic Sciences/methods ; Female ; Pregnancy ; *Microbiota ; },
abstract = {UNLABELLED: The issue of the effect of prenatal and perinatal pathological processes on the intestinal microbiome of the fetus and newborn requires increased attention.

OBJECTIVE: To analyze the results of scientific research reflecting the influence of the intestinal microbiome of a newborn on the stages of postembryonic development.

MATERIAL AND METHODS: A search for contemporary scientific studies relevant to the review's objectives was conducted in the scientific citation systems eLibrary (RSCI), Web of Science, PubMed, and Scopus. Thirty-three publications relevant to the review's subject matter were analyzed and included in the list.

RESULTS AND CONCLUSION: The idea of meconium non-sterility due to maternal-fetal transplantental microbial transition has been confirmed. The diagnostic value of detecting violations of the taxonomic composition of the microbiome lies in optimizing disease prevention and treatment strategies.},
}

Humans
*Meconium/microbiology
Infant, Newborn
*Gastrointestinal Microbiome/physiology
*Forensic Sciences/methods
Female
Pregnancy
*Microbiota

@article {pmid41428256,
year = {2025},
author = {Sivarajan, D and Pothayi, V and Devasia, SC and Ramachandran, B},
title = {Impact of dietary composition on behavioural expression and gut microbiome dynamics in zebrafish.},
journal = {Pflugers Archiv : European journal of physiology},
volume = {478},
number = {1},
pages = {13},
pmid = {41428256},
issn = {1432-2013},
support = {CSIR-UGC-JRF-905/2018//University Grants Commission/ ; (ECR/2018/002479)//DST-SERB, India/ ; },
mesh = {Animals ; *Zebrafish/microbiology/physiology ; *Gastrointestinal Microbiome/physiology ; *Behavior, Animal/physiology ; *Diet ; Brain/physiology ; *Animal Feed ; Aggression ; },
abstract = {Diet is a key physiological factor shaping brain function and gut microbiota, which together form the dynamic gut-brain axis. This bidirectional communication system plays a pivotal role in regulating behavioural outcomes. Therefore, it is worth investigating various behavioural aspects and connecting them with gut microbial dynamics shaped by differential dietary composition. Using zebrafish, we examined the effects of monotypic and combined diets of live feed and commercial feed on behavioural outcomes, morphometry, and gut microbiota. After chronic dietary intervention, fish receiving a mixed diet (Artemia, pellet, and spirulina) showed behavioural profile with enhanced exploration, reduced anxiety-like behaviour, and moderate aggression, alongside a balanced gut microbial composition. In contrast, monotypic diets produced distinct effects: Artemia-only fish displayed reduced boldness, heightened anxiety, and pathogenic microbial enrichment, while pellet-only fish showed greater growth but increased aggression. These findings highlight the importance of mixed feeding regimens for maintaining healthy gut-brain-behaviour interactions and support zebrafish as a model for studying diet-microbiota-behaviour relationships.},
}

Animals
*Zebrafish/microbiology/physiology
*Gastrointestinal Microbiome/physiology
*Behavior, Animal/physiology
*Diet
Brain/physiology
*Animal Feed
Aggression

@article {pmid41427854,
year = {2025},
author = {Wang, Y and Yu, J and Gao, L},
title = {Targeting Intratumoral Bacteria for Cancer Nanotherapeutics.},
journal = {ACS applied materials & interfaces},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsami.5c16720},
pmid = {41427854},
issn = {1944-8252},
abstract = {Intratumoral microbiota has emerged as a key modulator of cancer progression and therapeutic response, significantly influencing treatment outcomes. Although conventional microbiome-modulating approaches such as antibiotic administration can enhance cancer treatment efficacy, they frequently lead to inconsistent therapeutic results and disrupt beneficial microbial communities. Nanotechnology, with its capacity for precise interactions at microscopic and molecular scales, offers a promising solution for selectively regulating tumor-associated microbiota and reshaping the tumor microenvironment. This review elucidates current knowledge by conducting a comprehensive analysis of the literature, with a focus on classifying the antibacterial mechanisms of nanotechnology against intratumoral bacteria into physical, chemical, and biological modalities, and further discusses the precision design of nanomaterials, therapeutic outcomes, and antimicrobial mechanisms within each modality. Furthermore, we discuss challenges in precise targeting and safety, examine the translational progress of nanotechnology-based antimicrobial strategies, and propose future directions for research and clinical application.},
}

@article {pmid41427744,
year = {2025},
author = {Burnside, M and Helliwell, E and Treerat, P and Rozendal, T and Merritt, J and Baker, JL and Kreth, J},
title = {Comparative characterization reveals conserved and divergent ecological traits of oral corynebacteria.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0297325},
doi = {10.1128/spectrum.02973-25},
pmid = {41427744},
issn = {2165-0497},
abstract = {Corynebacteria are abundant members of the oral microbiome and increasingly recognized as key structural organizers of supragingival biofilms. Despite their prevalence, the ecological roles and phenotypic traits of many oral corynebacterial species remain poorly defined. Here, we isolated and characterized two new strains, Corynebacterium durum JJ2 and Corynebacterium argentoratense MB1, and compared them with previously characterized and published Corynebacterium durum JJ1 and reference strain Corynebacterium matruchotii ATCC 14266. Phenotypic assays revealed that C. durum strains displayed robust aggregation, thick biofilm formation, and extensive extracellular polymeric substance (EPS) networks, whereas C. argentoratense MB1 and C. matruchotii ATCC 14266 formed thinner biofilms with minimal EPS production. All four strains secreted extracellular membrane vesicles capable of inducing chain elongation in Streptococcus sanguinis, underscoring a conserved interspecies signaling function. Genomic analysis demonstrated close relatedness between C. durum and C. matruchotii, while C. argentoratense MB1 was more distantly related, with a reduced genome, fewer metabolic pathways, and the absence of nitrate reductase genes, consistent with its inability to grow under anaerobic conditions. These findings suggest that C. argentoratense MB1 may represent a less specialized or transient inhabitant of the oral cavity, whereas C. durum and C. matruchotii are well adapted to the oral niche. Together, this study expands our understanding of phenotypic diversity, metabolic capacity, and interspecies interactions among selected oral corynebacteria, highlighting their potential importance as biofilm organizers and contributors to oral microbial ecology.IMPORTANCEOral corynebacteria contribute to the structural and ecological stability of supragingival communities. Yet, their species-level functions remain poorly defined. By isolating and characterizing new strains of Corynebacterium durum and Corynebacterium argentoratense, and comparing them with reference strains including Corynebacterium matruchotii, we provide new insight into their phenotypic diversity, metabolic capacity, and ecological roles. Our results demonstrate that C. durum strains form robust biofilms enriched in extracellular polymeric substances, while C. argentoratense produces thinner biofilms and lacks the genomic features required for anaerobic growth, suggesting a less specialized or transient role in the oral cavity. Importantly, we show that extracellular membrane vesicles secreted by all tested strains promote chain elongation in Streptococcus sanguinis, highlighting a conserved mechanism of interspecies communication. These findings advance our understanding of how oral corynebacteria contribute to biofilm organization and microbial homeostasis and position them as critical but understudied players in oral microbial ecology.},
}

@article {pmid41427732,
year = {2025},
author = {O'Brien, CE and Frese, SA and Cernioglo, K and Damian-Medina, K and Mitchell, RD and Casaburi, G and Melnyk, RA and Henrick, BM and Smilowitz, JT},
title = {Randomized, placebo-controlled trial reveals the impact of dose and timing of Bifidobacterium infantis probiotic supplementation on breastfed infants' gut microbiome.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0051825},
doi = {10.1128/msphere.00518-25},
pmid = {41427732},
issn = {2379-5042},
abstract = {UNLABELLED: A dysfunctional gut microbiome has become increasingly common in infants born in high-income countries as Bifidobacterium strains no longer dominate the gut microbiome. Probiotics containing Bifidobacterium infantis have been used in breastfed newborns to successfully restore the gut microbiome; however, no studies to date have demonstrated this effect in older breastfed infants whose gut microbiomes are transitioning toward stability and maturity. This is a 9-week randomized controlled trial wherein 2-4 months old exclusively breastfed infants (n = 40) received 0 CFU/day B. infantis EVC001 (placebo), 4.0 × 10[9] CFU/day B. infantis EVC001 (low), 8.0 × 10[9] CFU/day B. infantis EVC001 (medium), or 1.8 × 10[10] CFU/day B. infantis EVC001 (high) in equal allocation for 28 consecutive days beginning on day 8. Stool samples were collected on study days 7, 10, 14, 21, 28, 35, 42, and 63. Fecal B. infantis levels were significantly higher in all supplement groups compared with placebo on day 28 and day 63. On day 28, fecal B. infantis levels were significantly higher in infants who received any (low, medium, and high) dose compared with baseline. The abundance of fecal Bifidobacteriaceae significantly increased nearly 2-fold in response to B. infantis EVC001 supplementation. No matter the dose, probiotic supplementation with B. infantis in 2- to 4-month-old exclusively breastfed infants resulted in colonization until at least 1 month post-supplementation.

IMPORTANCE: This study found that supplementing exclusively breastfed infants with a probiotic, Bifidobacterium infantis EVC001, between 2 and 4 months of age can successfully restore beneficial bacteria in their gut, even after the newborn period. Although previous research showed this effect in newborns, this is the first study to demonstrate that older infants, whose gut microbiomes are typically more stable, can still benefit. The probiotic was effective at all tested doses, with higher levels of B. infantis and overall Bifidobacteriaceae in infants' stool during and even 1 month after supplementation. This study demonstrates that B. infantis can take hold in the gut and potentially improve gut health in older breastfed babies, offering a promising approach to support infant health in settings where beneficial gut bacteria are often missing.

CLINICAL TRIALS: This study was registered at clinicaltrials.gov as NCT03476447.},
}

@article {pmid41427714,
year = {2025},
author = {Bell, AG and Cable, J and Temperton, B and Tyler, CR},
title = {Assessment of the effectiveness of host depletion techniques for profiling fish skin microbiomes and metagenomic analysis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0183825},
doi = {10.1128/spectrum.01838-25},
pmid = {41427714},
issn = {2165-0497},
abstract = {UNLABELLED: Microbiomes on fish mucosal surfaces play crucial roles in nutrient absorption, immune priming, and defense, and disruptions in these microbial communities can lead to adverse health outcomes, including disease. Studying fish microbiomes relies on sequencing microbiota within mucosal-rich samples; however, nucleic acid extraction from these samples is composed predominantly of host DNA, making subsequent bioinformatic processes difficult. Host depletion techniques address this issue by either selectively degrading host DNA before sequencing or retaining bacterial DNA post-extraction. However, their application to fish mucosal samples has been largely unexplored. Here, we assessed the efficacy of various host depletion techniques on fish skin mucosal swabs via either selectively removing CpG-methylated (predominantly eukaryotic) DNA or selectively lysing eukaryotic cells before DNA extraction. Surprisingly, none of the existing methods we assessed effectively reduced host DNA to be practically useful. Furthermore, some methods introduced a bias toward certain bacterial taxa, including the Bacilli class and the Proteobacteria phylum. Our findings illustrate that the currently available host depletion techniques are largely ineffective for reducing host DNA in fish mucosal samples. This poses a major limitation for developing an understanding of the functional composition of fish mucosal microbiomes, as enriching microbiota (and excluding host DNA) is fundamental for cost-effective metagenomic studies and facilitating more accurate analyses of the microbiota metabolome and proteome.

IMPORTANCE: Microbial communities on fish mucosal surfaces are vital for immune function and disease resistance. However, sequencing these communities is hindered by the dominance of host DNA in mucosal samples, which can exceed 99% of total nucleic acids. While host depletion techniques are routinely used in human and mammalian systems to enrich microbial DNA, their efficacy on fish samples remains uncharacterized. In this study, we assessed multiple commercial and published host depletion methods on fish skin microbiomes. None significantly reduced host DNA to levels suitable for high-quality metagenomic sequencing, and some introduced taxonomic bias. We suggest methodological reasons, including differences in fish cell structure and mucus composition compared to mammalian systems, that may explain these shortcomings. Based on our findings, we propose protocol modifications and highlight key areas for improvement. This work identifies critical limitations and offers a foundation for developing optimized host depletion strategies tailored to fish mucosal microbiome research.},
}

@article {pmid41427705,
year = {2025},
author = {Wang, J and Qu, R and Huang, W and Chen, Y and Li, Y and Lin, Q and Wu, Z and Yan, H and Yu, T and Wang, C and Ren, X and Wang, X and Wu, J},
title = {Progressive and concordant alterations in transcriptional and gut microbiota across aortic valve calcification severity.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0213725},
doi = {10.1128/spectrum.02137-25},
pmid = {41427705},
issn = {2165-0497},
abstract = {UNLABELLED: Calcific aortic valve disease (CAVD) is a common disorder associated with substantial morbidity and mortality. Although the gut microbiome has complex associations with cardiovascular disease, its variation across the calcification spectrum in CAVD remains poorly defined. We profiled aortic-valve transcriptomes from 31 patients spanning graded calcification and paired these with matched stool microbiome profiles. We identified subtle yet widespread transcriptional changes in mild CAVD (m-CAVD), consistent with a progressive relationship between calcification burden and gene-expression remodeling. At the community level, the gut microbiome in m-CAVD exhibited an intermediate configuration between non- and higher-calcification profiles, suggesting an early shift in the gut ecosystem along the disease continuum. At the genus level, we identified 11 taxa associated with stage; notably, Anaerococcus increased with calcification burden, whereas Rheinheimera declined across stages. These results refine the pathophysiology landscape of CAVD by connecting stage-dependent valvular transcriptional changes with coordinated shifts in the gut microbiome and indicate that early, microbiome-targeted interventions may be promising.

IMPORTANCE: Calcific aortic valve disease is a common valvular heart disease. Due to the difficulty in sampling arterial calcified tissues, research on the interaction between their gene expression and the gut has been limited. In this study, by analyzing the transcriptional profiles of calcified aortic valve tissues from patients with different levels of calcification and the characteristics of their corresponding gut microbiota, we identified consistent features between lesion gene expression and gut microbiota variation. This provides important evidence for the association between the gut microbiota and disease development stages, offering a new perspective for understanding disease progression and early intervention.},
}

@article {pmid41427586,
year = {2026},
author = {Newman, KL and Standke, AK and James, G and Vendrov, KC and Inohara, N and Bergin, IL and Higgins, PDR and Rao, K and Young, VB and Kamada, N},
title = {Miniature bioreactor arrays for modeling functional and structural dysbiosis in inflammatory bowel disease.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2604875},
doi = {10.1080/19490976.2025.2604875},
pmid = {41427586},
issn = {1949-0984},
mesh = {*Dysbiosis/microbiology ; Humans ; *Gastrointestinal Microbiome ; Animals ; Mice ; *Bioreactors/microbiology ; Feces/microbiology ; *Inflammatory Bowel Diseases/microbiology ; Clostridioides difficile/growth & development ; Colitis, Ulcerative/microbiology ; Disease Models, Animal ; Crohn Disease/microbiology ; Female ; Male ; Interleukin-10/genetics/deficiency ; Bacteria/classification/isolation & purification/genetics ; Mice, Inbred C57BL ; },
abstract = {Alterations in the gut microbiota, known as gut dysbiosis, are associated with inflammatory bowel disease (IBD). There is a need for model systems that can recapitulate the IBD gut microbiome to better understand the mechanistic impact of differences in microbiota composition and its functional consequences in a controlled laboratory setting. To this end, we introduced fecal samples from patients with Crohn's disease (CD) and ulcerative colitis (UC), as well as from healthy control subjects, to miniature bioreactor arrays (MBRAs) and analyzed the microbial communities over time. We then performed two functional assessments. First, we evaluated the colitogenic potential of the CD microbiotas in genetically susceptible germ-free IL-10-deficient mice and found that colitogenic capacity was preserved in a bioreactor-cultivated CD microbiota. Second, we tested impaired colonization resistance against Clostridioides difficile in UC microbiotas using the MBRA system and found that UC microbiotas were innately susceptible to C. difficile colonization while healthy microbiotas were resistant, consistent with what is seen clinically. Overall, our results demonstrate that IBD microbiotas perform comparably to healthy donor microbiotas in the MBRA system, successfully recapitulating microbial structure while preserving IBD-specific functional characteristics. These findings establish a foundation for further mechanistic research into the IBD microbiota using MBRAs.},
}

*Dysbiosis/microbiology
Humans
*Gastrointestinal Microbiome
Animals
Mice
*Bioreactors/microbiology
Feces/microbiology
*Inflammatory Bowel Diseases/microbiology
Clostridioides difficile/growth & development
Colitis, Ulcerative/microbiology
Disease Models, Animal
Crohn Disease/microbiology
Female
Male
Interleukin-10/genetics/deficiency
Bacteria/classification/isolation & purification/genetics
Mice, Inbred C57BL

@article {pmid41427415,
year = {2025},
author = {Bernate, E and Shi, Y and Franck, E and Crofts, TS},
title = {A functionally selected Acinetobacter sp. phosphoethanolamine transferase gene from the goose fecal microbiome confers colistin resistance in E. coli.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.09.693354},
pmid = {41427415},
issn = {2692-8205},
abstract = {Polymyxins are last-resort antibiotics for infections caused by multidrug resistant Gram-negative bacteria such as Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii . This makes the rise of bacteria exhibiting polymyxin E (colistin) resistance, largely through modification of lipid A moieties, concerning and suggests that it is important to document potential sources of the corresponding resistance genes. This study searched for potential emerging colistin-resistance genes from the environment by investigating a previously performed functional metagenomic selection for colistin resistance of a goose fecal microbiome. We found that the selection captured Acinetobacter sp. DNA fragments which all contained eptA genes. We confirmed their ability to confer significant colistin resistance in E. coli via modification of lipid A in the outer membrane. Furthermore, we found evidence for mobilization of closely related eptA genes in Acinetobacter strains, marking them as potential mcr genes or their precursors. This study highlights the goose fecal microbiome as a potential source for colistin resistance in the environment.},
}

@article {pmid41427374,
year = {2025},
author = {Suzuki, E and Deleray, V and Zemlin, J and Kousha, A and Nonoguchi, H and Sun, D and Tsai, CM and Zuffa, S and Kvitne, KE and Dorrestein, PC and Tsunoda, SM and Nizet, V and Liu, GY and Askarian, F},
title = {Effect of Perinatal Ampicillin or Amoxicillin/Clavulanate Exposure on Maternal and Infant Gut Microbiome, Metabolome, and Infant Responses to the 20-valent Pneumococcal Conjugate Vaccine.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.08.692990},
pmid = {41427374},
issn = {2692-8205},
abstract = {Emerging studies suggest that antibiotics can disrupt the gut microbiome and alter vaccine-induced immune responses, but the specific consequences of early-life exposure on neonatal immune development remains poorly understood. Here, we examined how two antibiotics frequently used in perinatal care, broad-spectrum ampicillin (AMP) and the extended-spectrum combination amoxicillin/clavulanate (AMOX/CLAV), administered during gestation and lactation, influence neonatal gut microbiome composition, fecal metabolome profiles, and responses to the 20-valent pneumococcal conjugate vaccine (PCV20). Maternal treatment with AMOX/CLAV, but not AMP, significantly reduced PCV-specific IgG titers at 4-and 6-weeks post-prime immunization compared to untreated controls. Exclusive exposure to AMOX/CLAV also impaired neutrophil-mediated opsonophagocytic killing, indicating diminished antibody functionality. These effects were transient, with immune parameters normalizing by week 8 post-prime immunization. Metabolomic and microbiome profiling revealed that maternal AMP and AMOX/CLAV differentially perturbed specific metabolite classes including bile acids, N -acyl lipids, and indole-derivatives, as well as key commensal taxa including Bacteroidales and Coriobacteriales within the gut microbiota. Together, these findings reveal a previously underappreciated maternal-offspring route of antibiotic influence that transiently disrupts neonatal vaccine responsiveness through microbiome and metabolome alterations. These results highlight maternal antibiotic exposure as a modifiable factor shaping early-life immunity.},
}

@article {pmid41426949,
year = {2025},
author = {Allshouse, T and Amendano, M and Caruso, B and Del Campo, R and Murphy, G and Shaffer, L and Steinberg, E and Sullivan, A and Stowe, E},
title = {The Microbiota of Homemade Tepache Includes Antibiotic-Resistant Microorganisms.},
journal = {microPublication biology},
volume = {2025},
number = {},
pages = {},
pmid = {41426949},
issn = {2578-9430},
abstract = {Tepache is a traditional, homemade Mexican drink made by fermenting pineapple rinds. The natural probiotic bacteria in tepache are said to promote a healthy gut microbiome. This study assessed the microbial community in homemade tepache for diversity, survival in simulated gastric fluid, and antibiotic resistance. Simulated gastric passaging reduced total community numbers but the community density was not strongly impacted by exposure to tetracycline. Metagenomic analysis reveals a community dominated by Bacillus, Meyerozyma and Talaromyces. These results indicate that consuming home fermented beverages may provide helpful probiotic bacteria but could also expose the gut microbiome to antibiotic resistance genes.},
}

@article {pmid41426590,
year = {2025},
author = {Zhang, J and Xu, X and Chen, L and Yang, X and Matsubara, JK and Tian, Y and Liu, J and Jin, X and Chang, H and Xu, M and Zhu, C and Wang, X and Ren, L and Xie, J and Liu, J and Liu, G and Lu, M and Wang, X and Du, L and Ma, Z and Liu, X and Zhao, H and Chen, W and Huo, X and Zheng, G and Xie, C and Xu, C and Zhang, X and Qi, W and Feng, Z},
title = {Circulating microbiome profiling in transjugular intrahepatic portosystemic shunt patients: 16S rRNA vs. shotgun sequencing.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1662837},
pmid = {41426590},
issn = {2296-858X},
abstract = {BACKGROUND AND AIM: Current efforts to characterize the circulating microbiome are constrained by the lack of standardized protocols for isolating and sequencing microbial communities in blood. To address this challenge, our study compared 16S rRNA (V3-V4 region) and shotgun metagenomic sequencing for circulating microbiome detection.

MATERIALS AND METHODS: After obtaining ethics committee approval and informed consent, samples were aseptically collected from 10 patients undergoing transjugular intrahepatic portosystemic shunt (TIPS) procedures. Shotgun metagenomic reads were taxonomically classified using the Kraken2-Bracken pipeline. 16S rRNA (V3-V4) data were analyzed through an ASV-based approach, with USEARCH for denoising and VSEARCH for taxonomic annotation. The results from both sequencing methods were then systematically compared.

RESULTS: Shotgun metagenomic sequencing generated 7,024,580,376 raw reads (mean depth: 234,152,679.2 reads/sample), while 16S rRNA sequencing produced 6,612,678 raw reads (mean depth: 220,422.6 reads/sample). 16S rRNA amplicon sequencing captured a broader range of microbial signals. Although the taxonomic profiles from both sequencing methods showed limited overlap, the core microbiota common to both were still identified. These conserved core microbial communities exhibited stable α- and β-diversity indices across separate vascular compartments.

CONCLUSION: In our study, 16S rRNA amplicon sequencing captured more diverse microbial signals than shotgun metagenomics. A stable microbial community structure was observed across vascular compartments, suggesting a homogeneous microbial composition throughout the circulatory system.},
}

@article {pmid41426531,
year = {2025},
author = {Jijón, G and Hough, C and Gedris, D and Frandsen, PB and Chaston, JM},
title = {Gut microbiome composition of Trichoptera larvae across functional feeding groups: a case study from the Provo River, Utah, USA.},
journal = {ZooKeys},
volume = {1263},
number = {},
pages = {165-177},
pmid = {41426531},
issn = {1313-2989},
abstract = {Diet is known to be a major factor in the gut microbiome of many groups of insects. Larvae from the insect order Trichoptera have varied feeding behaviors, encompassing all functional feeding groups, making them an excellent group for studying the links between diet and gut microbe community variation. However, no previous study has examined these links in caddisflies. Here, we characterize the gut microbiome composition of four caddisfly genera belonging to four different functional feeding groups over two sampling periods using 16S metabarcoding. We found that the sampling date had the strongest influence on gut microbiome variation. Host functional feeding groups and phylogeny also influenced gut community composition; however, improved sampling is necessary to confirm this relationship. Our preliminary results point to interesting differences among larvae from different feeding groups and suggest future areas for research, including performing species-level identification of the caddisfly larvae, using more taxa within and between functional feeding groups, using temporal and larval stage-matched replicates, assessing the degree of microbiome residency in caddisfly guts, and performing deeper sequencing.},
}

@article {pmid41426377,
year = {2025},
author = {Li, Z and Zhang, Y and Luo, X and Wang, Y and Peng, L and Zou, L},
title = {Dynamic relationships between bilirubin concentrations and the gut microbiota in the neonatal period: A pilot prospective cohort study.},
journal = {Pediatric investigation},
volume = {9},
number = {4},
pages = {347-360},
pmid = {41426377},
issn = {2574-2272},
abstract = {IMPORTANCE: Understanding the dynamic interplay between gut microbiota development and bilirubin metabolism may provide new insights into the pathophysiology of neonatal jaundice. Identifying microbial taxa associated with bilirubin fluctuations could help inform early prediction and microbiota-targeted interventions for hyperbilirubinemia.

OBJECTIVE: To investigate the correlation between dynamic changes in the gut microbiota and bilirubin concentrations during the neonatal period.

METHODS: Bilirubin concentrations were monitored daily throughout the neonatal period. Fecal samples were collected from neonates on days 1, 3, 7, 14, 21, and 28 after birth. The composition of the gut microbiome was assessed by 16S rRNA gene amplicon sequencing of the fecal samples. Within-subject, same-day associations between transcutaneous bilirubin (TcB) and genus-level abundance were quantified using a repeated-measures correlation.

RESULTS: Thirty neonates were included in the final analysis. Among the top-30 genera, six exhibited false discovery rate significant, same-day within-subject associations with TcB under the repeated-measures correlation framework (|rrm| ≥0.30). Changes in the abundances of the genera Streptococcus (r rm = +0.416, 95% confidence interval [CI] 0.272-0.543, P = 2.084 × 10[-7]; P-adj = 3.126 × 10[-6]) and Rothia (r rm = +0.340, 95% CI 0.187-0.476; P = 3.134 × 10[-5]; P-adj = 1.567 × 10[-4]) were positively correlated with bilirubin concentrations throughout the neonatal period. In complementary cross-sectional analyses centered on meconium, additional genus-bilirubin correlations were identified for TcB measured on postnatal days 3-7 and for the neonatal TcB peak, with multiplicity controlled separately for each endpoint.

INTERPRETATION: A correlation was found between dynamic changes in the gut microbiome and bilirubin concentrations during the neonatal period. The identified genera might be potential markers or targets for intervention for neonatal jaundice.},
}

@article {pmid41426333,
year = {2025},
author = {Turgeman, I and Henick, BS and Mezquita, L},
title = {Editorial: Nature and nurture in early onset lung cancer.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1750797},
pmid = {41426333},
issn = {2234-943X},
}

@article {pmid41426250,
year = {2025},
author = {Dai, YK and Li, DY and Cong, LL and Liao, Y and Wang, XC and Fan, JW and Chen, WJ and Fan, CH and Ma, T and Wu, YJ},
title = {Mechanism of Chronic Atrophic Gastritis: A 20-Year Bibliometric Analyses.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {17457-17475},
pmid = {41426250},
issn = {1178-7031},
abstract = {BACKGROUND AND PURPOSE: Chronic atrophic gastritis (CAG), affecting approximately 20-30% in high-risk populations, contributes to significant morbidity and mortality due to its progression to gastric cancer. Despite two decades of research into its pathogenesis, the vast body of literature has not yet been systematically mapped. A comprehensive bibliometric analysis mapping the field's evolution, collaborative networks, and knowledge gaps remains lacking. Therefore, we conduct a 20-year bibliometric analysis (2005-2024) of research on the mechanism of CAG to identify seminal works, emerging themes, evaluate global collaboration networks, and highlight translational challenges and opportunities.

PATIENTS AND METHODS: Data were retrieved from the Web of Science Core Collection (WoSCC) spanning from January 1, 2005, to December 31, 2024. Bibliometric analysis was performed using CiteSpace and VOSviewer to analyze publication trends, influential authors and institutions, keyword clusters, and citation bursts.

RESULTS: A total of 954 papers were identified, with China leading in publication output (41.51%), followed by the USA (15.20%). The USA demonstrated high centrality in international collaboration. Key journals included WORLD J GASTROENTERO and GASTROENTEROLOGY. Prolific authors such as Liu Yuetao and co-cited authors like CORREA P were identified. Keyword analysis revealed "Helicobacter pylori" as the most prominent term, with clusters focusing on traditional Chinese medicine, macrophage biology, and gastric intestinal metaplasia.

CONCLUSION: The study highlights the significant research output and collaboration in CAG, emphasizing the importance of interdisciplinary approaches and international partnerships. Future research should focus on integrating traditional knowledge with modern mechanistic studies and addressing emerging themes such as microbiome dysbiosis and precision medicine.},
}

@article {pmid41426219,
year = {2025},
author = {Jeong, JY and Park, SH and Kim, M and Kang, HK and Park, NG},
title = {Comparative gut microbiota, growth performances, and cytokine indices in broiler chickens with or without litter.},
journal = {Journal of animal science and technology},
volume = {67},
number = {6},
pages = {1328-1342},
pmid = {41426219},
issn = {2055-0391},
abstract = {Developmental patterns of the gut microbiota are important for improving chicken health and productivity. However, the influence of litter and litter microbes on cecal microbiota is still unclear. This study aimed to identify broiler cecal microbiota at different ages according to litter usage in cage (without litter) and conventional (with litter) conditions. The cecal contents of the broilers from each group were collected from 1-5 wk. The development and function of the gut microbiota were evaluated using 16S rRNA gene sequencing. The final body weight of the chickens was higher in the cage group than that in the conventional group. In particularly, α-diversity was higher at 3 wk than that at 1 wk. The phyla Firmicutes predominated at 3 wk. In contrast, the abundance of Bacteroidetes and fibrinolytic bacteria increased significantly at 1 and 2 wk compared to that at 3 and 5 wk. Corynebacterium was the most abundant genus in the conventional group after 3 wk. In conclusion, the cecal microbiota are influenced by environmental factors, such as cage, which improves the chicken gut environment.},
}

@article {pmid41425942,
year = {2025},
author = {Li, Z and Peng, X and Wang, Q and Guo, L and Liu, S and Xu, L},
title = {Host sweet preference modulates the salivary microbiome and its divergent associations with plaque-associated and non-plaque-related oral diseases.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1732083},
pmid = {41425942},
issn = {1664-302X},
abstract = {BACKGROUND: Microorganisms play a critical role in the progression of oral diseases. However, it remains unclear whether the frequency of sweet consumption influences the salivary microbiota in both plaque-associated and non-plaque-related oral diseases.

METHODS: Based on salivary microbiome analysis, unstimulated saliva samples were collected from university students aged 17-20, including healthy controls (HC), dental caries (DC), and dental fluorosis (DF) groups, under different sweet consumption frequencies. Microbiota potentially critical in disease development were identified.

RESULTS: No significant differences in α- and β-diversity were observed among the three groups. However, distinct microbial structures at the genus and species levels were evident under different sweet consumption conditions. Under high sweet consumption, the caries group exhibited enrichment of microbiota closely associated with sugar metabolism and acid production (e.g., Streptococcus, Rothia), while Ralstonia was significantly enriched in the caries group, suggesting its potential role in high-sweet-induced caries development. Under low sweet consumption, the healthy control group showed enrichment of taxa such as Stenotrophomonas, potentially linked to ecological stability, whereas the dental fluorosis group demonstrated significant enrichment of Fastidiosipila, reflecting specific fluoride-induced selective pressure on the microbiome. This study indicates that although sweet consumption frequency did not significantly alter overall microbial diversity, it reshaped the oral microbiota structure in a disease-specific context. The caries group was more prone to developing a cariogenic microbial profile under high-sugar conditions, while the fluorosis group exhibited unique ecological adaptive characteristics.},
}

@article {pmid41425940,
year = {2025},
author = {Zheng, B and Wang, L and Sun, S and Yuan, X and Liang, Q},
title = {The molecular interplay between the gut microbiome and circadian rhythms: an integrated review.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1712516},
pmid = {41425940},
issn = {1664-302X},
abstract = {This integrated review synthesizes current evidence on the molecular interplay between the gut microbiome and circadian rhythms, emphasizing a sophisticated bidirectional communication system crucial for maintaining metabolic, immune, and neurological homeostasis. The host circadian clock orchestrates microbial composition and function through rhythmic changes in feeding-fasting cycles, hormone secretion, immune responses, and bile acid metabolism. In return, microbial metabolites, including short-chain fatty acids such as butyrate, secondary bile acids like lithocholic acid, and tryptophan derivatives, act as timing cues that influence core clock gene expression via epigenetic mechanisms, receptor-mediated signaling (GPR41/43, FXR), and neuroendocrine pathways. Disruption of this finely tuned dialogue, known as chronodisruption, often driven by modern lifestyles, predisposes individuals to a range of pathologies, including metabolic syndrome, inflammatory bowel disease (IBD), neurodegenerative disorders, and cancer. The review also evaluates promising chronotherapeutic interventions such as time-restricted eating (TRE), targeted probiotic use, and chronopharmacology, which aim to resynchronize host-microbe rhythms and restore physiological balance. Elucidating these mechanisms provides a foundational framework for developing personalized health strategies that target the gut-clock axis.},
}

@article {pmid41425933,
year = {2025},
author = {Zhai, C and Sun, W and Li, Y and Han, H and Zhang, Y and Ma, B},
title = {Pre-release environmental acclimation enhances wild adaptability of endangered Kaluga sturgeon (Huso dauricus): insights from digestive, immune, and gut-microbiome perspectives.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1720688},
pmid = {41425933},
issn = {1664-302X},
abstract = {INTRODUCTION: Pre-release environmental acclimation is an effective strategy for improving post-stocking survival and restoring wild genetic resources in hatchery-reared juveniles. However, environmental acclimation protocols for the endangered Kaluga sturgeon (Huso dauricus) are currently non-existent.

METHODS: Here, cultured H. dauricus were transferred to a tributary of the Songhua River in autumn and exposed to an in-situ environmental acclimation protocol for 30 days. Subsequently, a hatchery control (HK) and seven environmental acclimation groups-HC1 (day 2), HC2 (day 5), HC3 (day 10), HC4 (day 15), HC5 (day 20), HC6 (day 25) and HC7 (day 30)-were monitored for feeding rate, digestive and immune enzyme activities, immune-gene expression, and gut microbiota change.

RESULTS: During the initial phase of wild conditioning, feeding rate remained negligible until HC2 group, then increased to 66%, 88.89% and 100% in groups HC4, HC5 and HC6, respectively. Meanwhile, digestive enzyme activities stabilized between groups HC4 and HC5, and immune enzyme activities in the wild-conditioned sturgeon were markedly higher than those of the control group. In addition, compared with the control group, the pro-inflammatory cytokine Interleukin-6 (IL-6) was significantly up-regulated, whereas the anti-inflammatory genes Interleukin-10 (IL-10) and Transforming growth factor-beta (TGF-β) were significantly down-regulated in HC4 group (P < 0.05). At the phylum level, the dominant microbiota shifted from Pseudomonadota to Bacillota by day 20 (HC5 group) and thereafter remained stable.

DISCUSSION: This study provides a theoretical framework for characterizing the physiological and biochemical responses of H. dauricus during environmental acclimation and provides a scientific basis for conserving its wild genetic resources.},
}

@article {pmid41425932,
year = {2025},
author = {Quijia-Pillajo, J and Chapin, LJ and Owen, JS and Altland, JE and Jones, ML},
title = {Fertilization influences the substrate, rhizosphere, and endosphere bacteriome of Petunia × hybrida.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1719754},
pmid = {41425932},
issn = {1664-302X},
abstract = {INTRODUCTION: In controlled environment agriculture (CEA), soil is replaced with soilless substrates that have poorly understood microbiome dynamics. We investigated the rhizosphere and endosphere bacteriome of Petunia × hybrida 'Picobella Blue' (Picobella) and 'Wave Purple' (Wave) grown in a soilless substrate (80% sphagnum peat and 20% perlite) under three fertilization rates (25, 100, and 200 mg·L[-1] N).

METHODS: Plant growth was assessed with the TraitFinder phenotyping platform, shoot dry weight, and nutrient analysis. Bacteriomes were profiled by 16S rRNA amplicon sequencing from unplanted substrate, bulk substrate, rhizosphere, and endosphere samples.

RESULTS: Both cultivars grew largest and healthiest at 200 mg·L[-1] N. Picobella fertilized with 100 and 200 mg·L[-1] N were equally green, whereas Wave was greenest at 200 mg·L[-1] N. Distinct bacteriomes were observed across unplanted substrate, rhizosphere, and endosphere. In unplanted substrate, fertilizer rate shaped bacterial community composition but not alpha diversity. In the rhizosphere, pH changes driven by fertilization strongly influenced bacterial community structure and reduced diversity. Endosphere and rhizosphere communities were further shaped by cultivar and fertilization rate.

DISCUSSION: These findings highlight nutrient management as a key driver of bacteriome dynamics across the substrate-plant continuum, underscoring the complex interactions between fertilization, plant genotype, and microbial communities in soilless culture.},
}

@article {pmid41425929,
year = {2025},
author = {Li, P and Yu, J and Li, T and Gong, X and Li, L and Cui, Y and He, J and Li, B and Wu, S and Guan, Q and Zhang, Z and Dai, X and Li, Z},
title = {The metabolite ILA of Akkermansia muciniphila improves AP-related intestinal injury by targeting and inhibiting CASP3 activity.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1669383},
pmid = {41425929},
issn = {1664-302X},
abstract = {OBJECTIVE: Acute Pancreatitis (AP) is a common acute abdominal disease in clinical practice. The gut microbiome is recognized as a key regulator in the development of acute pancreatitis. Akkermansia muciniphila (AKK) is recognized as a functional probiotic strain and has a beneficial effect on the progression of many diseases. However, the role of the AKK in the development of AP remains unclear. Here, we evaluated the potential contribution of AKK to AP.

DESIGN: Relative abundance of gut microbial AKK in AP was evaluated. A rat model of acute pancreatitis was established by retrograde pancreatic duct infusion of sodium taurocholate. Non-targeted and targeted metabolomics analysis were used for metabolites analysis.

RESULTS: We first found that the relative abundance of gut microbial AKK in AP patients was significantly reduced compared with that in healthy subjects. Live AKK supplementation, as well as supplementation with its culture supernatant, remarkably alleviates AP-related intestinal injury in AP rat models. Metabolomics studies found that the live AKK was able to generate Indole-3-lactic acid (ILA). ILA exerted a protective effect against AP-related intestinal injury, and significantly reduce inflammatory cell activation and pro-inflammatory factor overproduction. The mechanistic study revealed that ILA inhibits the apoptosis of intestinal epithelial cells by suppressing the activity of CASP3, and improves the role of intestinal barrier dysfunction in the AP model.

CONCLUSION: We revealed that ILA, derived from live AKK, may act as a novel endogenous agonist for CASP3. ILA may serve as a new potential treatment method for intestinal injury in AP after successfully translating its efficacy into clinical practice.},
}

@article {pmid41425928,
year = {2025},
author = {Rodríguez-Moreno, A and Martín-Blázquez, S and de Heredia, UL and Soto, Á and Lázaro, E},
title = {Impact of simulated microgravity in short-term evolution of an RNA bacteriophage.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1680651},
pmid = {41425928},
issn = {1664-302X},
abstract = {INTRODUCTION: Microgravity is a critical environmental factor in space that can alter microbial physiology and virus-host interactions. Understanding these effects is essential for planetary protection and crew health during long-term missions. Bacteriophage Qβ, an RNA virus infecting Escherichia coli F+ strains, provides a relevant model due to its potential presence in the human gut microbiome and its well-characterized evolutionary dynamics.

METHODS: We simulated microgravity using a custom-built 3D-clinostat and compared Qβ infections in semisolid medium under standard gravity and simulated microgravity. Twelve evolutionary lines were propagated for ten serial transfers under four experimental conditions combining bacterial growth and infection environments. Viral titers were quantified by plaque assay, and consensus sequences were determined by Sanger sequencing.

RESULTS: Initial infections under simulated microgravity yielded significantly lower viral titers than those in standard gravity, likely due to hindered phage diffusion and delayed infection initiation. After ten transfers, mutation C2011A (amino acid substitution T222N in the A1 virus protein) was fixed in all lines evolved under simulated microgravity but remained absent or polymorphic in standard gravity lines. Under simulated microgravity, the mutation increased virus titers and promoted faster initiation of infections in semisolid medium. However, those effects were not appreciable in normal gravity.

DISCUSSION: Our findings highlight the adaptability of Qβ and the potential impact of microgravity on phage-host interactions, offering insights into virus evolution in extraterrestrial conditions and its implications for space missions and planetary protection.},
}

@article {pmid41425927,
year = {2025},
author = {Qin, R and Li, C and Yuan, X and Chen, Y},
title = {Microbiome-targeted Alzheimer's interventions via gut-brain axis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1729708},
pmid = {41425927},
issn = {1664-302X},
abstract = {Alzheimer's disease (AD) is a progressive neurodegenerative disorder with limited treatment options, underscoring the need for novel therapeutic targets. The gut-brain axis has emerged as a critical bidirectional communication system, with growing evidence establishing gut dysbiosis as a causal factor in AD pathogenesis. This dysbiosis, characterized by a reduction in beneficial microbes and an increase in pro-inflammatory taxa, compromises intestinal and blood-brain barrier integrity, promoting systemic inflammation and the translocation of neurotoxic agents like lipopolysaccharide (LPS). Consequently, the balance of key microbial metabolites is disrupted, reducing neuroprotective short-chain fatty acids (SCFAs) and indoles while elevating inflammatory mediators, which collectively exacerbate neuroinflammation, amyloid-β (Aβ) deposition, and tau pathology. This review evaluates promising interventions, including probiotics, anti-inflammatory diets, exercise, and phytochemicals that can restore microbial balance, enhance barrier function, and improve cognitive outcomes in preclinical and early clinical studies. However, clinical translation is hindered by an overreliance on animal models, short-term studies, and insufficient mechanistic insight. Future research must prioritize large-scale human trials, multi-omics integration to elucidate signaling pathways, and personalized approaches that account for host genetics and baseline microbiome composition to fully harness the therapeutic potential of the gut-brain axis for AD.},
}

@article {pmid41425925,
year = {2025},
author = {Sukchawalit, R and Goryluk-Salmonowicz, A and Hobman, JL and Popowska, M},
title = {Editorial: Impacts of metal and xenobiotic-induced stress on antibiotic resistance in microbial communities.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1745065},
doi = {10.3389/fmicb.2025.1745065},
pmid = {41425925},
issn = {1664-302X},
}

@article {pmid41425919,
year = {2025},
author = {Kasani, PH and Yun, CH and Cho, KH and Jeong, SJ},
title = {Neonatal gut microbiota stratification and identification of SCFA-associated microbial subgroups using unsupervised clustering and machine learning classification.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1668451},
pmid = {41425919},
issn = {1664-302X},
abstract = {BACKGROUND: The neonatal gut microbiome plays a critical role in infant health through the production of short-chain fatty acids (SCFAs). However, the organization of SCFAs-producing microbial communities in neonates remains poorly characterized. This study applied unsupervised clustering and machine learning to classify microbial subgroups associated with SCFAs production, providing insight into their composition and metabolic potential.

METHODS: This study recruited 71 mother-infant pairs from Kangwon National University Hospital and Bundang CHA Hospital, collecting meconium samples within five days postpartum. Microbial diversity was analyzed by 16S rRNA gene sequencing (V3-V4 region) at the genus level, and SCFAs were quantified from the same samples. To identify functionally distinct microbial subgroups, K-Means, Agglomerative, Spectral, and Gaussian Mixture Model clustering were applied. Clustering validity was assessed using Silhouette Score, Calinski-Harabasz Index, Davies-Bouldin Index, and Prediction Strength Validation, with t-distributed Stochastic Neighbor Embedding (t-SNE) visualization to evaluate cluster separation. SCFAs distributions across clusters were compared, while random forest and logistic regression models were used to classify SCFAs-associated microbial clusters through Receiver Operating Characteristic curves (ROC).

RESULTS: The clustering analysis identified distinct microbial subgroups linked to SCFAs production, with Agglomerative clustering outperforming K-Means in capturing functionally relevant structures. Cluster 1 had higher SCFAs levels, enriched in Bacteroides, Prevotella, and Enterococcus, while Cluster 2 exhibited lower SCFAs concentrations with a more heterogeneous composition. The introduction of a third cluster in multi-class analysis revealed an intermediate metabolic profile, suggesting a continuum in microbial metabolic function. Classification analysis confirmed random forest model superiority, achieving ROC score of 91.05% (Agglomerative) and 87.74% (K-Means) in binary classification, and 92.98% (Agglomerative) and 89.84% (K-Means) in multi-class classification, demonstrating RF's strong predictive ability for SCFAs-based clusters.

CONCLUSION: Unsupervised clustering combined with classification analysis effectively predict SCFAs-associated subgroups and paving the way for future research on longitudinal tracking and functional genomic integration in early-life metabolic health.},
}

@article {pmid41425837,
year = {2025},
author = {Oladele, P and Johnson, TA},
title = {Trehalose and maltodextrin preserve microbial community structure in freeze-dried fecal samples for fecal microbiota transplantation.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf204},
pmid = {41425837},
issn = {2730-6151},
abstract = {Fecal microbiota transplantation (FMT) is a promising approach for restoring gut microbial balance in both humans and animals. However, the logistical limitations of transplanting fresh fecal samples have increased interest in freeze-dried (lyophilized) fecal material as a transplant inoculum. While lyophilization facilitates storage, it can compromise bacterial viability, which is essential for FMT effectiveness. Lyoprotectants are often used to protect bacterial cultures during freeze-drying, but their effect on complex microbial communities remains unclear, as they may preferentially preserve some taxa over others. This study investigated the impact of four lyoprotectants-mannitol, maltodextrin, trehalose, and a maltodextrin-trehalose mixture-on bacterial viability and community structure in pig fecal samples post-lyophilization. Propidium monoazide (PMA) treatment combined with 16S rRNA sequencing (PMAseq) was used to differentiate viable from non-viable bacteria. In the total community (without PMA), microbial profiles appeared similar across treatment groups. However, when focusing on the viable community (PMA-treated), lyoprotectant choice significantly influenced the post-lyophilization community composition. Gram-negative bacterial viability was especially sensitive to lyophilization. Trehalose and maltodextrin preserved bacterial viability and community structure more effectively than mannitol. Mannitol-treated samples had reduced viable bacterial cells and altered community composition, while trehalose and maltodextrin better maintained diversity and structure of the viable (PMA-treated) communities. Taken together, lyoprotectants have differential effects on microbial composition during lyophilization. Among those tested, trehalose and maltodextrin best preserved both viability and community structure, making them promising candidates for FMT applications. Future research should explore optimizing lyoprotectant formulations to enhance microbiome stability and functional outcomes.},
}

@article {pmid41425836,
year = {2025},
author = {Yin, X and Ang, LP and Zhu, RL and Azarbad, H and Ni, HH and Chai, ML and Liu, C and Kong, F and Liu, LJ and Liu, SL and Ma, Y and Zhou, HD and Luo, ZS and He, XK and Ye, LX and Li, H and Shu, L},
title = {Host-specific and environmental core bacteria differentially shape the stability and function of the Sphagnum phyllosphere.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf221},
pmid = {41425836},
issn = {2730-6151},
abstract = {Sphagnum mosses maintain peatland ecosystem stability through intimate associations with their microbiomes. As the foundational component of these communities, the core microbiome enables ecosystems to resist, absorb, and recover from environmental changes, yet the roles and processes of Sphagnum core members remain poorly understood, particularly in subtropical ecosystems. Here, we identified different components of core microbiomes and found that host-specific and environmental core microbiomes differentially shape the stability and function of Sphagnum phyllosphere bacteria by examining vertical stratification within a litter-Sphagnum-soil system in a subtropical mountain forest. Sphagnum harbors a microbial community that is significantly distinct from its surrounding environment (i.e. litter and soil), with community assembly primarily driven by deterministic processes, whereas litter and soil communities are more strongly shaped by stochastic processes. Sphagnum host-specific core taxa, enriched in carbon- and nitrogen-cycling lineages (i.e. Ca. Eremiobacterota), stabilized microbial composition, whereas environmental core taxa enhanced interaction strength and network robustness, and these groups responded differently to environmental filters (e.g. pH and elevation). Our framework highlights that core microbiomes are not functionally homogeneous, but instead reflect contrasting strategies that collectively shape ecosystem stability.},
}

@article {pmid41425703,
year = {2025},
author = {Feng, Y and Yang, H and Liang, G and Chen, J and Li, T and Wang, Y and Chang, J and Li, Y and Yang, M and Zhou, X and Wang, Z and Ge, C},
title = {Immune Checkpoint Inhibitors Combined with Oncolytic Virotherapy: Synergy, Heterogeneity, and Safety in Cancer Treatment.},
journal = {Oncology research},
volume = {33},
number = {12},
pages = {3801-3836},
pmid = {41425703},
issn = {1555-3906},
mesh = {Humans ; *Oncolytic Virotherapy/methods/adverse effects ; *Immune Checkpoint Inhibitors/therapeutic use/adverse effects/pharmacology ; *Neoplasms/therapy/immunology ; Combined Modality Therapy ; Tumor Microenvironment/immunology/drug effects ; Oncolytic Viruses/immunology ; Immunotherapy/methods ; Animals ; },
abstract = {Immune checkpoint inhibitor (ICI) has limited efficacy in the treatment of immune "cold" tumors. Due to insufficient T cell infiltration and heterogeneous programmed death ligand 1 (PD-L1) expression, the ORR is only 5%-8% compared with 30%-40% of "hot" tumors. This article reviews the synergistic mechanism, clinical efficacy and optimization strategy of oncolytic virus (OVs) combined with ICIs in the treatment of refractory malignant tumors. Systematic analysis of mechanistic interactions across tumor types and clinical trial data demonstrates that OVs transform the immunosuppressive microenvironment by inducing immunogenic cell death and activating innate immunity. Concurrently, ICIs enhance adaptive immunity by reversing T-cell exhaustion and expanding T-cell diversity. Clinical trials in melanoma, head and neck cancer and breast cancer showed superior efficacy. The Objective Response Rate (ORR) of combination therapy was 39%-62%, while the ORR of ICI monotherapy was 18%. Treatment heterogeneity is mainly attributed to virus-related factors, including targeting specificity and replication efficiency, tumor characteristics, such as antigen presenting ability and mutation load, and host immune status, including pre-existing antiviral antibodies and microbiome composition. This combined approach represents a paradigm shift in cancer immunotherapy, which effectively transforms immune "cold" tumors into "hot" tumors through the continuous activation of innate and adaptive immune responses. In the future, it is expected to improve the therapeutic effect of treatment-resistant malignant tumors through the integration of immune regulatory molecules, accurate biomarkers to guide the treatment scheme and triple combination strategy by a new generation of engineering viruses.},
}

Humans
*Oncolytic Virotherapy/methods/adverse effects
*Immune Checkpoint Inhibitors/therapeutic use/adverse effects/pharmacology
*Neoplasms/therapy/immunology
Combined Modality Therapy
Tumor Microenvironment/immunology/drug effects
Oncolytic Viruses/immunology
Immunotherapy/methods
Animals

@article {pmid41425618,
year = {2025},
author = {Fuller-Shavel, N and Davies, EJ and Peleg Hasson, S},
title = {Nutritional strategies in supporting immune checkpoint inhibitor, PI3K inhibitor, and tyrosine kinase inhibitor cancer therapies.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1670598},
pmid = {41425618},
issn = {2296-861X},
abstract = {Nutritional status of patients undergoing cancer treatment has been associated with cancer therapy and survival outcomes across multiple therapy types. Targeted therapies, including immune checkpoint inhibitors (ICIs), phosphatidylinositol 3-kinase (PI3K) inhibitors and EGFR-tyrosine kinase inhibitors (TKIs), are both influenced by and themselves influence the patients' nutritional and metabolic status. Precision nutrition approaches that address specific aspects of targeted therapies, from minimizing toxicities and treatment resistance to potential therapeutic synergies, offer an important avenue to optimize clinical outcomes for patients receiving targeted oncological treatments as a part of an overall precision integrative oncology approach. Optimizing ICI treatment may necessitate gastrointestinal microbiome modulation and managing systemic inflammation with a variety of dietary approaches under study, including the Mediterranean diet, increasing fiber and fermented food intake, fasting and fasting mimicking diet and the ketogenic diet. Supplementation approaches using live biotherapeutics alongside ICIs predominate over prebiotic, postbiotic and synbiotic studies, which require further attention and investment, alongside human research on mycotherapy and fucoidan-based combinations. Optimizing PI3K treatment tolerance requires close attention to monitoring and managing glycemic control through nutrition, lifestyle and pharmacological intervention as necessary, and in supporting patients with EGFR-TKIs both nutritional prehabilitation and close attention to managing gastrointestinal toxicities is paramount. Rational individualized approaches based on detailed and dynamic clinical assessment of patient-, cancer- and treatment-related factors, using validated prognostic scores and biomarkers, are needed to maximize the potential of precision nutrition now and in future trials in this arena.},
}

@article {pmid41425608,
year = {2025},
author = {Yaghoubi Khanghahi, M and AbdElgawad, H and Curci, M and Garrigues, R and Korany, SM and Alsherif, EA and Verbruggen, E and Spagnuolo, M and Addesso, R and Sofo, A and Beemster, GTS and Crecchio, C},
title = {Transcriptomic, biochemical, and microbiome assessments into drought and salinity tolerance in durum wheat mediated by plant growth-promoting bacteria.},
journal = {Physiology and molecular biology of plants : an international journal of functional plant biology},
volume = {31},
number = {12},
pages = {2121-2143},
pmid = {41425608},
issn = {0971-5894},
abstract = {UNLABELLED: This study investigates the efficacy of plant growth-promoting bacteria (PGPB) in improving stress tolerance in plants by analyzing the molecular and biochemical bases in durum wheat grain. An experiment was conducted where soil and seeds were inoculated with PGPB, under drought and salinity stress. 16 S rRNA sequencing indicated no change in grain bacterial communities in response to biofertilizers and stress. However, a genome-wide analysis identified 153 up-regulated and 33 down-regulated plant genes in response to PGPB, predominantly enriched in stress-related biological processes. These genes specifically encode for proteins involved in metabolite interconversion enzyme, chaperone, protein modifying enzyme, and transporters, which are functionally related groups assisting protein folding in the cell under stress conditions. Moreover, pathway analysis confirmed related changes at the metabolite and enzyme activity levels. In this regard, PGPB-treated plants exhibited heightened activity of both enzymatic and non-enzymatic (e.g., thioredoxins, peroxiredoxins, etc.) antioxidants under stress, showcasing significant enhancements ranging from + 27% to + 283% and + 36% to + 266%, respectively. Further elucidation of biochemical pathways revealed alterations in the activation of non-antioxidant enzymes in PGPB-treated plants, exemplified by increased activities of glutamate synthase (40-44%) and decreased activities of protein-tyrosine-phosphatase (29-31%) under both stresses, as well as elevated activities of anthocyanidin reductase (91%) and lipoxygenases (18%) specifically under drought. Overall, the present research highlighted the potential of beneficial bacteria in improving plant stress tolerance, especially under drought, through shifting transcriptome expression of plant genes and employing multiple protective strategies which can complement each other.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-025-01686-z.},
}

@article {pmid41425546,
year = {2025},
author = {Müller, L and Di Benedetto, S},
title = {Immunosenescence and inflammaging: Mechanisms and modulation through diet and lifestyle.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1708280},
pmid = {41425546},
issn = {1664-3224},
mesh = {Humans ; *Immunosenescence ; *Inflammation/immunology/metabolism ; *Life Style ; *Diet ; Animals ; Gastrointestinal Microbiome/immunology ; *Aging/immunology ; },
abstract = {Aging is associated with profound alterations in the immune system, characterized by immunosenescence and inflammaging, which together compromise host defense, promote chronic low-grade inflammation, and contribute to the development of age-related diseases. Immunosenescence involves thymic involution, hematopoietic stem cell skewing, accumulation of senescent immune cells, and impaired adaptive and innate responses. Inflammaging arises from persistent activation of innate immune pathways, senescence-associated secretory phenotype (SASP) signaling, metabolic dysregulation, and age-related alterations in the gut microbiome. These processes are interconnected through feedback loops and network-level interactions among immune, metabolic, and microbial systems, creating a self-perpetuating cycle of immune dysfunction and systemic inflammation. Emerging evidence indicates that immunosenescence and inflammaging can be modulated through integrative strategies that combine nutrition, microbiome modulation, and lifestyle interventions to sustain immune resilience across the lifespan. Nutrient-specific strategies, including polyphenols, omega-3 fatty acids, and micronutrients, regulate oxidative stress, cytokine signaling, and immune cell metabolism. Holistic dietary patterns such as the Mediterranean diet, caloric restriction, and microbiome-supportive diets enhance gut barrier integrity, modulate systemic inflammation, and improve adaptive immunity. Lifestyle factors, including regular physical activity, adequate sleep, and stress reduction, further support immune resilience. Personalized nutrition and lifestyle strategies, guided by immunobiological profiling, enable tailored approaches to mitigate immune aging. Collectively, these insights highlight a multidimensional framework for understanding and modulating immunosenescence and inflammaging. Integrating dietary, lifestyle, and pharmacological strategies offers a promising path toward enhancing immune function, reducing chronic inflammation, and promoting healthy longevity.},
}

Humans
*Immunosenescence
*Inflammation/immunology/metabolism
*Life Style
*Diet
Animals
Gastrointestinal Microbiome/immunology
*Aging/immunology

@article {pmid41425113,
year = {2025},
author = {Wang, D and Zhang, J and Wang, B and Gao, J and Zhang, G},
title = {Current Trends and Future Insights on Rosacea Treatment: A Bibliometric Analysis.},
journal = {Clinical, cosmetic and investigational dermatology},
volume = {18},
number = {},
pages = {3397-3412},
pmid = {41425113},
issn = {1178-7015},
abstract = {BACKGROUND: Rosacea involves immune, neurovascular, and microbial factors, but its complex mechanisms are poorly understood, hindering effective treatment development. This study aims to examine research trends and significant contributions in the treatment of rosacea.

METHODS: Publications related to rosacea treatment were retrieved from the Web of Science Core Collection (WoSCC). Bibliometric analysis and visualization were performed using VOSviewer, CiteSpace, and the R package "bibliometrix".

RESULTS: By June 7, 2024, 1389 English-language publications published between 1970 and 2024 were identified for analysis. The leading research countries were the United States (446 articles) and China (149 articles), with the Central South University (95 articles) being the most productive institution. Key journals included Journal of the American Academy of Dermatology (impact factor = 12.8) and the British Journal of Dermatology (impact factor = 11). James Q. Del Rosso was identified as a major contributor (h-index = 20). Keywords cluster analysis revealed five prominent themes: 1) pharmacological treatment and clinical trials, 2) epidemiology and associated risk factors, 3) pathophysiology and pathogenesis, 4) skin barrier function and related dermatoses, and 5) laser and physical therapies. Representative terms of emerging trends include "pathogenesis", "pathophysiology", and "standard classification", suggesting increasing focus on immune dysregulation, neurovascular mechanisms, and microbiome-related pathways. These insights indicate that future rosacea treatment research may shift toward targeted, mechanism-based therapeutic strategies.

CONCLUSION: This study underscores the dynamic landscape of research in rosacea treatment, synthesizes current areas of emphasis, and forecasts future trends. Future developments in rosacea research may concentrate on integrating precision medicine approaches by linking molecularly defined pathogenic mechanisms with standardized classification systems, thereby facilitating targeted and multidisciplinary treatment strategies.},
}

@article {pmid41424975,
year = {2025},
author = {Ma, L and Wang, H and Jin, Q and Sun, Z and Yu, S and Zhang, Y},
title = {The Gut-Liver Axis: Molecular Mechanisms and Therapeutic Targeting in Liver Disease.},
journal = {International journal of general medicine},
volume = {18},
number = {},
pages = {7531-7546},
pmid = {41424975},
issn = {1178-7074},
abstract = {The gut microbiota, often termed the "second genome", demonstrates profound therapeutic potential through its intricate biological network connecting multiple distal organs. Although microbial diversity is strongly correlated with intestinal health, its systemic implications on overall physiological homeostasis remain incompletely understood. This review synthesizes the latest evidence from clinical trials, randomized controlled trials (RCTs), systematic reviews, and meta-analyses to elucidate the biological pathways and therapeutic applications of the gut-liver axis. Through comprehensive schematic illustrations, we delineate the molecular mechanisms underlying bidirectional gut-liver communication, including microbial metabolite signaling, immune modulation networks, and enterohepatic circulation dynamics. Although interventional studies have confirmed the beneficial physiological effects of microbial modulation, current mechanistic insights are predominantly derived from animal models with limited clinical translation. While large-scale cohort studies with long-term follow-up data remain imperative, the existing evidence strongly supports the clinical value of microbiome-targeted strategies for treating hepatic diseases and related complications. These findings establish a critical theoretical framework for the development of next-generation microbial therapeutics targeting the gut-liver axis. The novelty of this review lies in its systematic classification of gut microbiota and their metabolites in the pathogenesis and treatment of various liver diseases, its detailed elaboration on signaling pathways, and its dedicated focus on the role of Traditional Chinese Medicine (TCM) in modulating the gut-liver axis.},
}

@article {pmid41424906,
year = {2025},
author = {Goswami, A and Ghosh, S and Bandyopadhyay, A and Saha, RG and Sengupta, P and Bhuniya, U and Mandal, P},
title = {Comparative Analysis of Vaginal Microbiome Associated with Oncogenic HPV Infection Among Different Ethnic Groups of Women of the Eastern Region of India.},
journal = {Indian journal of microbiology},
volume = {65},
number = {4},
pages = {1877-1890},
pmid = {41424906},
issn = {0046-8991},
abstract = {The study aimed to identify the influence of vaginal bacterial composition on HPV infection among tribal women of the eastern region of India compared to non-tribal women of the same region. For this study, 13 tribal women and 12 non-tribal women were recruited. DNA was isolated from vaginal swab samples, and subsequently, 16S rRNA gene analysis was performed. We identified two distinct clusters of samples based on taxonomic profiling and bacterial diversity. One cluster belonged to HPV negative samples and the other to HPV16/18 positive samples. The abundance of three bacterial species was significantly lower (p value < 0.05) among oncogenic HPV positive samples (mean abundance = 4.33, 0, and 0, respectively) compared to HPV negative samples (mean abundance = 29.71, 45.73, and 19.01, respectively) irrespective of their ethnicities, such as Lactobacillus amylolyticus, Bacillus coagulans, and Costridium sensu stricto. HPV16/18 positive samples also represent the differential microbiome composition between the two ethnic groups of women. Ethnicity specific variations in human vaginal microbiome composition might be recommended for geographically tailored microbiome-based therapeutic strategies.},
}

@article {pmid41424898,
year = {2025},
author = {Chattopadhyay, P and Biswas, I and Banerjee, G},
title = {Analysing the Metagenomic Dynamics of Soil Microbiota Affected by Tea Pruning and Skiffing Methods in Tea Plantations of Dibrugarh, Assam, India.},
journal = {Indian journal of microbiology},
volume = {65},
number = {4},
pages = {2015-2020},
pmid = {41424898},
issn = {0046-8991},
abstract = {Beginning with the centralization of young tea (Yt) to encourage low branch growth, subsequent light pruning (LP) and deep skiffing (DS) techniques are employed to promote branch spread, ensuring an ideal leaf area index and manageable plucking height. This study investigates the effects of LP and DS compared to Yt on soil biota, a previously unexplored topic. Soil samples from Yt, LP, and DS sites within the Rajgarh Tea Estate in Assam, India, were analyzed for standard parameters and metagenomic DNA using Illumina sequencing. While all samples exhibited a clay loam texture with minimal parameter variation, significant variations in soil phyla abundance were observed. Acidobacteria dominated across all samples, but linear discriminant analysis revealed distinct phyla compositions. At the genus level, Geobacter, Verticiella, and Glaciihabitans were most abundant in S11, S7, and S9 samples, respectively. However, the relative abundance of phyla in the soil samples from Yt, LP, and DS sites varies significantly. But the difference in bacterial community at genus level resolution was not significant at p value 0.05 level. These findings indicate that pruning and skiffing primarily impact on the relative abundance of soil phyla, not microbial diversity. Understanding the soil microbiota in relation to tea cultivation practices through metagenomics can pave the way for developing new microbial consortia for an integrated crop management system in tea cultivation.},
}

@article {pmid41424782,
year = {2025},
author = {Xu, M and Yu, Y and Li, L and Zhao, K and Lai, J and Wei, L and Ge, L},
title = {Rhein ameliorates inflammation, gut dysbiosis, and renal injury in obesity-related glomerulopathy mice.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1654062},
pmid = {41424782},
issn = {1663-9812},
abstract = {OBJECTIVE: Obesity-related glomerulopathy (ORG) lacks targeted therapies. Rhein, a bioactive anthraquinone from Rhei Radix et Rhizoma, was evaluated for its effects on inflammation, renal function, and gut microbiota in high-fat diet-induced ORG mice.

METHODS: C57BL/6J mice were fed a 60% fat diet for 12 weeks to establish ORG, followed by 300 mg/kg/day rhein free intake for 12 weeks. Serum cytokines (IL-6, TNF-α), renal histopathology, and 16S rRNA microbiome sequencing were analyzed.

RESULTS: Rhein significantly reduced body weight (P < 0.001), serum triglycerides (P < 0.01), and proteinuria (P < 0.001), while improving glomerular lesions. It also markedly lowered serum levels of IL-6, TNF-α, and creatinine. 16S rRNA sequencing revealed that rhein restored gut microbiota diversity (e.g., Chao1 index increased from 303.58 to 425.78) and reversed the Firmicutes/Bacteroidetes imbalance (76.86%-62.15%). Analysis of similarities (ANOSIM) further confirmed a significant difference in microbial community structure between the Rhein and Model groups (R = 0.926, p = 0.008).

CONCLUSION: Rhein mitigates ORG progression is associated with anti-inflammatory, lipid-lowering, and microbiota-modulating mechanisms, offering a novel therapeutic strategy.},
}

@article {pmid41424704,
year = {2025},
author = {Araújo, JPM and Przelomska, NAS and Smith, RJ and Drechsler-Santos, ER and Alves-Silva, G and Martins-Cunha, K and Hosoya, T and Luangsa-Ard, JJ and Perrigo, A and Repullés, M and Matos-Maraví, P and Woods, R and Pérez-Escobar, OA and Antonelli, A},
title = {A new species of Purpureocillium (Ophiocordycipitaceae) fungus parasitizing trapdoor spiders in Brazil's Atlantic Forest and its associated microbiome revealed through in situ "taxogenomics".},
journal = {IMA fungus},
volume = {16},
number = {},
pages = {e168534},
pmid = {41424704},
issn = {2210-6340},
abstract = {Our planet is inhabited by an estimated 2.5 million species of fungi, of which fewer than 10% have been scientifically described. Some of the most understudied yet remarkable fungal species are those capable of parasitizing arthropods, notably insects and spiders. Here, we explore the hidden diversity of a spider-attacking (araneopathogenic) fungus and its associated microbiome in one of the world's most biodiverse yet threatened biomes, the Atlantic Forest. We apply a field-based "taxogenomic" approach, comprising the integration of classical fungal taxonomy and genomic characterization of a sample's endogenous, associated, and incidental DNA. The data we produced in the field reveal a new species of Purpureocillium fungus belonging to the P. atypicola group, parasitizing trapdoor spiders, and provide a snapshot of its associated bacterial and fungal microbiota. Molecular, morphological, and ecological data support P. atypicola as a complex of cryptic species infecting a variety of ecologically distinct spider species globally. We call for consolidated efforts to accelerate and facilitate the publication of both new species and the characterization of the genomic composition of their associated taxa.},
}

@article {pmid41424695,
year = {2025},
author = {Wang, X and Yue, R and Wen, J and Wu, H and Zhou, X and Chen, Y and Luo, L and Lin, S and Ai, Q and He, Y and Zhao, W},
title = {Alanyl-Glutamine Attenuates Soybean Meal-Induced Intestinal Dysfunction and Growth Retardation in Largemouth Bass (Micropterus salmoides).},
journal = {Aquaculture nutrition},
volume = {2025},
number = {},
pages = {7842137},
pmid = {41424695},
issn = {1365-2095},
abstract = {This study investigated the mitigating effects of alanyl-glutamine (AG) on soybean-meal-induced enteritis (SBMIE) in largemouth bass (Micropterus salmoides). Three experimental diets were prepared: a fishmeal (FM) diet as a positive control, a 50% soybean meal (SBM) replacement FM protein (SBM50) diet as a negative control, and the SBM50 diet supplemented with 1% AG (SBM50 + 1% AG). Fish (initial weight: 10.20 ± 0.20 g) were distributed into three groups in triplicate (25 fish per tank) and fed for 8 weeks. Results demonstrated that the SBM50 + 1% AG group exhibited markedly higher final body weight, weight gain rate, and specific growth rate compared to the SBM50 (p < 0.05). The SBM50 + 1% AG group markedly elevated serum levels of free glycine, lysine, and total essential amino acids compared to the FM group (p < 0.05). In addition, the SBM50 + 1% AG group markedly increased the intestinal plica height (PH) and goblet cell numbers compared to the SBM50 group (p < 0.05). Pathological alterations, including villous atrophy, nuclear pyknosis, mitochondrial matrix dissolution, and inner membrane disruption, were shown in the SBM50 group, all of which were ameliorated by AG supplementation. In addition, the addition of AG significantly reduced Caspase3 activity compared to the FM group (p < 0.05). Microbiome analysis revealed dietary AG significantly increased α-diversity and the proliferation of potentially beneficial taxa (Bacteroidota, Bacteroides, and Prevotella) (p < 0.05). Transcriptomics showed dietary AG upregulated intestinal barrier-related pathways (including focal adhesion, cell adhesion molecules, and adherens junction), along with tight junction gene expression (zo-1, claudin-3, and filamin-B). In conclusion, high dietary SBM inclusion impairs growth performance and induces intestinal inflammation in largemouth bass. Dietary AG effectively mitigates SBMIE by remodeling the intestinal microbiota, enhancing intestinal barrier integrity, and modulating immune responses.},
}

@article {pmid41424621,
year = {2025},
author = {Shangguan, Y and Zhu, J and Ye, J and Korpelainen, H and Li, C},
title = {Selenium phytofortification: enhanced stress resistance and nutraceutical enrichment in horticultural crops.},
journal = {Horticulture research},
volume = {12},
number = {12},
pages = {uhaf236},
pmid = {41424621},
issn = {2662-6810},
abstract = {As a bridge between human health and plant nutrition, Selenium (Se) phytofortification represents a promising strategy for achieving a safe and effective dietary Se supplementation. Due to chemical similarities, Se absorption, transformation, and storage in crops primarily follow the sulfur metabolic pathway. Se enhances horticultural crop resilience against abiotic and biotic stresses by: (i) boosting antioxidant capacity, (ii) inducing hormonal cascades, (iii) promoting the accumulation of key metabolites (e.g. amino acids, flavonoids), (iv) strengthening cellular functions, and (v) harnessing plant-microbiome interactions. In horticultural crops, most Se exists in organic forms, such as selenoamino acids, selenoproteins, selenium-polysaccharides, and selenium-polyphenols, which contribute to unique quality traits. Additionally, Se regulates the synthesis of core nutrients, including amino acids, flavonoids, phenolic compounds, soluble sugars, mineral elements, alkaloids, and volatile compounds. It also extends postharvest shelf life by delaying senescence and deterioration. Current phytofortification strategies focus on enhancing bioavailable Se in edible parts through agronomic interventions and plant breeding. Artificial Se fertilization is the most common agronomic approach, classified by the application method (soil fertilization, foliar spraying, hydroponic supplementation, and seed soaking) and fertilizer type (inorganic, organic, nano-Se, and biosynthesized fertilizers). Optimizing plant species, fertilization methods, dosage, timing, and elemental synergies maximize phytofortification efficiency.},
}

@article {pmid41424618,
year = {2025},
author = {Pandey, SN and Goyal, K and Rana, M and Menon, SV and Ray, S and Ali, H and Kumbhar, PS and Disouza, J and Singh, SK and Gupta, G and Wong, LS and Kumarasamy, V and Subramaniyan, V},
title = {Microbiome-derived bile acids as endogenous regenerative mediators in liver repair.},
journal = {Regenerative therapy},
volume = {30},
number = {},
pages = {681-690},
pmid = {41424618},
issn = {2352-3204},
abstract = {The liver's extraordinary capacity for self-repair is often compromised by chronic injury, fibrosis, or extensive resection, creating an urgent need for innovative regenerative therapies to restore liver function. Emerging evidence suggests that microbiome-derived bile acid metabolites are potent endogenous mediators of hepatic regeneration. Beyond their canonical role in lipid emulsification, these chemically diverse molecules engage nuclear and membrane receptors, most notably the farnesoid X receptor (FXR) and Takeda G protein-coupled receptor 5 (TGR5), to stimulate hepatocyte proliferation, modulate inflammatory responses, and reactivate quiescent progenitor cells. In this review, we integrate mechanistic insights from partial hepatectomy, germ-free, and antibiotic-treated animal models with early clinical observations to illuminate how primary and secondary bile acids orchestrate cell cycle progression, cytokine balance, and extracellular matrix remodeling. We then examined the therapeutic landscape, from synthetic FXR/TGR5 agonists to live-biotherapeutic approaches, genetically modified probiotic strains, and fecal microbiota transplantation. We highlight the preliminary indicators of efficacy and challenges in manufacturing consistency, safety profiling, and regulatory classification. We address the interindividual variability in microbiome composition, potential biomarkers such as serum FGF19, imaging-based measures of functional liver mass, and considerations for optimal trial design. This is the first comprehensive review to frame microbiome-driven bile acids as direct modulators of liver regeneration and chart a coherent translational development pathway. By integrating stem cell biology, hepatology, microbiology, and bioengineering perspectives, we demonstrate the underexplored therapeutic potential of these approaches to transform the future of hepatic repair.},
}

@article {pmid41424605,
year = {2025},
author = {Kay, E and Kazi, M and Burton, J and Parvathy, SN},
title = {Therapeutic properties of plant-derived prebiotics in melanoma.},
journal = {Exploration of targeted anti-tumor therapy},
volume = {6},
number = {},
pages = {1002354},
pmid = {41424605},
issn = {2692-3114},
abstract = {Immune checkpoint inhibitor (ICI) therapy has revolutionized metastatic melanoma treatment, yet only a subset of patients respond effectively, and the treatment can induce a variety of immune-related adverse events (irAEs), including colitis. The gut microbiome plays a critical role in determining patient responses to immunotherapy, prompting exploration of gut-modifying strategies such as prebiotics, probiotics, and fecal microbiota transplantation (FMT) to overcome both primary and acquired resistance and improve treatment outcomes. Prebiotics, defined as dietary substrates that selectively support the growth and/or activity of beneficial gut microorganisms, represent a feasible and safe strategy for microbiome reshaping. Plant-derived prebiotics like castalagin, inulin, fructooligosaccharides, galactooligosaccharides, mushroom extract, kale extract, and konjac glucomannan offer unique advantages over synthetic or animal-derived alternatives due to their natural fiber content alongside their ability to enhance gut microbial diversity. Prebiotics are known to achieve health benefits by selectively stimulating beneficial gut bacteria, producing short-chain fatty acids (SCFAs) that modulate the host immune system, suppressing pathogenic microbes, enhancing mucin production, and modulating systemic and gut-associated immune responses. SCFAs generated through prebiotic fermentation influence host innate and adaptive immunity and regulate metabolic activity via inhibition of histone deacetylases (HDACs), influencing mTOR/MAPK signaling and cytokine production. They also act as ligands for G-protein-coupled receptors (GPCRs), altering intracellular calcium and cAMP to modulate immune cell gene expression. However, the specific mechanisms by which individual prebiotics interact with host genetics, beneficial gut bacteria, and their metabolites are not very well understood. This is crucial to optimize their therapeutic potential in cancer immunotherapy. This review synthesizes current evidence on plant-derived prebiotics, highlighting the impact of beneficial gut bacteria and their metabolites. Given their established safety for human consumption, prebiotics represent a promising, low-risk option to improve gut microbiome composition and potentially enhance immunotherapy and clinical outcomes in cancer.},
}

@article {pmid41424562,
year = {2025},
author = {Andargie, YE and Lee, G and Kim, MJ and Fentie, EG and Jeong, M and Tagele, SB and Lim, K and Azizoglu, U and Shin, JH},
title = {Soil microbial load modulation improves plant-microbe interactions and bioinoculant efficacy in pathogen-stressed soils.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1712997},
pmid = {41424562},
issn = {1664-462X},
abstract = {Plants establish a close association with a community of microbes naturally living in the soil, known as resident soil microbiome, which typically maintains a dynamic equilibrium that confers resilience against biotic and abiotic perturbations. However, this microbiome can also reduce the success of adding new helpful microbes (bioinoculants) by reducing their functional integration with the host plant. Although bioinoculants often perform well under controlled conditions, their efficacy in pathogenic soils is frequently compromised even after repeated applications. While several factors influencing inoculation success have been examined, the impact of soil microbial load, its dynamics, and associated transcriptomic consequences remain largely overlooked. To address this gap, we induced dysbiosis in the resident soil microbiome using moist heat treatment (MHT) thereby generating a gradient in microbial load. We then assessed the phenotypic and transcriptomic responses of Cucumis sativus L., for bioinoculants alongside relative and quantitative rhizosphere microbiome profiling. MHT reduced resident soil bacterial abundance by 96.4% ± 0.9%, with 78% recovery observed after planting. This recolonization promoted plant growth and overall health by restructuring the rhizosphere microbiome and activating plant-microbe interaction pathways such as sugar metabolism, nitrogen metabolism, and aromatic compound degradation. In contrast, moist heat untreated (native) rhizosphere, with a microbial load threefold higher, resisted restructuring, favoring metabolic pathways that preserve microbial stability, such as cell wall and signal molecule biosynthesis, at the expense of plant health. Transcriptomic analyses revealed that, in moist heat treated (dysbiotic) soil conditions, bioagent inoculation triggered induced systemic resistance in cucumber, characterized by downregulation of PAL and POX gene families together with SAMDC, and upregulation of auxin-regulatory and calcium uniporter genes. This response reflected a reallocation of metabolic energy from defense to growth, while maintaining active signaling for beneficial colonization and pathogen perception via modulation of calcium influx. Our findings highlight microbial load modulation as a key strategy to facilitate rhizosphere remodeling, enhance bioinoculant efficacy, and promote plant transcriptomic responses.},
}

@article {pmid41424555,
year = {2025},
author = {Qiao, J and Shen, L and Liu, J and Sun, J and Dai, Z and Hu, J and Du, C and Yang, J and Li, J and Zhao, J and Chen, X},
title = {Graphene oxide promotes soybean growth by reshaping the rhizosphere microbiome and enhancing soil fertility.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1683882},
pmid = {41424555},
issn = {1664-462X},
abstract = {Soybean (Glycine max L.) one of the world's most important crops that is prized for its high protein and lipid content. As a prominent member of the carbon nanomaterial family, graphene oxide (GO) exhibits remarkable fertilizer adsorption and slow-release capabilities owing to its high specific surface area and abundant oxygen-containing functional groups, demonstrating broad application prospects in agricultural production. However, its potential role in regulating soybean growth and modulating the rhizosphere microbiome remains poorly understood. To elucidate the mechanism by which GO modulates soybean growth, we investigated eight cultivars (SN24, CD5, 7534, 15GI-16, ZH75, G135, L2012-7, and CD13) with a 30 mg/L GO treatment. The results demonstrate that GO application significantly enhanced key agronomic traits, increasing plant height by 7.17-51.05%, stem diameter by 12.39-63.34%, and the number of root nodules by 33.33-328.57%, along with increase in root biomass. Rhizosphere microbiome analysis revealed that GO restructured microbial communities in L2012-7 and significantly increased bacterial and fungal abundance or diversity based on operational taxonomic unit (OTU) levels (p < 0.05). Taxonomic profiling identified GO-enriched beneficial genera (Sinorhizobium, Sphingomonas and Trichoderma), with LEfSe and Random Forest analyses confirming that Sinorhizobium is a keystone taxon. Mechanistically, Sinorhizobium fredii (Sf01) was successfully isolated and identified from soybean rhizosphere soil, which was shown to promote soybean growth. Treatment with 5, 30, and 50 mg/L GO promoted the colony growth of S. fredii (Sf01) by 40.2%, 42.9%, and 55.5%, respectively, whereas 100 mg/L GO inhibited its growth compared to the control. Furthermore, soil nutrient analysis demonstrated that GO significantly enhanced the contents of soil organic matter, total nitrogen, available potassium, available phosphorus, ammonium nitrogen, and humic acid in soybean rhizosphere soil. Our experimental results demonstrate that GO reshapes the soybean rhizosphere microbial community, which in turn enriches keystone beneficial microbes S. fredii (Sf01) and enhances soil fertility retention capacity. This cascade of effects collectively promotes soybean plant growth, offering a nano-enabled strategy to reduce reliance on synthetic fertilizers.},
}

@article {pmid41424302,
year = {2026},
author = {Meng, X and Hao, R and Liu, K and Zhang, P and An, C and Zhang, Y and Li, H and Wu, B and Li, M and Yu, X and Tong, X},
title = {The trilateral nexus of autoimmune thyroiditis: integrating immunological triggers, endocrine disruption, and gut microbiome alterations for treatment strategies.},
journal = {Autoimmunity},
volume = {59},
number = {1},
pages = {2601015},
doi = {10.1080/08916934.2025.2601015},
pmid = {41424302},
issn = {1607-842X},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Thyroiditis, Autoimmune/immunology/therapy/metabolism/etiology/microbiology ; Dysbiosis/immunology ; Animals ; Thyroid Hormones/metabolism ; Thyroid Gland/immunology/metabolism ; Autoantibodies/immunology ; },
abstract = {The pathogenesis of autoimmune thyroiditis (AIT) is intricately linked to immune dysregulation, endocrine imbalance, and gut microbiota dysbiosis. The immune system drives autoimmune attacks against thyroid tissue through Th1/Th2 cell imbalance, Treg dysfunction, and excessive release of proinflammatory cytokines. Thyroid hormone regulation primarily occurs via the hypothalamic-pituitary-thyroid (HPT) axis. Elevated levels of TPOAb and TgAb in AIT patients can lead to hypothyroidism by affecting the HPT feedback loop. Thyroid hormone regulation of immune cell metabolism and differentiation, in turn, affects immune homeostasis, forming a bidirectional regulatory network. Recent studies further reveal that the gut microbiota influences systemic immune tolerance by regulating intestinal barrier integrity and metabolites (e.g. short-chain fatty acids and secondary bile acids). Abnormal abundance of specific genera (e.g. Bacteroides and Prevotella) can promote the production of thyroid autoantibodies (TPOAb/TgAb), and increased intestinal permeability caused by microbiota dysbiosis may facilitate cross-reactivity between microbial antigens and thyroid antigens. Furthermore, the gut microbiota indirectly regulates thyroid function through the HPT axis. This review aims to summarize the current knowledge regarding the specific molecular mechanisms of gut microbiota-immune-endocrine interactions in AIT, offer important references for researching the treatment directions of AIT.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Thyroiditis, Autoimmune/immunology/therapy/metabolism/etiology/microbiology
Dysbiosis/immunology
Animals
Thyroid Hormones/metabolism
Thyroid Gland/immunology/metabolism
Autoantibodies/immunology

@article {pmid41424105,
year = {2025},
author = {Sangavi, R and Malligarjunan, N and Pandian, SK and Gowrishankar, S},
title = {Ricinoleic Acid Potentiates Sodium Fluoride's Antibacterial Action Against Streptococcus mutans: A Synergistic Approach for Caries Control.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {133},
number = {12},
pages = {e70125},
doi = {10.1111/apm.70125},
pmid = {41424105},
issn = {1600-0463},
support = {CMRG2023BBT05036//Directorate of Technical Education/ ; ANRF/IRG/2024/001173/LS//Anusandhan National Research Foundation/ ; //University Grants Commission/ ; },
mesh = {*Sodium Fluoride/pharmacology ; *Streptococcus mutans/drug effects ; Drug Synergism ; *Anti-Bacterial Agents/pharmacology ; Biofilms/drug effects ; Microbial Sensitivity Tests ; *Dental Caries/prevention & control/microbiology/drug therapy ; *Ricinoleic Acids/pharmacology ; Reactive Oxygen Species/metabolism ; Humans ; },
abstract = {Dental caries arises from dysbiosis of the oral microbiome, wherein acidogenic pathogens such as Streptococcus mutans dominate over protective commensals. Sodium fluoride (NaF) remains a cornerstone in caries prevention; however, its limited efficacy in high-risk individuals and the emergence of fluoride-resistant strains highlight the need for enhanced therapeutic strategies. The present study investigates the synergistic antibacterial potential of NaF combined with ricinoleic acid (RA), a bioactive fatty acid with established antimicrobial activity. Checkerboard and time-kill assays revealed a strong synergistic interaction between RA and NaF, with a combinatorial minimum inhibitory concentration (CMIC) of 64 + 128 μg/mL, respectively. Complete eradication of S. mutans was achieved within 120 min at CMIC (64 + 128 μg/mL). The combination significantly disrupted mature biofilms, resulting in an 82% reduction in total biomass as confirmed by confocal microscopy. Mechanistic analyses indicated that RA triggered reactive oxygen species (ROS) generation and membrane perturbation, which facilitated enhanced NaF uptake and intracellular antibacterial action. Moreover, the RA-NaF combination markedly inhibited key virulence attributes of S. mutans, including acidogenesis and aciduricity, by approximately 76% and 71%, respectively. The treatment also exhibited a sustained post-antimicrobial effect lasting up to 12 h and did not induce bacterial resistance upon repeated exposure. Collectively, these findings highlight that RA potentiates the anticariogenic efficacy of NaF through a multi-targeted cellular mechanism involving oxidative stress induction, membrane disruption, and metabolic suppression. This synergistic combination represents a promising and fluoride-efficient strategy for the prevention and management of dental caries.},
}

*Sodium Fluoride/pharmacology
*Streptococcus mutans/drug effects
Drug Synergism
*Anti-Bacterial Agents/pharmacology
Biofilms/drug effects
Microbial Sensitivity Tests
*Dental Caries/prevention & control/microbiology/drug therapy
*Ricinoleic Acids/pharmacology
Reactive Oxygen Species/metabolism
Humans

@article {pmid41424069,
year = {2025},
author = {Prokopidis, K},
title = {Probiotics, prebiotics, and synbiotics to counteract sarcopenia: Where are we now and what challenges need to be faced?.},
journal = {The Proceedings of the Nutrition Society},
volume = {},
number = {},
pages = {1-17},
doi = {10.1017/S0029665125102036},
pmid = {41424069},
issn = {1475-2719},
abstract = {Sarcopenia, the age-related decline in muscle mass and strength, is a contributor to frailty and reduced quality of life. Emerging evidence suggests an emerging role of the gut microbiome in modulating skeletal muscle through microbial species and metabolites, such as short-chain fatty acids (SCFAs), potentially influencing glucose profile, inflammation, nutrient absorption, and protein metabolism. This review considers the potential of probiotics, prebiotics, and synbiotics as interventions to mitigate sarcopenia based on animal and human studies, while providing a critique of present barriers that need to be addressed. Preclinical models, including germ-free mice and faecal microbiota transplantation, demonstrate that gut microbiota from healthy or young donors may enhance overall muscle health via reductions in inflammatory and muscle atrophy markers. Limited human studies show that probiotics such as Lactobacillus and Bifidobacterium could improve branched chain amino acid (BCAA) bioavailability and potentially sarcopenia indices, although findings have been inconsistent. Particularly, challenges including inconsistent microbial assessments, lack of dietary control, and interindividual variability due to diet, age, genetics, comorbidities, and medications may hinder progress in this field. Delivery methods (e.g., capsules, fermented foods, or fortified products) could further complicate efficacy through probiotic stability and dietary restrictions in older adults. Standardized protocols (e.g., Strengthening The Organization and Reporting of Microbiome Studies (STORMS) checklist), and multi-omics approaches may be critical to address these limitations and identify microbial signatures linked to sarcopenia outcomes. While preclinical evidence highlights mechanistic pathways pertinent to amino acid metabolism, translating findings to humans requires rigorous experimental trials.},
}

@article {pmid41423966,
year = {2025},
author = {Rosales, SM and Klinges, JG and Clark, AS and Muller, EM and Huebner, LK},
title = {Stony Coral Tissue Loss Disease Results in Persistent Microbial-Level Disturbances on Coral Reef Ecosystems.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70264},
doi = {10.1111/1758-2229.70264},
pmid = {41423966},
issn = {1758-2229},
support = {X7-01D00820-0//U.S. Environmental Protection Agency/ ; //University of Miami/ ; NA 20OAR4320472//National Oceanic and Atmospheric Administration/ ; },
mesh = {*Anthozoa/microbiology ; Animals ; *Coral Reefs ; Florida ; *Microbiota ; Ecosystem ; *Bacteria/classification/genetics/isolation & purification ; Geologic Sediments/microbiology ; Seawater/microbiology ; Biodiversity ; },
abstract = {Stony coral tissue loss disease (SCTLD) has reduced coral diversity and homogenised benthic communities. Beyond coral loss, SCTLD may disrupt microbiome composition and function, affecting reef recovery. We examined microbiome changes of apparently healthy corals, water, and sediment at three patch reefs in the Lower Florida Keys during three SCTLD stages: before (vulnerable), during (epidemic), and after (endemic) the outbreak. SCTLD significantly altered microbial diversity and functional potential within apparently healthy corals and the surrounding reef environment. In corals, microbial alpha and beta diversity were highest at the vulnerable stage before declining by the endemic stage, indicating lingering impacts of SCTLD on microbial diversity. Network neighbour and betweenness analyses revealed a loss in connectivity in microbial communities in coral and sediments during the endemic stage. Microbial functional prediction indicated an increase in multidrug resistance and sulphur cycling genes in corals in the epidemic stage. Predicted nitrogen fixation genes were enriched in epidemic coral and seawater, and endemic coral and sediments. SCTLD-associated taxa increased in apparently healthy corals, water and sediments during the epidemic stage, with some taxa persisting in the reef environment during the endemic stage. Thus, SCTLD likely has lasting taxonomic and functional microbial disruptions in coral reef ecosystems.},
}

*Anthozoa/microbiology
Animals
*Coral Reefs
Florida
*Microbiota
Ecosystem
*Bacteria/classification/genetics/isolation & purification
Geologic Sediments/microbiology
Seawater/microbiology
Biodiversity

@article {pmid41423811,
year = {2025},
author = {Gordon, ES and Goc, J and Grier, A and Thomas, C and Lentine, J and Sockolow, RE and Sonnenberg, GF},
title = {Altered Gut Microbiota in Pediatric Quiescent Crohn's Disease Patients with Iron Deficiency Anemia.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf295},
pmid = {41423811},
issn = {1536-4844},
support = {//Weill Cornell Medicine Department of Pediatrics/ ; },
abstract = {BACKGROUND: Iron deficiency anemia (IDA) is the most common extra-intestinal complication in inflammatory bowel disease (IBD). The persistence of iron deficiency in patients living with quiescent IBD remains poorly understood. Given the extensive body of research linking IBD pathogenesis to microbiome disruptions, it is hypothesized that alterations in the microbiota or immune responses may drive the persistence of IDA in quiescent Crohn's disease. This study aimed to determine whether changes in the gut microbiota or immune phenotypes contribute to IDA, while uncovering potential mechanisms driving IDA in quiescent disease.

METHODS: This cross-sectional, descriptive, and analytical study utilized 141 samples from pediatric Crohn's disease patients with and without iron deficiency as well as healthy controls for initial 16S microbiome analysis and a smaller subset for Shotgun Metagenomics and immunologic analyses. Fecal and peripheral blood samples were obtained from the Jill Roberts Institute Live Cell Bank.

RESULTS: While no major differences were observed in the overall gut microbiome composition between pediatric patients with quiescent Crohn's disease, with or without IDA, notable shifts in specific microbial strains were identified. Specifically, levels of Anaerobutyricum soehngenii and Alistipes shahii were significantly altered. Metagenomic analysis revealed an enrichment of pathways related to short-chain fatty acid metabolism and ascorbate degradation, indicative of functional change in these microbes.

CONCLUSIONS: This is the first comprehensive microbiome analysis of quiescent pediatric Crohn's disease with concomitant IDA. The findings indicate modest but significant microbial strain-level differences and associated functional pathways, potentially implicating microbiota-mediated mechanisms in the persistence of IDA.},
}

@article {pmid41423748,
year = {2025},
author = {Wang, C and Zhan, D},
title = {Gut Microbiome and Paediatric Inflammatory Bowel Disease: Emerging Mechanistic and Therapeutic Insights Into Pathogenesis and Microbiota-Based Approaches.},
journal = {IET systems biology},
volume = {19},
number = {1},
pages = {e70047},
doi = {10.1049/syb2.70047},
pmid = {41423748},
issn = {1751-8857},
support = {202101AY070001-049//The Joint Project of Kunming Medical University and Science and Technology Agency/ ; 202101AT070199//Yunnan Fundamental Research Projects/ ; XDYC-QNRC-2022-0293//Yunnan Revitalization Talent Support Program/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology/therapy ; Child ; Dysbiosis/microbiology ; },
abstract = {The gut microbiome is crucial for paediatric intestinal development and holds therapeutic potential for inflammatory bowel disease (IBD). This review explores the link between gut microbiome dysbiosis and paediatric IBD pathogenesis. Microbial colonisation during early developmental windows establishes immune tolerance, reinforces epithelial barrier integrity and regulates metabolic functions. Dysbiosis contributes to disease through reduced beneficial microbial metabolites, impaired mucosal barriers and aberrant immune activation. Distinct dysbiosis signatures in paediatric patients correlate with clinical phenotypes and treatment responses, suggesting potential biomarkers. Emerging therapies include targeted nutritional therapies, designed microbial consortia, microbiota transplantation and tailored diets. By correcting underlying microbial imbalances, these approaches may offer more sustainable disease control with fewer side effects than conventional anti-inflammatory treatments. However, challenges persist, such as limited paediatric cohort sizes, a lack of causal mechanistic data and variability in microbiome profiles due to diet, geography and developmental stage. Future research requires larger longitudinal studies to develop paediatric-specific interventions that restore microbial equilibrium, ultimately transforming IBD management in children.},
}

Humans
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases/microbiology/therapy
Child
Dysbiosis/microbiology

@article {pmid41423687,
year = {2025},
author = {Han, S and Yang, Y and Xiong, S and Zheng, H and Yan, M and Yang, Y and Guo, S and Liu, H and Li, J and Yin, J and Li, R},
title = {Plant-microbiome interactions suppress Fusarium wilt by enriching beneficial Aspergillus in the tobacco rhizosphere.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00836-w},
pmid = {41423687},
issn = {2524-6372},
support = {SCYC202304//the Science and Technology Project of Sichuan Branch of China National Tobacco Corporation/ ; KTTQ2025018//the Fundamental Research Funds for the Central Universities/ ; PAPD//the Priority Academic Program Development of the Jiangsu Higher Education Institutions/ ; },
}

@article {pmid41423676,
year = {2025},
author = {Tian, M and Soleimani Samarkhazan, H and Alemohammad, SS and Manesh, MF and Tavakoli, F and Shams, A and Zeynalabadi, A},
title = {Microbiome dysbiosis and chemotherapy resistance in acute myeloid leukemia (AML).},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00891-8},
pmid = {41423676},
issn = {2055-5008},
abstract = {AML often relapses due to chemotherapy resistance, increasingly linked to gut microbiome dysbiosis. Microbial drug modification, immune modulation, and metabolite-driven survival/epigenetic changes (e.g., SCFAs, kynurenine) promote resistance. Clinical data associate reduced diversity, loss of Faecalibacterium, and Enterococcus overgrowth with poorer outcomes. Microbiome interventions (FMT, probiotics, diet) show promise; priorities are standardizing methods and defining microbe-metabolite mechanisms to guide trials.},
}

@article {pmid41423651,
year = {2025},
author = {Ammari, F and Mousavi, SN and Rad, ZA and Afshar, D},
title = {Relationship of dietary macronutrient intake with the relative abundance of bifidobacteria and lactobacilli in breast milk of normal-weight mothers compared to the obese: a case-control study.},
journal = {BMC nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40795-025-01226-8},
pmid = {41423651},
issn = {2055-0928},
abstract = {BACKGROUND: Lactobacillus and Bifidobacterium are members of the probiotic bacteria with many health benefits. Breast milk is an important source of these beneficial genera, which are affected by several factors. In the present study, the population of these genera was measured in milk of obese vs. normal-weight lactating women and their relationship with dietary macronutrient's intake was investigated.

METHODS: Twenty women with high body mass index (BMI) enrolled as obese (≥ 30 kg/m2) and 20 women with normal BMI (18.5-24.9 kg/m2) were selected as controls. Breast milk samples were collected 4 months after delivery (due to stabilization of milk microbiome). Dietary information was collected using a food frequency questionnaire. DNA was extracted from milk. The population of Bifidobacterium and Lactobacillus was measured against 16 S rRNA gene amplification method.

RESULTS: Bifidobacterium was significantly higher in breast milk of controls than the obese (p = 0.04). Bifidobacterium was 89% lower in breast milk of obese mothers than the controls, adjusting for the assessed parameters (p < 0.001). Pre-pregnancy weight showed a significant effect on the population of Bifidobacterium (p < 0.001). Energy, protein, carbohydrates, total fiber, soluble and insoluble fiber showed a positive effect on Bifidobacterium population, while dietary fat showed a negative effect (p < 0.001 in all cases).

CONCLUSIONS: The breast milk population of Bifidobacterium is associated with maternal weight. Maternal dietary intake of energy, carbohydrate, protein and fibre showed a positive effect on this genus, while dietary fat showed a negative effect.},
}

@article {pmid41423629,
year = {2025},
author = {Cunningham-Oakes, E and Price, V and Mphasa, M and Mallewa, J and Darby, AC and Feasey, NA and Lewis, JM},
title = {Quantifying the bystander effect of antimicrobial use on the gut microbiome and resistome in Malawian adults.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67677-6},
pmid = {41423629},
issn = {2041-1723},
support = {109105z/15/a//Wellcome Trust (Wellcome)/ ; 206545/Z/17/Z//Wellcome Trust (Wellcome)/ ; CL-2019-07-001//DH | National Institute for Health Research (NIHR)/ ; NIHR200632//DH | National Institute for Health Research (NIHR)/ ; },
abstract = {Antibiotic treatment for sepsis has an unintended yet crucial consequence: it exerts a bystander effect on the microbiome, changing its bacterial composition and resistome. Antimicrobial stewardship aims, in part, to minimise this effect to prevent development of subsequent drug-resistant infection, but data evaluating and quantifying these changes are largely lacking, especially in low-income settings which are disproportionately affected by antimicrobial resistance. Such data are critical to creating evidence-based stewardship protocols. Here, we address this data gap in Blantyre, Malawi. We use longitudinal sampling of human stool and metagenomic deep sequencing to describe microbiome composition and resistome pre-, during- and post-antimicrobial exposure. We develop Bayesian regression models to link these changes to individual antimicrobial agents. We find that ceftriaxone, in particular, exerts strong off-target effects, both increasing abundance of Enterobacterales, and the prevalence of macrolide and aminoglycoside resistance genes. Simulation from the fitted models allows exploration of different stewardship strategies and can inform practice in Malawi and elsewhere.},
}

@article {pmid41423312,
year = {2025},
author = {Bertin, L and Caldart, F and Savarino, EV},
title = {Non-pharmacological approaches in gastroesophageal reflux disease: Evidence-based dietary and lifestyle interventions.},
journal = {Best practice & research. Clinical gastroenterology},
volume = {79},
number = {},
pages = {102083},
doi = {10.1016/j.bpg.2025.102083},
pmid = {41423312},
issn = {1532-1916},
mesh = {Humans ; *Gastroesophageal Reflux/diet therapy/physiopathology/therapy/epidemiology/diagnosis ; Treatment Outcome ; Evidence-Based Medicine ; Diet, Carbohydrate-Restricted ; *Risk Reduction Behavior ; *Life Style ; Diet, Vegetarian ; Esophageal pH Monitoring ; },
abstract = {Gastroesophageal reflux disease (GERD) affects 18-28 % of Western populations, with 10-40 % experiencing refractory symptoms despite proton pump inhibitor therapy. We conducted a comprehensive narrative review of dietary interventions in GERD, analyzing studies that measured clinical efficacy through validated symptom scores (GERD-Q, RDQ) and objective reflux parameters (24-h pH-impedance monitoring, acid exposure time). We examined pathophysiological mechanisms, intervention efficacy, and clinical implementation strategies across diverse patient populations. Structured dietary interventions demonstrate clinically meaningful outcomes with robust mechanistic rationale. Low-carbohydrate approaches achieved significant reductions in esophageal acid exposure time (mean difference -2.83 %, 95 % CI: -4.554 to -1.114, p < 0.001), while systematic trigger food elimination protocols achieved 23 % improvement in GERD-Q scores, enabling 45 % of patients to discontinue pharmacological therapy. Plant-based dietary patterns showed remarkable protective effects with 50 % reduction in GERD prevalence (OR = 1.96, 95 % CI 1.22-3.17 for animal food consumption). Weight management interventions demonstrated exceptional efficacy in overweight patients, with GERD prevalence decreasing from 37 % to 15 % (p < 0.01) and 65 % achieving complete symptom resolution. Individual dietary trigger identification achieved high success rates with standardized protocols. Evidence-based dietary interventions offer clinically meaningful alternatives or adjuncts to pharmacological therapy. However, significant study heterogeneity and predominance of short-term trials limit definitive clinical recommendations. Future research should prioritize developing validated precision medicine algorithms integrating clinical phenotyping, genetic markers, and microbiome profiling to optimize personalized dietary prescriptions and investigate long-term sustainability of dietary modifications.},
}

Humans
*Gastroesophageal Reflux/diet therapy/physiopathology/therapy/epidemiology/diagnosis
Treatment Outcome
Evidence-Based Medicine
Diet, Carbohydrate-Restricted
*Risk Reduction Behavior
*Life Style
Diet, Vegetarian
Esophageal pH Monitoring

@article {pmid41423295,
year = {2025},
author = {Jeong, H and Seo, H and Kim, S and Rahim, MA and Barman, I and Shuvo, MSH and Jo, S and Hossain, MS and Yoo, JJ and Kim, YH and Jung, SS and Song, HY and Jeon, CH},
title = {Alterations in the Gut Microbiome in Ankylosing Spondylitis and Their Correlation with Disease Activity.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2508043},
doi = {10.4014/jmb.2508.08043},
pmid = {41423295},
issn = {1738-8872},
mesh = {Humans ; *Spondylitis, Ankylosing/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Male ; Adult ; Female ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Dysbiosis/microbiology ; C-Reactive Protein/analysis ; Biomarkers ; DNA, Bacterial/genetics ; Case-Control Studies ; },
abstract = {The microbiome significantly influences immune dysfunction and gut dysbiosis in patients with ankylosing spondylitis (AS). This study focuses on defining the distinct microbial characteristics within AS and biomarkers associated with disease activity. 44 patients with AS and 50 healthy controls (HC) were recruited. 16S rRNA sequencing was conducted to assess the microbiome of stool samples. The Ankylosing Spondylitis Disease Activity Score with C-reactive protein (ASDAS-CRP) was calculated for all AS patients; scores ≥ 2.1 indicated high disease activity, while < 2.1 indicated low disease activity. Similar alpha diversity profiles were maintained in both AS and HC cohorts, whereas significant differences were identified in beta diversity. The compositional prevalence of Proteobacteria, particularly Gammaproteobacteria, and Enterobacterales, including Escherichia spp., in the AS group was significantly increased. On the other hand, beneficial taxa, including Firmicutes, Clostridia, Clostridiales, Lachnospiraceae, Ruminococcaceae, and Faecalibacterium, were highly abundant in the HC group. Among patients with AS, alpha diversity decreased in the high disease activity group compared to the low disease activity group, while beta diversity did not differ significantly. Moreover, Coprobacter spp. abundance positively correlated with the Bath Ankylosing Spondylitis Disease Activity Index (p = 0.032) and the ASDAS-CRP (p = 0.023). Patients with AS exhibit distinct gut microbiota profiles, with increased Proteobacteria and decreased beneficial taxa such as Firmicutes. Greater disease activity is accompanied by reduced alpha diversity, while Coprobacter spp. abundance correlates with disease activity, suggesting its potential as a biomarker.},
}

Humans
*Spondylitis, Ankylosing/microbiology
*Gastrointestinal Microbiome/genetics
RNA, Ribosomal, 16S/genetics
Male
Adult
Female
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
Middle Aged
Dysbiosis/microbiology
C-Reactive Protein/analysis
Biomarkers
DNA, Bacterial/genetics
Case-Control Studies

@article {pmid41423183,
year = {2025},
author = {Zhang, Y and Su, Z and Jiang, H and Zhao, Y and Gao, F and Cai, K and Fang, S and Hu, K},
title = {Bacillus coagulans controls grass carp overwintering syndrome through the intestinal microbiota-metabolite-immunity network.},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {111084},
doi = {10.1016/j.fsi.2025.111084},
pmid = {41423183},
issn = {1095-9947},
abstract = {Grass carp winter syndrome is a low-temperature disease that has severely impacted freshwater fish farming in China in recent years. Characterized by rapid onset, high transmissibility, and elevated mortality, it proves difficult to control with conventional treatments. Bacillus coagulans, which combines the acid-producing antibacterial properties of Lactobacillus with the heat resistance and feed pellet compatibility of Bacillus subtilis, has gained attention as an alternative to antibiotics in livestock and poultry. This study represents the first integrated multi-dimensional analysis combining gut morphology, immunological enzyme activity, gut microbiome and metabolomics. It systematically elucidates the mechanism by which feeding grass carp with a bacterial suspension of Bacillus coagulans BC66 at a concentration of 100 billion CFU/g for 20 days ameliorates wintering syndrome through regulation of the gut metabolism-immune network. The findings reveal the therapeutic efficacy of this approach for grass carp wintering syndrome. The results demonstrated that B. coagulans BC66 improved the survival rate of grass carp affected by winter syndrome and promoted the repair of intestinal tissue. Antioxidant enzyme activities, such as those of SOD, CAT, and GSH-Px, were significantly elevated, while the expression of inflammatory genes (IL-8, TNF-α, NF-κB, and IL-12) decreased and that of IL-10 increased. A significant enrichment of Firmicutes, Bacteroidota, and Actinobacteriota occurred, with a notable increase in beneficial bacterial phyla, indicating a shift towards a more balanced microbial ecosystem. Meanwhile, pathogenic genera such as Aeromonas, Escherichia-Shigella, and Vibrio were markedly reduced. Metabolite analysis revealed downregulation of SDMA, Dibutylamine, and Involucrin, suggesting a reduction in inflammatory signaling and pathological metabolites. Conversely, Bifidobacterium-associated phospholipids (PC-O-15:0), pristanic acid, britannilactone derivatives, and antioxidant phenols were upregulated, alongside activation of the ABC transporters metabolic pathway and suppression of neuroactive ligand signaling and receptor interactions. These findings indicate that B. coagulans BC66 partially restored detoxification of exogenous toxins, distribution of endogenous metabolites, pathogen resistance, and osmoregulatory functions in grass carp. These findings provide scientific evidence supporting the application of Bacillus coagulans BC66 as an effective green alternative to antibiotics for preventing and controlling winter syndrome in grass carp, offering new strategies for improving health management in freshwater aquaculture.},
}

@article {pmid41423131,
year = {2025},
author = {Buckner, JE and Vo, L and Herrera, MJ and French, KB and Rankins, DR and Vasquez, J and Pande, A and Connor, KM and Peña Gonzalez, VI and German, DP},
title = {The Captive Gut: the impacts of long-term captivity on the intestinal digestive enzyme activities of a marine herbivorous fish.},
journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology},
volume = {},
number = {},
pages = {111965},
doi = {10.1016/j.cbpa.2025.111965},
pmid = {41423131},
issn = {1531-4332},
abstract = {Given that digestion is largely a chemical process in fishes that do not masticate or triturate their food, digestive enzyme activities are frequently measured as indicators of what nutrients a fish can readily digest. Here, we explored what happens to digestive tract length and digestive enzyme activities in a marine herbivorous fish (Xiphister mucosus) fed in captivity for more than two years. Captivity is known to impact nearly all aspects of an animal's biology, but the gut microbiome has received more attention than digestive biochemistry in this regard. After consuming a prepared diet primarily composed of algae collected from the same site from which the fish were collected for over two years, the lab-fed fish showed a marked reduction in amylase, trypsin, and aminopeptidase activities in comparison to wild-caught fish. Moreover, the gradient of activity moving along the intestine (activities decreasing distally for amylase and trypsin, increasing for aminopeptidase) completely disappeared in the lab-fed fish. The relative gut length decreased by about 18 % in the lab-fed fish, suggesting that they ate less than their wild counterparts, which likely led to slower gut transit and more time for enzymes to interact with substrates. Hence, digestive enzyme activities were lower in the lab-fed fish. A formulated diet in the laboratory presents a different gut environment for the herbivorous X. mucosus, and perhaps feeding them a live algal diet would better replicate the wild-gut phenotype if this fish is to be held for lengthy periods of time for display or aquaculture purposes.},
}

@article {pmid41423130,
year = {2025},
author = {Giakoumis, T and O'Shea, JP and Clarke, G and Griffin, BT},
title = {Assessment of pectin-ethyl cellulose coated pellets for bacterially enhanced colonic drug delivery in progressively complex in vitro and in vivo models.},
journal = {International journal of pharmaceutics},
volume = {},
number = {},
pages = {126521},
doi = {10.1016/j.ijpharm.2025.126521},
pmid = {41423130},
issn = {1873-3476},
abstract = {Microbially triggered drug delivery technologies have long been recognized for their potential to achieve targeted site-specific drug release in the colon. Yet, despite extensive research and ever-increasing knowledge of the role of gut microbiome, few microbially-tiggered formulations have successfully transitioned to the clinic. A major challenge lies in the poor translation of promising in vitro results to in vivo performance, compounded by the lack of physiologically relevant preclinical models that can reliably guide formulation optimization. In this study, a comprehensive evaluation was conducted using a toolkit of in vitro and in vivo models of increasing complexity and biorelevance to investigate polysaccharide-based pellets as a microbiota-responsive material for targeted colonic drug release. Theophylline pellets were coated with a pectin-ethylcellulose film and tested in vitro in the presence of microbial enzymes or bacteria. Pectin-ethylcellulose, ethylcellulose alone coated and uncoated pellets were further assessed in both healthy pigs and microbiota-depleted porcine models in a cross over design. While pectin-ethylcellulose coatings demonstrated microbially enhanced drug release in vitro, this effect was not replicated in vivo. The lack of in vivo response is likely attributable to the low pectinase activity observed in pig faecal samples. This study underscores the need for more predictive, compendial in vitro systems to better anticipate drug release behaviour prior to animal testing. Notably, this study is the first to demonstrate the utility of a porcine microbiota-depletion model for investigating the impact of microbiome alterations on drug pharmacokinetics, using a crossover design that allows comparisons between healthy and microbiota-depleted pigs.},
}

@article {pmid41422940,
year = {2025},
author = {Manoharan-Basil, SS and Vanbaelen, T and Kenyon, C},
title = {Threshold effects of doxycycline post-exposure prophylaxis (PEP) on the gut resistome and microbiome: evidence from change-point analyses.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108322},
doi = {10.1016/j.ijid.2025.108322},
pmid = {41422940},
issn = {1878-3511},
abstract = {BACKGROUND: Doxycycline post-exposure prophylaxis (doxy-PEP) is recommended to prevent bacterial sexually transmitted infections (STIs) in high-risk populations in some countries, but its potential to promote antimicrobial resistance (AMR) remains a concern. We aimed to determine the cumulative doxycycline intake threshold at which significant shifts occur in antimicrobial resistance genes (ARGs) and gut microbial community composition.

METHODS: We analysed data from the US DoxyPEP trial, a randomized clinical trial that enrolled men who have sex with men (MSM) and transgender women who received either doxy-PEP (200 mg doxycycline after condomless sex) or standard of care (SOC). Change-point analysis was applied to six-month cumulative doxycycline exposure to identify dosing thresholds associated with shifts in the gut resistome and microbiome.

RESULTS: Segmented change-point analysis identified a resistome threshold of 64.68 (95% CI: [64.06, 65.3]) doxycycline doses over six months, above which significant increases in ARG abundance were observed. For the microbiome, segmented breakpoints were estimated for 133 genera: the median breakpoint was 43.22 doses (IQR 38.42 - 49.21). Using prespecified significance criteria, 4/133 (3%) genera exhibited significant abundance shifts, which included Acutalibacter, Anaerotignum, Petrimonas, and Sphingobacterium.

CONCLUSIONS: Doxy-PEP is associated with a dose-dependent enrichment of gut ARGs, with a threshold effect at ∼65 doses over six months and taxon-specific abundance shifts in the gut microbiome centered around 43 doses. These dose thresholds provide actionable data to optimize safe doxy-PEP implementation and highlight the need for monitoring strategies that mitigate AMR and microbiome disruption risks.},
}

@article {pmid41422915,
year = {2025},
author = {Levine, BA and Lynch, AJ and Bailey, MT and Loman, BR},
title = {Prebiotic fructan chain length influences enteric microbiota-host GABAergic signaling and intestinal motility.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110234},
doi = {10.1016/j.jnutbio.2025.110234},
pmid = {41422915},
issn = {1873-4847},
abstract = {Dietary fiber ingestion serves as a critical regulator of intestinal motility and the structure and function of the enteric microbiome. Yet, the extent to which subtle structural differences among fibers modulate motility via microbiota-host interactions remains undefined. GABA is a microbial metabolite intimately related to microbial fructan fermentation and host intestinal motility. The purpose of this study was to investigate how fructan chain length influenced microbiota-host signaling underlying ileal and colonic contractions. Male and female mice were pair-fed diets containing no fiber (fiber-free diet, FFD) or the same diet containing cellulose (CELL, fiber control), short-chain fructooligosaccharides (scFOS), or inulin (INU) for two weeks. scFOS and INU similarly enhanced total microbial load (fluorescence in situ hybridization), relative abundances of GABA-synthesizing bacteria (16S rRNA sequencing), and luminal GABA concentrations (ELISA) in the ileum and colon versus FFD. Conversely, scFOS altered expression (Fluidigm qPCR) of more motility- and GABA-related genes than INU in the ileum, whereas INU altered expression of more motility and GABA-related genes than scFOS in the colon. Incubation of ileal segments with GABA potentiated contraction force in INU but not scFOS ex vivo. Conversely, incubation of colon segments with GABA repressed contraction force in scFOS, reducing them to levels observed in INU with or without GABA. Notably, GABA altered contraction forces only in female mice. Our study highlights dietary fructan chain length as a determinant of segment- and sex-specific GABA-mediated intestinal motility and creates a rationale and framework for investigation of how prebiotic fiber structures influence microbiota-host interactions and physiology.},
}

@article {pmid41422660,
year = {2025},
author = {Zhao, Y and Gao, M and Wang, F and Pang, L and Li, H and Lin, X and Chen, L},
title = {GCHFR-gut microbiota axis in gout: an integrative multi-omics and Mendelian randomization study with clinical and molecular validation.},
journal = {International immunopharmacology},
volume = {170},
number = {},
pages = {116064},
doi = {10.1016/j.intimp.2025.116064},
pmid = {41422660},
issn = {1878-1705},
abstract = {BACKGROUND: Gout is a systemic metabolic disease with rising prevalence and complex etiology, yet its molecular mechanisms remain incompletely defined. Multi-omics Mendelian randomization (MR) enables causal prioritization of genes implicated in gout. Because the gut microbiota (GM) can modulate urate metabolism and inflammation, integrating microbiome analyses may help nominate potential therapeutic candidates. This study aimed to nominate candidate targets for gout by integrating multi-omics MR, clinical validation, GM analysis, and in-silico druggability assessment.

METHODS: We performed multi-omics MR (pQTL/eQTL/mQTL) to prioritize genes with putative causal effects on gout risk. Candidate gene expression patterns were examined in a public single-cell RNA sequencing dataset to determine their distribution across immune cell subtypes and functional context. Associations between identified candidate genes and GM composition were evaluated using the MiBioGen database. Potential therapeutic interactions were predicted through the Comparative Toxicogenomics Database (CTD). Expression of candidate genes was validated in peripheral blood samples from 51 gout patients and 50 healthy controls by quantitative real-time polymerase chain reaction (qRT-PCR). Finally, molecular docking and molecular dynamics (MD) simulations were conducted to explore binding poses and stability between prioritized proteins and predicted drugs.

RESULTS: MR analysis identified four gout-associated genes (BAIAP2, CD248, GCHFR, and ABHD14B). Among them, BAIAP2, CD248, and GCHFR showed significant causal relationships with specific gut microbial taxa in MiBioGen, whereas ABHD14B showed no GM associations. CTD-based drug prediction further highlighted three compounds-benzbromarone, calcitriol, and cyclosporine-potentially targeting these genes. In an independent cohort (51 gout vs. 50 controls), qRT-PCR confirmed GCHFR dysregulation consistent with MR estimates, and molecular docking plus MD simulations supported stable binding of benzbromarone to GCHFR, providing mechanistic plausibility.

CONCLUSIONS: This integrative framework convergently prioritizes GCHFR as a candidate for therapeutic investigation in gout and identifies CD248, BAIAP2, and ABHD14B as additional gout-related candidates. These results generate testable hypotheses for GCHFR-focused mechanistic and therapeutic studies, as well as further functional studies of the other genes.},
}

@article {pmid41422344,
year = {2025},
author = {Carstensen, M and Philipp, LM and Basu, M and Hoffmann, P and Klenig, JN and Wandmacher, AM and Sebens, S},
title = {Intratumoral microbiome and pancreatic cancer: an enabling hallmark and path to novel treatments?.},
journal = {British journal of cancer},
volume = {},
number = {},
pages = {},
pmid = {41422344},
issn = {1532-1827},
support = {RTG 2501 TransEvo//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Clinician Scientist in Evolutionary Medicine Program (Projektnummer 413490537)//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; RTG 2501 TransEvo//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; RTG 2501 TransEvo//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; RTG 2501 TransEvo//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; RTG 2501 TransEvo//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Clinician Scientist in Evolutionary Medicine Program (Projektnummer 413490537)//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {In 2022, Hanahan integrated polymorphic microbiomes to the hallmarks of cancer, resulting in 14 overarching features that are considered fundamental to initiation and progression of cancers. It is well acknowledged that genomic instability/genetic alterations together with tumor-associated inflammation are so called "enabling hallmarks" as they drive the acquisition of the other traits. The microbiome is a key component of the inflammatory tumor stroma. Pancreatic ductal adenocarcinoma (PDAC) in particular is characterized by a pronounced stromal compartment whose role in the acquisition of malignant properties is well documented. Recent studies indicate massive alterations of the microbiome in PDAC tissues compared to healthy pancreas or precursor lesions. However, the mechanistic role of the PDAC-associated microbiome, its influence on the hallmarks of cancer, and how this relates to PDAC malignancy remain poorly understood. This raises the question of whether the tumor-associated microbiome through its direct influence on PDAC cells, their precursors, and the surrounding non-neoplastic cells promotes the acquisition of other hallmarks that drive PDAC development and progression. This perspective article outlines the current knowledge of the impact of the PDAC-associated microbiome on the hallmarks of cancer in PDAC. These current findings support the altered microbiome as a third enabling hallmark of PDAC and emphasize that further mechanistic studies are urgently needed to further substantiate its fundamental importance for this tumor entity. This knowledge will provide the basis for clinical translation to develop more effective therapeutic approaches for PDAC. The intratumoral microbiome in PDAC exhibits numerous interactions with the hallmarks of cancer. Hallmarks indicated in blue have demonstrated interactions with the microbiome, while others still remain underexplored. These extensive interactions substantiate the role of the intratumoral microbiome in PDAC as an enabling hallmark, underlining its potential as a therapeutic target. Partially created with biorender.com.},
}

@article {pmid41422338,
year = {2025},
author = {Wu, Y and Ling, Z and Peng, L and Wang, X and He, Y and Khan, A and Salama, ES and Kulshreshtha, S and Liu, P and Li, X},
title = {Vitamin B6 form produced by Lactobacillus induces metabolic disorder and suppresses multi-pathogenic bacteria.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-025-09348-2},
pmid = {41422338},
issn = {2399-3642},
support = {32370110//National Natural Science Foundation of China (National Science Foundation of China)/ ; 323B2004//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Vitamin B6 comprises six vitamers, pyridoxal, pyridoxine, pyridoxamine, pyridoxal 5'-phosphate (PLP), pyridoxine 5'-phosphate (PNP), and pyridoxamine 5'-phosphate (PMP), recognized for pleiotropic functions in mitigating oxidative stress and modulating metabolic homeostasis. This study reveals that PMP exhibits broad-spectrum antibacterial activity against pathogens, including Aeromonas hydrophila (A. hydrophila), Staphylococcus aureus, Pseudomonas aeruginosa, and Salmonella. In vitro assays demonstrated that high-dose PMP disrupts bacterial membrane integrity, triggering extensive extracellular DNA leakage and bactericidal effects. Furthermore, we identified Pediococcus acidilactici GR-6 and Lactobacillus fermentum GR-7, isolated from crucian carp gut, that synergistically synthesize vitamin B6 de novo during pathogens co-culture, achieving ≥63% inhibition of polymicrobial pathogens. Integrated genomic, proteomic and metabolomic analyses confirm that GR-6/GR-7 consortium regulates pyridoxal kinase and pyridoxine 4-dehydrogenase, maintaining vitamin B6 primarily as pyridoxine (84%) and PMP (16%). In A. hydrophila-infected crucian carp, dietary supplementation with GR-6/GR-7 consortium increases survival by 50%, with restored gut microbiota diversity and attenuated systemic inflammation (Alkaline phosphatase, Lysozyme and GSH/GSSG ratio). Metabolomics showed that probiotics-mediated elevation of intestinal content PMP level directly inhibits A. hydrophila infection. Collectively, this study establishes PMP as a novel probiotic metabolite that directly eliminates pathogens and resolving gut microbiome-host metabolic dysregulation.},
}

@article {pmid41422274,
year = {2025},
author = {Jin, Y and He, J and Fan, D and Wang, L and Cui, N and Liu, Y and Liu, D},
title = {Application of edible fungi in gut microbiota regulation.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-025-00671-w},
pmid = {41422274},
issn = {2396-8370},
support = {82003985, 81973712, and 82004030//National Natural Science Foundation of China/ ; 82003985, 81973712, and 82004030//National Natural Science Foundation of China/ ; 2022JP06//Graduate Training Innovation Demonstration Project/ ; 010301104//Jilin Postdoctoral Foundation Program/ ; Grant No. 20230401062YY//Jilin Province Science and Technology Development Project in China/ ; },
abstract = {The human gut microbiota serves as a critical hub for host metabolic and immune regulation. Disruption of its homeostasis is closely associated with diseases such as Inflammatory Bowel Disease (IBD), metabolic syndrome, and colorectal cancer. Modern dietary and environmental factors are known to exacerbate this dysbiosis, highlighting the need for innovative interventions capable of modulating the gut ecosystem. Within this context, this review explores the potential of edible fungi, focusing on culinary mushrooms (e.g., Lentinula edodes) and medicinal fungi such as Ganoderma lucidum and Phellinus linteus, which are widely studied in Asia for their health benefits. While consumed as functional foods for their nutritional properties in some countries, they are used in traditional medicine in others. This review examines the role of their bioactive components (e.g., polysaccharides, terpenoids) in remodeling the gut microbiome, thereby highlighting their application in functional foods and dietary interventions. This review systematically examines the pathological mechanisms underlying gut dysbiosis and elucidates how bioactive fungal components (e.g., β-glucans, ganoderic acids) improve intestinal barrier function and immune homeostasis by modulating the composition of the gut microbiota, enhancing the production of SCFAs (short-chain fatty acids), and inhibiting the colonization of pathogens. Current evidence, primarily from preclinical studies, suggests that bioactive fungal components, such as β-glucans from Ganoderma lucidum and polysaccharides from Trametes versicolor, may impart health benefits against metabolic disorders and neoplasms. These benefits are mediated through the modulation of microbiota-derived metabolites (e.g., SCFAs) and epigenetic remodeling mechanisms (e.g., HDAC (Histone Deacetylase) inhibition), suggesting their potential application in functional foods and nutritional strategies. metabolites (e.g., SCFAs) and epigenetic remodeling mechanisms (e.g., HDAC inhibition). However, critical gaps persist, particularly in translating these preclinical findings to humans. Key challenges include understanding their bioavailability, establishing human-relevant dose-response relationships, and elucidating spatiotemporal dynamics within microbiota-host interaction networks. Addressing these gaps requires integration with multi-omics technologies and well-designed clinical trials. Multi-omics and organoid models should be integrated by future research to advance precision medicine applications of fungal-derived therapies.},
}

@article {pmid41422269,
year = {2025},
author = {Wang, Y and Xu, J and Liang, G and Liang, S and Hou, M and Sun, L and Wang, J and Chen, H and Zhao, Y and Chen, W and Wang, E and Huang, J and Jiao, X and Zhang, Y},
title = {Gut microbiome profiling of a migratory Anser serrirostris population reveals two groups with distinct pathogen and ARG contents.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00888-3},
pmid = {41422269},
issn = {2055-5008},
abstract = {Migratory birds are key vectors of pathogens and antibiotic-resistance genes (ARGs), yet intrapopulation variation and its microbiome-mediated basis remain poorly understood. Here, we characterized the gut microbiome of 70 individuals from a migratory Anser serrirostris population using full-length 16S rDNA sequencing, followed by metagenomic analysis of 25 representative samples. Both approaches consistently identified two distinct groups (E1 and E2). Network analysis revealed impaired microbial interactions in E1 compared to E2. E1 exhibited higher abundances of opportunistic pathogens (e.g., Pseudomonas, Erwinia) and enriched functions related to pathogenicity and ARGs, predominantly driven by these taxa. Conversely, E2 showed function enrichment in short-chain fatty acid biosynthesis and plant metabolite degradation, mediated mainly by Bradyrhizobium and Ligilactobacillus. Genome-centric analysis identified several pathogenic genomes (e.g., Salmonella, Vibrio parahaemolyticus) harboring critical virulence factors and ARGs predominantly in E1. These results provide valuable insights into microbiome-driven variation in pathogen/ARG loads within migratory bird populations.},
}

@article {pmid41422165,
year = {2025},
author = {Wehnes, T and Wang, W and Tay, JH and Guan, L and Feng, L and Ho, CMR and Ng, TP and Kennedy, BK and Venkitaraman, A and Koh, WP and Chong, YS and Maier, AB},
title = {Oral short-chain fatty acid-producing bacteria may be associated with biological age and cognition among the oldest old.},
journal = {Communications medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s43856-025-01288-6},
pmid = {41422165},
issn = {2730-664X},
abstract = {BACKGROUND: Biological age derived from DNA methylation (mAge) reflects aging-related physiological changes and the risk of age-related diseases. However, the association between oral microbiome and mAge remains unclear.

METHODS: We examined associations between mAge, physical and cognitive function, and the oral microbiome in 311 community-dwelling, predominantly Chinese adults aged 85 years or older. Oral microbial composition was assessed using 16S rRNA sequencing, and mAge was estimated using four established epigenetic clocks: HorvathAge, HannumAge, PhenoAge, and GrimAge.

RESULTS: In this cohort (median chronological age = 88.6 years; median DNA methylation-based biological age = 81.4 years), individuals with lower mAge deviation, corresponding to a younger biological age, exhibit lower oral microbial alpha diversity based on Simpson's index. While no taxa differences reach significance after correction for multiple testing, several short-chain fatty acid-producing genera, such as Prevotella_7 and Veillonella, show nominal associations with both mAge deviation and methylation at aging-related CpG sites, particularly in neurologically relevant genes. Higher abundance of Prevotella_7 species is associated with better cognitive performance (Mini-Mental State Examination), whereas Alloprevotella is linked to poorer cognition.

CONCLUSION: Our findings highlight that, as far as we aware, previously unrecognized oral microbiome composition links to lower mAge deviation and better cognitive function among the oldest-old, suggesting a potential role of the oral microbiome in promoting healthy aging and informing future mechanistic investigations.},
}

@article {pmid41421973,
year = {2025},
author = {Jensen, R and McKenney, EA and Beasley, JC and Cloete, CC and Melton, M and Lafferty, DJR},
title = {Phylogenetic influence on gut microbiome diversity within an African herbivore community.},
journal = {BMC ecology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12862-025-02489-2},
pmid = {41421973},
issn = {2730-7182},
support = {Excellence in Education Award//Northern Michigan University/ ; Faculty Research Grant//Northern Michigan University/ ; DE-EM0005228//U.S. Department of Energy/ ; },
abstract = {BACKGROUND: The microbial community within the gastrointestinal tract, known as the gut microbiome (GMB), is a complex micro-ecosystem that is modulated by the life history and physiological traits of the host as well as environmental conditions experienced by the host. In addition, phylogeny can be an important driver of GMB variability across mammalian species, with closely-related species sharing more similar microbial communities than distantly-related species, an eco-evolutionary pattern known as phylosymbiosis. In this study, we examined GMB diversity across 11 species of large herbivores in Etosha National Park (ENP), Namibia, to determine whether host species exhibit phylosymbiosis and whether different herbivore families host distinct microbial communities. The large herbivore community of ENP is an excellent model system because the herbivore species represent distinct evolutionary lineages and have evolved a variety of gut morphologies, dietary niches, and habitat requirements, all of which shape gut microbial diversity.

RESULTS: While we found no evidence of phylosymbiosis across the greater ENP herbivore community, phylosymbiosis was detected among bovid species based on a positive correlation between microbial relative abundance and host evolutionary divergence times. Our results also revealed distinct microbial membership (e.g., Bacteroides, Treponema, and Alistipes) that distinguished bovid species from elephants and giraffes.

CONCLUSIONS: Our study provides new insights into the impact of phylogeny on GMB diversity in a closely-related African herbivore community. In particular, phylosymbiosis patterns observed in bovids but not all herbivore species demonstrates that microbial communities are dynamic and respond to a mixture of host evolutionary strategies and corresponding adaptations.},
}

@article {pmid41421910,
year = {2025},
author = {Zeng, H and Xu, H and Liu, G and Wei, Y and Zhang, J and Shi, H},
title = {Corrigendum to "Physiological and metagenomic strategies uncover the rhizosphere bacterial microbiome succession underlying three common environmental stresses in cassava" [J Hazard Mater 411 (2021) 125143].},
journal = {Journal of hazardous materials},
volume = {},
number = {},
pages = {140878},
doi = {10.1016/j.jhazmat.2025.140878},
pmid = {41421910},
issn = {1873-3336},
}

@article {pmid41421774,
year = {2025},
author = {Liu, X and Li, J and Ding, Y and Wang, T and Li, H and Xu, Y},
title = {Waste-derived cultivation substrates drive the dominance of nitrogen-functional microbes in the rhizosphere microbiome to improve nitrogen use efficiency.},
journal = {Environmental research},
volume = {291},
number = {},
pages = {123593},
doi = {10.1016/j.envres.2025.123593},
pmid = {41421774},
issn = {1096-0953},
abstract = {Nitrogen (N) loss and low nitrogen use efficiency (NUE) pose major sustainability challenges in facility agriculture. Cultivation substrates have been developed as an alternative to traditional soil for better N management. However, it is unknown what kind of substrates are effective in addressing N loss and improving NUE. Herein, this study investigated the effects of various substrates on N loss and NUE through a five-year continuous tomato cultivation experiment, revealing the underlying biological mechanisms. The substrates tested included soil with recommended fertilizer, grass biochar (GB), coconut coir, and vegetable waste (VM), with soil without fertilizer application set up as a negative control. And structural equation modeling revealed that the rhizosphere microbiome composition was the primary driver of nitrogen utilization in substrates. Notably, GB and VM substrates reshaped the microbial community related to N transformation, and promoted the evolution of N-functional microorganisms into core microbial members, thereby strengthening their ability for N transformation and utilization. These substrates regulated key processes such as fixation and nitrification, which collectively improved nitrogen conversion efficiency and minimized N loss. Further, the relative abundance of N-functional genes (e.g., nirB, narI, nifH, hao), which are closely associated with these processes, markedly increased, ranging from 22.16 % to 109.22 %. This significant rise in gene abundance underscored the enhanced N transformation processes and further validated the effectiveness of GB and VM substrates in optimizing NUE. This study provides a technical solution for reducing N loss and improving NUE in facility agriculture, and offering theoretical guidance for optimizing substrate design.},
}

@article {pmid41421745,
year = {2025},
author = {Mandelbrot, L and Kennedy, S and Rousseau, J and Goffinet, F and Landraud, L and Plainvert, C and Marcou, V and Desfrère, L and Barral, T and Allal, L and Baud, A and Grall, N and Poyart, C and Ancel, PY and Tazi, A},
title = {Predicting neonatal infection in PPROM with vaginal microbiology and metagenomics: a prospective cohort study.},
journal = {American journal of obstetrics and gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajog.2025.12.042},
pmid = {41421745},
issn = {1097-6868},
abstract = {OBJECTIVE: Early-onset neonatal sepsis (EONS) due to ascending infection is a potentially preventable complication of preterm premature rupture of membranes (PPROM). Our objective was to determine whether the analysis of bacteria from vaginal swab samples is predictive of the risk of EONS in PPROM.

STUDY DESIGN: In a prospective 3-center observational cohort, patients with PPROM were enrolled between 22 and 36 weeks' gestation (WG) + 6 days. Vaginal swab samples at delivery were analyzed using two different approaches, classical bacterial cultures and shotgun metagenomic sequencing analysis. A metagenomics score was constructed combining the characterization of the vaginal microbiome and the presence of pathogens and the optimal cut-off to predict EONS was tested on a receiver operating curve.

RESULTS: 563 PPROM cases were enrolled, with 646 liveborn neonates. PPROM occurred < 32 WG in 41.9% and deliveries were < 34 WG in 41.0%. The incidence of EONS was 29/646 (4.5%). When considering all central and peripheral microbiological samples available for 26 neonates, the main pathogens isolated were Escherichia coli in 14 cases (53.8 %), other gram-negatives in 5 (19.2%), strict anaerobes in 3 (11.5%); there was a single case (3.8%) each with Group B Streptococcus (GBS), Streptococcus anginosus, Staphylococcus aureus and Ureaplasma urealyticum. We studied the prediction of EONS among 272 mothers and their 310 neonates (20 EONS, 6.4%) with both culture and metagenomic data available. A culture positive for a major or intermediate pathogen in the vaginal sample at delivery had a sensitivity of 80.0 % (95% CI=56.3-94.3) and a specificity of 37.9% (95% CI=32.3-43.8), adjusted odds ratio (aOR) of 1.6 (95 % CI [0.5-5.0]) to predict EONS. The presence of E. coli was associated with an EONS risk of 10.6% vs 4.9%, in the absence of E. coli (p=0.07). The metagenomics score was highly associated with EONS, with an area under the receiver operating curve of 0.75 (95% CI, 0.61-0.90). At the optimal cutoff value, sensitivity was 70% (95% CI, 64-95%), specificity was 85% (95% CI, 81-89%). A metagenomics score greater than 40 was associated with a significantly increased risk of EONS with an aOR of 8.9 (95 % CI [3.5; 22.3]) in multivariate analysis adjusted for latency period and gestational age, p<0.001.

CONCLUSION: In PPROM, conventional microbial culture of maternal vaginal samples was associated with EONS, but its predictive values remain insufficient to guide perinatal care. Metagenomic microbial signatures improved predictive values. This opens the perspective for a rapid point-of-care test.},
}

@article {pmid41421681,
year = {2025},
author = {Fu, Q and Shi, JS and Lai, JL and Zhang, Y and Huang, Y and Luo, XG},
title = {Maize adaptation to low-dose nanoplastic-lead co-contamination: Foliar metabolic reprogramming and phyllospheric microbiome restructuring.},
journal = {NanoImpact},
volume = {41},
number = {},
pages = {100606},
doi = {10.1016/j.impact.2025.100606},
pmid = {41421681},
issn = {2452-0748},
abstract = {Nanoplastics (NPs) and lead (Pb), as emerging environmental pollutants, have been rarely studied in terms of their combined effects on crop growth and metabolic processes under low-dose co-exposure conditions. This study simulated rain-mediated co-exposure of maize seedlings to NPs and Pb at environmentally relevant concentrations (400 μg/L) to elucidate the metabolic responses in leaves and the dynamics of phyllosphere microbial communities. Short-term exposure (45 days) to NPs and Pb did not significantly impair maize seedling growth; however, it induced the accumulation of essential macronutrients in leaves. The metabolic adaptation of maize leaves to NPs and Pb exposure was characterized by a reduction in carbon metabolic flux coupled with an enhancement in lipid metabolic flux. Furthermore, plants responded to co-exposure by activating key metabolic pathways such as those involving ABC transporters, nucleotide metabolism, and amino acid metabolism. Concurrently, the phyllosphere microbiome exhibited structural reorganization, with enrichment of stress-tolerant microbial taxa (e.g., Acidobacteria, Chloroflexi), activation of microbial redox systems, and enhanced capacity of the leaf microbiota to adapt to NPs and Pb exposure. The findings offer theoretical insights into assessing agricultural environmental impacts associated with combined exposure to emerging pollutants, phyllosphere microbial ecology, and plant stress resistance.},
}

@article {pmid41421639,
year = {2025},
author = {Espinosa, AC and Gómez, RJV and Duque-Granda, D and Cadavid-Restrepo, GE and Junca, H and Herrera, CXM},
title = {Evidence of eurythermal behavior and microbiota differentiation in Aedes aegypti and Aedes albopictus from the Colombian Amazon biome.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107951},
doi = {10.1016/j.actatropica.2025.107951},
pmid = {41421639},
issn = {1873-6254},
abstract = {Temperature is one of the most important factors influencing mosquito development, vector competence, and microbiome composition, affecting the disease transmission cycle by either facilitating or inhibiting pathogen establishment. This study aimed to estimate temperature preference and its correlation with bacterial communities in populations of Ae. aegypti and Ae. albopictus from the urban area of Leticia, Amazonas. Temperature preference profiles were obtained by introducing 50 individuals of each species and sex in six replicates for one hour into a device with a temperature gradient of 19-36°C. Subsequently, a metataxonomic analysis of bacterial communities was performed using DNA extracted from whole mosquito body groups associated with temperature ranges defined by their statistical significance. First, it was determined that females of both species preferred temperatures between 23-28°C. Meanwhile, Ae. aegypti males showed a larger temperature preference range (21-28°C) than Ae. albopictus males (25-28°C). Regarding bacterial communities, an increase in diversity was observed in males of both species with rising temperatures, whereas the opposite occurred in females. The Amplicon Sequence Variants (ASVs) associated with Asaia (2.88%), Cedecea (45.80%), Elizabethkingia (77.78%), and Klebsiella (8.90%) were the most abundant genera in Ae. aegypti. In comparison, Ae. albopictus exhibited a high abundance of Elizabethkingia (36.34%), Pseudomonas (95.08%), and Wolbachia (12.73%). Interestingly, Elizabethkingia varied in abundance according to sex and temperature in both species. It was determined that the structure of Aedes bacterial communities in the Amazon was influenced by sex, species, and temperature, indicating high plasticity and ubiquity according to temperature profiles.},
}

@article {pmid41421627,
year = {2025},
author = {Kubáňová, M and Kirakci, K and Boudesocque-Delaye, L and Divoux, L and Kaňa, A and Zelenka, J and Ruml, T and Munnier, E and Lang, K and Verger, A},
title = {Blue-light activated molybdenum cluster-based photosensitizers in NaDES - formulated creams for dermatological photodynamic therapy.},
journal = {International journal of pharmaceutics},
volume = {689},
number = {},
pages = {126491},
doi = {10.1016/j.ijpharm.2025.126491},
pmid = {41421627},
issn = {1873-3476},
abstract = {Photodynamic therapy (PDT) emerges as an innovative strategy combining light and drug treatment. The most prevalent use of this therapy is for the elimination of cancerous and pre-cancerous cells. However, in recent years PDT has been shown to be a suitable approach to combat the rising threat of antimicrobial resistance through the photoinactivation of pathogenic bacteria. Photosensitizers predicated on octahedral hexa-molybdenum cluster (Mo6) complexes activated by blue light were formulated into semi-solid topical pharmaceutics containing three distinct types of Mo6 clusters as potential novel actives for cosmetics purposes. For the first time, semi-solid cosmetic formulations were developed utilizing natural deep eutectic solvents as carriers of these active compounds and tested for their stability, viscosity, skin penetration, and singlet oxygen formation. After that, negligible toxicity for human cells was confirmed using in vitro testing on HaCaT cell lines. Finally, photoinactivation of the most prevalent skin bacterial pathogens Staphylococcus aureus and Cutibacterium acnes was demonstrated under mild conditions that preserve viability of natural symbiotic skin microflora.},
}

@article {pmid41421597,
year = {2025},
author = {P, C and L, L and J, A},
title = {An oral microbiome from 1929: paleoproteomic study of a toothbrush belonging to Georges Clemenceau (1841-1929).},
journal = {Journal of stomatology, oral and maxillofacial surgery},
volume = {},
number = {},
pages = {102691},
doi = {10.1016/j.jormas.2025.102691},
pmid = {41421597},
issn = {2468-7855},
}

@article {pmid41421562,
year = {2025},
author = {Jesenak, M and Bobcakova, A and Golebski, K and Krohn, IK and Seys, SF and Rennerova, Z and Durdik, P and Tufvesson, E and Markocsy, A and Kosturiak, R and Diamant, Z},
title = {Airway epithelial barrier integrity: an emerging treatable trait in asthma management.},
journal = {Respiratory medicine},
volume = {},
number = {},
pages = {108579},
doi = {10.1016/j.rmed.2025.108579},
pmid = {41421562},
issn = {1532-3064},
abstract = {The airway epithelium not only acts as a physical barrier between the environment and the host, but also functions as an active immunological interface, facilitating crosstalk between the epithelial cells, immune cells and the microbiome aimed at protecting the host. Therefore, maintaining airway epithelial barrier integrity and its function is crucial for prevention of chronic inflammatory airway diseases, such as allergy, asthma and chronic obstructive pulmonary disease. The potential to restore the epithelial barrier by therapeutic interventions has increasingly gained interest over recent years. As part of their disease-modifying properties, various treatment modalities including small molecule drugs, biologics, bronchial thermoplasty and allergen immunotherapy, showed beneficial effects on epithelial barrier integrity in select patient populations. In this review, we summarize current knowledge, discuss recent evidence of therapeutic interventions on restoring epithelial barrier function and highlight unmet needs and future research directions.},
}

@article {pmid41421530,
year = {2025},
author = {Ghaffari, MH and Sadri, H and Hemmert, KJ and Ostendorf, CS and Schuchardt, S and Koch, C and Sauerwein, H},
title = {Longitudinal characterization of fecal lipids in dairy heifers from birth to first calving.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27816},
pmid = {41421530},
issn = {1525-3198},
abstract = {The developmental phases of dairy heifers, from birth to first calving, are characterized by major changes in nutrition, gastrointestinal tract physiology and metabolism. Fecal metabolomics offers a powerful, noninvasive approach to understanding the intricate interplay between host metabolism, gut health, and the evolving gut microbiota. However, the longitudinal dynamics of fecal lipids are poorly characterized across these phases. The aim of this study was to characterize and quantify fecal lipid classes and their temporal dynamics in Holstein heifers at key time points from birth to first calving. For this purpose, 10 Holstein heifers were prospectively enrolled and sampled at 5 critical developmental stages: within 12 h after birth, preweaning (wk 6), at weaning (wk 14), postweaning (mo 8), and at first calving (mean age 26 ± 2.3 mo). Fecal samples were collected rectally at each stage and analyzed by targeted metabolomics (MxP Quant 500 kit) using flow injection analysis-tandem mass spectrometry with normalization to internal standards and strict quality control. Multivariate analyses, including principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), and hierarchical clustering, were used to assess temporal changes in fecal lipid composition. The PCA model explained 69.3% of the total variance (principal components 1, 2, and 3: 39.7%, 18.8%, and 10.8%, respectively). Subsequent permutational multivariate ANOVA (999 permutations) indicated significant stage effects (R[2] = 0.76). Additionally, PLS-DA, employing 5 components, demonstrated high explanatory power (R[2] = 0.98, Q[2] = 0.87), validated through permutation testing. Fecal fatty acids profiling showed a persistent dominance of myristic acid (C14:0) throughout the observation period, suggesting a process independent of direct dietary inputs and possibly related to microbial synthesis or lipid metabolism between host and microbe. Further consideration of the microbial contribution to myristic acid production may have implications of intestinal lipid metabolism processes as well as host-microbe interactions with physiological relevance to gut health. Longitudinal assessments on triglycerides, diglycerides, and monoglycerides revealed stage-dependent changes in lipid metabolism in relation to the process of digestive lipolysis and dietary transition from birth to calving. Additionally, the data indicated shifts toward phospholipids and sphingolipids after the colostrum phase and particularly increased abundances of phosphatidic acid, phosphatidylinositol, and lysophospholipids during the preweaning developmental stage, signaling membrane remodeling via the Lands cycle associated with developmental changes in gut function and immunity. Stage-dependent changes were also evident for fecal cholesteryl esters and acylcarnitines, with early elevations after birth and again during the preweaning stages. This may infer distinct lipid transport and energy metabolism and later fluctuations in signaling physiological changes in response to dietary transitions and rumen development. These findings provide a comprehensive overview of fecal lipid dynamics throughout heifer development, detailing the metabolic signatures related to key physiological changes. Collectively, the findings underscore the potential of fecal lipidomics as a noninvasive approach to monitoring gut maturation, dietary adaptation, and host-microbiota interactions from birth to calving.},
}

@article {pmid41421479,
year = {2025},
author = {Schneller-Pavelescu, L and Mora-Martínez, C and Sánchez-Pujol, MJ and Sanz, Y and Caparrós-Cayuela, E and Francés-Guarinos, R and Ramos-Rincón, JM and Belinchón-Romero, I},
title = {Relation between gut microbiome and inflammatory interleukins in psoriasis patients compared to healthy controls: an observational study.},
journal = {Actas dermo-sifiliograficas},
volume = {},
number = {},
pages = {104579},
doi = {10.1016/j.ad.2025.104579},
pmid = {41421479},
issn = {1578-2190},
abstract = {BACKGROUND: The gut microbiota interacts with the immune system and plays an important role in many inflammatory diseases such as psoriasis, although the exact mechanisms in this disease are not yet well understood.

OBJECTIVES: To characterize differences in the microbiota between patients with psoriasis and healthy controls, and to assess the relationship between these differences and the interleukins involved in psoriasis.

METHODS: A cross-sectional observational study was conducted in which sociodemographic data, blood samples, and stool samples were collected from patients with psoriasis and healthy controls attending our center between June 2019 and May 2020. Cytokines (interleukin (IL) 17, 22, 23, 31, 33, 36, interferon (IFN) γ, and transforming growth factor (TGF) β) were analyzed using ELISA, and microbiota was analyzed through 16S amplicon sequencing.

RESULTS: Thirty-six patients and 23 controls were included. Absolute abundance analysis found a higher abundance of the phylum Synergistota in the control group (p<0.05). Differential abundance analysis found higher abundance of the genus Subdoligranulum and Lactobacillus, and the species Bacteroides plebeius (p<0.05), and lower abundance of the species Senegalimassilia anaerobia and the genus Ruminococcus (p<0.05) in the psoriasis group. A relationship was observed between Subdoligranulum and TNFα, IL17, IL22, IL23, IL31, IL33, IL36, IFNγ, and TGFβ (p<0.05), as well as between Lactobacillus and IL17, IL23, IL36, TNFα, and TGFβ (p<0.05).

CONCLUSIONS: Significant alterations in the gut microbiota of patients with psoriasis were detected and a relationship with inflammatory interleukins, suggesting their involvement in the disease. These findings could aid in the development of future probiotic treatments for psoriasis.},
}

@article {pmid41421426,
year = {2025},
author = {Nam, J and Lee, Y and Lee, S and Choi, H and Lee, SY and Yang, D},
title = {Synthetic biology strategies for engineering probiotics and commensal bacteria for diagnostics and therapeutics.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108782},
doi = {10.1016/j.biotechadv.2025.108782},
pmid = {41421426},
issn = {1873-1899},
abstract = {Microorganisms inhabit diverse environments, including nearly every organ in the human body. The human microbiome-a complex community of microorganisms residing in the human body-has gained increasing attention as a key contributor to human health and disease, making it an important target for the development of diagnostic and therapeutic strategies. However, the inherent complexity of microbial communities and the challenges of engineering diverse, non-model microorganisms present significant barriers. To address these challenges, synthetic biology has provided powerful tools and strategies to engineer microorganisms capable of sensing disease-specific environments and performing targeted therapeutic functions. In particular, the development of synthetic genetic circuits has significantly improved the precision and reliability of disease diagnosis and treatment, enabling real-time disease monitoring, therapeutic, and even preventive interventions. This review highlights state-of-the-art synthetic biology tools and strategies for engineering the probiotics and commensal bacteria aimed at the diagnosis and treatment of human diseases, with accompanying examples. Future challenges and prospects are also discussed.},
}

@article {pmid41421411,
year = {2025},
author = {Chaudhary, R and Bag, S and Bansal, N and Lal, R and Bishnoi, M and Kondepudi, KK and Chopra, K and Bansal, S},
title = {Soy Isoflavone Ameliorates Gut-brain axis Dysfunction via ER-β Activation and β-glucuronidase Modulation in Estrogen-Deficient Rats.},
journal = {European journal of pharmacology},
volume = {},
number = {},
pages = {178503},
doi = {10.1016/j.ejphar.2025.178503},
pmid = {41421411},
issn = {1879-0712},
abstract = {The Gut-brain axis (GBA) plays a crucial role in neuroendocrine homeostasis, and its dysregulation due to estrogen deficiency is associated with cognitive decline, mood disorders, and gut microbiome disturbances in postmenopausal women. The gut microbiome involved in estrogen metabolism, known as the estrobolome, regulates β-glucuronidase activity, which influences estrogen reactivation and systemic availability. Reduced estrobolome function and altered β-glucuronidase activity in post-menopause may exacerbate GBA dysfunction. Thus, strategies that modulate the estrobolome and enhance β-glucuronidase may be beneficial in improving postmenopausal GBA dysfunction. With this background, our study aims to determine the effect of soy isoflavone (SIF) on GBA dysfunction in estrogen-deficient rats. To induce GBA dysfunction, rats were first bilaterally ovariectomized (OVX) and, after one week, treated with SIF (40 and 80 mg/kg)/17β-estradiol (17βE2) for 28 days. In OVX rats, one-month administration of SIF maintained estrogen receptor-β (ER-β) expression over estrogen receptor-α (ER-α), preserved gut eubiosis by modulating the estrobolome, increased β-glucuronidase enzyme and GUSB gene levels. Additionally, SIF also restores physiological and neurobehavioral parameters. In addition to this, SIF regulates mucosal integrity, tight junction genes, inflammatory markers, oxidative stress, monoamine neurotransmission, hypothalamic-pituitary axis regulations, and apoptosis. Comparative profiling of SIF with 17βE2 shows that 17βE2 improves gut and brain health, while preserving serum estradiol levels and uterine horn weight. This may enhance the feminizing side effects of 17βE2. However, SIF did not show any uterotrophic effect. SIF at doses of 40 and 80 mg/kg may offer a safer alternative to 17βE2 for managing GBA dysfunction in postmenopausal women.},
}

@article {pmid41421358,
year = {2025},
author = {Wang, J and Qian, X and Li, Q and Jin, Z and Liu, N and Zhao, J and Chen, W and Wang, S and Tian, P},
title = {Bacteriocin gene-mediated ecological adaptation of Bifidobacterium breve in the adult human gut.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {101106},
doi = {10.1016/j.xgen.2025.101106},
pmid = {41421358},
issn = {2666-979X},
abstract = {The ecological persistence of Bifidobacterium breve across life stages reflects adaptive strategies beyond the classical infant- versus adult-type dichotomy, historically attributed to differential nutrient utilization. Here, comparative genomics revealed no major differences in shared carbohydrate-related genes or accessory genome content between infant- and adult-derived strains. Instead, a distinct type III lanthipeptide bacteriocin cluster, lanKC, was specifically detected in adult-derived isolates. Functional assays combining gene knockout, in vitro co-cultivation, and human intervention demonstrated that lanKC enhances strain-level competitive fitness and promotes community stability. Phylogenetic and metagenomic analyses of 5,475 lanKC homologs and 6,122 infant gut metagenomes further suggested a possible early-life acquisition via intra-genus horizontal gene transfer. These findings uncover a previously unrecognized genetic basis underlying B. breve adaptation to the gut environment and support a multi-factorial model in which metabolic flexibility and interference competition jointly sustain bifidobacterial persistence and host-microbe symbiosis throughout life.},
}

@article {pmid41421351,
year = {2025},
author = {Newsome, RC and Liu, H and Agbodzi, B and Gharaibeh, RZ and Zhou, L and Jobin, C},
title = {Microbial-derived immunostimulatory small molecule augments anti-PD-1 therapy in lung cancer.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102519},
doi = {10.1016/j.xcrm.2025.102519},
pmid = {41421351},
issn = {2666-3791},
abstract = {We previously showed that enrichment of the Bacteroides genus is associated with improved anti-PD-1-mediated tumor therapy. Here, we isolate 183 Bacteroides isolates from the feces of humanized anti-PD-1 responder mice. Supernatants from 6 of 183 isolates stimulate IFNγ production from primary CD8[+] T cells. These six isolates (6-consort) enhance anti-PD-1-induced anti-tumor efficacy in syngeneic and orthotopic lung cancer models compared to non-responder feces-colonized mice, an effect dependent on the production of IFNγ. Bioassay-guided fractionation and comparative metabolomics lead to the discovery of an active N-acyl amide (cis-Bac429) produced by Bacteroides. cis-Bac429 stimulates IFNγ production by CD8[+] T cells but not synthetic saturated Bac429 (sat-Bac429), indicating structural specificity. Intratumorally administered cis-Bac429, but not sat-Bac429, significantly decreases subcutaneous lung and colon tumor growth in combination with anti-PD-1 therapy and drives IFNγ+ CD8[+] T cell tumor infiltration. These findings pave the way for development of Bacteroides-type N-acyl-amides as adjuvant treatments for anti-PD-1-refractory NSCLC.},
}

@article {pmid41421350,
year = {2025},
author = {Chen, W and Wang, X and Zhu, R and Gao, W and Tao, L and Yang, R and Wei, Q and Zhang, Y and Gong, Y and Zhong, H and Huang, L and Zhu, X and Yang, Y and Zhang, L and Wan, L and Yang, G and Li, Y and Jiao, N and Wang, J and Qin, H and Zhu, L},
title = {Integrative multi-omics reveals microbial genomic variants driving altered host-microbe interactions in autism spectrum disorder.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102516},
doi = {10.1016/j.xcrm.2025.102516},
pmid = {41421350},
issn = {2666-3791},
abstract = {Emerging evidence links the gut microbiome to autism spectrum disorder (ASD), yet the role of microbial genomic variation remains underexplored. We generated a large-scale metagenomic and metabolomic dataset from over 1,100 children, integrating public datasets, to characterize ASD-associated microbial changes. We identified 35 species, 213 genes, 28 pathways, and 99 metabolites, alongside 1,369 single-nucleotide variants, 233 insertions/deletions, and 195 structural variants with differential abundance. Profiling of microbial genomic variation revealed 33 species and 196 enzymes lacking abundance differences, yet exhibiting significant sequence variation. Integrated analysis of microbial variants and metabolites uncovered 357 neurological associations, with mediation analysis showing that several metabolites link microbial variants to the ASD phenotype. Importantly, diagnostic models incorporating microbial variant and/or metabolite features achieved superior performance and generalizability. Our findings highlight microbial genomic variation as a critical, previously overlooked dimension of ASD-associated dysbiosis, offering valuable insights for diagnosis and mechanistic studies.},
}

@article {pmid41421305,
year = {2025},
author = {Zhou, H and McCarthy, FM and Kim, TH and Warren, W and Zhang, G},
title = {Emerging technologies in poultry genomics: Unlocking innovation for the future of sustainable production.},
journal = {Poultry science},
volume = {105},
number = {2},
pages = {106240},
doi = {10.1016/j.psj.2025.106240},
pmid = {41421305},
issn = {1525-3171},
abstract = {Over the past decade, poultry genomics has undergone a transformative shift from genome assembly to functional annotation, mechanistic discovery, and integrative applications that advance sustainable poultry production. This symposium highlights emerging tools and resources that enable researchers to move beyond statistical associations toward biological causality and breeding application. Functional annotation through the FAANG (Functional Annotation of Animal Genomes) initiative and ChickenGTEx Project has produced comprehensive regulatory maps and expression QTL datasets across tissues, cell types, and developmental stages, forming a foundation for identifying causal regulatory variants. Advances in CRISPR-based editing provide scalable platforms for in vitro validation of regulatory elements and dissect gene function, bridging genotype to phenotype. Single-cell RNA sequencing technologies are now delivering high-resolution immune cell atlases and developmental maps, offering novel insights into host defense and tissue regulation. Integrative omics frameworks that combine genomics, transcriptomics, epigenomics, and 3D chromatin data are revealing systemic regulatory networks controlling complex traits such as egg production, growth, and fat deposition, with functional validation of candidate variants accelerating their translation into precision breeding. Equally important, microbiome-based approaches are emerging as powerful tools to improve poultry health, nutrient utilization, and disease resistance, providing environmentally sustainable strategies that complement genetic selection. Challenges remain in statistical power, tissue- and development-specific context specificity, and bridging discoveries to genomic prediction. However, new opportunities, including multi-omics integration, causal inference, and iterative validation pipelines facilitate the development of predictive and mechanistically informed approaches to genetic improvement. Together, these advances mark a paradigm shift in poultry genomics, positioning the field to close the genotype-molecular-phenotype loop, and equipping the industry with tools to enhance production efficiency, resilience, and animal welfare for long-term sustainability.},
}

@article {pmid41420986,
year = {2025},
author = {Kao, CS and Jiang, CB and Yang, CC and Wang, YL and Chen, YH and Chao, HJ and Hsi, HC and Chien, LC},
title = {Combined exposure to microplastics and cadmium alters gut microbiota composition in preschool children: A cross-sectional study.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140854},
doi = {10.1016/j.jhazmat.2025.140854},
pmid = {41420986},
issn = {1873-3336},
abstract = {Early childhood is a critical developmental stage during which the gut microbiota strongly influences nutrient absorption, immunity, and neurodevelopment. Diet is considered a primary route of exposure to both microplastics (MPs) and cadmium (Cd), raising concerns about their potential joint impacts on child health. However, the effects of combined exposure to MPs and Cd on the early-life gut microbiota remain poorly understood. Fecal samples from 68 preschool children under 6 years of age were analyzed using pyrolysis-gas chromatography-mass spectrometry (Py-GC/MS) and inductively coupled plasma mass spectrometry (ICP-MS) to quantify MPs and Cd, respectively. MPs were detected in all samples, with a median concentration of 123.7 μg/g dry weight (DW) (interquartile range, IQR: 70.6-197.8). The predominant polymers were polyethylene (PE, 100 %), polyamide-66 (PA66, 100 %), and polyvinyl chloride (PVC, 93 %). Cd was also detected in all children, with a median concentration of 0.31 μg/g DW (range: 0.21-0.48). Cd concentrations were significantly higher in the low-MP-exposure group compared to the high-exposure group, indicating an inverse association between fecal MP and Cd levels in children. Under combined exposure to MPs and Cd, children with lower Cd levels exhibited higher abundances of beneficial taxa, such as Bifidobacterium and Faecalibacterium. In contrast, higher MP exposure was associated with enrichment of Bacilli and enhanced Bacilli-associated functional activity, particularly in amino acid, energy, and carbohydrate metabolism. KEGG functional predictions also showed that carbohydrate and nucleotide metabolism pathways are more prominent in both low Cd-MP and high Cd-MP exposure groups, indicating a non-monotonic trend. These findings provide novel evidence that combined exposure to MPs and Cd is associated with distinct alterations in the gut microbiota of preschool children, underscoring the need to consider multiple pollutants in early-life microbiome research.},
}

@article {pmid41420859,
year = {2025},
author = {Beghini, F and Brito, IL and Gerstein, M and Christakis, NA},
title = {Characterization of gut microbiomes in rural Honduras reveals uncharacterized species and associations with human genetic variation.},
journal = {Cell reports},
volume = {45},
number = {1},
pages = {116724},
doi = {10.1016/j.celrep.2025.116724},
pmid = {41420859},
issn = {2211-1247},
abstract = {The gut microbiome is integral to human health, yet research data to date have emphasized industrialized populations. Here, we performed large-scale shotgun metagenomic sequencing on 1,893 individuals from rural Honduras, providing the most comprehensive microbiome dataset from Central America. We identify a distinct microbial composition enriched in Prevotella species. Longitudinal analysis in 301 individuals reveals microbiome instability, with shifts in taxonomic diversity and metabolic potential, including changes associated with severe acute respiratory syndrome coronavirus 2 infection. Additionally, we characterize the gut virome and eukaryotic microbiome, identifying uncharacterized viral taxa and a high prevalence of Blastocystis species in individuals with greater microbial diversity. Finally, by integrating host genomic data, we uncover significant host-microbiome associations, highlighting the influence of human genetic variation on microbial composition. These findings expand our understanding of microbiome diversity in non-industrialized populations, underscoring the need for global microbiome research.},
}

@article {pmid41420751,
year = {2025},
author = {Varia, J and Herbert, M and Hooker, B},
title = {The Neuroimmunology of Autism.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {316},
pmid = {41420751},
issn = {1559-1182},
mesh = {Humans ; Animals ; *Autism Spectrum Disorder/immunology ; *Neuroimmunomodulation ; *Autistic Disorder/immunology ; Microbiota ; *Immune System/immunology ; },
abstract = {Alterations and maladaptations of the immune system remain some of the most controversial concepts in autism spectrum disorder (ASD). Nonetheless, intensifying evidence confirms that much of what ASD involves is related not to a static encephalopathy-based model of autism but rather to the consequences of environmental insult and complex and dynamic psychological and physiological processes involving the interdependence of the nervous, immune, and host microbiome. This narrative review provides a conceptual framework, focuses on clinical research, and is written for specialists and non-specialists. To provide access to multi- and interdisciplinary perspectives with wide-ranging cutting-edge implications for all people with ASD. Beginning with historical, epidemiological, and etiological underpinnings, we elaborate on a contemporary understanding of the immune system in the pathophysiology of ASD. Theoretical and scientific discourse on the relationship of the immune system with the nervous system and host microbiota in homeostasis/allostasis, neurodevelopment, and psychological and physiological health and disease is also provided. As a basis for conceptual advances detailing the interconnection, interdependence, and interference with or subjugation (as would be the case for autoinflammatory and autoimmune conditions) of the nervous system and host microbiota by the immune system, and the role of these interactions in the pathogenesis of ASD. This gives us a platform for not only examining the role of the immune system in the etiology, pathogenesis, and pathophysiology of ASD but also understanding social and higher-level processes of consciousness for individuals on the spectrum. Finally, taking a neuroimmunological perspective, we highlight the need for a multi-scale, holistic approach to understanding and developing future therapeutic modalities to address the core symptoms of ASD that go beyond the current reductionist and "magic-bullet" medical paradigm.},
}

Humans
Animals
*Autism Spectrum Disorder/immunology
*Neuroimmunomodulation
*Autistic Disorder/immunology
Microbiota
*Immune System/immunology

@article {pmid41420750,
year = {2025},
author = {Motevalli, H and Mehrani, A and Zolfaghari, K and Khodaee, P and Yazdanpanah, N and Saleki, K and Rezaei, N},
title = {TLRs and NLRs modulate oral microbiome involvement in Alzheimer's disease.},
journal = {Metabolic brain disease},
volume = {41},
number = {1},
pages = {7},
pmid = {41420750},
issn = {1573-7365},
mesh = {Humans ; *Alzheimer Disease/metabolism/microbiology ; *Microbiota/physiology ; *Toll-Like Receptors/metabolism ; Animals ; *Mouth/microbiology ; Dysbiosis/metabolism ; },
abstract = {Alzheimer's disease (AD) is the most common and irreversible type of dementia, accounting for more than half of all dementia cases. Early diagnosis of AD plays a role in slowing the progression of the disease and also preserving the quality of life of patients. However, there is often a time lag of several decades between the biological onset of the disease and the time of clinical diagnosis. At the time of diagnosis, the patient often has noticeable cognitive decline, which reduces the effectiveness of available treatments. This diagnostic time lag from onset to the onset of symptoms highlights the need to identify accessible and cost-effective screening tools, such as biomarker-based diagnostic and screening methods. Studies have implicated disorders of the oral-brain axis in the pathogenesis of neurodegenerative diseases such as AD. Oral dysbiosis has been epidemiologically associated with an increased risk of cognitive decline and AD, making the oral microbiome a potential biomarker for screening and early diagnosis of AD. Oral dysbiosis also plays a role in the pathogenesis of AD by increasing systemic inflammation and neuroinflammation. TLR/NLR signaling has been identified as a key intrinsic pathway in the pathogenesis of these neuroinflammations and systemic inflammation, which may suggest the use of inhibitors such as TAK-242/MCC950 as a potential therapeutic approach in the treatment of AD, although preclinical and clinical evidence for the use of these inhibitors in the course of AD is still very limited. In this review, we discuss oral dysbiosis in AD and review studies investigating the mouth-brain axis as an effective pathway in AD from diagnosis to treatment.},
}

Humans
*Alzheimer Disease/metabolism/microbiology
*Microbiota/physiology
*Toll-Like Receptors/metabolism
Animals
*Mouth/microbiology
Dysbiosis/metabolism

@article {pmid41420663,
year = {2025},
author = {Frederick, RM and Lam, K and Han, JK},
title = {Acute Exacerbations of Chronic Rhinosinusitis.},
journal = {Current allergy and asthma reports},
volume = {25},
number = {1},
pages = {61},
pmid = {41420663},
issn = {1534-6315},
mesh = {Humans ; *Sinusitis/diagnosis/drug therapy ; Chronic Disease ; *Rhinitis/diagnosis/drug therapy ; Acute Disease ; Disease Progression ; Asthma ; Anti-Bacterial Agents/therapeutic use ; Rhinosinusitis ; },
abstract = {PURPOSE OF REVIEW: We aim to highlight recent advancements on the evolving chronic rhinosinusitis (CRS) phenotype: acute exacerbations of chronic rhinosinusitis (AECRS). We focused on studies that expanded the current understanding of its pathophysiology, patient characteristics, and disease burden.

RECENT FINDINGS: Defining AECRS has been a topic of discussion for many years. A recent regulatory definition of AECRS in the literature incorporates a > 3 day requirement of worsened symptoms and an escalation of treatment. It is important not to rely on patient-reported rescue medication frequency as it was recently demonstrated these are only obtained for 1/3 of reported AECRS episodes. The pathophysiology behind AECRS is still being evaluated but it appears irritants such as viral insult to the sinonasal microbiome can create a dysbiosis and worsens host immune system breakdown, facilitating a subsequent bacterial infection. Many studies are using loose definitions of AECRS because no formal definition has existed until recently. Clinical trials and other studies are relying on patient-reported illnesses, CRS-related antibiotics, and CRS-related corticosteroids to determine an episode of AECRS. Formally defining AECRS is vital in order to conduct future literature on its etiology and clinical outcomes so results may be translatable. Additionally, our review demonstrates that CRS patients with asthma and/or concomitant allergic rhinitis appear to be at an increased risk for developing AECRS and future research should continue to investigate their interplay. Many patients are being overprescribed antibiotics and corticosteroids for reported AECRS episodes. This increases total healthcare spending and increases the risk for adverse effects from corticosteroids and antibiotic resistance. Future research should investigate methods to mitigate this practice.},
}

Humans
*Sinusitis/diagnosis/drug therapy
Chronic Disease
*Rhinitis/diagnosis/drug therapy
Acute Disease
Disease Progression
Asthma
Anti-Bacterial Agents/therapeutic use
Rhinosinusitis

@article {pmid41420661,
year = {2025},
author = {Ngangbam, AK and Nongmaithem, BD and Haojam, RS and Khundrakpam, L and Singh, LL and Meetei, KB},
title = {First functional and taxonomic insights into the microbiome of edible snail, Cipangopaludina lecythis via shotgun metagenomics.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {1},
pages = {18},
pmid = {41420661},
issn = {1572-9699},
mesh = {*Snails/microbiology ; *Metagenomics/methods ; Animals ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The freshwater snail Cipangopaludina lecythis holds both ecological and medicinal importance, yet its microbiome remains unexplored. This study presents the first shotgun metagenomic profiling of edible tissues of C. lecythis. Illumina HiSeq sequencing generated over 42 million high-quality reads, revealing 38 bacterial phyla dominated by Pseudomonadota (32%), followed by Bacillota and Actinomycetota. At the genus level, Pseudomonas, Klebsiella, Acinetobacter, Bacillus, Clostridium, Staphylococcus, and Streptomyces were prevalent. Functionally important genera such as Aeromonas, Vibrio, and Pseudoalteromonas which are known for their probiotic and immunomodulatory properties were also detected. The dominant species included Pseudomonas sp. REST10, Escherichia coli, Klebsiella pneumoniae, and Streptomyces sp. T12, many of which were associated with fermentation and host microbe interactions. Interestingly, the microbial profiles differed from those in marine snails, indicating environment-specific microbiome signatures. Functional annotation revealed key enzymes including 17 beta-hydroxysteroid dehydrogenase type 3 (HSD17B3) and malonyl-CoA:ACP transacylase, involved in fatty acid metabolism and energy regulation. Enzymes such as glutathione S-transferase and arylacetamide deacetylase were also detected, along with chitinase and chitin synthases, suggesting host microbe interactions in chitin metabolism. High alpha diversity showed a rich and functional microbiome. Overall, this study highlights the metabolic potential and ecological relevance of the C. lecythis microbiome, supporting its application in biotechnology and nutraceutical industry.},
}

*Snails/microbiology
*Metagenomics/methods
Animals
*Bacteria/classification/genetics/isolation & purification
*Microbiota
Phylogeny
RNA, Ribosomal, 16S/genetics

@article {pmid41420422,
year = {2025},
author = {Cao, S and Yang, L and Wang, R and Liu, J},
title = {Worldwide Research Trends on Substance Use Disorder-Related Inflammatory Imbalances: A Bibliometric Analysis.},
journal = {CNS neuroscience & therapeutics},
volume = {31},
number = {12},
pages = {e70719},
doi = {10.1002/cns.70719},
pmid = {41420422},
issn = {1755-5949},
support = {1053320230244//the Fundamental Research Funds for the Central Universities of Central South University/ ; U22A20303//National Natural Science Foundation of China/ ; 2019SK2131//Innovative Province Special Construction Foundation of Hunan Province/ ; 2021RC4016//the Science and Technology Innovation Program of Hunan Province/ ; 2020SK4001//Clinical Research Center For Medical Imaging In Hunan Province in China/ ; },
mesh = {*Bibliometrics ; Humans ; *Substance-Related Disorders/epidemiology/complications ; *Inflammation ; *Biomedical Research/trends ; Animals ; },
abstract = {BACKGROUND: Substance use disorder (SUD) is a complex, chronic, and relapsing encephalopathy associated with inflammatory processes. This study aims to conduct a bibliometric analysis to elucidate the current landscape, research hotspots, and evolving trends in the field of SUD-related inflammation imbalance.

METHODS: Original research and review articles pertaining to "SUD-inflammation" subject were systematically retrieved from the Web of Science Core Collection (WoSCC) database, encompassing publications from its inception to January 1, 2025. Co-authorship, collaboration, co-citation, and co-occurrence analyses were performed using VOSviewer, and CiteSpace was utilized to identify strongest citation bursts and keyword trends.

RESULTS: A total of 2318 publications on "SUD-inflammation" realm were included. A marked increase in publication output was observed starting in 2019. The United States (US) and China emerged as the most prolific countries. The journal, institution, and author, with the largest number of total publications (NP), were respectively JOURNAL OF ETHNOPHARMACOLOGY, UNIVERSITY OF CALIFORNIA SYSTEM, and Michael Maes. Core terms "microglial activation," "oxidative stress," and "TLR4 signaling" were among the most frequently studied topics. Additionally, the roles of the "gut-immune-brain" axis and N-acetylcysteine in drug addiction have been receiving significant attention.

CONCLUSION: This bibliometric study delineates the foundational knowledge structural and mapping of the "SUD-inflammation" field over the past 25 years. The findings provide a comprehensive and data-driven perspective on the evolving research landscape, offering valuable insights for future investigations and resource allocation.},
}

*Bibliometrics
Humans
*Substance-Related Disorders/epidemiology/complications
*Inflammation
*Biomedical Research/trends
Animals

@article {pmid41420183,
year = {2025},
author = {Dai, Y and Song, J and Bai, G and Liu, J},
title = {A literature-based gut microbiota dietary index and its association with obstructive sleep apnea risk: a population-based, cross-sectional study.},
journal = {BMC nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40795-025-01199-8},
pmid = {41420183},
issn = {2055-0928},
support = {[2022] No.1//Zunyi Oral Disease Immune Prevention and Medical Biomaterials Research and Development Innovation Talent Team, Zunyi Science Talent/ ; [2022] No.1//Zunyi Oral Disease Immune Prevention and Medical Biomaterials Research and Development Innovation Talent Team, Zunyi Science Talent/ ; [2022] No.1//Zunyi Oral Disease Immune Prevention and Medical Biomaterials Research and Development Innovation Talent Team, Zunyi Science Talent/ ; },
abstract = {BACKGROUND: Limited research has explored the link between the Literature-Based Dietary Index for Gut Microbiota (LBDI-GM) and Obstructive Sleep Apnea (OSA). This study aims to examine the relationship between these two conditions.

METHODS: This cross-sectional analysis utilized data from the 2015-2018 National Health and Nutritional Examination Survey (NHANES). Obstructive sleep apnea (OSA) served as the independent variable, evaluated through self-reported questionnaires. The dependent variable was the novel literature-Based Dietary Index for Gut Microbiota, which quantified dietary patterns linked to intestinal microbiome characteristics. Weighted multivariable logistic regression modeling explored associations between LBDI-GM and OSA. Supplementary subgroup and interaction evaluations were performed.

RESULT: A total of 8,707 participants were included in the final analysis, with a mean age of 47.66 years (SD = 0.43). The study population was nearly equally distributed by sex, with 4,460 males (51.2%) and 4,247 females (48.8%). Following comprehensive adjustment for potential confounders in the weighted logistic regression model (Model III), LBDI-GM demonstrated a statistically significant inverse association with OSA risk (OR = 0.967, 95% CI: 0.938-0.996, p = 0.025). Sex-stratified analyses indicated that this protective association was particularly evident among female participants.

CONCLUSIONS: This cross-sectional study identified an inverse association between LBDI-GM and OSA, suggesting that dietary patterns promoting gut microbiota health may play a role in reducing the risk of OSA. These findings highlight the potential for integrating dietary interventions into clinical practice to improve OSA management.},
}

@article {pmid41420109,
year = {2025},
author = {McCormick, C and Degregori, S and Johnson, GC and Blumstein, DT and Barber, PH},
title = {Marmot gut microbiomes are stable against dietary variation.},
journal = {Oecologia},
volume = {208},
number = {1},
pages = {15},
pmid = {41420109},
issn = {1432-1939},
support = {1557130//National Science Foundation/ ; },
mesh = {*Gastrointestinal Microbiome ; Animals ; *Diet ; *Marmota/microbiology ; RNA, Ribosomal, 16S ; Feces/microbiology ; },
abstract = {Animal gut microbiomes, particularly those of herbivorous mammals, are strongly shaped by the host diet. However, how dietary composition impacts gut microbiome variation across a population of wild hosts is unknown. To examine the relationship between gut microbiome composition and diet composition across individuals, we employed a multi-omic approach leveraging both 16S rRNA amplicon sequencing and plant DNA metabarcoding (tRNL primer) in 39 wild yellow-bellied marmot fecal samples from the Rocky Mountains. We utilized the 16 s rRNA primer to target microbes and the tRNL primer to target plants. Our results indicate that the marmot gut microbiomes appear to be stable against dietary variation, even across individuals with significantly different diets. We also show that colony membership significantly impacts marmot dietary variation, while age does not. Thus, while diet clearly plays a significant role in shaping mammalian gut microbiomes, our study suggests that diet composition within the same species has a minimal impact on gut microbiome variation, particularly in the absence of experimental manipulations and dietary interventions.},
}

*Gastrointestinal Microbiome
Animals
*Diet
*Marmota/microbiology
RNA, Ribosomal, 16S
Feces/microbiology

@article {pmid41419805,
year = {2025},
author = {Hussain, M and Ahmed, N and Xie, X and Teng, Z and Hou, X and Li, X and Yang, Z and Zhu, Z},
title = {Characterization of the mango phyllosphere microbiome during fruit-setting unveils unique community assembly and coexisting beneficial-pathogenic microbiota.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-07943-3},
pmid = {41419805},
issn = {1471-2229},
support = {2025KY0769//Basic Ability Enhancement Projects for Young and Middle-aged Teachers/ ; 2024011670 and 2019011394//Scientific Research Startup Fund of Baise University/ ; 2024011670 and 2019011394//Scientific Research Startup Fund of Baise University/ ; },
abstract = {BACKGROUND: Mango is an economically important fruit tree with rich genetic diversity, but has been threatened by a diverse range of pathogens, causing substantial losses annually. While the plant-associated microbiomes are well studied, the assembly patterns and composition of phyllosphere microbial communities for deciphering potential pathogenic and beneficial microbiota during the mango fruit-setting phase remain largely unexplored.

RESULTS: This study profiled the bacterial and fungal communities in mango leaves, flowers, and fruitlets using high-throughput amplicon sequencing. Both flowers and fruitlets exhibited significantly less diverse microbial communities than leaves, and the bacterial and fungal microbiota compositions of all three organs were distinct from one another. Importantly, organ-specific preferences were observed among the dominant bacterial families, with mango flowers characterized by a high abundance of Erwiniaceae, fruitlets by Acetobacteraceae, and leaves by Microbacteriaceae and Bifidobacteriaceae. In contrast, fungal families were less differentiated, with only Didymellaceae and Symmetrosporaceae showing leaf-specific enrichment relative to flowers and fruitlets. Analysis of the shared microbial genera across the three phyllosphere organs revealed the presence of core bacterial taxa Pseudomonas and Sphingomonas, while the fungal core genera were Alternaria, Aureobasidium, Cladosporium, Epicoccum, Fusarium, Hannaella, Nectria, Neodidymella, and Vishniacozyma. Notably, several of these concurrently detected microbial genera have been previously documented as either pathogenic (e.g., Alternaria, Cladosporium and Fusarium) or beneficial (Aureobasidium, Vishniacozyma, Sphingomonas and Pseudomonas). Furthermore, we found that the mango phyllosphere bacterial and fungal communities were established by parallel selection of the microbiota, instead of consecutive selection. Deciphering the functional profile of the phyllosphere microbiota revealed the association of microbial taxa with functions such as chemoheterotrophy, aerobic chemoheterotrophy, fermentation, aromatic compound degradation, plant pathogens, endophytes, and saprotrophs, indicating a balanced ecosystem in which future fruit health outcomes may be determined by subtle shifts in the microbial community structure.

CONCLUSION: Our findings offer a checklist of the core beneficial and pathogenic microbes inhabiting the mango phyllosphere, while also highlighting the selective role of mango organs in recruiting specific subsets of microbiota, which can be harnessed for disease protection and improving mango production.},
}

@article {pmid41419476,
year = {2025},
author = {Gustin, AT and Broedlow, CA and Hager, K and Coronado, E and Wangari, S and Iwayama, N and Ahrens, CY and Garrison, WD and Guerriero, KA and De Paris, K and Londono-Renteria, B and Gale, M and Klatt, NR and Kublin, JG and Manuzak, JA},
title = {Distinct gastrointestinal microbial signatures predict parasite levels in controlled Plasmodium infections in both rhesus macaques and humans.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67241-2},
pmid = {41419476},
issn = {2041-1723},
support = {K01OD024876//U.S. Department of Health & Human Services | NIH | NIH Office of the Director (OD)/ ; },
abstract = {Functions of the gastrointestinal (GI) microbiome include maintenance of immune homeostasis and protection against infectious disease. Current assessments of the role of the GI microbiome in Plasmodium infection have been primarily conducted using mouse models and observational human cohorts. Here, we experimentally assessed associations between pre-infection GI microbiome composition and acute Plasmodium parasitemia using 16S rRNA sequencing and samples from rhesus macaques (RMs) and adult humans enrolled in a previously conducted controlled human malaria infection (CHMI) trial (NCT04072302) originally designed to test the efficacy of KAF156, a novel imidazolopiperazine class of antimalarial drugs. We identified distinct pre-infection 16S microbial signatures that were associated with increased risk for above median parasitemia in RMs infected with P. fragile and CHMI participants infected with P. falciparum. Further, we identified a Bifidobacterium feature set that accurately stratified parasitemia risk and could therefore serve as a foundation for a potential biomarker panel to aid prevention efforts in malaria endemic regions. Together, our findings demonstrate that pre-infection GI microbiome composition is indicative of risk for Plasmodium parasitemia, and our observation that the pre-infection microbiome-P. fragile dynamic in RMs mirrors the pre-infection microbiome-P. falciparum interaction in CHMI participants supports the future use of this model in pre-clinical investigations of novel microbiome-targeting approaches to reduce malaria burden.},
}