@article {pmid41175312,
year = {2025},
author = {Miller, BC and Haggler, JA and Chaudhari, DS and Shukla, R and Kumar, V and Mishra, SP and Masternak, MM and Holland, P and Labyak, C and Golden, A and Dangiolo, M and Arikawa, AY and Kociolek, J and Fraser, A and Williams, C and Agronin, M and Aymat, M and Pledger, W and Yadav, H and Jain, S},
title = {Gut microbiome signatures predict cognitive impairment in older cancer survivors.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {41175312},
issn = {2509-2723},
support = {22A17//Florida Department of Health/ ; },
abstract = {Cancer treatments are improving, and the population of cancer survivors is steadily increasing. However, many survivors experience long-term side effects, including chemobrain and other age-related geriatric disorders like cognitive impairment (CI), severely impacting their quality of life. Emerging studies suggest that the gut microbiome plays a central role in cognitive health. However, the long-term effects of cancer treatments on the microbiome, and how these changes impact cognitive health in survivors, remain largely unknown. Shotgun metagenomic data from 150 older adults (≥ 60 years old, including 49 cancer survivors and 101 controls) from the Microbiome in Aging Gut and Brain (MiaGB) consortium revealed that Tyzzerella, Eggerthella lenta, and Bacteroides vulgatus were specific markers of the cancer survivor gut and could differentiate cancer survivorship in this cohort. Microbiome signatures were distinct in cancer survivors with CI compared to those without and differed from those seen in non-cancer individuals with CI. Bacterial taxa including Streptococcus thermophilus and Firmicutes bacterium CAG 114 were significantly reduced in cancer survivors and strongly associated with CI. Importantly, metabolic pathway analysis revealed that microbial neurotransmitter synthesis was significantly depleted in the gut of cancer survivors, suggesting a mechanistic link to CI. Our results suggest that microbiome signatures predict cancer survivorship and the risk of CI in older adults, potentially by depleting neurotransmitter synthesis in the gut. These findings aid in establishing the role of the microbiome in predicting cancer survivorship and CI risk, which is valuable in the development of novel therapies to support the growing population of cancer survivors.},
}

@article {pmid41175215,
year = {2025},
author = {Ichibakase, F and Naito, T and Kaji, N},
title = {Fabrication and installation of a flexible polydimethylsiloxane (PDMS) porous membrane as a substitute for a rigid, conventional, track-etched polyethylene terephthalate (PET) membrane on cell culture inserts for gut barrier co-culture.},
journal = {Analytical and bioanalytical chemistry},
volume = {},
number = {},
pages = {},
pmid = {41175215},
issn = {1618-2650},
support = {24K01322//Japan Society for the Promotion of Science/ ; },
abstract = {We report a simple, clean-room-free strategy for fabricating an ultrathin (≈ 5 µm) and highly flexible polydimethylsiloxane (PDMS) porous membrane that functions as a mechanically dynamic scaffold for an intestine-on-a-chip platform capable of co-culturing human epithelial cells and gut bacteria. The membrane is produced by a two-dimensional phase separation process in which polystyrene (PS) of defined molecular weight (MW = 1300-170,000) acts as the sacrificial layer in a PDMS/toluene matrix. Systematic variation of phase separation time (3-24 h), PS molecular weight, and PS:PDMS:toluene mixing ratio revealed that PS of MW = 5780 at a 1:7.5:7.5 weight ratio generated through pores 10-100 µm in diameter, whereas PS of MW = 1300 yielded sub-2 µm pores but required optimization to secure pore continuity. Scanning electron microscopy images confirmed homogeneous lateral distribution of the pores and negligible surface collapse after sacrificial removal of PS by overnight toluene extraction and subsequent thermal curing. Fluorescein permeability assays demonstrated that membranes fabricated with PS of MW = 5780 or 1300 displayed solute transport rates that showed a similar trend to 1.0 µm track-etched polyethylene terephthalate (PET) inserts at 12 h, underscoring successful formation of through pores despite an order of magnitude reduction in overall thickness. Importantly, Caco-2 colon epithelial cells adhered, proliferated, and formed confluent monolayers within 7 days on collagen-coated PDMS membranes, whereas confluent cultures on PET required 10 days. Long-term culture experiments (up to 18 days in our setting) highlighted contrasting behaviors: cells cultured on the larger-pore (10-100 µm) membranes detached after ≈13 days, likely due to accumulation of autocrine inhibitors on the impermeable basal side; in contrast, cells on the smaller pore (≈2 µm) PDMS membranes remained viable, although some cells migrated through the membrane to the lower chamber, illustrating the need to match pore size distribution to cell diameter. The present methodology eliminates photolithography and plasma bonding steps commonly associated with PDMS microfabrication and can be completed with benchtop spin coating and solvent-casting equipment in <48 h. Because the resulting membrane combines (i) compliance suitable for pneumatically driven peristaltic deformation, (ii) molecular permeability that showed a similar trend to conventional PET inserts, and (iii) optical transparency for real-time microscopy, it provides a versatile foundation for constructing gut-on-a-chip systems that more faithfully recapitulate the biochemical and mechanical microenvironment of the intestinal epithelium. Beyond microbiome-epithelium interaction studies, the platform is readily adaptable to barrier-function assays, drug-transport screening, and host-pathogen investigations involving mechanically active mucosal tissues.},
}

@article {pmid41175138,
year = {2025},
author = {Balan, P and Leite, FRM and Tay, JRH and Hartanto, J and Nascimento, GG and Romandini, M},
title = {Oral Microbiome Signatures in Periodontitis and Edentulism-A Population-Based Study.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70046},
pmid = {41175138},
issn = {1600-0765},
abstract = {AIM: To examine the association between the oral microbiome, periodontitis, and edentulism in a nationally representative sample of the U.S.

METHODS: A total of 5299 adults aged 30-69 years were examined (NHANES 2009-2012). Oral rinse samples were collected and analyzed through 16S rRNA gene sequencing. Periodontitis presence, stage, extent, and grade were assessed according to the 2017 AAP/EFP classification using the ACES framework, with edentulism considered as a distinct category. Bacterial diversity and taxonomic composition were evaluated using alpha and beta diversity metrics and multivariable linear models (MaAsLin2), adjusted for relevant confounders.

RESULTS: Alpha diversity increased with periodontitis severity, extent, and grade, peaking in Stage III generalized periodontitis. In Stage IV, extensive tooth loss was associated with a decrease in alpha diversity. Edentulous individuals exhibited the lowest alpha diversity, falling below levels observed in those without periodontitis. Beta diversity differences across periodontitis severity, extent, and grade were subtle (< 0.2%). Taxonomically, increasing severity, extent, and grade of periodontitis were associated with enrichment of established periodontitis-related genera (e.g., Dialister, Filifactor, Fusobacterium, Porphyromonas, Prevotella, Tannerella) and Jonquetella, alongside depletion of health-related genera (e.g., Rothia, Veillonella). A total of 13 genera were commonly altered in both edentulous individuals and those with Stage III-IV periodontitis, relative to participants with no or localized Stage I-II disease.

CONCLUSION: Periodontitis is characterized by an increase in alpha diversity with advancing severity, extent, and grade, followed by a decline with extensive tooth loss and edentulism. However, it accounted for only a small fraction of the overall variation in oral microbiome composition. Taxonomic shifts included enrichment of established periodontitis-related genera and Jonquetella, alongside depletion of health-related genera. The persistence of periodontitis-associated bacteria in edentulous individuals may have important implications for implant dentistry.},
}

@article {pmid41174950,
year = {2025},
author = {Vega-Abellaneda, S and Román, E and Soler, Z and Ortiz, MÀ and Rossi, G and Biagini, L and Sánchez, E and Pons-Tarin, M and Laghi, L and Mengucci, C and Kaur, N and Poca, M and Cuyàs, B and Serrano-Gomez, G and Alvarado, E and Manichanh, C and Soriano, G},
title = {A Metagenomics Approach to Frailty in Patients With Cirrhosis Undergoing a Multifactorial Intervention.},
journal = {Liver international : official journal of the International Association for the Study of the Liver},
volume = {45},
number = {12},
pages = {e70418},
doi = {10.1111/liv.70418},
pmid = {41174950},
issn = {1478-3231},
support = {PI19/00275//Instituto de Salud Carlos III/ ; PR-455/2020//Col.legi Oficial d'Infermeres i Infermers de Barcelona/ ; //MENDES SA/ ; //Infisport/ ; },
mesh = {Humans ; *Liver Cirrhosis/complications/therapy/microbiology ; *Frailty/therapy/microbiology ; Male ; Metagenomics ; *Gastrointestinal Microbiome ; Female ; *Probiotics/therapeutic use ; Middle Aged ; Aged ; Feces/microbiology ; Amino Acids, Branched-Chain/therapeutic use ; },
abstract = {The relationship between frailty and gut microbiota has not been previously addressed in patients with cirrhosis. We studied by metagenomic shotgun sequencing the faecal microbiota composition associated with frailty in 29 patients with cirrhosis from a previous study (Román, Hepatol Commun 2024). Frail and prefrail patients were randomised to a multifactorial intervention (home exercise, branched-chain amino acids and a multistrain probiotic) or control for 12 months. We observed a positive correlation between the abundance of Rothia dentocariosa and the Liver frailty index (LFI), and between Bacteroides faecis and gait speed. After the multifactorial intervention, LFI improved and the main changes in the microbiota composition were a decrease in the abundance of Akkermansia muciniphila, and an increase in Streptococcus thermophilus, Lactobacillus acidophilus and several species of Bifidobacterium. We conclude that frailty in patients with cirrhosis was associated with a distinct microbiome signature. After a long-term multifactorial intervention, frailty improved in parallel with changes in microbiome composition. Trial Registration: ClinicalTrials.gov identifier: NCT04243148.},
}

Humans
*Liver Cirrhosis/complications/therapy/microbiology
*Frailty/therapy/microbiology
Male
Metagenomics
*Gastrointestinal Microbiome
Female
*Probiotics/therapeutic use
Middle Aged
Aged
Feces/microbiology
Amino Acids, Branched-Chain/therapeutic use

@article {pmid41174806,
year = {2025},
author = {Dong, Q and Ma, B and Zhou, X and Huang, P and Gao, M and Yang, S and Jiao, Y and Zhou, Y and Shi, Z and Deng, Q and Hua, D and Wang, X and Liu, L and Zhang, C and Zhang, C and Kong, M and He, C and Wu, T and Zou, H and Shi, J and Sheng, Y and Wang, Y and , and Tang, L and Hu, S and Zhong, H and Sun, W and Chen, W and Zhai, Q and Kong, X and Zheng, Y and Chen, L},
title = {Expanded gut microbial genomes from Chinese populations reveal population-specific genomic features related to human physiological traits.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {137},
pmid = {41174806},
issn = {1756-994X},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Asian People/genetics ; Phylogeny ; China ; *Genome, Bacterial ; *Genomics/methods ; East Asian People ; },
abstract = {BACKGROUND: A comprehensive and representative reference database is crucial for accurate taxonomic and functional profiling of the human gut microbiome in population-level studies. However, as approximately 70% of current microbial reference data originate from European and North American populations, other regions, including East Asia-and particularly China-remain significantly underrepresented.

METHODS: We constructed the human Gut Microbiome Reference (GMR), comprising 478,588 high-quality microbial genomes from Chinese (247,134) and non-Chinese (231,454) populations. Species-level clustering and protein annotations were performed to characterize microbial diversity and function. We further integrated novel microbial genomes into taxonomic profile database and validated the improvements using independent cohort data.

RESULTS: The GMR dataset spans 6664 species, including 26.4% newly classified species, and encodes over 20 million unique proteins, with 47% lacking known functional annotations. Notably, we observed that 35.35 and 32.46% of species unique to Chinese and non-Chinese populations, respectively. For 2145 species shared between populations, 74% of 304 species with balanced prevalence between populations exhibited population-specific phylogenetic stratification, involving health relevant functionalities such as antibiotic resistance. Integration of novel genomes into taxonomic improved population-level species profiling by up to 23% and uncovered replicable associations between novel species and host physiological traits.

CONCLUSIONS: Our study largely expands the compositional and functional landscape of the human gut microbiome, providing a crucial resource for studying the role of gut microbiome for regional health disparities.},
}

Humans
*Gastrointestinal Microbiome/genetics
Asian People/genetics
Phylogeny
China
*Genome, Bacterial
*Genomics/methods
East Asian People

@article {pmid41174753,
year = {2025},
author = {Xing, Y and Liu, C and Zhang, C and Zhou, D and Hu, B and Jiang, Q and Chen, J and Lin, Z and Wang, T and Yan, H and Liu, A and Lu, W and Ben, X and Yang, K and Yuan, JX and Zhan, W and Wang, J},
title = {Antibiotic-driven and microbiota-targeted therapy for advanced management of pulmonary hypertension.},
journal = {Respiratory research},
volume = {26},
number = {1},
pages = {303},
pmid = {41174753},
issn = {1465-993X},
support = {82120108001//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Hypertension, Pulmonary/drug therapy/microbiology/physiopathology ; *Anti-Bacterial Agents/therapeutic use/pharmacology/administration & dosage ; Male ; Retrospective Studies ; Rats ; Humans ; Middle Aged ; Female ; *Gastrointestinal Microbiome/drug effects/physiology ; Aged ; Rats, Sprague-Dawley ; *Disease Management ; Cohort Studies ; *Microbiota/drug effects ; },
abstract = {BACKGROUND: Pulmonary hypertension (PH), particularly secondary to hypoxic lung diseases like chronic obstructive pulmonary disease (COPD), lacks effective targeted therapies. Emerging evidence suggests that microbiota imbalances contribute to PH progression, raising the possibility of microbiome-targeted interventions. This study explores the role of antibiotics in modulating microbiota and ameliorating PH.

METHODS: A retrospective cohort analysis was conducted using the Medical Information Mart for Intensive Care (MIMIC) database to assess changes in mean pulmonary artery pressure (mPAP) after antibiotic treatment. Subsequently, clinical data of 220 PH patients (including group 1, 3, and 4 PH) from single clinical center were analyzed, with 16S rRNA sequencing performed on pharyngeal and fecal samples to evaluate microbiota composition. A hypoxia-induced PH rat model was used to investigate the effects of antibiotic treatment on hemodynamics, pulmonary vascular remodeling, and gut microbiota.

RESULTS: Antibiotic use was associated with reduced mPAP in PH patients, particularly in hypoxic associated PH. Microbiota diversity decreased with antibiotic treatment, but probiotic species like Lactobacillus were enriched. In hypoxia-induced PH rats, antibiotics attenuated right ventricular systolic pressure (RVSP), reduced pulmonary vascular thickening, and preserved gut villi integrity. Lactobacillus and Anaerostipes correlated negatively with PH severity, suggesting a protective role.

CONCLUSION: Antibiotic-driven microbiota modulation may alleviate PH progression by targeting dysbiosis and reducing inflammation. These findings support further investigation into optimized antibiotic regimens as a therapeutic strategy for PH, particularly in hypoxic lung disease-associated cases.},
}

Animals
*Hypertension, Pulmonary/drug therapy/microbiology/physiopathology
*Anti-Bacterial Agents/therapeutic use/pharmacology/administration & dosage
Male
Retrospective Studies
Rats
Humans
Middle Aged
Female
*Gastrointestinal Microbiome/drug effects/physiology
Aged
Rats, Sprague-Dawley
*Disease Management
Cohort Studies
*Microbiota/drug effects

@article {pmid41174528,
year = {2025},
author = {Sharma, D and Valmiki, H and Chayal, P and Kumar, S and Chhotaray, S},
title = {Microbiome study of Murrah buffalo mastitis milk with emphasis on Acinetobacter species.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {703},
pmid = {41174528},
issn = {1471-2180},
}

@article {pmid41174251,
year = {2025},
author = {Dass, M and Abbai, NS and Ghai, M},
title = {The human skin microbiome: factors affecting individuality and application in forensic investigations.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {41174251},
issn = {1437-1596},
abstract = {Differences in microbial communities have been observed across various skin sites, such as dry, moist, and sebaceous areas. These skin types influence the diversity of microbials present in each microenvironment. Commonly found skin microbes include Staphylococcus epidermidis, Cutibacterium acnes and Corynebacterium sp. Ethnicity, age, gender and health status are a few individual-specific factors that shape the skin microbiome. Every individual retains unique and distinct skin microbial communities despite constant exposure to environmental changes. In forensic investigations, human identification can be achieved through skin microbial trace analysis left behind on surfaces and objects. Temporal stability of the microbial profile, on skin, for up to two weeks, is an attractive feature for the implementation of skin microbiome analysis in forensic applications. Additionally, microbial traces can assist in determining geolocation and estimating postmortem interval. Although high-throughput sequencing technologies have accelerated microbiome research and provide species-level information, the skin is a low-biomass sample, and there are currently no standardised protocols from sample collection to analysis. Machine learning is rapidly advancing skin microbiome research by enabling the analysis of large and complex datasets to uncover patterns. These patterns can be used for predicting skin health conditions, matching skin samples to specific microenvironments, identifying individuals and inferring biogeographic origins. The present review highlights current research in the application of skin microbiome analysis for forensics and future potential applications for age and gender determination. Additionally, the factors affecting the skin microbiome diversity are discussed. Skin microbiome research will accelerate enrichment of microbiome databases, which could complement the standard STR typing in accurate human identification.},
}

@article {pmid41173905,
year = {2025},
author = {Adhikary, R and Alkhatib, AEA and Hazra, S},
title = {Resistome profiling and bacterial community structure of semi-urban gutter ecosystems of India.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38127},
pmid = {41173905},
issn = {2045-2322},
mesh = {India ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; *Drug Resistance, Bacterial/genetics ; beta-Lactamases/genetics/metabolism ; Gastrointestinal Microbiome ; Metagenomics/methods ; Humans ; Microbiota ; Metagenome ; },
abstract = {Environmental factors contribute to antimicrobial resistance, a global health threat. Contaminated gutter water in urban areas spreads resistant bacteria, disrupting ecosystems and promoting biofilm formation, causing widespread concern. This study aimed to evaluate antibiotic-resistant bacterial populations across six gutter ecosystems in Roorkee, Uttarakhand, India during summer against different classes of antibiotics, identify presence of beta-lactamase, and explores total bacterial communities, and predicting metabolic pathways through 16S rRNA based metagenomic approach of V3 region. The highest resistant bacterial population was found in HL_NS-6, and HL_NS-2, with highly resistance to Penicillin (ampicillin and oxacillin), Cephalosporin (Cephalothin), aminoglycoside (Kanamycin), fluoroquinolone (ciprofloxacin), and Antifolate (Trimethoprim) class antibiotics. Beta-lactamase activity was detected in all samples except HL_NS-5, indicated by nitrocefin hydrolysis. The microbial community in the six samples were composed with the major families enterobacteriaceae (15.4%) and pseudomonadaceae (8.29%), covering 23.7% of the total population. The highest taxa were found in HL_NS-2 and HL_NS-4, while the largest genera were Pseudomonas (8.3%), Escherichia (8.2%), Hydrogenophaga (6.85%), and Candidatus Moranella (5.4%). There were 21.25% common bacterial genera were present as core microbiome and rest were signified the population diversity among the six-gutter microbiome. The coexistence of common metabolic pathways (citric acid cycle, carbon, nitrogen metabolism etc.), and streptomycin, glycosphingolipid, lipopolysaccharide, cyanoamino acid metabolism pathways might be induced the development of antibiotic resistance in gutter microbiome. This study suggests the presence of antibiotic-resistant bacteria with antibiotic resistant metabolic pathways, and beta-lactamase genes in urban gutter water, which could be harmful to both human health and environmental ecosystems.},
}

India
Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects/classification
RNA, Ribosomal, 16S/genetics
*Ecosystem
*Drug Resistance, Bacterial/genetics
beta-Lactamases/genetics/metabolism
Gastrointestinal Microbiome
Metagenomics/methods
Humans
Microbiota
Metagenome

@article {pmid41173853,
year = {2025},
author = {Huang, Y and Li, H and Zhu, B and Feng, S and Liu, C and Zhang, Z and Ning, Y and Wu, K and Wu, F},
title = {The association between gut microbiota and functional connectivity in cognitive impairment of first-episode major depressive disorder.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {449},
pmid = {41173853},
issn = {2158-3188},
support = {82301688//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82301688//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82301688//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82301688//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82301688//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82301688//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82301688//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82301688//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Cognitive Dysfunction/physiopathology/microbiology/diagnostic imaging ; *Depressive Disorder, Major/microbiology/physiopathology/complications/diagnostic imaging ; Male ; Female ; Adult ; Magnetic Resonance Imaging ; Young Adult ; *Brain/physiopathology/diagnostic imaging ; Case-Control Studies ; *Nerve Net/physiopathology/diagnostic imaging ; Connectome ; },
abstract = {The pathogenesis of major depressive disorder(MDD) and cognitive impairment has been linked to gut microbiota; however, the relationship between cognitive impairment and gut microbiota in patients with MDD and their underlying mechanisms remain unclear. This study aimed to investigate the brain-gut axis involved in cognitive impairment among patients with first-episode MDD through neuroimaging and microbiome analyses. 43 microbial species were different between patients with first-episode MDD and healthy controls. Notably, the relative abundances of Amycolatopsis sp. Hca4 and Shewanella livingstonensis were lower in patients with MDD compared to healthy controls, with Amycolatopsis sp. Hca4 negatively correlated with processing speed and Shewanella livingstonensis positively correlated with verbal learning. Brain network analysis revealed significant connectivity between subnetworks in patients with MDD, with cognitive function closely associated with connections between somatomotor-limbic, default mode-limbic and frontoparietal-limbic networks. Additionally, Amycolatopsis sp. Hca4 was found to modulate the relationship between the functional connectivity of the middle frontal gyrus and parahippocampal gyrus and working memory, with this correlation varying according to the abundance of Amycolatopsis sp. Hca4. These findings suggest that gut microbiota disturbances in patients with first-episode MDD serve as a regulatory factor for brain dysfunction and cognitive impairment.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Cognitive Dysfunction/physiopathology/microbiology/diagnostic imaging
*Depressive Disorder, Major/microbiology/physiopathology/complications/diagnostic imaging
Male
Female
Adult
Magnetic Resonance Imaging
Young Adult
*Brain/physiopathology/diagnostic imaging
Case-Control Studies
*Nerve Net/physiopathology/diagnostic imaging
Connectome

@article {pmid41173690,
year = {2025},
author = {Strunk, T and Steer, J and Currie, A},
title = {Neonatal skin: barrier, immunity and infection prevention in the NICU.},
journal = {Seminars in fetal & neonatal medicine},
volume = {},
number = {},
pages = {101681},
doi = {10.1016/j.siny.2025.101681},
pmid = {41173690},
issn = {1878-0946},
abstract = {The neonatal skin is central to early survival and immune development. Far from being a passive mechanical barrier, it integrates physical, chemical, and microbial defences that together protect the infant in the immediate postnatal period. In preterm infants, structural immaturity, reduced antimicrobial capacity, and altered microbial colonisation confer heightened vulnerability to infection and inflammation. At the same time, the neonatal period represents a critical window during which skin-microbe interactions shape tolerance and long-term immune trajectories. This review summarises recent advances in understanding the development of the skin barrier, antimicrobial and innate immune defences, and the role of commensals in immune programming. Translational opportunities for neonatal care are discussed, including skin protective practices, antisepsis, and emollient use that may reduce infection risk in the neonatal intensive care unit. Finally, we consider future directions in microbiome-informed and skin-centred strategies.},
}

@article {pmid41173568,
year = {2025},
author = {Díaz Perdigones, CM and Hinojosa Nogueira, D and Rodríguez Muñoz, A and Subiri Verdugo, A and Vilches-Pérez, A and Mela, V and Tinahones, FJ and Moreno Indias, I},
title = {Taxonomic and functional characteristics of the gut microbiota in obesity: A systematic review.},
journal = {Endocrinologia, diabetes y nutricion},
volume = {72},
number = {9},
pages = {501624},
doi = {10.1016/j.endien.2025.501624},
pmid = {41173568},
issn = {2530-0180},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Obesity/microbiology/metabolism ; Bacteria/classification ; },
abstract = {Obesity is a growing public health problem. In recent decades, scientific evidence has linked gut microbiota to obesity. This systematic review summarizes current knowledge on the composition and functional differences in gut microbiota between individuals with obesity and those with normal weight. Following PRISMA 2020 recommendations, studies published in adult populations between January 2014 and May 2024 were reviewed. PubMed, Web of Science, and Scopus databases were searched for observational studies that had used advanced sequencing methods, such as 16S rRNA and shotgun metagenomics, to assess gut microbiota. The quality of these studies was also analyzed using the Newcastle-Ottawa scale. Our review of 16 studies shows a reduction in microbial diversity in individuals with obesity. In addition, a higher relative abundance of the phylum Firmicutes, the families Enterobacteriaceae, Gemellaceae, Prevotellaceae, Streptococcaceae and Veillonellaceae, as well as the genera Blautia, Butyricimonas, Collinsella, Megamonas, and Streptococcus, while beneficial bacteria such as the families Porphyromonadaceae and Rikenellaceae, and the genera Bifidobacterium spp. and Faecalibacterium prausnitzii, were depleted. Functional analysis showed a tendency to an increase in metabolic pathways associated with carbohydrate and lipid metabolism, with reduced pathways related to short-chain fatty acid production. Obesity is associated with altered gut microbiota composition and function. However, the variability across studies regarding population characteristics, dietary pattern, and sequencing techniques limits the comparability of findings. Future research should prioritize standardized methodologies and confounding factors to elucidate the role of the gut microbiome in obesity.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Obesity/microbiology/metabolism
Bacteria/classification

@article {pmid41173369,
year = {2025},
author = {Goerdten, J and Rattner, J and Merdas, M and Achaintre, D and Yuan, L and Russo, P and Veidebaum, T and Molnár, D and Lissner, L and De Henauw, S and Moreno, LA and Aleksandrova, K and Foraita, R and Nöthlings, U and Keski-Rahkonen, P and Floegel, A},
title = {Reproducibility and sources of variation of urinary biomarkers of food intake of fruits, vegetables and chocolate in European children and adolescents.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.10.039},
pmid = {41173369},
issn = {1541-6100},
abstract = {BACKGROUND: Biomarkers of food intake (BFI) may improve dietary assessment. Thereby, a key concern is their reproducibility over time. In epidemiological studies this is important to accurately estimate habitual food intake, and consequent disease risk associations.

OBJECTIVE: We aimed to assess the reproducibility of twelve urinary metabolites linked to food intake and to investigate potential sources of their variation.

METHODS: The analyses are based on previously identified urinary metabolites associated with dietary intake of fruits, vegetables, and chocolate in the large-scale European IDEFICS/I.Family study. Metabolites were measured in 1,788 urine samples from 599 children at study baseline (2007/2008, n=597), at the first follow-up (2009/2010, n=596), and the third follow-up (2013/2014, n=595) using high-resolution liquid chromatography-mass spectrometry. Unadjusted and adjusted intra-class correlation coefficients (ICC) were calculated for 2-year and 4-year intervals. To identify sources of biomarker variability, various factors, including dietary intake, were analysed. The amount of variance explained by each factor was quantified using the partial coefficient of determination (R[2]).

RESULTS: The median ICCs were 0.27 (range: 0.11; 0.54) and 0.28 (range: 0.15; 0.51) over 2- and 4-years interval, respectively. Individual factors explained a median of 17% (range: 9.8%; 42.4%) of the variance for the 2-year interval and 14.6% (range: 8.3%; 43.8%) for the 4-year interval. Country of residence explained the largest proportion of variance (median 5% for the 2-year interval; 4.5% for the 4-year interval). Dietary intake explained only a variation of 0.7% (0.0%; 1.5%) and 0.6% (0.0%; 1.1%) for the 2- and 4-year interval, respectively.

CONCLUSION: The reproducibility of urinary metabolites was poor to moderate over the 2- to 4- year periods, and only part of the variability could be explained by the studied factors. Future studies should explore shorter time intervals and other sources of variation e.g., the influence of the gut microbiome and genetic factors.},
}

@article {pmid41173282,
year = {2025},
author = {Fu, Z and Li, W and Qiu, H and Romero-Freire, A and He, E},
title = {Critical role of crosstalk through the gut-liver and gut-kidney axes in mediating organ-specific toxicity induced by foodborne and waterborne rare earth elements.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {387},
number = {},
pages = {127327},
doi = {10.1016/j.envpol.2025.127327},
pmid = {41173282},
issn = {1873-6424},
abstract = {The escalating contamination of rare earth elements (REEs) in agricultural soils and rivers from intensive mining activities necessitates urgent investigation into their potential health risks. This study systematically compared the organ-specific toxicological effects of foodborne versus waterborne REE exposure in murine model, focusing on toxicity mechanisms mediated by the gut-liver and gut-kidney axes crosstalk. Elevated REE concentrations were detected in both liver and kidney tissues, as well as feces following exposure, with accumulation dependent on exposure level and duration, indicating that REEs can accumulate in mice despite existing excretion mechanisms. Histopathological analysis and immunofluorescence staining revealed that tissue damage related to inflammation and oxidative stress in the liver and kidney was caused by REE exposure, supported by altered metabolite profiles. Both foodborne and waterborne REEs disrupted hepatic metabolism related to amino acids and arachidonic acid, driving inflammation and oxidative stress. Whereas waterborne REEs preferentially impaired renal tryptophan and riboflavin metabolism associated with oxidative stress. Notably, both pathways disturbed the urea cycle in target organs, impacting nitrogen metabolism. Furthermore, REE exposure triggered a significant shift in intestinal flora composition, characterized by an elevated Firmicutes/Bacteroidota ratio. Correlation network analysis indicated significant crosstalk within the gut-kidney axis (p < 0.01), underscoring the critical role of gut microbiota in mediating REE toxicity. While the gut-liver axis exhibits comparatively weaker interactions. Overall, our study offers new insights into the distinct toxic action mechanisms of REEs through varied exposure patterns and highlights the gut microbiota as a key modulator of host health outcomes.},
}

@article {pmid41172985,
year = {2025},
author = {Padhi, P and Abdalla, A and Schneider, B and Backes, N and Otto, AA and Scheibe, IJ and Thomas, JP and Khadse, G and Samidurai, M and Jochmans, AK and George, A and Zenitsky, G and Jin, H and Anantharam, V and Kanthasamy, A and Mishra, A and Allenspach, K and Mochel, J and Phillips, GJ and Kanthasamy, AG},
title = {Bioengineered gut bacterium synthesizing levodopa alleviates motor deficits in models of Parkinson's disease.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.10.005},
pmid = {41172985},
issn = {1934-6069},
abstract = {L-3,4-Dihydroxyphenylalanine (L-DOPA), synthesized from L-tyrosine, is a direct precursor to dopamine. L-DOPA is the gold-standard treatment for Parkinson's disease (PD), given orally alongside decarboxylase inhibitors (e.g., benserazide) to enhance bioavailability. However, its chronic daily pulsatile-like delivery is associated with complications. Herein, we show the construction and in vivo efficacy of a programmable, titratable, genetically engineered E. coli Nissle 1917 system (EcNL-DOPA) that continuously synthesizes L-DOPA from L-tyrosine for systemic distribution. Oral administration of EcNL-DOPA with benserazide maintains therapeutic plasma L-DOPA concentrations and increases brain dopamine levels. EcNL-DOPA improves motor performance and limits depressive-like behaviors without adverse side effects in healthy mice, Parkinsonian mice, and canine models. Simulated physiological models from pharmacokinetic and pharmacodynamic studies in canines demonstrate the translational feasibility of this biotherapeutic system for potential human studies. This work lays the groundwork for EcNL-DOPA as a continuous, non-invasive microbial drug delivery platform for PD and chronic neurological diseases.},
}

@article {pmid41172954,
year = {2025},
author = {Suri, H and Suri, H and Nagda, N and Misra, T and Vuppu, S},
title = {Current perspectives on the human skin microbiome: Functional insights and strategies for therapeutic modulation.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {193},
number = {},
pages = {118655},
doi = {10.1016/j.biopha.2025.118655},
pmid = {41172954},
issn = {1950-6007},
abstract = {Human skin is inhabited by commensal microbiota comprising bacteria, fungi, viruses, and demodex mites. The skin microbiome is associated with several vital functions for the host, such as maintaining barrier integrity, modulating lipid homeostasis, eliminating pathogens, and stimulating the immune reactions. However, alterations in the composition of the skin microbiome are often found to be linked with inflammatory dermatological conditions like atopic dermatitis, psoriasis, acne vulgaris, rosacea, and wound-associated infections. These conditions can be diagnosed using culture-dependent and advanced culture-independent analyses, including multi-omics platforms and high-throughput sequencing technologies. Developments in microbiome research and biotechnology have catalysed initiatives to modify the skin microbiota as a therapeutic intervention. Current strategies encompass precision medicine utilising biomarkers, transplantation of complete microbial consortia, application of specific commensal microbes, bacteriophage therapy, use of pre- and probiotic metabolites, as well as sanitizers and antibiotics. This study consolidates existing knowledge regarding the composition and functional roles of the skin microbiome, investigates dysbiosis in skin pathologies, and examines potential microbiome-targeted therapeutic interventions. The study intends to address the challenges and future directions related to the clinical implementation of microbiome-targeted approaches, encompassing the regulatory aspects necessary to guarantee the efficacy and safety of innovative diagnostic and therapeutic applications.},
}

@article {pmid41172807,
year = {2025},
author = {Huang, KC and Lin, CY and Chuang, PY and Yang, TY and Tsai, YH and Li, YY and Chang, SF},
title = {Microbiota diversity and its influence on diabetic osteoporosis development.},
journal = {Biochemical and biophysical research communications},
volume = {790},
number = {},
pages = {152884},
doi = {10.1016/j.bbrc.2025.152884},
pmid = {41172807},
issn = {1090-2104},
abstract = {Diabetic osteoporosis represents a form of secondary osteoporosis whereby diabetes, particularly through chronic hyperglycemia, compromises bone quality and elevates fracture risk. Recent studies using type II diabetes mellitus (T2DM) rat models induced by a high-fat diet (HFD) and low-dose streptozotocin (STZ) have revealed both gut microbiota dysbiosis and osteoporotic bone changes. However, the mechanisms by which the gut microbiota contributes to diabetic osteoporosis remain poorly understood. This study aimed to elucidate the underlying mechanisms of diabetic osteoporosis through microbiome profiling and pathway enrichment analysis. A male T2DM rat model was established via HFD feeding and STZ injection. Bone structural integrity was assessed using micro-computed tomography, while gut microbiota composition was analyzed via 16 S rRNA gene pyrosequencing and subsequent bioinformatic processing. The results showed that T2DM rats exhibited significantly elevated levels of proinflammatory cytokines, which were negatively correlated with bone density and bone turnover markers. Microbiota diversity analysis revealed a decrease in beneficial bacterial taxa, including Lactobacillus, Romboutsia, Turicibacter, and Clostridia UCG-014, alongside an increase in potentially pathogenic Enterococcus, despite a modest increase in other beneficial genera such as Parabacteroidetes, Intestinomonas, and Faecalibaculum. Functional enrichment analysis indicated impaired short-chain fatty acid (SCFA) metabolism, specifically reduced propanoate and butanoate pathway, and enhanced tryptophan metabolism, both of which were associated with decreased bone mass. These findings suggest that microbiota-driven alterations in SCFA production contribute to systemic inflammation and bone loss. Identification of key microbial metabolites and pathways may guide the development of microbiome-targeted therapies to improve metabolic and skeletal health in diabetic populations.},
}

@article {pmid41172523,
year = {2025},
author = {Matishov, G and Rudoy, D and Tkacheva, I and Prazdnova, E and Neidorf, A and Kulikov, M and Nedina, N},
title = {Prospects of the BFT development for utilization of heterotrophic microbiome as a feed raw material source and maintenance of optimal parameters of the cultivation environment.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {85},
number = {},
pages = {e295017},
doi = {10.1590/1519-6984.295017},
pmid = {41172523},
issn = {1678-4375},
mesh = {*Microbiota/physiology ; *Aquaculture/methods ; *Animal Feed ; *Sewage/microbiology ; *Bioreactors/microbiology ; Heterotrophic Processes ; Animals ; },
abstract = {The need of the aquaculture development intensification is related with the growing demand of the world community for quality food products produced with minimal environmental impact. The trend of implementing industries that contribute to the achievement of sustainable development of mankind implies the development of new environmentally friendly technologies. The introduction of the biofloc system in aquaculture implies not only an increase in the production profitability due to effective water treatment in cultivation pools, but also the possibility to use the formed activated sludge flocs as raw material for feed additives. However, the formation of the BFT system microbiome is accompanied by significant changes in the species composition of the microbial community. The technology efficiency is largely related to the possibility of microbiome community management, so the study of species composition, quantitative characteristics and biological features of the BFT system components is of great interest. The dynamics of microbiome development, its influence on marketable qualities and morphophysiological characteristics of hydrobionts, as well as the biochemical features of floc raw materials, are investigated comprehensively.},
}

*Microbiota/physiology
*Aquaculture/methods
*Animal Feed
*Sewage/microbiology
*Bioreactors/microbiology
Heterotrophic Processes
Animals

@article {pmid41172500,
year = {2025},
author = {Silva, RM and Petean, GBF and Pannuti, CM and Souza, NV and Silva-Sousa, YTC and Gavini, G and Duarte, MAH and Estrela, C and Bueno, M and Mazzi-Chaves, JF and Paula-Silva, FWG and Sipert, C and Basso, F and Damião Sousa-Neto, M},
title = {Advances in clinical and translational research in endodontics: A comprehensive overview.},
journal = {Brazilian dental journal},
volume = {36},
number = {},
pages = {e236723},
pmid = {41172500},
issn = {1806-4760},
mesh = {Humans ; *Translational Research, Biomedical ; *Endodontics/trends ; },
abstract = {Clinical and translational research play a decisive role in advancing evidence-based endodontics by bridging basic science with clinical applications. This narrative review provides a comprehensive overview of the current state and advances in clinical and translational research in Endodontics, addressing methodological foundations, diagnostic challenges, and emerging technologies. It highlights the importance of well-designed randomized controlled trials, robust outcome definitions, and the inclusion of patient-reported outcome measures. The integration of advanced imaging, particularly cone-beam computed tomography, has significantly improved diagnostic accuracy and treatment monitoring. Molecular biology techniques, including polymerase chain reaction and biomarker profiling, have expanded the understanding of endodontic microbiome, immune responses, and host factors related to treatment outcomes. Despite these advances, persistent limitations include diagnostic imprecision, lack of standardized criteria, and underutilization of biomarkers and omics data in clinical practice. The rise of precision dentistry, propelled by genomics, bioinformatics, and artificial intelligence, holds the potential to revolutionize endodontic care through personalized diagnostic and therapeutic strategies. Bridging existing gaps will require rigorous study designs, coordinated multicenter efforts, and the effective integration of molecular diagnostics, all of which are critical to advancing endodontic science and optimizing patient outcomes. Likewise, the full potential of translational science can be harnessed to reshape the future of endodontics.},
}

Humans
*Translational Research, Biomedical
*Endodontics/trends

@article {pmid41172333,
year = {2025},
author = {Athreya, GS and Czuppon, P and Gokhale, CS},
title = {The Evolution of Dependence and Cohesion in Incipient Endosymbioses.},
journal = {The American naturalist},
volume = {206},
number = {5},
pages = {435-451},
doi = {10.1086/737588},
pmid = {41172333},
issn = {1537-5323},
mesh = {*Symbiosis ; *Biological Evolution ; Models, Biological ; Animals ; Reproduction ; },
abstract = {AbstractEukaryogenesis is the prototypical example of an egalitarian evolutionary transition in individuality, and endosymbiosis, more generally, is central to the origins of many complex biological systems. Why do only some symbioses undergo such a transition, and how does the host-symbiont relationship change during this process? Here, we characterize endosymbiosis by two emergent collective-level properties: host and symbiont survival as a collective ("mutual dependence") and the level of synchronized reproduction ("reproductive cohesion"). Using adaptive dynamics, we study the evolution of the traits underlying these properties. First, by adding a carrying capacity for the collective population-a realism omitted in previous models-we find novel reasons why complete dependence or cohesion might not evolve, thus providing further theoretical support for the rarity of transitions in individuality. Second, our model suggests that asymmetries in evolutionary outcomes of hosts and symbionts can be explained by a difference in their population growth parameters, coupled with their shared fate when in a collective. Last, we show that during the early stages of an endosymbiosis, even if investments in dependence and cohesion are uncorrelated, mutual dependence arises faster than reproductive cohesion. Our results hence shed light on three aspects of endosymbiosis: coevolution between the host and symbiont, coevolution between dependence and cohesion, and ultimately the opportunity to undergo an evolutionary transition. Connecting to ecological factors, this work uncovers fundamental properties of endosymbioses, providing a clear way forward for theoretical and empirical investigations.},
}

*Symbiosis
*Biological Evolution
Models, Biological
Animals
Reproduction

@article {pmid41172301,
year = {2025},
author = {Wang, Y and Le Roy, CI and Li, J and Han, S and Liu, Z and Lahiry, A and Sahu, H and Li, Q and Dong, J and Mondragon, A and Samuel, TM and Cai, W},
title = {Efficacy of a Ready-to-Feed Starter Liquid Infant Formula Containing 2-Fucosyllactose and Lacto-N-Neotetraose in Chinese Infants: Protocol for a Double Blind, Randomized Controlled Trial.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e66489},
doi = {10.2196/66489},
pmid = {41172301},
issn = {1929-0748},
mesh = {Humans ; *Infant Formula/chemistry ; Double-Blind Method ; *Trisaccharides/administration & dosage/pharmacology ; Infant ; *Oligosaccharides/administration & dosage/pharmacology ; Gastrointestinal Microbiome/drug effects ; China ; Infant, Newborn ; Female ; Male ; Milk, Human/chemistry ; Bifidobacterium ; Randomized Controlled Trials as Topic ; Quality of Life ; Feces/microbiology ; Breast Feeding ; East Asian People ; },
abstract = {BACKGROUND: Bioactive compounds, such as human milk oligosaccharides (HMOs), impact the development of the intestinal microbiome and immune maturation in early life. They have been shown to result in positive benefits, including improved gut health, reduced frequency of infections, and age-appropriate growth when added to infant formula. However, data supporting the added value of including these HMOs in early-stage infant formula is currently lacking among Chinese infants.

OBJECTIVE: In this double-blind randomized controlled trial including a nonrandomized reference breastfed group, we will test the efficacy of ready-to-feed infant formula containing 2 HMOs (2-fucosyllactose and lacto-N-neotetraose) on Bifidobacteria abundance, gut microbiome, gut and immune health, growth, and quality of life.

METHODS: Healthy infants will be enrolled between 3 and 14 days after birth at 5 sites in China and randomized to either the experimental group (fed ready-to-feed infant formula containing 2 HMOs) or the control group (fed the same ready-to-feed infant formula without the 2 HMOs), using a dynamic allocation algorithm with double blinding. Infants will receive trial formula until age 6 months and will be followed up until age 12 months. The breastfed group will serve as a reference. The primary end point will be Bifidobacteria abundance in fecal samples at 3 months, measured via quantitative polymerase chain reaction. Secondary end points will include fecal microbiome (including taxonomy, diversity, functionality, and metabolites), fecal markers of immune health, gastrointestinal tolerance, stooling patterns, immune competence (overall state of the immune system), sleep quality, growth, quality of life, medication use, and physician-reported adverse events. A 2-sided test at the 5% significance level will be used for statistical testing.

RESULTS: The study received ethical approval in March 2024 and will be completed by the end of 2026, which will be followed by a publication in a peer-reviewed journal.

CONCLUSIONS: The Starter Liquid Infant Formula Trial (STARLIT) will be one of the first to assess the efficacy of these 2 HMOs among Chinese infants on gut and immune health, in addition to clinically relevant outcomes such as quality of life, growth, and adverse events. This study should help to demonstrate that an increase in the growth of beneficial Bifidobacteria in response to intake of 2-fucosyllactose and lacto-N-neotetraose may have a broader impact on overall gut microbiome composition and infant gut and immune health.

TRIAL REGISTRATION: ClinicalTrials.gov NCT06361719; https://clinicaltrials.gov/study/NCT06361719.

PRR1-10.2196/66489.},
}

Humans
*Infant Formula/chemistry
Double-Blind Method
*Trisaccharides/administration & dosage/pharmacology
Infant
*Oligosaccharides/administration & dosage/pharmacology
Gastrointestinal Microbiome/drug effects
China
Infant, Newborn
Female
Male
Milk, Human/chemistry
Bifidobacterium
Randomized Controlled Trials as Topic
Quality of Life
Feces/microbiology
Breast Feeding
East Asian People

@article {pmid41171541,
year = {2025},
author = {Joseph, JS and Selvamani, SB and Thiruvengadam, V and Ramasamy, GG and Subramanian, S and Menon, G and Sivakumar, G and Manjunath, C},
title = {Gut microbiota profiling of Apis cerana indica across biodiversity hotspots in the Western Ghats, India.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {35},
pmid = {41171541},
issn = {1573-4978},
mesh = {Bees/microbiology ; Animals ; *Gastrointestinal Microbiome/genetics ; India ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; },
abstract = {BACKGROUND: The gut microbiome of honey bees plays a crucial role in regulating key physiological traits and metabolic processes, including digestion, detoxification, nutrient assimilation, development and immunity. However, information on the gut bacterial diversity of Apis cerana indica bee populations in India remains limited. This study aims to address this critical knowledge gap in Western Ghats, India with outcomes that may provide valuable insights for improving beekeeping practices in the region.

METHODS AND RESULTS: To fill this gap, we investigated and characterized the gut bacteriome of A. cerana indica collected from two ecologically distinct regions within the Western Ghats. We employed a combination of next-generation sequencing (NGS) using the Oxford Nanopore platform and traditional culture-based methods targeting the 16S rRNA gene to analyze the microbial communities. Our results revealed that the gut bacterial communities of foraging A. cerana indica bees from both locations displayed unique and overlapping microbiome profiles. A total of 225 bacterial species across 30 bacterial orders were identified via 16S rRNA amplicon sequencing, with 92 species shared between the two sites. Prominent symbiotic bacterial groups included Gammaproteobacteria, Betaproteobacteria, Flavobacteria, Actinobacteria, Firmicutes, Proteobacteria, and Actinomycetota. Notably, core bee-associated symbionts exhibited a negative correlation with pathogenic bacterial taxa.

CONCLUSION: These findings offer valuable insights into the ecological and functional roles of the gut microbiome in A. cerana indica, a native honeybee species of the Western Ghats. The presence of shared bacterial species across regions suggests their potential significance in formulating conservation strategies for indigenous bee populations.},
}

Bees/microbiology
Animals
*Gastrointestinal Microbiome/genetics
India
RNA, Ribosomal, 16S/genetics
Biodiversity
Bacteria/genetics/classification
High-Throughput Nucleotide Sequencing/methods
Phylogeny

@article {pmid41171386,
year = {2025},
author = {Singh, S and Kriti, M and Sharma, P and Pal, N and Sarma, DK and Verma, V and Tiwari, RR and Kumar, M},
title = {From Gut to Reproductive Health: Exploring Microbiome Interactions and Future Interventions.},
journal = {Reproductive sciences (Thousand Oaks, Calif.)},
volume = {},
number = {},
pages = {},
pmid = {41171386},
issn = {1933-7205},
abstract = {Recent advances in microbiome research have illuminated the complex bidirectional interactions between gut health and reproductive well-being. Understanding the gut microbiome's influence on the reproductive system and vice versa reveals how both of them can affect hormone production, immune function, and ultimately overall reproductive health. Dysbiosis, an imbalance in the gut microbial community, has been linked with a range of reproductive issues, including decreased sperm count and motility, erectile dysfunction, polycystic ovary syndrome (PCOS), endometriosis, infertility, and adverse pregnancy outcomes. This review critically evaluates emerging therapeutic interventions aimed at restoring microbial balance and enhancing reproductive health, such as use of prebiotics, probiotics, bacteriophage therapy, and fecal microbiota transplantation (FMT). By exploring the intricate interplay between gut microbiota and reproductive health, this review also emphasizes the need for integrated approaches in research and clinical practice to develop effective microbiome-based therapies for better reproductive health outcomes.},
}

@article {pmid41171303,
year = {2025},
author = {Shi, J and Zhang, R and Zhang, L and Wang, Y and Xu, Y and Wang, Y and Raghavan, V and Wang, J},
title = {Urban Allergic Diseases Are Exacerbated by Adverse Environmental Factors.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c09233},
pmid = {41171303},
issn = {1520-5851},
abstract = {Allergic disease prevalence differs between urban and rural populations. We aimed to evaluate the relationships between environmental and dietary factors and allergic diseases in both urban and rural settings. The results showed that the alarming increase in the incidence and severity of allergic diseases coincided with environmental and lifestyle changes, such as global warming, extreme weather and dietary modifications. Higher greenhouse gas emissions, consumption of fast food and fried meat, use of pesticides, and less exposure to pets, greenery, and environmental microbes are associated with increased rates of urban allergic diseases. The living environment influenced the microbiota of rural and urban children. Changes in environments and lifestyles influence the commensal gut, skin, respiratory, and nasal microbiomes and their human hosts, contributing to the rising incidence of allergic diseases.},
}

@article {pmid41171140,
year = {2025},
author = {Zhang, Z and Zhao, H and Wang, T},
title = {PRIME: a database for 16S rRNA microbiome data with phenotypic reference and comprehensive metadata.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1057},
pmid = {41171140},
issn = {1362-4962},
support = {12222111//National Natural Science Foundation of China/ ; 12331009//National Natural Science Foundation of China/ ; 12571306//National Natural Science Foundation of China/ ; //Fundamental Research Funds for the Central Universities/ ; //Shanghai Jiao Tong University/ ; //National Natural Science Foundation of China/ ; },
abstract = {PRIME (Phenotypic Reference for Integrated Microbiome Enrichment) is a curated and standardized database of human microbiome 16S rRNA amplicon sequencing data, designed to facilitate cross-study analysis, reproducibility, and phenotype-driven discovery. PRIME aggregates 53 449 samples from 111 public studies, covering 93 body sites and 101 phenotypic categories, with detailed harmonization of sample-level metadata such as disease status, demographics, body sites, sequencing protocols, and experimental design. Each sample includes taxonomic abundance profiles generated via a consistent pipeline using both SILVA (138.2) and Greengenes2 (2024.09) reference databases, with results reported at multiple taxonomic levels as observed abundances (read counts) and relative abundances (proportions). A major strength of PRIME is its extensive manual curation, which standardizes phenotypic and contextual metadata across studies, enabling precise querying and robust phenotype-based comparisons. Users can interactively explore the database through a modern web interface, filter and visualize data by metadata fields, and download customized subsets. Programmatic access is supported via RESTful APIs and R package. PRIME aims to advance microbiome data integration and is continuously updated to incorporate new studies and features. The database is freely available at https://primedb.sjtu.edu.cn.},
}

@article {pmid41171125,
year = {2025},
author = {Kuhn, M and Schmidt, TSB and Ferretti, P and Głazek, A and Robbani, SM and Akanni, W and Fullam, A and Schudoma, C and Cetin, E and Hassan, M and Noack, K and Schwarz, A and Thielemann, R and Thomas, L and von Stetten, M and Alves, R and Iyappan, A and Kartal, E and Kel, I and Keller, MI and Maistrenko, O and Mankowski, A and Nishijima, S and Podlesny, D and Schiller, J and Schulz, S and Van Rossum, T and Bork, P},
title = {Metalog: curated and harmonised contextual data for global metagenomics samples.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1118},
pmid = {41171125},
issn = {1362-4962},
support = {668031//Horizon 2020/ ; ERC-AdG-669830/ERC_/European Research Council/International ; 101059915//European Union's Horizon Europe research and innovation programme/ ; NNF15OC0016692//MicrobLiver/ ; //Novo Nordisk Foundation/ ; //Deutsche Forschungsgemeinschaft/ ; 460129525//German Research Foundation/ ; //Ministry of Science/ ; //MWK/ ; //German Federal Ministry of Research, Technology and Space/ ; //European Molecular Biology Laboratory/ ; },
abstract = {Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data is deposited in public databases, the associated contextual data is often not complete and needs to be retrieved from primary publications. This lack of access to sample-level metadata like clinical data or in situ observations impedes cross-study comparisons and meta-analyses. We therefore created the Metalog database, a repository of manually curated metadata for metagenomics samples across the globe. It contains 80 423 samples from humans (including 66 527 of the gut microbiome), 10 744 animal samples, 5547 ocean water samples, and 23 455 samples from other environmental habitats such as soil, sediment, or fresh water. Samples have been consistently annotated for a set of habitat-specific core features, such as demographics, disease status, and medication for humans; host species and captivity status for animals; and filter sizes and salinity for marine samples. Additionally, all original metadata is provided in tabular form, simplifying focused studies e.g. into nutrient concentrations. Pre-computed taxonomic profiles facilitate rapid data exploration, while links to the SPIRE database enable genome-based analyses. The database is freely available for browsing and download at https://metalog.embl.de/.},
}

@article {pmid41171124,
year = {2025},
author = {Lv, J and Ma, S and Ma, C and Liu, F and Duan, X and Huang, X and Geng, Q and Liu, F and Li, G and Li, Y and Wang, J and Li, C and Zheng, H and Zhang, Y and Sun, Z and Wang, J and Fan, G and Huang, S and Zhang, L and Bao, Z and Wang, S},
title = {Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1098},
pmid = {41171124},
issn = {1362-4962},
support = {2024YFC2816000//National Key Research and Development Program of China/ ; LSKJ202202804//Marine S&T Fund of Shandong Province for Laoshan Laboratory/ ; 2025B1111180001//Guangdong Provincial Key Areas R&D Program Project/ ; SOLZSKY2025013//Hainan Province Science and Technology Special Fund/ ; 32573498//Natural Science Foundation of China/ ; 32222085//Natural Science Foundation of China/ ; QDLYY-2024011//Blue Seed Industry Science and Technology Innovation Project/ ; GZB20250215//Postdoctoral Fellowship Program of CPSF/ ; },
abstract = {Multi-omics analyses have significantly advanced the understanding of complex marine microbial communities and their interactions. Despite notable progress from recent large-scale ocean meta-analysis efforts, the effective integration and accessibility of these diverse datasets remain challenging. To address this, we introduce Ocean-M (http://om.qnlm.ac), a comprehensive and publicly accessible platform for marine microbial multi-omics data integration, analysis, and visualization. Ocean-M provides a systematic view of 54 083 high-quality metagenome-assembled genomes, including genome assembly statistics, genome clustering, gene annotation, and interactive tools for global-scale taxonomic profiling. The platform also incorporates microbial community networks, host-microbiome interactions, and environmental DNA datasets to support an integrated ecological framework for studying microbial interactions and ecosystem functions. Additionally, Ocean-M enables large-scale mining of ecologically and biotechnologically important genes, with curated catalogs of 151 798 biosynthetic gene clusters, 52 699 antibiotic resistance genes, and millions of carbohydrate-active enzymes and plastic-active enzymes. By combining multi-omics data with environmental metadata, Ocean-M serves as a valuable resource for advancing marine microbial ecology, global biogeography, and functional gene discovery.},
}

@article {pmid41171074,
year = {2025},
author = {Zhou, Y and Wang, Y and Xiao, B and Wang, S and Zhang, Z and Wang, X and Liu, B and Yang, Y and Wang, C and Zhou, C and Liao, M and Song, F and Luo, H},
title = {Predicting age from binarized human oral microbial data combined with an ensemble of classifiers.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0118225},
doi = {10.1128/msystems.01182-25},
pmid = {41171074},
issn = {2379-5077},
abstract = {It is well established that the composition of the human microbiome changes with age; however, limited research has explored the association between the oral microbiome and aging, as well as its potential for age prediction. In this study, we investigated the correlation between the oral microbiome and age by analyzing samples from 150 individuals across a wide age range (6-78 years). The observed species richness and Chao1 index significantly increased with age. Permutational multivariate analysis of variance (PERMANOVA), using both Bray-Curtis and Jaccard distances, identified age as a major factor influencing microbial variation. After a comprehensive comparison of four different oral microbiome data processing approaches, we then developed an ensemble model based on binarized oral microbial data, incorporating an eXtreme Gradient Boosting (XGBoost) algorithm with 32 classifiers. This ensemble model achieved a mean absolute error (MAE) of 7.20 years in the independent validation set (n = 15) and 4.33 years in the 20-59 age subgroup (n = 12), significantly outperforming traditional models. When the sample size increased to 2,550, the MAE in the independent validation set (n = 255) was reduced to 4.80 years, with the 20-59 age subgroup (n = 232) achieving an MAE of 3.76 years, highlighting its generalizability and robustness. Additionally, compared to the previously published model for age prediction based on oral microbiome, our model demonstrated significantly superior performance. These findings support the potential of integrating binarized microbial data with ensemble modeling as a promising direction for human age prediction based on the microbiome.IMPORTANCEPERMANOVA analysis with Jaccard distances revealed age as a major determinant of variation in microbial composition, highlighting the potential of binarized oral microbial data as a novel predictor for human age prediction. Furthermore, we developed an ensemble model combining an XGBoost algorithm and 32 classifiers to predict age from binarized oral microbial data. The model achieved an MAE of 7.20 years in the independent validation set (n = 15) and 4.33 years in the 20-59 age subgroup (n = 12). When applied to predict age in 2,550 samples from previous studies, the ensemble model outperformed the prior model, achieving an MAE of 4.44 years compared to the previous model's 4.94 years. These findings demonstrate that binarized oral microbial data, along with the ensemble model we developed, can effectively predict human age and provide a solid foundation for future age-related research.},
}

@article {pmid41168692,
year = {2025},
author = {Mo, X and Shi, S and Siddique, KHM and Li, Y and Zhang, Z and Zhang, M},
title = {Community interactions and functions drive bacteriome assembly in soil-plant continua of fragile estuarine wetland.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1477},
pmid = {41168692},
issn = {1471-2229},
support = {2022YFF1301004//Ministry of Science and Technology of the People's Republic of China/ ; },
abstract = {UNLABELLED: Restoration of degraded estuarine wetlands relies heavily on rhizosphere bacterial communities that support vegetation colonization and persistence. However, the mechanisms driving microbiome assembly across soil–plant continua in these fragile ecosystems remain poorly understood. Here, we examined plant traits, soil physicochemical properties, and α-diversity and community structure in rhizosphere and non-rhizosphere soils of two dominant species (Suaeda salsa and Phragmites australis) in a degraded estuary in China. We further assessed bacteriome assembly processes, β-diversity, and the relative influence of abiotic and biotic factors. Bacterial community structure differed significantly between the two plant continua, though diversity did not. Across both rhizosphere and non-rhizosphere soils, bacteriome assembly was governed predominantly by heterogeneous selection. Within this deterministic framework, intrinsic biotic factors—including keystone taxa, metabolic functions, and host plants—exerted stronger effects on community assembly than abiotic drivers. Moreover, available phosphorus facilitated this assembly pattern through indirect pathways. These findings highlight the pivotal role of biotic interactions in shaping bacteriomes and maintaining functional stability in fragile estuarine ecosystems, with implications for guiding ecological restoration.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-07341-9.},
}

@article {pmid41171001,
year = {2025},
author = {Smolkova, D and Rusin, M and Dobrowolska-Iwanek, J and Woźniakiewicz, M and Lavicka, J},
title = {Sensitive Profiling of Human Milk Oligosaccharides in Human Colostrum and Breast Milk by Capillary Electrophoresis-Mass Spectrometry.},
journal = {Journal of separation science},
volume = {48},
number = {11},
pages = {e70309},
doi = {10.1002/jssc.70309},
pmid = {41171001},
issn = {1615-9314},
mesh = {Humans ; *Milk, Human/chemistry ; *Colostrum/chemistry ; *Oligosaccharides/analysis ; Electrophoresis, Capillary ; Mass Spectrometry ; Female ; },
abstract = {Human milk oligosaccharides are pivotal for shaping the infant gut microbiome and immune development, yet their structural diversity hampers routine identification and quantification. We report an optimized capillary electrophoresis-mass spectrometry workflow that enables sensitive, isomer‑selective profiling of 10 biologically relevant human milk oligosaccharides in colostrum and early‑lactation breast milk. Human milk oligosaccharides were first neutralized to stabilize sialic acids and derivatized with Girard's reagent P, introducing a permanent positive charge to enhance electrophoretic resolution and electrospray ionization efficiency. Separation in a linear‑polyacrylamide‑coated capillary (0.25 M formic acid, 30 kV) and mass spectrometry detection with a nanoCEasy interface achieved baseline resolution of all targets except positional isomers lacto-N-difucohexaose I/II. Incorporation of Girard's reagent P‑labeled maltoheptaose as an internal standard improved migration time precision to < 0.5% RSD and reduced peak‑area repeatability to 9%-25% RSD. Limits of detection were 0.8-290 ng/mL, corresponding to fg-pg on‑column amounts and outperforming precedent APTS-based CE/LIF methodologies. Application to colostrum and milk samples from a single donor (1-3 months postpartum) revealed pronounced variation. Colostrum was dominated by 2'‑fucosyllactose and fucosylated lacto-N-fucopentaose isomers, whereas sialylated human milk oligosaccharides were present in smaller amounts. Longitudinally, 2'‑fucosyllactose remained the most abundant species, while lacto-N-fucopentaose and lacto-N-neotetraose/lacto-N-tetraose diminished markedly by Month 3. The presented capillary electrophoresis-mass spectrometry platform delivers reasonably fast (< 70 min), high‑sensitivity human milk oligosaccharide fingerprinting from minimal sample volumes and is readily adaptable to large‑cohort studies, offering new opportunities to elucidate the nutritional dynamics of the maternal milk glycome during lactation.},
}

Humans
*Milk, Human/chemistry
*Colostrum/chemistry
*Oligosaccharides/analysis
Electrophoresis, Capillary
Mass Spectrometry
Female

@article {pmid41170939,
year = {2025},
author = {Blondin-Brosseau, M and Zhang, W and Gravel, C and Harlow, J and Li, X and Nasheri, N},
title = {Survival of influenza virus H1N1 and murine norovirus in raw milk cheeses.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0188125},
doi = {10.1128/aem.01881-25},
pmid = {41170939},
issn = {1098-5336},
abstract = {The spillover of highly pathogenic avian influenza (HPAI) to dairy cattle and its presence at high titers in raw milk has created a concern that consumption of dairy products made from unpasteurized milk could result in human exposure. We examined whether H1N1, as a surrogate for HPAI viruses, and murine norovirus (MNV), as a surrogate for unenveloped enteric viruses, can survive the cheese-making process by making cream cheese-style and feta-style cheeses from artificially inoculated raw milk. We used the modified ISO 15216 method for viral extraction, which has a limit of detection of 3.0-3.7 log for infectious H1N1 in soft cheeses. Infectious H1N1 virus was detected in the curd from both types of cheeses and in the whey from cream cheese but not in the whey from feta cheese. Infectious MNV particles were detected in the curd and in the whey for both types of cheeses. To study the effect of salt, pH, aging, and microbiome of various unpasteurized milk cheeses on viral survival, we artificially inoculated different commercial unpasteurized milk cheeses with 7 log PFU of H1N1 and 6 log PFU of MNV and examined viral survival over an 8 week period at 4°C. We observed that H1N1 survived for 8 weeks, with an average of 2.6, 2.75, and 4.0 log reductions on cheddar, washed rind firm cheese, and semisoft brie-like cheese, respectively (P < 0.001). The level of infectious H1N1 fell below the limit of detection in cream cheese after 2 weeks of inoculation. It is noteworthy that the sensory qualities of soft and semisoft cheeses deteriorated in 2 weeks, but the sensory qualities of firm cheeses did not change drastically, demonstrating that, as expected, they endure the aging process better than the soft and semisoft cheeses. Furthermore, the limit of detection for soft cheeses is approximately 1 log lower compared to firm cheeses, and the extraction method has a lower efficiency for soft cheeses compared to firm cheeses. MNV survived in firm cheeses for 8 weeks with only 1 log reduction on cheddar cheese and 2 log reductions on the washed rind firm cheese (P < 0.05). The data obtained in this study could help with the risk assessment of dairy products made from unpasteurized milk.IMPORTANCEThe rapid spread of H5N1 viruses among dairy cattle in the United States and the viral shedding at high titers raised concern regarding the safety of dairy products, specifically cheeses made with unpasteurized milk. In this study, we demonstrated that murine norovirus and influenza virus can survive the cheese-making and aging process. Therefore, it is recommended that milk contaminated with viruses be heat-treated to ensure safety.},
}

@article {pmid41170737,
year = {2026},
author = {Zhang, R and Zhang, L and Tian, B and Wang, Y and Kang, X and Zheng, J},
title = {The gut‑bone‑cartilage triad: Microbial regulation of the Wnt/β‑catenin signaling pathway in osteoarthritis joint remodeling (Review).},
journal = {Molecular medicine reports},
volume = {33},
number = {1},
pages = {},
doi = {10.3892/mmr.2025.13733},
pmid = {41170737},
issn = {1791-3004},
mesh = {Humans ; *Osteoarthritis/metabolism/microbiology/pathology ; *Wnt Signaling Pathway ; *Gastrointestinal Microbiome ; Animals ; *Cartilage, Articular/metabolism/pathology ; *Bone Remodeling ; *Bone and Bones/metabolism ; },
abstract = {Osteoarthritis (OA) is a prevalent chronic joint disorder with a notable global health burden, characterized by articular cartilage degeneration, abnormal bone remodeling and synovial inflammation. Traditional treatments mainly focus on symptom management rather than addressing the underlying disease mechanisms. The gut microbiome serves a potential role in OA through the gut‑bone‑cartilage axis. Notably, the gut microbiome and its metabolites can influence bone and cartilage homeostasis, and the Wnt/β‑catenin signaling pathway has been implicated in OA pathogenesis. The present study comprehensively reviews the emerging evidence supporting the gut‑bone‑cartilage axis in OA and the role of microbial regulation of Wnt/β‑catenin signaling in joint remodeling. The current understanding of the influence of the gut microbiome on OA pathogenesis is summarized, discussing the mechanisms underlying the gut‑bone‑cartilage axis and exploring the therapeutic potential of targeting this axis. Future research should focus on developing targeted therapies that modulate the gut microbiome and the Wnt/β‑catenin pathway, as well as exploring the potential of gene editing and carrier technologies for OA treatment.},
}

Humans
*Osteoarthritis/metabolism/microbiology/pathology
*Wnt Signaling Pathway
*Gastrointestinal Microbiome
Animals
*Cartilage, Articular/metabolism/pathology
*Bone Remodeling
*Bone and Bones/metabolism

@article {pmid41170399,
year = {2025},
author = {Hasanthi, M and Chotikachinda, R and Medagoda, N and Lee, KJ},
title = {Exogenous protease supplementation in high- and low-fishmeal diets for Pacific white shrimp (Penaeus vannamei): Comparative effect on growth, immunity, nutrient digestibility and gut health.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {22},
number = {},
pages = {36-49},
pmid = {41170399},
issn = {2405-6383},
abstract = {The present study evaluated the effects of exogenous protease supplementation in low- and high-fishmeal (FM) diets on growth performance, feed utilization, innate immunity, digestive enzyme activity, nutrient digestibility, gut microbiota and intestinal morphology of Pacific white shrimp (Penaeus vannamei). A 2 × 3 factorial experiment was designed with two dietary FM levels (200 g/kg, positive control [PC]; and 100 g/kg, negative control [NC]) and three protease levels (0, 400 and 800 mg/kg) to obtain six experimental diets designated as PC, PC400, PC800, NC, NC400, and NC800. Six replicate groups of 30 shrimp (initial weight 0.30 ± 0.01 g) were fed the diets for 8 wk. Protease supplementation significantly improved (P < 0.001) growth performance and feed utilization efficiency in both high- and low-FM diets. Innate immunity and antioxidant enzyme activities were significantly enhanced (P < 0.001) with increasing FM and protease levels. Furthermore, the inclusion of protease in low-FM diets significantly increased (P < 0.001) total hemocyte count and phagocytic, phenoloxidase, lysozyme and superoxide dismutase activities, reaching levels comparable to the PC group. Increasing FM and protease levels significantly upregulated (P < 0.001) the expression of proPO, crustin, TGF-β, Lv IKK-β and TLR3 genes, while downregulating TNF-α. The inclusion of protease in the low FM diet significantly increased (P < 0.05) digestive enzyme activities, intestinal villi length, whole-body amino acid composition and nutrient digestibility to the levels comparable to the PC group. The relative abundance of heterotrophic marine bacteria (P < 0.001), Gram-positive bacteria (P = 0.034) and Lactobacilli spp. (P < 0.001) in the gut significantly increased (P < 0.05) with increasing protease levels, while an inverse relationship was observed for Vibrio spp. (P < 0.001). These results demonstrated that protease supplementation in either the high- or low-FM diets could improve shrimp growth, feed utilization efficiency, immunity, nutrient digestibility, intestinal morphology and gut microbiome. Notably, supplementing the low-FM diet with 800 mg/kg protease improved shrimp performance, reaching levels comparable to those obtained with the PC diet.},
}

@article {pmid41170114,
year = {2025},
author = {Sharma, E and Thind, S and Ohri, T and Goyal, R and Dhawan, R and Singh, J and Krishna, S and Sangha, R},
title = {The crippling grip of antimicrobial resistance in dentistry: A review.},
journal = {Bioinformation},
volume = {21},
number = {7},
pages = {1871-1874},
pmid = {41170114},
issn = {0973-2063},
abstract = {A primary challenge for dentists is maintaining or restoring a balanced oral microbiome, as it plays a significant role in determining oral health and disease states. However, oral diseases such as gingivitis, dental caries, periodontitis and peri-implantitis can occur when pathogenic microbes settle in the oral cavity and become part of the oral biofilm. There are several preventative and therapeutic strategies available today, but the majority of them are centered on antibiotics. Antibiotic stewardship in dentistry might be a helpful strategy to maximize and prevent inappropriate or even needless antibiotic usage, marking a step towards precision medicine, given the current context of antimicrobial resistance (AMR). Additionally, efforts are being made to discover novel, efficient treatments that can take the place of antibiotics.},
}

@article {pmid41169518,
year = {2025},
author = {Drovetski, SV and Shearn-Bochsler, VI and Hofmeister, EK and Karouna-Renier, NK and Dusek, RJ},
title = {A short-term sublethal oral exposure to microcystin-LR disrupts cecal microbiome homeostasis in mallard.},
journal = {Frontiers in toxicology},
volume = {7},
number = {},
pages = {1634241},
pmid = {41169518},
issn = {2673-3080},
abstract = {INTRODUCTION: The frequency of cyanobacterial blooms seems to have increased globally in recent decades due to human induced eutrophication and climate change. Cyanobacterial blooms can produce several groups of toxins, among which microcystin-LR (MC-LR) is one of the most abundant. Effects of MC-LR on avian microbiome have not been studied and studies in laboratory murines have been limited to metabarcoding of prokaryotes.

METHODS: Using RNA shotgun sequencing, we compared the richness and composition of metabolically active prokaryotes, expressed virulence factors, antimicrobial resistance genes, metabolic pathways, Gene Ontology terms, enzymes, and proteins in mallards (Anas platyrhynchos) that were orally exposed to a sublethal dose of MC-LR for one week and unexposed birds.

RESULTS: Richness and composition of all compared features did not differ between exposed and control birds and none were differentially expressed between exposure groups. However, richness and/or composition of all features except virulence factors and Carbohydrate Active enzymes had multiple-fold greater dispersion in exposed birds than in controls. This effect was especially pronounced in expressed metabolic (MetaCyc) pathways.

DISCUSSION: Our results suggest that MC-LR exposure had a stochastic (rather than deterministic) effect on cecal microbiota, especially its function. Observed disturbance of the microbiota homeostasis is consistent with the Anna Karenina Principle. This principle has been documented in a wide range of eukaryotes using primarily microbial community metabarcoding. Although stochastic disturbance of microbiota function has been hypothesized, our study seems to be the first to demonstrate this in an experimental study.},
}

@article {pmid41169482,
year = {2025},
author = {Cao, F and Yi, W and Wu, M and Gao, A and Kang, T and Hou, X},
title = {Characteristics of the gut microbiome of asymptomatic hyperuricemia.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1557225},
pmid = {41169482},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Hyperuricemia/microbiology ; Male ; Female ; Middle Aged ; Uric Acid/blood ; Adult ; Case-Control Studies ; Feces/microbiology ; Asymptomatic Diseases ; Biomarkers/blood ; Aged ; },
abstract = {PURPOSE: Asymptomatic hyperuricemia(AH) is characterized by elevated blood uric acid levels without symptoms,posing risks like gout, kidney stones, and cardiovascular diseases. This study aims to investigate the role of the gut microbiota in uric acid metabolism in AH.

METHODS: Clinical data from 30 AH patients and 30 healthy controls were collected. Fecal microbiota genomic DNA was extracted, PCR amplified, library constructed, and sequenced. Bioinformatics and statistical analyses were conducted to study the gut microbiota of the two groups.

RESULTS: The AH group exhibited significantly elevated levels of body mass index (BMI), Triglycerides (TG), Total Cholesterol (TC), as along with a history of smoking, hypertension, and fatty liver disease compared to the healthy group (P < 0.05). The overall richness and ecological diversity of gut microbiota in the AH group decreased, with differences in the distribution at the phylum and genus levels compared to the healthy group. Uric acid demonstrated significant correlations with various gut microbiota (e.g., Granulicatella), suggesting their potential as biomarkers for AH. Despite limitations such as a small sample size and lack of long-term follow-up, our findings provide new insights for the early diagnosis and personalized treatment of AH. Looking ahead, these discoveries may advance the clinical management of AH and the exploration of associated biomarkers.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Hyperuricemia/microbiology
Male
Female
Middle Aged
Uric Acid/blood
Adult
Case-Control Studies
Feces/microbiology
Asymptomatic Diseases
Biomarkers/blood
Aged

@article {pmid41169397,
year = {2025},
author = {Hu, X and Li, B and Li, Y and Liang, Y and Huang, T},
title = {Communication between gut microbiota-derived metabolites and the tumor microenvironment.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1649438},
pmid = {41169397},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Tumor Microenvironment/immunology ; *Neoplasms/metabolism/immunology/therapy/microbiology ; Animals ; Immunotherapy/methods ; },
abstract = {The gut microbiota has been increasingly recognized as a critical player in maintaining human health and influencing disease development. The tumor microenvironment (TME) is pivotal in tumor development and progression, comprising immune cells, stromal elements, extracellular matrix components, and cytokines. Recent studies have highlighted the promising potential of gut microbiota-derived metabolites (e.g., short-chain fatty acids, bile acids, polyamines, and tryptophan derivatives) to reshape the TME in various ways, generating significant interest for the development of novel therapeutic strategies. Beyond their established effects on traditional cancer treatments, emerging evidence suggests that microbiome-based interventions can substantially enhance cancer immunotherapy. However, the variable role of gut microbiota in modulating therapeutic responses complicates the prediction of clinical outcomes. Therefore, understanding the crosstalk between the gut microbiota and the TME is crucial and holds promise for the development of personalized and comprehensive cancer management strategies. This review aims to summarize the reciprocal regulatory mechanisms between gut microbiota-derived metabolites and the TME, and to explore how these interactions can be leveraged to improve cancer immunotherapy.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Tumor Microenvironment/immunology
*Neoplasms/metabolism/immunology/therapy/microbiology
Animals
Immunotherapy/methods

@article {pmid41169369,
year = {2025},
author = {Pentimalli, F and Krstic-Demonacos, M and Costa, C and Mutti, L and Bakker, EY},
title = {Correction: Intratumor microbiota as a novel potential prognostic indicator in mesothelioma.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1703111},
doi = {10.3389/fimmu.2025.1703111},
pmid = {41169369},
issn = {1664-3224},
abstract = {[This corrects the article DOI: 10.3389/fimmu.2023.1129513.].},
}

@article {pmid41169367,
year = {2025},
author = {Ren, J and Niu, Z and Wang, J and Guo, J and Hao, H and Gao, F and Liu, R and Wang, Z},
title = {The link between gut microbiota and multiple sclerosis from the perspective of barrier function.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1652796},
pmid = {41169367},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Multiple Sclerosis/microbiology/immunology/metabolism/etiology ; *Blood-Brain Barrier/immunology/metabolism ; Animals ; Dysbiosis/immunology ; },
abstract = {Recently, more and more studies have begun to focus on the role of gut microbiota in neurological diseases, especially immune-mediated disorders including multiple sclerosis (MS). The bidirectional communication between the gut microbiome and the central nervous system (CNS) is known as the gut-brain axis, which includes two key barriers, namely blood-brain barrier (BBB) and the gut barrier, and has become a crucial framework for understanding the pathophysiological mechanisms of various neurological disorders. Gut microbes co-evolved with humans and play important roles in maintaining steady state via various pathways, including immune regulation. An altered gut microbiota, referred to as dysbiosis, not only induces increased intestinal permeability locally, but also promotes systemic immune responses in the CNS. Increased BBB permeability has been considered the core mechanism for MS, and a "leaky" gut has also been reported in MS as well as its animal models. Therefore, the gut-brain axis is increasingly being considered as playing a crucial role in the pathogenesis of MS, with a major focus on specific gut microbiota alterations associated with the disease. Here, we review how the possible dysfunction of the gut-brain axis might impact MS, with particular emphasis on the barrier function.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Multiple Sclerosis/microbiology/immunology/metabolism/etiology
*Blood-Brain Barrier/immunology/metabolism
Animals
Dysbiosis/immunology

@article {pmid41169357,
year = {2025},
author = {Xiao, Y and Gong, B and Li, J and Xu, N},
title = {The oral microbiome and atherosclerosis: current evidence on association, mechanisms, and clinical implications.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1640904},
pmid = {41169357},
issn = {1664-3224},
mesh = {Humans ; *Atherosclerosis/microbiology/etiology/immunology ; *Microbiota ; *Mouth/microbiology ; Animals ; Disease Susceptibility ; },
abstract = {Atherosclerosis, the primary pathology of cardiovascular disease (CVD), is not fully explained by traditional risk factors. The oral microbiome has emerged as a key environmental contributor, yet the evidence for its role remains complex. This review moves beyond summarizing established associations to critically appraise the evidence, synthesize novel mechanistic insights, and outline future clinical frameworks. While traditional mechanisms such as direct bacteremia and systemic inflammation are covered, this review highlights emerging pathways including the oral-gut-vascular axis, epigenetic reprogramming ("inflammatory memory"), and the role of the multi-kingdom microbiome. We critically evaluate the evidence landscape, reconciling conflicting findings from observational studies, Mendelian randomization, and randomized controlled trials (RCTs) by systematically examining methodological heterogeneity. Furthermore, future directions are explored, focusing on the application of artificial intelligence (AI) for biomarker discovery and the development of novel interventions like engineered microbial therapeutics. Finally, the review translates scientific consensus into actionable clinical frameworks for interdisciplinary patient care. This comprehensive synthesis underscores the need to move towards mechanism-based, personalized strategies for CVD prevention.},
}

Humans
*Atherosclerosis/microbiology/etiology/immunology
*Microbiota
*Mouth/microbiology
Animals
Disease Susceptibility

@article {pmid41169232,
year = {2025},
author = {Church, ME and Hernandez, SI and Alvarez, JI},
title = {Neuroinflammatory canine disorders: unveiling disease mechanisms from a One Health perspective.},
journal = {Journal of immunology (Baltimore, Md. : 1950)},
volume = {214},
number = {10},
pages = {2535-2542},
doi = {10.1093/jimmun/vkaf236},
pmid = {41169232},
issn = {1550-6606},
support = {/NH/NIH HHS/United States ; 5UL1TR001878/TR/NCATS NIH HHS/United States ; //Institute of Translational Medicine and Therapeutics/ ; //University of Pennsylvania/ ; },
mesh = {Animals ; Dogs ; Humans ; Disease Models, Animal ; *Multiple Sclerosis/immunology ; *Neuroinflammatory Diseases/immunology/veterinary ; One Health ; *Dog Diseases/immunology ; *Meningoencephalitis/immunology/veterinary ; },
abstract = {While rodent models remain foundational in biomedical research for their manipulability, genetics, and reproducibility, spontaneous diseases in companion animals provide relevant models to study naturally occurring conditions. Pathogenic processes underlying diseases in humans and dogs are similar or identical, which exemplifies the One Health concept. Companion animals share physiological and genetic traits with humans, have similar exposure to microorganisms and toxic insults, and due to cohabitation, share our microbiome. Dogs have intact immune systems and tolerate drugs at dosages comparable to humans. Dogs with naturally occurring neuroinflammatory disorders can serve as spontaneous models for those affecting humans. Granulomatous meningoencephalomyelitis, the most common canine neuroinflammatory disorder, recapitulates key immunopathological features of multiple sclerosis. The clinical course of granulomatous meningoencephalomyelitis is prolonged from months to years, rather than days to weeks as in rodents, a key aspect when modeling multiple sclerosis chronicity and assessing drug response over time. Thus, establishing natural models of human diseases constitutes a significant advancement to understanding mechanisms of disease while benefiting veterinary medicine and accelerating new therapies for humans.},
}

Animals
Dogs
Humans
Disease Models, Animal
*Multiple Sclerosis/immunology
*Neuroinflammatory Diseases/immunology/veterinary
One Health
*Dog Diseases/immunology
*Meningoencephalitis/immunology/veterinary

@article {pmid41169153,
year = {2025},
author = {Boccacino, JM and Velasco-Herrera, MDC and Beale, MA and Billington, J and Vermes, I and Obolenski, S and Wong, K and Torrens, L and Moody, S and Perdomo, S and Cheema, S and Francis, B and Offord, V and Butler, AP and Adams, DJ},
title = {SPARKI: a tool for the statistical analysis of pathogen identification results.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf596},
pmid = {41169153},
issn = {1367-4811},
abstract = {MOTIVATION: Many pathogen identification and microbiome analysis tools have been developed in recent years, with Kraken 2 by Wood et al. 2019 being one of the most popular. While tools downstream of Kraken 2 can assist in the interpretation of its outputs, a statistical framework to assess the likelihood that a taxon/organism is present in a single sample alongside an automated end-to-end analysis pipeline has not yet been fully implemented.

RESULTS: Here we introduce SPARKI, an R package that performs statistical analysis of Kraken 2 outputs and aids in the identification of pathogens present in next-generation sequencing samples. SPARKI adds to the field by bringing a probabilistic view to Kraken 2 data, serving as a discovery tool and complementing other methods such as KrakenTools (Lu et al. 2022), Bracken (Lu et al. 2017) and Pavian (Breitwieser et al. 2020).

AVAILABILITY: SPARKI code is available on GitHub at https://github.com/team113sanger/sparki. SPARKI is also part of an end-to-end pathogen identification pipeline, sparki-nf, which is available at https://github.com/team113sanger/sparki-nf. An additional pipeline for further exploration and validation of SPARKI results is also available at https://github.com/team113sanger/map-to-genome.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid41169135,
year = {2025},
author = {Lalwani, A and Singh, S and Parua, S and Ahuja, D and Adhikary, K and Maiti, R and Bhattacharya, K and Banerjee, SK and Syamal, AK},
title = {Novel Targets and Nanotechnology Approaches in Treating Vulvovaginal Candidiasis: Insights into Host-Microbe Interactions and Immunotherapy.},
journal = {Current pharmaceutical design},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113816128388596251001075837},
pmid = {41169135},
issn = {1873-4286},
abstract = {The aim of this article is to study recent developments in the management of vulvovaginal candidiasis (VVC) with emphasis on overcoming antifungal resistance and recurrent VVC by examining hostmicrobe interaction, new molecular targets, immunotherapeutic interventions, and nanotechnology-based strategies. This review integrates recent VVC pathogenesis, immune response, and therapeutic development literature with a focus on immunomodulation, vaccine development, and nanotechnology interventions. Literature on immunotherapy and nanoparticle-based drug delivery systems was comprehensively reviewed. Immunotherapeutic concepts, such as cytokine modulation and vaccine therapy candidates, hold promise to substitute or supplement current antifungals. Nanoparticles exhibit efficacy in advancing drug solubility, reaching fungal cells, and minimizing unwanted effects. The synergy between nanotechnology and immunotherapy provides combined advantages over the multiple drawbacks of current therapies. Although novel methodologies have shown strong promise, aspects of safety, clinical relevance, and regulatory issues continue to remain key challenges. Nanotechnology-based host-targeted immunotherapy is most probably going to transform the scenario of VVC treatment, especially in drug-resistant cases. Additional research is needed to elucidate molecular host-fungal interaction mechanisms, validate vaccine efficacy in the clinic, and design standardized, reproducible nanotherapeutic platforms. Personalized regimens of treatment through immunological and microbiome profiling can enhance long-term outcomes in VVC treatment.},
}

@article {pmid41169038,
year = {2025},
author = {Buccola, MJ and Satheesh Babu, AK and Paz, HA and Porter, ND and Srinivasan, H and Ricks, RL and Rosquist, K and Torres, JL and Zhong, Y and Jalili, T and Wankhade, UD and Anandh Babu, PV},
title = {Dietary Prebiotics Modulate Omeprazole-Induced Alterations in the Gut Microbial Signature.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70307},
doi = {10.1002/mnfr.70307},
pmid = {41169038},
issn = {1613-4133},
abstract = {Proton pump inhibitors (PPIs) are commonly used to treat heartburn and acid-related disorders. However, their misuse and prolonged use contribute to gut dysbiosis. This study investigated whether well-known prebiotic dietary sources, blueberries or strawberries, can reverse PPI (omeprazole) induced dysbiosis and gut inflammation by modulating gut microbes. Male C57BL/6J mice (7 weeks old) were fed a diet with or without omeprazole (40 mg/kg diet), blueberry (3.7% in the diet; ∼1.5 human servings) or strawberry (2.35% in the diet; ∼2 human servings) for 12 weeks. Metabolic parameters, gut microbes (in the cecum and colon), and inflammatory markers were assessed. In this study, no changes were observed in metabolic parameters in mice fed a diet supplemented with omeprazole or berries. Second, blueberry or strawberry supplementation at nutritional dosages improved alterations in gut microbial ecology induced by omeprazole, with effects varying between the cecum and colon. Third, strawberry supplementation reduced omeprazole-induced gut inflammation. Fourth, selected genera were either positively or negatively associated with markers of gut inflammation, suggesting that dietary berries can ameliorate inflammatory signaling through modifications in the gut microbiome. Dietary berries represent a potential nutritional strategy for improving PPI-induced gut dysbiosis and inflammation.},
}

@article {pmid41168883,
year = {2025},
author = {Gabashvili, E and Küsel, K and Pratama, AA and Wang, H and Taubert, M},
title = {Growth of candidate phyla radiation bacteria in groundwater incubations reveals widespread adaptations to oxic conditions.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {224},
pmid = {41168883},
issn = {2049-2618},
support = {390713860//Deutsche Forschungsgemeinschaft/ ; B 715-09075//Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft/ ; 2016 FGI 0024 "BIODIV"//Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft,Germany/ ; },
mesh = {*Groundwater/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/growth & development/genetics/classification/isolation & purification/metabolism ; *Microbiota/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Adaptation, Physiological ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The candidate phyla radiation (CPR) comprises a widespread but poorly understood group of bacteria with limited cultured representatives, largely due to their metabolic dependencies on microbial hosts. In laboratory incubations, CPR often decline sharply in relative abundance, even when samples originate from natural environments where they dominate, such as groundwater, where they can represent over 50% of the microbiome. Suitable enrichment conditions and host interactions remain poorly defined.

RESULTS: Here, we analyzed 16S rRNA gene amplicon data from 397 groundwater incubation samples across 31 treatments, including 22 under oxic conditions, to identify factors that promote CPR survival and growth. Despite an initial decline, CPR abundances recovered over longer incubation times, reaching up to 11-30% of the microbial community. In total, we detected 1410 CPR amplicon sequence variants (ASVs), spanning six major CPR classes commonly found in groundwater. Enrichment success was treatment-specific: Cand. Saccharimonadia dominated in incubations with polysaccharides (up to 31.4%), while Cand. Parcubacteria were enriched (> 23%) in treatments stimulating methylotrophs and autotrophs. ASV-specific growth rates based on quantitative PCR showed that some CPR doubled within 1-2 days, comparable to faster-growing non-CPR groundwater bacteria, while most CPR had doubling times around 15 days. Strikingly, although the relative abundance of many CPR ASVs showed positive correlation with anoxic conditions, overall CPR reached higher absolute abundances under oxic conditions than under anoxic conditions. Metabolic network analysis based on metagenome-assembled genomes revealed that up to 62% of annotated genes were associated with functions linked to oxic conditions. In fact, 25 CPR genomes encoded enzymes that directly utilize oxygen, challenging the long-standing view of CPR as strictly anaerobic, fermentative organisms.

CONCLUSIONS: Our findings demonstrate that diverse CPR lineages not only survive but actively grow in groundwater incubations, even under oxic conditions. The discovery of genes for oxygen-dependent reactions and substantial CPR enrichment in oxic treatments reveals unexpected metabolic flexibility, helping to explain their persistence and ecological success across a wide range of environments.},
}

*Groundwater/microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/growth & development/genetics/classification/isolation & purification/metabolism
*Microbiota/genetics
Phylogeny
DNA, Bacterial/genetics
Adaptation, Physiological
Sequence Analysis, DNA

@article {pmid41168882,
year = {2025},
author = {Bowers, RM and Bennett, S and Riley, R and Villada, JC and Da Silva, IR and Woyke, T and Frank, AC},
title = {Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {222},
pmid = {41168882},
issn = {2049-2618},
support = {10.46936/10.25585/60000936//U.S. Department of Energy/ ; DEB-1442348//Directorate for Biological Sciences/ ; },
mesh = {*Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; *Tracheophyta/microbiology ; Metagenome ; Phylogeny ; *Plant Leaves/microbiology ; Pinus/microbiology ; },
abstract = {BACKGROUND: The aerial surface of plants, known as the phyllosphere, hosts a complex and dynamic microbiome that plays essential roles in plant health and environmental processes. While research has focused on root-associated microbiomes, the phyllosphere remains comparatively understudied, especially in forest ecosystems. Despite the global ecological dominance and importance of conifers, no previous study has applied shotgun metagenomics to their phyllosphere microbiomes.

RESULTS: This study uses metagenomic sequencing to explore the microbial phyllosphere communities of subalpine Western conifer needle surfaces from 67 trees at six sites spanning the Rocky Mountains, including 31 limber pine, 18 Douglas fir, and 18 Engelmann spruce. Sites span ~ 1,075 km and nearly 10° latitude, from Glacier National Park to Rocky Mountain Biological Laboratory, capturing broad environmental variation. Metagenomes were generated for each of the 67 samples, for which we produced individual assemblies, along with three large coassemblies specific to each conifer host. From these datasets, we reconstructed 447 metagenome-assembled genomes (MAGs), 417 of which are non-redundant at the species level. Beyond increasing the total number of extracted MAGs from 153 to 294, the three coassemblies yielded three large MAGs, representing partial sequences of host genomes. Phylogenomics of all microbial MAGs revealed communities predominantly composed of bacteria (n = 327) and fungi (n = 117). We show that both microbial community composition and metabolic potential differ significantly across host tree species and geographic sites, with site exerting a stronger influence than host.

CONCLUSIONS: This dataset offers new insights into the microbial communities inhabiting the conifer needle surface, laying the foundation for future research on needle microbiomes across temporal and spatial scales. Variation in functional capabilities, such as volatile organic compound (VOC) degradation and polysaccharide metabolism, closely tracks shifts in taxonomic composition, indicating that host-specific chemistry, local environmental factors, and regional microbial source pools jointly shape ecological roles. Moreover, the observed patterns of mobile genetic elements and horizontal gene transfer suggest that gene exchange predominantly occurs within microbial lineages, with occasional broader transfers dispersing key functional genes (e.g., those involved in polysaccharide metabolism), which may facilitate microbiome adaptation.},
}

*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
*Tracheophyta/microbiology
Metagenome
Phylogeny
*Plant Leaves/microbiology
Pinus/microbiology

@article {pmid41168838,
year = {2025},
author = {Sabeel, Z and Yang, Z},
title = {Microbiome-targeted nanoplatforms and engineering approaches in breast cancer therapy.},
journal = {Molecular cancer},
volume = {24},
number = {1},
pages = {276},
pmid = {41168838},
issn = {1476-4598},
mesh = {Humans ; *Breast Neoplasms/therapy/microbiology/etiology/pathology/drug therapy ; Female ; *Microbiota/drug effects ; Animals ; *Nanoparticles/chemistry ; Tumor Microenvironment/drug effects ; Drug Delivery Systems ; },
abstract = {Breast cancer (BC) presents persistent therapeutic challenges due to tumor heterogeneity, therapy resistance, and immune dysfunction, further compounded by emerging evidence of microbiome involvement in disease progression. Pathogenic bacteria such as Fusobacterium nucleatum have been implicated in modulating immune evasion, remodeling the extracellular matrix, and influencing therapy outcomes. Conventional microbiome-modulating strategies (e.g., antibiotics, probiotics) suffer from non-specificity and potential dysbiosis. Nanomaterial (NM)-based microbiome modulation offers a transformative alternative by enabling: targeted elimination of tumor-associated pathogens (e.g., Gal/GalNAc-functionalized nanoparticles for F. nucleatum), bacterial membrane-coated nanoplatforms for precision antimicrobial delivery, and multifunctional nanosystems that modulate the tumor microenvironment (TME) while preserving beneficial microbiota. This review explores NM-based microbiome modulation across BC contexts, including localized drug delivery, immunomodulation, and microbial niche editing. Highlighted strategies include lipid-based antimicrobial nanoparticles (NP), metallic NPs enhancing therapy sensitivity, and Traditional Chinese Medicine (TCM)-inspired nanoformulations for microbiome balance. Synergies with chemotherapy, immunotherapy, and radiotherapy are evaluated, alongside preclinical findings demonstrating improved tumor control and microbiome resilience. Finally, challenges in clinical translation, including toxicity, immunogenicity, and scalability, are discussed, with future directions emphasizing smart nanosystems capable of microbiome-responsive, biomarker-guided, and immune-integrated interventions in BC therapy.},
}

Humans
*Breast Neoplasms/therapy/microbiology/etiology/pathology/drug therapy
Female
*Microbiota/drug effects
Animals
*Nanoparticles/chemistry
Tumor Microenvironment/drug effects
Drug Delivery Systems

@article {pmid41168776,
year = {2025},
author = {Heng Wu, and Dong, T and Li, A and Chen, J and Zhang, H and Lv, H and Yang, C and Guo, X and Yang, X and Qiu, L and Miao, C and Yao, Y},
title = {An innovative strategy for overcoming ultra-high ammonia nitrogen inhibition on anaerobic methanogenesis via stepwise domestication.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {223},
pmid = {41168776},
issn = {2049-2618},
mesh = {*Methane/biosynthesis/metabolism ; Anaerobiosis ; *Ammonia/metabolism ; Animals ; Cattle ; Methanosarcina/metabolism/genetics ; *Nitrogen/metabolism ; Bioreactors/microbiology ; Bacteria/metabolism/classification/genetics ; Manure/microbiology ; Domestication ; Metagenomics/methods ; },
abstract = {BACKGROUND: The world is facing both an increasingly severe energy crisis and a growing problem of agricultural pollution. The utilization of agricultural waste by anaerobic digestion (AD), has received increasing attention. AD using representative waste cow dung results in total ammonia nitrogen (TAN) accumulation and inhibition of methanogens resulting in reduced CH4 production. However, there is a lack of highly efficient in-situ biological domestication strategies to enhance the TAN tolerance of methanogens in AD systems.

RESULTS: In this study, an incremental approach to gradually increasing the TAN concentration has been used for overcoming the problem. The results showed that at an ultra-high concentration of 6124.09 mg/L TAN, a 48-day domesticated AD system functioned stably and the cumulative CH4 production reached 72.81 mL/g volatile solids, whereas the undomesticated AD system failed to produce CH4. After domestication, the lactate dehydrogenase concentration decreased to 96.44 ng/L and the adenosine triphosphate concentration increased to 48.77 nmol/L, confirming that microbial activity improved. Hydrolytic and acidogenic bacteria were enriched, with Methanosarcina (79.73%) dominating the domesticated AD system, primarily Methanosarcina mazei. Metagenomic analysis showed that with two-component system enrichment, the key inhibited steps from glycerate-1,3P2 to pyruvate (2.498‰), and from acetyl-CoA and acetyl phosphate to acetic acid (1.141‰ and 0.798‰), as well as vital methanogenic genes mcrA (0.128‰), mcrB (0.127‰), and mcrG (0.065‰), were both enriched, which favored a stable methanogenic system. More importantly, this ultra-high resistance AD system also showed the potential to increase the CH4 production per unit substrate at the Minhe biogas plant with 24,000 m[3] operation scale in Shandong Province, China.

CONCLUSIONS: Stepwise increase the TAN concentration is a novel method that was demonstrated to be a practical and sustainable way to overcome ultra-high TAN inhibition (6124.09 mg/L). During domestication, the two-component system may regulate the microbial collaborative network to ensure microbial activity and high abundance enrichment, thus potentially constructing a methanogenic system dominated by hydrogenotrophic and acetoclastic methanogenesis, holding a promising application prospect. This study helped recognize the potential of methanogens in tolerating ultra-high inhibition and developed an achievable AD technology for robustly treating fecal residue and wastewater in practice.},
}

*Methane/biosynthesis/metabolism
Anaerobiosis
*Ammonia/metabolism
Animals
Cattle
Methanosarcina/metabolism/genetics
*Nitrogen/metabolism
Bioreactors/microbiology
Bacteria/metabolism/classification/genetics
Manure/microbiology
Domestication
Metagenomics/methods

@article {pmid41168767,
year = {2025},
author = {Meng, L and Fan, G and Xie, H and Tye, KD and Xia, L and Luo, H and Tang, X and Huang, T and Lin, J and Ma, G and Xiao, X and Li, Z},
title = {Maternal-to-neonatal microbial transmission and impact of prenatal probiotics on neonatal gut development.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1198},
pmid = {41168767},
issn = {1479-5876},
support = {81771664//National Natural Science Foundation of China/ ; 202201010952//Department of Science and Technology of Guangzhou/ ; },
mesh = {Humans ; *Probiotics/pharmacology ; Female ; Pregnancy ; Infant, Newborn ; *Gastrointestinal Microbiome/drug effects ; Adult ; Meconium/microbiology ; Feces/microbiology ; *Prenatal Care ; },
abstract = {BACKGROUND: Maternal microbiota during pregnancy plays a crucial role in establishing the neonatal gut microbiota, which is essential for infant health. This study aimed to trace maternal microbial sources contributing to early neonatal gut colonization and assess the effect of prenatal probiotic supplementation on maternal-to-neonatal microbial transmission.

METHODS: A total of 26 mother-neonate pairs undergoing full-term vaginal delivery were enrolled. From gestational week 32 until delivery, the intervention group received a probiotic supplement containing Bifidobacterium longum, Lactobacillus delbrueckii bulgaricus, and Streptococcus thermophilus twice daily, while the control group received no supplementation. Maternal fecal, vaginal, and placental samples were collected at full term, and neonatal fecal samples were collected longitudinally at Days 1, 3, 14, and 6 months postpartum. Microbial community profiling was performed using 16 S rRNA gene sequencing. Microbial source attribution was conducted using the FEAST algorithm.

RESULTS: Alpha and beta diversity analyses showed that prenatal probiotics transiently altered the composition of neonatal meconium microbiota, with no significant differences observed at later time points. Volatility analysis revealed enhanced microbial stability in the probiotic group during Days 1 to 3 (P < 0.001). FEAST source-tracking indicated that maternal gut and placenta were the major contributors to neonatal meconium colonization, with gut-derived input increasing over time and vaginal contributions remaining minimal throughout. Probiotic supplementation significantly increased the placental contribution to meconium microbiota (P = 0.02), with a sustained but non-significant elevation observed through later stages. Meanwhile, gut-derived and vaginal-derived inputs were consistently reduced in the probiotic group, though these differences did not reach statistical significance.

CONCLUSION: This study highlights the dynamic nature of maternal-to-neonatal microbial transmission and demonstrates that prenatal probiotic supplementation can transiently reshape early colonization patterns by modulating source contributions.

TRIAL REGISTRATION: ClinicalTrials.gov, NCT06241222 (https://clinicaltrials.gov/study/NCT06241222); retrospectively registered on 2024-01-17 (study start 2018-01-01; completion 2021-12-31; first posted 2024-02-05).},
}

Humans
*Probiotics/pharmacology
Female
Pregnancy
Infant, Newborn
*Gastrointestinal Microbiome/drug effects
Adult
Meconium/microbiology
Feces/microbiology
*Prenatal Care

@article {pmid41168741,
year = {2025},
author = {Nita, IB and Văcărean-Trandafir, IC and Amărandi, RM and Ilie, OD and Dobrin, PR and Bejenariu, AC and Ivanov, IC and Doroftei, B},
title = {Exploring gut microbiota profile induced by antipsychotics in schizophrenic patients: insights from an Eastern European pilot study.},
journal = {BMC psychiatry},
volume = {25},
number = {1},
pages = {1037},
pmid = {41168741},
issn = {1471-244X},
}

@article {pmid41168652,
year = {2025},
author = {Iancu, L and Mosby, R and Bonicelli, A and Procopio, N},
title = {Impact of flunitrazepam on Calliphora vicina (Diptera: Calliphoridae) microbiome dynamics.},
journal = {Journal of forensic sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/1556-4029.70208},
pmid = {41168652},
issn = {1556-4029},
support = {//Undergraduate Research/Creative Activity Fund 2023-2024, College of Arts and Sciences, University of North Dakota/ ; MR/S032878/1//UKRI/ ; MR/Y019989/1//UKRI/ ; },
abstract = {This study explored the effects of flunitrazepam, a benzodiazepine, on the microbiome diversity of Calliphora vicina Robineau-Desvoidy, 1830 (Diptera: Calliphoridae). By examining the microbial shifts throughout developmental stages, the research contributes valuable data to the field of forensic entomotoxicology. Two colonies of 500 adults were fed minced beef liver, spiked and non-spiked with 25 mg of flunitrazepam, and reared under controlled conditions (24°C, relative humidity of 45%, 12:12 light-dark cycle). Following oviposition, egg clusters were transferred, and the experiment was carried out in triplicate under the same experimental conditions. A total of 54 specimens, including all developmental stages, were collected for microbiome investigation via Illumina MiSeq. Both colonies had a 19-day development cycle from eggs to teneral. However, flunitrazepam-fed specimens were heavier, particularly during the pupa and teneral stages. Microbiome analysis revealed significant differences in diversity and composition between the colonies and across developmental stages. Pseudomonadota (Proteobacteria) dominated the control adults, while Bacteroidota and Bacillota (Firmicutes) were more prevalent in flunitrazepam-fed adults. Additionally, Enterobacterales, Lactobacillales, and Morganellaceae showed notable variations across different stages. This study highlights the significant impact of flunitrazepam on the microbiome dynamics of C. vicina, revealing notable morphological changes related to the specimens' weight toward the end of the development cycle and alterations in microbiome composition. These findings have important implications for forensic entomotoxicology, particularly in the accurate estimation of the minimum postmortem interval (mPMI).},
}

@article {pmid41168431,
year = {2025},
author = {Jabbar, KS and Priya, S and Xu, J and Das Adhikari, U and Pishchany, G and Mohamed, ATM and Johansen, J and Thurimella, K and McCabe, C and Vlamakis, H and Okello, S and Delorey, TM and Lankowski, A and Mosepele, M and Siedner, MJ and Plichta, DR and Kwon, DS and Xavier, RJ},
title = {Human immunodeficiency virus and antiretroviral therapies exert distinct influences across diverse gut microbiomes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41168431},
issn = {2058-5276},
support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 HL141053/HL/NHLBI NIH HHS/United States ; K24 HL166024/HL/NHLBI NIH HHS/United States ; DK120485//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Human immunodeficiency virus (HIV) infection alters gut microbiota composition and function, but the impact of geography and antiretroviral therapy remains unclear. Here we determined gut microbiome alterations linked to HIV infection and antiretroviral treatment in 327 individuals with HIV and 260 control participants in cohorts from Uganda, Botswana and the USA via faecal metagenomics. We found that while HIV-associated taxonomic differences were mostly site specific, changes in microbial functional pathways were broadly consistent across the cohorts and exacerbated in individuals with acquired immunodeficiency syndrome. Microbiome perturbations associated with antiretroviral medications were also geography dependent. In Botswana and Uganda, use of the non-nucleoside reverse transcriptase inhibitor efavirenz was linked to depletion of Prevotella, disruption of interspecies metabolic networks, exacerbation of systemic inflammation and atherosclerosis. Efavirenz-associated Prevotella depletion may occur through cross-inhibition of prokaryotic reverse transcriptases involved in antiphage defences, as shown by computational and in vitro experiments. These observations could inform future geography-specific and microbiome-guided therapy.},
}

@article {pmid41168291,
year = {2025},
author = {Arjmand, E and Moghadam, A and Afsharifar, A and Faghihi, MM and Izadpanah, K and Taghavi, SM},
title = {Metagenome analysis of Citrus sinensis rhizosphere infected with Candidatus liberibacter asiaticus reveals distinct structure in bacterial communities.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37987},
pmid = {41168291},
issn = {2045-2322},
mesh = {*Rhizosphere ; *Plant Diseases/microbiology ; *Metagenome ; *Microbiota/genetics ; *Citrus sinensis/microbiology ; *Rhizobiaceae ; Plant Roots/microbiology ; Soil Microbiology ; *Bacteria/genetics/classification ; Phylogeny ; *Liberibacter ; High-Throughput Nucleotide Sequencing ; },
abstract = {The rhizosphere microbiome plays crucial roles in different root-associated biological functions, especially regulating plant defense systems. Huanglongbing (HLB) disease, caused by Candidatus Liberibacter species, is a disaster threat to the global citrus industry. This study investigates changes in rhizosphere bacterial communities of Citrus sinensis trees infected by Candidatus Liberibacter asiaticus (CLas). We performed the high-throughput sequencing of the rhizosphere-associated bacterial metagenome and identified taxonomic profiles. Alpha diversity based on Shannon and Chao1 indices, and beta diversity based on Bray-Curtis dissimilarity and the UniFrac indices, revealed significant differences in the composition and structure of the rhizosphere microbiome between CLas-infected and CLas-free trees. We achieved significant relative abundance at the phylum and family, and genus levels. The abundance of Pseudomonas, Chryseobacterium, and an unknown genus belonging to Aurantimonadaceae was significantly suppressed in infected trees, while Planococcus and an unknown genus belonging to Caulobacteraceae were significantly enriched. These results confirm that CLas have dramatically altered the structure and composition of the rhizosphere microbiome. These changes discovered some valuable biomarkers related to this disease. These clues might be applied in microbial engineering of the rhizosphere to control HLB.},
}

*Rhizosphere
*Plant Diseases/microbiology
*Metagenome
*Microbiota/genetics
*Citrus sinensis/microbiology
*Rhizobiaceae
Plant Roots/microbiology
Soil Microbiology
*Bacteria/genetics/classification
Phylogeny
*Liberibacter
High-Throughput Nucleotide Sequencing

@article {pmid41168195,
year = {2025},
author = {Shan, L and Guo, X and Hu, Y and Zhou, H and Meng, X and Liu, K and Shi, L and Hu, F and Liu, Y and Zhang, T and Zhou, Y},
title = {L-citrulline protects testicular Sertoli cell function by mitigating DNA damage via the gut-testis axis of sheep fed a high-concentrate diet.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {202},
pmid = {41168195},
issn = {2055-5008},
support = {YLXKZX-ND-029//Inner Mongolia Autonomous Region Department of Education first-class scientific research project/ ; YLXKZX-ND-029//Inner Mongolia Autonomous Region Department of Education first-class scientific research project/ ; YLXKZX-ND-029//Inner Mongolia Autonomous Region Department of Education first-class scientific research project/ ; 2022JBGS0024//the Inner Mongolia Autonomous Region Open Competition Projects/ ; 2022JBGS0024//the Inner Mongolia Autonomous Region Open Competition Projects/ ; 2022JBGS0024//the Inner Mongolia Autonomous Region Open Competition Projects/ ; 2023ZD0407504//Biological Breeding-National Science and Technology Major Project/ ; 2023ZD0407504//Biological Breeding-National Science and Technology Major Project/ ; 2023YFHH0114//Inner Mongolia Autonomous Region Science and Technology Plan/ ; 32260180//the National Natural Science Foundation of China/ ; 32260181//the National Natural Science Foundation of China/ ; 2024SKYPT0068//the Science and Technology Major Project of Inner Mongolia Autonomous Region of China to the State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock/ ; },
mesh = {Male ; Animals ; *DNA Damage/drug effects ; *Sertoli Cells/drug effects/metabolism/physiology ; *Gastrointestinal Microbiome/drug effects ; *Citrulline/metabolism/pharmacology ; Sheep ; *Testis/drug effects ; Fecal Microbiota Transplantation ; Blood-Testis Barrier/drug effects ; Metabolomics ; *Diet/adverse effects ; Infertility, Male ; Dysbiosis ; },
abstract = {Mounting evidence underscores that high-concentrate diets (HCD) significantly impair male reproductive health, leading to infertility, and are closely associated with dysregulation of the gut microbiome and metabolome. However, effective therapeutic strategies targeting these alterations remain elusive. Notably, compelling evidence implicates the gut-testis axis as a critical mediator in the etiology of poor semen quality. Gut-derived metabolites, as key players in the gut-testis axis, warrant in-depth investigation as potential therapeutic targets for addressing male infertility caused by environmental factors, particularly dietary stressors. In this study, through an integrated multi-omics approach employing 10× Genomics single-cell mRNA sequencing, 16S ribosomal DNA sequencing and metabolomic profiling, we demonstrate that HCD induces DNA damage in Sertoli cells and disrupts the integrity of the blood-testis barrier (BTB), resulting in a significant decline in spermatozoa quality. Moreover, HCD impairs gut microbiota homeostasis and arginine biosynthesis, particularly leading to a remarkable decrease in L-citrulline levels. Additionally, fecal microbiota transplantation (FMT) experiments confirm that gut microbiota dysbiosis contributes to Sertoli cell DNA damage and BTB dysfunction. Interestingly, the effect of HCD-induced aberrant Sertoli cells function can be rescued by supplementation with L-citrulline. Collectively, these findings highlight the therapeutic potential of L-citrulline in protecting male reproductive health under dietary stress conditions, particularly through its action on the gut-testis axis.},
}

Male
Animals
*DNA Damage/drug effects
*Sertoli Cells/drug effects/metabolism/physiology
*Gastrointestinal Microbiome/drug effects
*Citrulline/metabolism/pharmacology
Sheep
*Testis/drug effects
Fecal Microbiota Transplantation
Blood-Testis Barrier/drug effects
Metabolomics
*Diet/adverse effects
Infertility, Male
Dysbiosis

@article {pmid41168153,
year = {2025},
author = {Querdasi, FR and Uy, JP and Labus, JS and Xu, J and Karnani, N and Tan, AP and Broekman, BBFP and Gluckman, PD and Chong, YS and Chen, H and Fortier, MV and Daniel, LM and Yap, F and Eriksson, JG and Cai, S and Chong, MF and Toh, JY and Godfrey, KM and Meaney, MJ and Callaghan, BL},
title = {Childhood gut microbiome is linked to internalizing symptoms at school age via the functional connectome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9359},
pmid = {41168153},
issn = {2041-1723},
support = {T32MH015750//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; F32MH135657//U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH)/ ; ARUK-PG2022A-008//Alzheimer's Research UK (ARUK)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; *Connectome ; Child ; Magnetic Resonance Imaging ; Male ; Female ; *Brain/diagnostic imaging/physiology ; RNA, Ribosomal, 16S/genetics ; *Anxiety/microbiology ; Child, Preschool ; Feces/microbiology ; *Depression/microbiology ; },
abstract = {The microbiome-gut-brain-axis plays a critical role in mental health. However, research linking the microbiome to brain function is limited, particularly during development, when tremendous plasticity occurs and many mental health issues, like depression and anxiety, initially manifest. Further complicating attempts to understand interactions between the brain and microbiome is the complex and multidimensional nature of both systems. In the current observational study (N = 55), we use sparse partial least squares to identify linear combinations of brain networks (brain signatures) derived from resting state fMRI scans at age 6 years that maximally covary with internalizing symptoms at age 7.5 years, before identifying microbe abundances (microbial profiles) derived from 16S rRNA sequencing of stool samples at age 2 years that maximally covary with those brain signatures. Finally, we test whether any early microbial profiles are indirectly associated with later internalizing symptoms via the brain signatures, highlighting potential microbial programming effects. We find that microbes in the Clostridiales order and Lachnospiraceae family are associated with internalizing symptoms in middle childhood through connectivity alterations within emotion-related brain networks.},
}

Humans
*Gastrointestinal Microbiome/physiology/genetics
*Connectome
Child
Magnetic Resonance Imaging
Male
Female
*Brain/diagnostic imaging/physiology
RNA, Ribosomal, 16S/genetics
*Anxiety/microbiology
Child, Preschool
Feces/microbiology
*Depression/microbiology

@article {pmid41168105,
year = {2025},
author = {Wang, Z and Lin, X},
title = {The association between periodontitis and hypothyroidism: A comprehensive review.},
journal = {The Journal of international medical research},
volume = {53},
number = {10},
pages = {3000605251388870},
doi = {10.1177/03000605251388870},
pmid = {41168105},
issn = {1473-2300},
mesh = {Humans ; *Periodontitis/complications/pathology ; *Hypothyroidism/complications ; Animals ; },
abstract = {This narrative review aimed to critically synthesize and evaluate the current evidence on the association between hypothyroidism and periodontitis, with a particular focus on elucidating the underlying pathophysiological mechanisms. A comprehensive literature search was conducted on PubMed, encompassing animal, cellular, and clinical studies. The synthesized findings indicate that hypothyroidism exacerbates periodontitis through multiple interconnected pathways, including dysregulated bone metabolism, induction of systemic osteoporosis, amplification of immune-inflammatory responses, and disruption of oral microbiome homeostasis. Furthermore, evidence suggests a potential bidirectional relationship, wherein periodontal therapy may positively influence thyroid function parameters. A key takeaway from this review is the importance of interdisciplinary collaboration between endocrinologists and dental professionals. Incorporating thyroid function evaluation into periodontal management may enhance treatment outcomes. This review concludes that although existing evidence supports a significant association, further high-quality longitudinal human studies are required to definitively establish causality and elucidate the precise underlying molecular mechanisms.},
}

Humans
*Periodontitis/complications/pathology
*Hypothyroidism/complications
Animals

@article {pmid41167751,
year = {2025},
author = {Bi, XX and Zhou, LX and Zhang, YP and Jiang, XW and Li, LN},
title = {[Correlation between short chain fatty acids in saliva and salivary microbiota in patients with laryngopharyngeal reflux disease].},
journal = {Zhonghua er bi yan hou tou jing wai ke za zhi = Chinese journal of otorhinolaryngology head and neck surgery},
volume = {60},
number = {10},
pages = {1298-1307},
doi = {10.3760/cma.j.cn115330-20250101-00002},
pmid = {41167751},
issn = {1673-0860},
support = {7242136//Beijing Municipal Natural Science Foundation/ ; },
mesh = {Humans ; *Saliva/microbiology/chemistry ; Male ; Female ; Adult ; *Fatty Acids, Volatile/analysis/metabolism ; *Microbiota ; Case-Control Studies ; *Laryngopharyngeal Reflux/microbiology/metabolism ; Middle Aged ; Retrospective Studies ; Young Adult ; Adolescent ; },
abstract = {Objective: This study aimed to compare short-chain fatty acid (SCFA) levels in saliva between patients with laryngopharyngeal reflux disease (LPRD) and healthy controls, and to explore the relationship between these SCFAs and the salivary microbiota. Methods: A retrospective case-control study was conducted, enrolling 36 patients with laryngopharyngeal reflux disease (LPRD) who visited the Department of Otorhinolaryngology Head and Neck Surgery, the Eighth Medical Center, Chinese PLA General Hospital between February and November 2023. All patients were diagnosed via pharyngeal pH monitoring. The LPRD group included 30 males and 6 females, aged 20-53 years (30.61±7.83 years). In addition, 39 healthy volunteers were recruited as the control group, comprising 25 males and 14 females, aged 18-58 years (28.64±7.97 years). Unstimulated mixed saliva samples were collected from all participants. Concentrations of eight SCFAs (acetic acid, propionic acid, isobutyric acid, butyric acid, valeric acid, isovaleric acid, hexanoic acid, and heptanoic acid) in saliva were quantified using gas chromatography-mass spectrometry (GC-MS). Salivary DNA was extracted, followed by amplification and sequencing of the 16S rRNA gene to analyze the microbiota composition at the genus level. The SCFA concentrations and the differences in bacterial species between the LPRD and control groups were compared, and the correlation between SCFA concentrations and the relative abundance of different bacterial genera in the salivary microbiota was analyzed. All statistical analyses were performed using R version 3.6.1 and SPSS version 26.0, while, microbiome analyses were conducted using R language. Results: Salivary hexanoic acid concentration was significantly higher in the LPRD group than in the control group [(29.50±19.61) ng/ml vs. (10.15±3.65) ng/ml; t=-2.72, P<0.05]. Significant differences in the relative abundance of 17 bacterial genera were observed between the two groups (P<0.05), including Prevotella, Butyrivibrio, Streptococcus, and Actinomyces. Correlation analysis revealed that hexanoic acid concentration was significantly positively correlated with the abundance of Butyrivibrio (γ=0.73, P<0.05) and Streptococcus (γ=0.78, P<0.05), while showing a significant negative correlation with Actinomyces (γ=-0.73, P<0.05). Conclusion: Elevated salivary hexanoic acid levels may be associated with the development of LPRD. Dysbiosis of the salivary microbiota might contribute to LPRD pathogenesis by altering the concentrations of SCFA, particularly hexanoic acid.},
}

Humans
*Saliva/microbiology/chemistry
Male
Female
Adult
*Fatty Acids, Volatile/analysis/metabolism
*Microbiota
Case-Control Studies
*Laryngopharyngeal Reflux/microbiology/metabolism
Middle Aged
Retrospective Studies
Young Adult
Adolescent

@article {pmid41167732,
year = {2025},
author = {Ewell, TR and Bomar, MC and Abbotts, KSS and Kayne, BT and Risk, BD and Williams, NNB and Wei, Y and Dooley, GP and Weir, TL and Bell, C},
title = {Short-Term Low Dose Cannabidiol Does Not Influence Glucose Tolerance or the Gut Microbiome in Sedentary Adults with Overweight and Obesity: Pilot Study.},
journal = {Cannabis and cannabinoid research},
volume = {},
number = {},
pages = {},
doi = {10.1177/25785125251391085},
pmid = {41167732},
issn = {2378-8763},
abstract = {Introduction: Epidemiological data indicate that regular users of cannabis products may be protected from type 2 diabetes, although the mechanism is not understood. Observations from animal studies suggest that the cannabinoid, cannabidiol (CBD) may protect/improve glucose tolerance; an effect that may be partially mediated by favorable modifications to the gut microbiome. The aims of the current pilot project were to gain initial insight into the influence of short-term CBD ingestion on oral glucose tolerance, the gut microbiome, and inflammation in sedentary adults with overweight or obesity and free from diabetes. Materials and Methods: Using a randomized, double-blind, repeated measures, parallel design, oral glucose tolerance was determined in 16 adults (6 males, 10 females) prior to and following 4 weeks of daily ingestion of either placebo or CBD (30 mg every 12 h). Fecal samples were collected at baseline and post-intervention. Results: Compared with placebo, CBD did not influence glucose tolerance (Matsuda Index: placebo-pre 7.6 [5.5], placebo-post 10.1 [5.5], vs. CBD-pre 11.7 [7.9], and hCBD-post 10.1 [10.2]; median [interquartile range]; p > 0.05). Characteristics of the gut microbiome or inflammation were not appreciably modified by CBD or placebo. Discussion: Short-term daily ingestion of low-dose CBD did not appear to favorably modify glucose tolerance in sedentary adults with overweight or obesity. It is possible that CBD may not account for the previously reported protection from type 2 diabetes bestowed to regular users of cannabis products.},
}

@article {pmid41167655,
year = {2025},
author = {Akkoyunlu, DS and Celebi, A and Gur, B and Kanli, A and Ugurtas, C and Ozer, T and Sarikaya, NK and Keskin, SE and Cine, N and Savli, H},
title = {Functional Abdominal Bloating Is Associated With Gut Microbiota Dysbiosis and Altered Intestinal Barrier Function: Experimental Evidence.},
journal = {In vivo (Athens, Greece)},
volume = {39},
number = {6},
pages = {3320-3332},
doi = {10.21873/invivo.14130},
pmid = {41167655},
issn = {1791-7549},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Dysbiosis/microbiology ; Female ; Male ; Adult ; Middle Aged ; Feces/microbiology ; *Intestinal Mucosa/metabolism/microbiology ; Biomarkers ; Aged ; Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Intestinal Barrier Function ; },
abstract = {BACKGROUND/AIM: This study aimed to characterize gut microbiota alterations and intestinal barrier markers in patients with functional abdominal bloating (FAB) to explore its underlying biological mechanisms.

MATERIALS AND METHODS: Stool samples from 42 adults diagnosed with FAB per Rome IV criteria were analyzed using the intergenic spacer profiling, which profiles the 16S-23S ribosomal DNA intergenic spacer region to enhance species-level resolution. Targeted real-time polymerase chain reaction quantified key bacterial taxa. Microbial diversity, Firmicutes/Bacteroidetes (F/B) ratio, enterotype distribution, and levels of beneficial and pathogenic bacteria were assessed. Gastrointestinal immune and permeability markers (calprotectin, secretory IgA, zonulin, α1-antitrypsin, bile acids, pancreatic elastase) were measured by enzyme-linked immunosorbent assay.

RESULTS: A dysbiosis index ≥15 was observed in 90.5% of patients, indicating significant microbial imbalance. Most showed a low mean F/B ratio (<1.5) and microbial diversity index (<5), reflecting reduced microbiota resilience. Enterotype 1 (Bacteroides-dominant) was predominant (67%), with no detection of Enterotype 3 (Ruminococcus-dominant). Levels of beneficial bacteria, including Faecalibacterium prausnitzii, Akkermansia muciniphila, Bacteroides spp., and Bifidobacterium spp., were markedly decreased in over 80% of individuals. Conversely, Proteobacteria such as Sutterella wadsworthensis and Klebsiella spp. were at elevated levels. Calprotectin and sIgA were increased in >59.5% of cases; zonulin and α1-antitrypsin were elevated in 19% and 16.7%, respectively, suggesting mucosal immune activation and possible barrier dysfunction.

CONCLUSION: This study demonstrates that FAB is accompanied by profound alterations in gut microbiota composition and mucosal immune responses, indicating that its pathophysiology extends beyond functional disturbances to include measurable biological changes. These findings support the growing clinical relevance of microbiota-informed evaluation and open new avenues for targeted therapeutic strategies.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Dysbiosis/microbiology
Female
Male
Adult
Middle Aged
Feces/microbiology
*Intestinal Mucosa/metabolism/microbiology
Biomarkers
Aged
Bacteria/genetics/classification
RNA, Ribosomal, 16S/genetics
Intestinal Barrier Function

@article {pmid41167320,
year = {2025},
author = {Pandey, NK and Simon, M and Vishwakarma, RK and Sen, S and Joshi, H and Yadav, S and Mateo-Sagasta, J and Jampani, M and Sikka, A and Hazra, S},
title = {Exploring Microbial Diversity, Antibiotic Resistance, and their Environmental Drivers in Urban and Peri-Urban Riverbed Sediments of Sub-tropical River Basins.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123174},
doi = {10.1016/j.envres.2025.123174},
pmid = {41167320},
issn = {1096-0953},
abstract = {Rivers travel through diverse landscapes and carry natural and anthropogenic materials, which affect the dynamics of the biological and physicochemical properties of the river and riverbed sediments. Anthropological activities such as urbanization and industrialization release vast amounts of contaminants that can alter a river's ecology and contribute to the emergence of drug resistance. This study explores two subtropical river basins in India, focusing on the main river Song (flowing through a peri-urban sub-basin) and joined by its tributaries, viz. Rispana, Bindal, and Suswa (flowing through a heavily urbanised sub-basin). A total of 27 sediment samples were collected from 9 sites in winter, summer, and monsoon seasons of the year 2024 to explore microbial diversity, antibiotic-resistant bacteria (ARB), physicochemical properties, antibiotic residues, and heavy metal concentrations. Results highlight that heavily urbanised sub-basins sediments carry more contaminants and a high load of antibiotic-resistant bacteria, ESKAPE pathogen genera, and Enterobacterales in comparison to peri-urban river basins. However, both sub-basins predominantly carry the bacterial phyla Pseudomonadota and Bacillota, including pathogenic genera such as Pseudomonas, Staphylococcus, and Acinetobacter. Our analysis demonstrated that elevated concentrations of heavy metals and antibiotics are closely associated with increased levels of antimicrobial resistance. Overall, this study provided comparative insights into the peri-urban and heavily urbanised sub-basin river sediments microbiome, antibiogram, and their drivers. The results and findings of this study may help to develop a basic framework of policy recommendations for better managing subtropical river basins in urbanized areas.},
}

@article {pmid41167241,
year = {2025},
author = {Balasubramaniam, K and Mueller-Klein, N and Vink, T and Clutton-Brock, TH and Manser, MB and Sommer, S},
title = {Impact of animal socioecology on gut microbial communities: Insights from wild meerkats in the Kalahari.},
journal = {The Journal of animal ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1365-2656.70168},
pmid = {41167241},
issn = {1365-2656},
support = {RGP0051/2017//Human Frontier Science Program/ ; 294494//H2020 European Research Council/ ; 742808//H2020 European Research Council/ ; DFG SO428/15-1//Deutsche Forschungsgemeinschaft/ ; },
abstract = {The social organisation of animals likely shapes the composition, diversity and stability of microbiomes, giving rise to the concept of the 'social microbiome'-microbial communities shared within and across social units, or 'islands', ranging from individuals to entire ecosystems. Understanding the connections and their underlying drivers is crucial for revealing how socioecology influences microbiomes and associated health outcomes. However, empirical assessments are still limited, and the relative influence of social organisation compared to intrinsic (biological) and extrinsic (environmental) factors in shaping microbiomes is particularly unclear. Here, we used a long-term, individual-based study of Kalahari meerkats (Suricata suricatta) to test predictions from the social microbiome concept. We assessed the relative influence of social factors, biological traits and environmental variables on gut microbial communities, while also accounting for the effects of microbial phylogenetic relatedness and within-host associations or co-occurrence independent of phylogeny. Meerkat microbiomes exhibited highly 'nested' and weakly 'modular' structures: individuals with lower diversity hosted amplicon sequence variants (ASVs) that were subsets of the overall community, though some bacterial taxa clustered distinctly among hosts. Microbiomes were more similar within social groups than between them. Group membership strongly influenced the co-occurrence of many beneficial ASVs, as well as a few potentially harmful ones. This effect was stronger than that of kinship, though closer relatives shared more similar microbiomes within some groups. While a range of social, biological and environmental factors influenced bacterial abundance, group membership, individual age and sampling time since sunrise had the most significant impact. ASV-ASV co-occurrence within hosts, independent of phylogeny, also played a major role. In contrast, individual-level social traits (e.g. dominance, immigration), other environmental (e.g. sampling temperature, rainfall, hours since foraging), demographic (sex) and health-related factors (body condition, disease status) had weaker effects on bacterial abundance. We show that gut microbiomes are shaped by a combination of factors, highlighting the importance of separating the effects of social organisation from individual social traits, biological factors, environmental influences and microbe-microbe interactions. By identifying drivers of both beneficial and detrimental bacterial co-occurrence, we provide a foundation for assessing how the social microbiome affects animal health and fitness.},
}

@article {pmid41167188,
year = {2025},
author = {Cha, JH and Kim, N and Ma, J and Lee, S and Koh, G and Yang, S and Beck, S and Byeon, I and Lee, B and Lee, I},
title = {A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.10.001},
pmid = {41167188},
issn = {1934-6069},
abstract = {The oral microbiome is increasingly linked to human health. To further examine this microbial community, we present the human reference oral microbiome (HROM), with 72,641 high-quality genomes from 3,426 species, including 2,019 previously unidentified species, improving metagenomic sequence read classification over existing catalogs. Notably, HROM unveils 1,137 previously uncharacterized candidate phyla radiation (CPR) species, establishing Patescibacteria as the most prevalent phylum in the oral microbiota and distinct from environmental Patescibacteria. Additionally, an oral CPR subclade is associated with periodontitis, complementing Porphyromonas gingivalis in predicting disease. Finally, comparing HROM with reference genomes of the gut microbiome reveals taxonomic and functional divergence between these microbiomes. HROM contains 42 ectopic oral species, and their relative abundance in gut microbiota is predictive of intestinal, cardiovascular, and liver diseases. Thus, HROM offers an expanded view of the oral microbiome and highlights the clinical importance of further examining the links between oral microbes and systemic disorders.},
}

@article {pmid41167187,
year = {2025},
author = {Huang, Y and Tang, S and Liu, R and Yu, P and Liu, J and Xiao, T and Zhang, Y and Fan, M and Zhang, F and Ni, B},
title = {Soil organic carbon mediates plant immunity-rhizosphere microbiome interactions and controls colonization resistance to microbial inoculants.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.10.002},
pmid = {41167187},
issn = {1934-6069},
abstract = {Beneficial microbial inoculants can improve crop performance, but their effectiveness in the field is highly variable. Here, we provide experimental and ecological evidence suggesting that soil organic carbon (SOC) may influence colonization resistance, potentially through interactions between host immunity and microbiome assembly in the rhizosphere. Using greenhouse assays, field trials, multi-omics, and a global meta-analysis, we observed an inverted U-shaped (Kuznets-type) relationship between SOC and bioinoculant efficacy. Yield gains peaked at ∼1.5% SOC, coinciding with reduced immune and microbial barriers to inoculant establishment. At low or high SOC, enrichment of antagonistic bacterial consortia suppressed beneficial fungal colonization. Mechanistic analyses indicated SOC-dependent modulation of reactive oxygen species homeostasis, altered microbial network connectivity, and regulation of bioactive metabolites affecting plant immunity. These findings are consistent with the existence of a conceptual SOC-immune-microbiome axis, which may help explain resource-dependent colonization patterns and inform future microbiome engineering strategies across diverse hosts.},
}

@article {pmid41167178,
year = {2025},
author = {Chen, K and Zhang, X and Zeng, K and Zhong, J and Jin, S and Nie, Y and Yang, P and He, N and Chen, H and Cao, Y and Fu, Y and Fang, Z and Jiang, W and Liu, C},
title = {Bifidobacterium animalis subsp. lactis BLa80 for preventing allergic, respiratory, and gastrointestinal diseases in young children in China: a randomized double-blind placebo-controlled trial.},
journal = {Clinical and experimental pediatrics},
volume = {},
number = {},
pages = {},
doi = {10.3345/cep.2025.01256},
pmid = {41167178},
issn = {2713-4148},
abstract = {BACKGROUND: Respiratory, gastrointestinal, and allergic diseases can significantly affect children's physical and mental health and quality of life.

PURPOSE: This study aimed to assess the safety of Bifidobacterium animalis subsp. lactis BLa80, its preventive effects on morbidities related to respiratory, gastrointestinal, and allergic diseases, and its impact on the gut microbiome of children during the study period.

METHODS: Healthy children aged 0-3 years were randomly assigned to an intervention group (IG; n=180) or control group (CG; n=180). Participants received probiotics or placebo for 3 months, followed by a 3-month follow-up period. Children in the IG received one oral probiotic sachet daily for 90 consecutive days starting on the first day of the intervention. Each sachet contained maltodextrin and the BLa80 strain at 5×109 colony-forming units (CFUs). Children in the CG received placebo sachets containing maltodextrin only. The primary outcome measure was eczema morbidity during the 6-month study period. Secondary outcomes included acute upper respiratory tract infections (URTIs) and acute tracheitis/bronchitis. Fecal gut microbiota profiles were assessed by 16S rRNA sequencing. Fecal immune biomarkers including calprotectin, human beta-defensin-2 (HBD-2), cathelicidin (LL-37), and secretory immunoglobulin A were also determined. This study was registered with the China Clinical Trial Center (ChiCTR2300074956).

RESULTS: Per-protocol analyses were conducted of 156 and 164 subjects in the IG and CG, respectively. The morbidity rate of eczema during the 6-month period was significantly lower in the IG versus CG (intention-to-treat analysis: 26.1% [47 of 180] vs. 66.7% [120 of 180], P<0.01; per-protocol analysis: 30.1% [47 of 156] vs. 73.2% [120 of 164], P<0.01). Probiotic supplementation was also associated with a lower risk of URTIs (IG vs. CG: 40.3% vs. 20.7%; risk ratio [RR], 0.752; 95% confidence interval [CI], 0.653-0.866) and acute tracheitis/bronchitis (18.8% vs. 9.5%; RR, 0.897; 95% CI, 0.825-0.977). Bla80 intervention increased the relative abundance of Bifidobacterium bifidum, Bifidobacterium kashiwanohense PV20-2, Bifidobacterium longum, and Enterococcus dispar ATCC (American Type Culture Collection) 51266 while decreasing the abundance of Bacteroides thetaiotaomicron. Postintervention, the IG had significantly lower concentrations of LL-37 (3,509.31± 587.89 pg/g vs. 3,720.82±614.90 pg/g, P=0.006) and HBD-2 (202.36±56.35 pg/g vs. 222.65±56.23 pg/g, P=0.005) than the CG. No serious adverse events were reported in either group.

CONCLUSION: The daily administration of BLa80 at 5×109 CFU for 3 months in children aged 0-3 years reduced therisk of eczema, URTIs, and acute tracheitis/bronchitis and beneficially altered the gut microbiome composition, fecal immune biomarkers, and functional gene composition without any adverse effects.},
}

@article {pmid41166910,
year = {2025},
author = {Mao, YQ and Song, SY and Xu, Q and Zang, TT and Wang, LS and Shen, L and Ge, JB},
title = {Dietary fiber pectin supplement attenuates atherosclerosis through promoting Akkermansia-related acetic acid metabolism.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {148},
number = {},
pages = {157373},
doi = {10.1016/j.phymed.2025.157373},
pmid = {41166910},
issn = {1618-095X},
abstract = {BACKGROUND: Atherosclerosis (AS) is a vascular disease caused by chronic inflammation, and its incidence and mortality rates are still on the rise. Recent studies have revealed that the structure and function of gut microbiota are significantly correlated with the occurrence and development of AS, providing novel insights into the mechanisms of cardiovascular diseases. Multiple studies have clarified that dietary fiber pectin alter the structure and function of the gut microbiota. At the same time, it has also been found that dietary fiber pectin can alleviate atherosclerosis.

PURPOSE: The aim is to explore whether the gut microbiota mediates the anti-atherosclerotic effects of pectin, and to elucidate the underlying molecular mechanisms.

METHODS: We established an atherosclerosis model in ApoE[-/-] mice by feeding a high-fat and high-cholesterol diet. We combined antibiotic depleted gut microbiota and transplanted the fecal microbiota to demonstrate that the effect of dietary fiber pectin in alleviating atherosclerosis depends on the gut microbiota. Subsequently, we explored the material basis of the anti-atherosclerotic effect mediated by the gut microbiota through 16 s rRNA sequencing, targeted metabolomics detection, and bacterial culture methods.

RESULTS: We conducted experiments on ApoE[-/-] mice to deplete gut microbiota with antibiotics and then perform fecal microbiota transplantation, and the results showed that supplementation with dietary fiber pectin attenuates atherosclerosis in a gut microbiome dependent manner. Through 16S rRNA sequencing, we found that supplementation of dietary fiber pectin could enrich the abundance of Akkermansia (Akk). In addition, administration with Akk was sufficient to prevent the progression of atherosclerosis in a diet-induced model. Mechanistically, Akk produced acetic acid through fermentation of pectin, and then inhibited the proliferation of Lactococcus lactis (l.lactis) in arterial plaque to exert anti-atherosclerosis effect.

CONCLUSIONS: Our results suggest that dietary fiber pectin enriches the abundance of Akk, which inhibits the proliferation of the atherosclerotic-related bacterium, l.lactis, by producing acetic acid in ApoE[-/-] mice. Our findings first reveal that pectin prevents the development of atherosclerosis through gut microbiota. Additionally, based on the theory of the "gut-vessel" axis, we demonstrate that dietary fiber pectin enriched the abundance of Akk in the gut, which elevated the level of acetic acid and further inhibit the abundance of l. within atherosclerotic plaques. These data provide new clues and strategies for the clinical treatment of atherosclerosis.},
}

@article {pmid41166850,
year = {2025},
author = {Qiu, X and Wang, Y and Yu, T and Li, D and Tan, Y and Huo, Z and Yan, X},
title = {Vibrio parahaemolyticus infection in Manila clams (Ruditapes philippinarum): A case study of microbiome perturbation.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {57},
number = {},
pages = {101655},
doi = {10.1016/j.cbd.2025.101655},
pmid = {41166850},
issn = {1878-0407},
abstract = {The homeostasis of gill microbiota is essential for marine organisms' health, yet pathogen invasion disrupt this balance, impacting host physiology. As the farming density rises in the shellfish aquaculture industry, the Manila clam (Ruditapes philippinarum) has shown increased susceptibility to pathogens, with Vibrio parahaemolyticus representing a major economic threat. This study delves into the effects of V. parahaemolyticus on the gill microbiota of R. philippinarum (Ruditapes philippinarum) through histopathological analysis and 16S rRNA gene sequencing. At 72 hour post-infection (hpi), severe inflammatory reactions and gill damage were observed, accompanied by significant changes in microbial community structure. At 72 hpi, microbial diversity significantly shifted, with a decrease in Bacteroidota and Vibrionimonas, while Bradyrhizobium became dominant. By 96 hpi, Acidobacteriota and Chloroflexi increased, suggesting organic matter accumulation and redox alterations. LEfSe analysis identified Enterobacteriaceae, Streptomycetaceae, and Streptomycetales as biomarker taxa at 72 hpi. Metabolic pathways with increased abundance relative to 0 hpi included nucleoside metabolism, replication, and purine metabolism, while glycine, serine, and threonine metabolism showed a decreased abundance. Our findings illustrate that V. parahaemolyticus infection disrupts microbial and metabolic homeostasis in the gill of R. philippinarum, eliciting substantial inflammatory damage and offering insights into molecular mechanisms underlying clam susceptibility and potential mortality.},
}

@article {pmid41166814,
year = {2025},
author = {Li, H and Song, K and Zhang, X and Wang, S and Yang, L},
title = {Integrated untargeted and targeted metabolomics and microbiome profiling reveal the effects of storage duration on the flavor quality of Rizhao Jinhua white tea.},
journal = {Food chemistry},
volume = {496},
number = {Pt 2},
pages = {146811},
doi = {10.1016/j.foodchem.2025.146811},
pmid = {41166814},
issn = {1873-7072},
abstract = {The post-fermented tea develops enhanced quality attributes with prolonged storage. In this study, we explored the dynamic changes in sensory characteristics, untargeted and targeted metabolomics, and microbial communities of Rizhao Jinhua white tea (WFB) across different storage years. Storage process reduced bitterness and astringency, while improving overall mellowness. Levels of total polyphenols, amino acids, theaflavins, and thearubigins declined significantly, whereas theabrownin reached its peak at year 5. Among 118 identified differential metabolites, flavonoids exhibited the most pronounced variations. Further targeted quantification of flavonoids revealed catechin, epicatechin, epigallocatechin, quercitrin, and isorhamnetin as key flavor determinants. This was related to glycosylation, hydrogenation, hydroxylation, and hydrolysis reactions occurring during storage. Dominant microbial genera such as Aspergillus and Pseudomonas continuously promoted flavonoids transformations during storage. The outcomes of this research support better approaches to flavor quality optimization in stored Jinhua white tea.},
}

@article {pmid41166334,
year = {2025},
author = {Yang, S and Wang, K and Hu, Y and Zhang, L and Zhang, C and Liu, Y and Li, Z and Jiang, L and Han, Y and Naowarojna, N and Wei, Y and Zhang, Y},
title = {Studies on Two Convergently Evolved Cysteate Synthases in Sulfonolipid Biosynthesis.},
journal = {ACS chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschembio.5c00142},
pmid = {41166334},
issn = {1554-8937},
abstract = {Capnine-like sulfonolipids are sulfonate-containing analogs of sphingolipids found in many Bacteroidetes bacteria, where they govern essential functions such as gliding motility, outer membrane polysaccharide assembly, and antibiotic susceptibility. In gut-associated anaerobic Bacteroidetes, these sulfonolipids also modulate host-microbe interactions. In aerobic bacteria, the capnine precursor cysteate is produced by a pyridoxal phosphate (PLP)-dependent cysteate synthase (CapA1), a close homologue of cystathionine β-synthase (CBS). By contrast, the mechanism of cysteate production in anaerobic Bacteroidetes bacteria has not been biochemically studied. Herein, we report the characterizations of archaeal cysteate synthase homologue from the anaerobic bacteria Alistipes finegoldii (AfCapA2). Biochemical assays confirm its ability to catalyze the conversion of O-phosphoserine (OPS) to cysteate. Crystal structures of AfCapA2 in complex with PLP and OPS-PLP identify essential catalytic residues and reveal a structural similarity to threonine synthase, unlike CapA1, which is more similar to CBS. Comparative analysis of CapA1 and this nonorthologous CapA2, including structural differences, catalytic versatility, and phylogenetic distribution across Bacteroidetes, suggests convergent evolution of cysteate synthase activity. Our work clarifies the details of sulfonolipid synthesis in anaerobic bacteria and the biochemical origins of this structurally distinctive lipid in the gut microbiome.},
}

@article {pmid41166319,
year = {2025},
author = {Sanam, M and Hossain, CFTZ and Hyder, TB and Tarannum, R and Oishi, JF and Rahman, KMM and Islam, SBU and Bulbul, N and Sultana Jime, J and Shishir, MA and Safa, A and Fakruddin, M},
title = {Bridging two worlds: Host Microbiota crosstalk in health and dysregulation.},
journal = {Innate immunity},
volume = {31},
number = {},
pages = {17534259251392993},
doi = {10.1177/17534259251392993},
pmid = {41166319},
issn = {1753-4267},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Animals ; *Dysbiosis/immunology ; Signal Transduction ; Immunity, Innate ; Homeostasis ; *Host Microbial Interactions/immunology ; Adaptive Immunity ; Bile Acids and Salts/metabolism ; Fatty Acids, Volatile/metabolism ; },
abstract = {The gut microbiota plays a crucial role in various physiological functions, such as the production of microbial compounds and maintaining homeostatic equilibrium by complex host-microbial interactions. However, any shift in the constitution and diversity of the microbiota or abnormal interaction with the host can prompt the development of dysbiosis. This review thus illustrates that microbial metabolites, notably short-chain fatty acids, tryptophan metabolites, bile acids, and polyamines, exert significant regulatory effects on innate and adaptive immunological processes, immune response and intestinal barrier integrity through specific receptor activation, involving TLRs, NODs, GPCRs, nuclear receptors, and Wnt/β-catenin. It further explores the disruption of host signalling pathways, caused by dysbiosis, promoting the transcription of specific genes and activating pro-inflammatory pathways. Consequently, this suggests that microbiota acts beyond general health, eventually contributing to gastrointestinal, metabolic, and neurological disorders. Lastly, this review highlights therapeutic approaches required to restore balance and uphold physiological balance.},
}

Humans
*Gastrointestinal Microbiome/immunology
Animals
*Dysbiosis/immunology
Signal Transduction
Immunity, Innate
Homeostasis
*Host Microbial Interactions/immunology
Adaptive Immunity
Bile Acids and Salts/metabolism
Fatty Acids, Volatile/metabolism

@article {pmid41166306,
year = {2025},
author = {Zhang, ZF and Huang, JE and Phurbu, D and Qu, ZS and Liu, F and Cai, L},
title = {A deep metagenomic atlas of Qinghai-Xizang Plateau lakes reveals their microbial diversity and salinity adaptation mechanisms.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116483},
doi = {10.1016/j.celrep.2025.116483},
pmid = {41166306},
issn = {2211-1247},
abstract = {The Qinghai-Xizang Plateau (QXP), harboring the planet's highest density of plateau lakes, offers an exceptional biogeographic environment for studying extremophilic microbial communities and their adaptation to salinity. Through deep metagenomic sequencing, we construct the Qinghai-Xizang Lake Sediment Genome (QXLSG) catalog, a high-resolution genomic catalog comprising 5,866 metagenome-assembled genomes (MAGs), 58.16 million non-redundant protein encoding genes, and 19,008 biosynthetic gene clusters. Notably, 80.78% of the 2,742 species-level MAGs represent undescribed taxa, significantly expanding the known microbial diversity. Salinity emerges as the primary environmental factor influencing microbial community. Functional annotation highlights that the "salt-out" strategy, particularly the uptake of glycine betaine, is the main mechanism for salinity tolerance. This strategy is prevalent in both hypersaline lake communities and the dominant microbial phyla. Overall, this study provides a crucial genetic resource for future bioprospecting and deepens our understanding of the fundamental mechanisms of microbial adaptation to extreme saline environments.},
}

@article {pmid41166299,
year = {2025},
author = {Scully, S and Earley, B and Smith, PE and Finnie, MSJ and McAloon, C and Buckley, F and Kenny, DA and Waters, SM},
title = {Characterisation of the bacterial and archaeal microbiota in fresh colostrum collected from a single, spring-calving dairy herd.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0335718},
doi = {10.1371/journal.pone.0335718},
pmid = {41166299},
issn = {1932-6203},
mesh = {*Colostrum/microbiology ; Animals ; Cattle ; *Archaea/genetics/classification/isolation & purification ; Female ; *Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Dairying ; Pregnancy ; },
abstract = {There is increasing evidence to support the existence of a naturally occurring colostral microbiome, which may influence the development of the gastrointestinal microbiota and immune function of the calf. The objective of this study was to characterize the prokaryotic community of colostrum collected fresh (within 2h parturition) from primi- and multiparous Holstein-Friesian (n = 17) and Jersey (n = 10) cows. Extracted microbial DNA underwent qPCR and Illumina amplicon sequencing of the V4 region of the 16S rRNA gene. High throughput amplicon sequencing data was analysed using a variety of R packages. Taxonomy was assigned using the SILVA database (v. 138.1). No effect of breed or parity was observed on alpha (α; Shannon) diversity and community composition. The mean Shannon score was 3.33 (SE 0.14), indicating a diverse community within sample. A total of 681 genus-level amplicon sequence variant (ASV) groups were identified prior to filtering for relative abundance (RA) of >0.05%. Nineteen bacterial genera were identified as core. The predominant bacterial phyla observed were Bacillota, Pseudomonadota, and Actinomycetota. Community membership consisted of common gut commensals, with many members exhibiting diverse metabolic functions. Within the archaeal community, Methanobrevibacter had the highest RA, accounting for 85.99%. No observed differences between breeds suggests that farm origin may be more influential than breed on microbiota composition. The presence of archaea and strict anaerobes highlights the need to investigate the existence of an entero-mammary pathway in cattle. This is the first study jointly characterising bacteria and archaea in colostrum from different breeds from the same dairy herd under pasture-based conditions. The diverse bacterial community observed warrants further investigation into its role in calf health in early life. Specific microbes, like Lachnospiraceae, should be investigated for their potential in the development of probiotics and preventative practices for better calf health.},
}

*Colostrum/microbiology
Animals
Cattle
*Archaea/genetics/classification/isolation & purification
Female
*Bacteria/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Dairying
Pregnancy

@article {pmid41166275,
year = {2025},
author = {Kašperová, B and Mego, M and Čierniková, S and Ševčíková, A and Kašperová, S and Vranovský, A and Drgoňa, L},
title = {Nutrition of patients undergoing haematopoietic stem cell transplantation.},
journal = {Klinicka onkologie : casopis Ceske a Slovenske onkologicke spolecnosti},
volume = {38},
number = {5},
pages = {345-357},
doi = {10.48095/ccko2025345},
pmid = {41166275},
issn = {1802-5307},
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Nutritional Status ; *Malnutrition/etiology ; },
abstract = {BACKGROUND: Haematopoietic stem cell transplantation is associated with increased demands for adequate caloric intake and heightened risk of macronutrient and micronutrient depletion. Carbohydrates, proteins, and fats represent a key source of energy and structural components for transplanted patients, who often have limited oral intake because of mucositis and loss of appetite and increased nutritional requirements due to catabolism, inflammation, and tissue regeneration. Deficiencies in vitamins and trace elements occurring in some patients play a crucial role in enzymatic reactions, antioxidant defense, immune function, and tissue repair. Preparative regimen also causes damage of the intestinal mucosa and, in combination with antibiotic therapy, reduces the diversity of the microbiome. According to the latest evidence, patient nutrition has an impact on the short- and long-term outcomes of transplantation. Recognition of malnutrition and catabolism in these patients is difficult in routine practice; closer analysis of body composition and early intervention by a clinical nutritionist may be helpful. Adequate nutrient replacement is an important aspect of maintaining nutritional balance and good recovery.

AIM: The aim of this article is to provide an overview of nutrition, its specific components and nutritional disorders in oncology patients, as well as to summarize specific complications of aggressive treatment in patients undergoing hematopoietic stem cell transplantation and underline the need for early nutritional intervention in this group of patients.},
}

Humans
*Hematopoietic Stem Cell Transplantation/adverse effects
*Nutritional Status
*Malnutrition/etiology

@article {pmid41166162,
year = {2025},
author = {McMahan, RH and Najarro, KM and Giesy, LE and Evans, MR and Schnabl, B and Orlicky, DJ and Frank, DN and Kovacs, EJ},
title = {Intestinal REG3G Protects Against Gastrointestinal Dysfunction in a Murine Model of Ethanol Intoxication and Burn Injury.},
journal = {Shock (Augusta, Ga.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/SHK.0000000000002737},
pmid = {41166162},
issn = {1540-0514},
abstract = {Nearly half of the burn patients in the United States are under the influence of alcohol at the time of injury and alcohol intoxication is associated with poor clinical outcomes. Ethanol has been shown to worsen burn-induced intestinal dysfunction and inflammation, facilitating bacterial translocation from the intestine to the mesenteric lymph nodes and systemic circulation. Regenerating islet-derived protein 3-gamma (REG3G), an antimicrobial peptide crucial for maintaining intestinal homeostasis, protects mice from ethanol-induced bacterial translocation. In this study, we utilized a murine model to determine whether REG3G protects against the combined effects of acute ethanol exposure and burn injury. Mice with intestinal epithelial cell-specific overexpression of REG3G (Reg3g-Tg) were evaluated for gut barrier function, intestinal and hepatic inflammatory cytokines, and antimicrobial peptide expression after ethanol and burn injury. Additionally, we performed 16S rRNA gene sequencing of fecal microbiota. Our results demonstrate that ethanol exposure before burn injury downregulates the antimicrobial peptide REG3G in the ileum, when compared to burn alone. Intestine-specific overexpression of REG3G reversed several gastrointestinal effects of the combined injury, reducing intestinal inflammation and preventing bacterial translocation to the lymph nodes. Moreover, Reg3g-Tg mice exhibited reduced liver inflammation after combined injury, suggesting that improving intestinal function can also influence extra-intestinal organs. These findings highlight the therapeutic potential of REG3G in mitigating the effects of burn injury and alcohol intoxication.},
}

@article {pmid41166145,
year = {2025},
author = {Ding, W and Zhang, H and Wen, J and Xiong, G and Cheng, M and Liu, J and Zhao, Y and Miao, Q and Deng, H and Xu, Z and Mi, L and Tan, Z and Su, L and Long, Y and Ning, K},
title = {A multi-omics analysis reveals a gut microbiome-LPC metabolic axis driving postoperative inflammation in cardiopulmonary bypass patients.},
journal = {Shock (Augusta, Ga.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/SHK.0000000000002722},
pmid = {41166145},
issn = {1540-0514},
abstract = {BACKGROUND: Patients undergoing cardiac surgery with cardiopulmonary bypass (CSCPB) are at substantial postoperative risk, which may be influenced by alterations in gut microbiota and metabolites. The roles of these biological changes in postoperative outcomes remain inadequately explored.

METHODS: We collected 54 preoperative samples and 33 postoperative samples from 60 CSCPB patients. Metagenomic and metabolomic sequencing were performed to identify the gut microbiota and serum and fecal metabolites. We examined the dynamics pattern of these microbiota and metabolites, as well as their associations with the postoperative risk. Additionally, we developed a predictive model for postoperative risk based on preoperative microbiome and metabolome data.

RESULTS: We revealed significant alterations of gut microbiota (P = 0.012), serum metabolites (P = 3.50e-10) and fecal metabolites (P = 0.0081) in patients following CSCPB, among which lysophosphatidylcholines (LPCs) exhibited notable changes. Particularly, we identified a potential regulatory function of the microbiota on LPC metabolism, which further influence the postoperative risk. The predictive model for ICU stay duration achieved a mean absolute error (MAE) of 1.27 days and an R² of 0.63, suggesting its utility in assessing postoperative risk. Also, our study provides a valuable resource (catalogue GM3C) for further investigation into potential medical targets in CSCPB patients, comprising more than 2,000 metagenome-assembled genomes and 3 million unigenes.

CONCLUSIONS: Our study reveals that the gut microbiome and LPC-centered metabolism form a functional network influencing postoperative risk in CSCPB patients. These findings underscore the role of gut-derived signals in modulating non-infectious inflammatory responses and host imbalance, offering a multi-omics framework for decoding systemic complications beyond classical sepsis paradigms.

TRIAL REGISTRATION: ClinicalTrials.gov (NCT04032938). Registered 25 July 2019, https://clinicaltrials.gov/study/NCT04032938#study-record-dates.},
}

@article {pmid41165913,
year = {2025},
author = {de Farias, BO and Dos Santos Lopes, E and Pereira, BC and Pimenta, RL and Parente, CET and Seldin, L and Saggioro, EM},
title = {Poultry slaughterhouse wastewater as a driver of bacterial community shifts and the spread of antibiotic resistance genes in aquatic ecosystems.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {11},
pages = {1268},
pmid = {41165913},
issn = {1573-2959},
mesh = {*Wastewater/microbiology ; Animals ; *Abattoirs ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Poultry ; Genes, Bacterial ; Waste Disposal, Fluid ; RNA, Ribosomal, 16S ; Environmental Monitoring ; Anti-Bacterial Agents ; *Water Microbiology ; Microbiota ; },
abstract = {Poultry slaughterhouse wastewater (PSW) is a source of environmental pollutants, harboring pathogens and antibiotic resistance genes (ARGs). This study aimed to assess the effects of conventional biological treatment of PSW on the bacterial community and its efficiency in removing ARGs, as well as to evaluate the impact of its discharge on the receiving river. Samples were collected from raw sewage, treated effluent, and upstream and downstream river sites. Total metagenomic DNA was extracted for real-time PCR quantification of 16S rRNA, yccT gene (Escherichia coli), and ARGs, which were selected based on their ability to confer resistance to clinically relevant antibiotics and their prevalence in poultry-associated environments, including resistance to tetracyclines (tetM), beta-lactams (blaTEM), sulfonamides (sul1), and quinolones (qnrS). Amplicon sequencing of 16S rRNA V3-V4 region was used to assess bacterial community structure. Treated effluent significantly altered the downstream microbiome, reducing bacterial richness by up to 72.3% and diversity by 25.4%. Effluent-associated phyla such as Pseudomonadota (37%), Bacillota (28%), and Bacteroidota (26%) became dominant in the downstream river samples. Enterobacterales increased after treatment, and E. coli increased by 2.93 logs downstream. All ARGs increased after treatment and remained elevated downstream, with qnrS and sul1 rising by 3.77 and 3.87 logs, respectively. These findings highlight PSW treatment plants as a potential point of selection and dissemination of antimicrobial resistance (AMR)-related bacteria and genes. Inefficient treatment contributes to shifts in river bacterial communities and the spread of AMR.},
}

*Wastewater/microbiology
Animals
*Abattoirs
*Drug Resistance, Microbial/genetics
Bacteria/genetics
Poultry
Genes, Bacterial
Waste Disposal, Fluid
RNA, Ribosomal, 16S
Environmental Monitoring
Anti-Bacterial Agents
*Water Microbiology
Microbiota

@article {pmid41165889,
year = {2025},
author = {Sternau, M and Czajkowski, M and Błaczkowska, A and Żawrocki, A and Dolny, M and Matuszewski, M},
title = {Penile microbiome in histopathologically confirmed lichen sclerosus: a comparative study of urethral and preputial swabs.},
journal = {World journal of urology},
volume = {43},
number = {1},
pages = {653},
pmid = {41165889},
issn = {1433-8726},
mesh = {Humans ; Male ; *Lichen Sclerosus et Atrophicus/microbiology/pathology ; *Microbiota ; Prospective Studies ; *Urethra/microbiology ; Adult ; Middle Aged ; *Foreskin/microbiology ; *Penile Diseases/microbiology/pathology ; Young Adult ; },
abstract = {PURPOSE: The study examines the microbial compositions of patients with lichen sclerosus (LS) compared to control group, and individuals with other penile conditions. The aim is to address the critical question regarding the etiology of penile LS and to explore the potential involvement of the microbiome in its pathogenesis.

METHODS: In this prospective single-centre study, 73 uncircumcised male patients undergoing circumcision for phimosis were enrolled between January 2023 and April 2024. Foreskin and urethral swabs were obtained prior to surgery to isolate Candida, aerobic, and anaerobic microorganisms and sexually transmitted pathogens. Patients were categorised into LS (n = 44) and non-LS (n = 29) groups based on histopathological findings. Additionally, a control group, which consisted of patients with healthy foreskin, has been specified to conduct further analysis.

RESULTS: No statistically significant differences were observed in the prevalence of specific bacterial or viral pathogens between the LS and non-LS groups and between the LS/non-LS and control group. The most common commensal organisms were Staphylococcus coagulase-negative (48% and 34% respectively) and Corynebacterium spp. (27% and 17% respectively), whereas Enterococcus faecalis (14%) and Escherichia coli (16%) were the most frequent pathogens in LS group, and Streptococcus agalactiae (21%) was the most abundant pathogen in non-LS group. HPV was detected in 5% of patients with LS and in 14% of patients without LS. There were no statistically significant differences in CRP levels and BMI. In exploratory multivariable models adjusting for age and BMI, the presence of Streptococcus agalactiae was associated with lower odds of LS (OR 0.19; 95% CI 0.04-0.92; p = 0.04; FDR = 0.07); however, given limited power, these results should be interpreted cautiously.

CONCLUSIONS: Our study demonstrated no significant association between specific microbial or viral profiles and penile lichen sclerosus. However, due the fact that the culture-based approach employed in this study may underestimate the diversity of the penile microbiome, further research is warranted.},
}

Humans
Male
*Lichen Sclerosus et Atrophicus/microbiology/pathology
*Microbiota
Prospective Studies
*Urethra/microbiology
Adult
Middle Aged
*Foreskin/microbiology
*Penile Diseases/microbiology/pathology
Young Adult

@article {pmid41165775,
year = {2025},
author = {Dohadwala, S and Shah, P and Farrell, MK and Politch, JA and Marathe, J and Costello, CE and Anderson, DJ},
title = {Sialidases derived from Gardnerella vaginalis and Prevotella timonensis remodel the sperm glycocalyx and impair sperm function.},
journal = {Glycobiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/glycob/cwaf067},
pmid = {41165775},
issn = {1460-2423},
abstract = {Bacterial vaginosis (BV), a dysbiosis of the vaginal microbiome, affects approximately 30% of women worldwide (up to 50% in some regions) and is associated with several adverse health outcomes including preterm birth and increased incidence of sexually transmitted infections (STIs). BV-associated bacteria such as Gardnerella vaginalis and Prevotella timonensis damage the vaginal mucosa through the activity of sialidase enzymes that remodel the epithelial glycocalyx and degrade mucin glycoproteins. This damage may contribute to adverse health outcomes. However, whether BV-associated glycolytic enzymes also damage sperm has not yet been determined. Here, we show that sialidase-mediated glycocalyx remodeling of human sperm increases sperm susceptibility to damage and adversely affects their function in vitro. Specifically, we report that sperm motility was not adversely affected by sialidase treatment, but desialylated human sperm demonstrate increased susceptibility to agglutination and complement-mediated cytotoxicity as well as impaired transit through cervical mucus. Our results demonstrate mechanisms by which BV-associated sialidases affect sperm survival and function and potentially contribute to adverse reproductive outcomes such as infertility.},
}

@article {pmid41165608,
year = {2025},
author = {Velten Mendes, M and Lima, TC and Amormino, MS and de Oliveira, JS and Barroso, FLA and Boudry, G and Moreira-Júnior, RE and Brunialti-Godard, AL},
title = {Predicted functional alterations in colonic microbiota metabolism underlie ethanol consumption and preference behavior in mice.},
journal = {Alcohol, clinical & experimental research},
volume = {},
number = {},
pages = {},
doi = {10.1111/acer.70165},
pmid = {41165608},
issn = {2993-7175},
support = {406958/2022//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; //Pró-Reitoria de Pesquisa, Universidade Federal de Minas Gerais/ ; //Instituto Nacional de Ciências e Tecnologia sobre Substâncias Psicoativas/ ; //Pós-Graduação em Genética (ICB/UFMG)/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; APQ-03984-24//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; APQ-045517-22//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; },
abstract = {BACKGROUND: Alcohol use disorder (AUD) is a complex condition affecting several body systems. Gut microbiota alterations, intestinal-barrier disruption, and the consequent translocation of metabolites foster chronic inflammation, lower short-chain fatty acid (SCFA) output, and depleted beneficial bacteria may contribute to transcriptional, epigenetic, and metabolic changes that influence ethanol preference.

METHODS: Two experimental phases were used. T1 (8 weeks): mice received either the American Institute of Nutrition standard diet (AING) or a high-sugar-butter (HSB) diet. T2 (4 weeks): HSB animals switched to AING (SWITCH), while AING mice maintained the same diet. Each diet arm was split into ethanol (EtOH; free access to 10% ethanol) or H2O, generating four groups (AING + H2O, AING + EtOH, SWITCH + H2O, and SWITCH + EtOH). Sample processing involved colonic-content collection, 16S rRNA sequencing, microbiome profiling, functional inference, metabolic-network analysis, and SCFA/amino acid quantification.

RESULTS: SWITCH + EtOH mice displayed high ethanol consumption and preference, whereas AING + EtOH mice showed ethanol aversion. Their colonic microbiota differed markedly; amino acid metabolism fell, secondary bile acid synthesis rose, and SCFA production dropped in SWITCH + EtOH animals. Direct measurements confirmed significant reductions in butyrate, acetate, propionate, and selected amino acids. Network analysis revealed enrichment of bacterial metabolism, oxidative stress, and dopamine pathway genes.

CONCLUSIONS: Diet-induced dysbiosis, reflected in shifts in microbiota-derived metabolites, was associated with excessive alcohol intake; the metabolites identified can represent potential therapeutic targets for AUD.},
}

@article {pmid41165420,
year = {2025},
author = {Gonçalves, IC and Pontes, A and Gonçalves, C and Sá-Nogueira, Id},
title = {FrlP, an ABC type I importer component of Bacillus subtilis: regulation and impact in bacterial fitness.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0032025},
doi = {10.1128/jb.00320-25},
pmid = {41165420},
issn = {1098-5530},
abstract = {Bacillus subtilis is able to catabolize fructosamines, also known as Amadori rearrangement products. The frlBONMD-frlP operon mediates this process and is subjected to specific and global regulation. Although the degradation pathway favoring α-glycated amino acids is known, the mechanisms of substrate uptake have remained unclear. In this study, mutagenic and functional analyses revealed that FrlONM, a type I ABC importer, along with the nucleotide-binding domain (NBD) FrlP, is required for the uptake of fructosevaline. Transcriptional and translation frlP-lacZ fusions indicated that frlP is induced by fructosevaline and negatively regulated by the FrlR repressor. In addition, we show that MsmX, a multitask NBD of B. subtilis, is also able to serve as an energy motor of this type I ABC importer and that its presence alongside FrlP is vital for optimal growth on fructosevaline. To address the physiological significance of this functional redundancy, we assessed the distribution of ABC type I NBDs FrlP and MsmX across the Bacillaceae family. MsmX is homogeneously distributed in the Bacillaceae family tree, while FrlP is restricted to the Bacillus subtilis group, suggesting that the presence of FrlP together with other components of the fructosamines operon is important for bacterial fitness in plant-associated ecological niches.IMPORTANCEBacillus subtilis is widely applied in the industry as a microbial cell factory, as a biofertilizer for sustainable agriculture, in the animal feed industry and as human probiotic. In its natural environment, B. subtilis helps to shape the gut microbiome and the phytomicrobiome. Fructosamines, or Amadori rearrangement products, are ubiquitously found in nature and serve as precursors of toxic cell end-products implicated in the pathology of human diseases. This study provides a solid contribution to a deep knowledge of transport mechanisms, genetic regulation, and physiological relevance of fructosamines utilization in B. subtilis. Moreover, it highlights an unusual strategy to adapt to alterations in nutrient availability by swapping the energy providing domain of ABC transporters.},
}

@article {pmid41165402,
year = {2025},
author = {Nakatani, H and Suetake, N and Hori, K},
title = {Antimicrobial-producing bacteria from fish epidermal mucus alter the fish epidermal bacterial flora and host resistance to infection.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0145025},
doi = {10.1128/aem.01450-25},
pmid = {41165402},
issn = {1098-5336},
abstract = {The emergence of antimicrobial-resistant bacteria in aquaculture has raised the need for alternative strategies to control fish infections. Antimicrobial-producing bacteria have been explored as probiotics or biocontrol agents, but their mechanisms of action and impact on host-associated microbiota remain poorly understood. Here, we identified Pseudomonas mosselii KH-ZF1, a bacterium isolated from fish epidermal mucus, as a producer of antimicrobial substances. When applied to zebrafish, strain KH-ZF1 transiently adhered to the epidermal mucus and altered the composition of the skin microbiota. Under an appropriate administration condition, strain KH-ZF1 treatment significantly improved survival in zebrafish infected with Yersinia ruckeri and suppressed pathogen growth on the skin surface. However, in the absence of strain KH-ZF1 or inappropriate conditions, Y. ruckeri dominated the epidermal bacterial community. The antimicrobial compound produced by strain KH-ZF1 was identified as Fluviol C, a pigmented metabolite previously reported from Pseudomonas fluorescens. Fluviol C inhibited the growth of multiple fish pathogens at experimentally determined concentrations (0.5-32 µg/mL) but exhibited toxicity to zebrafish even below its minimum inhibitory concentration. Intriguingly, fluviol C, at sub-inhibitory levels, induced bacterial substitution in the epidermal microbiota, mimicking the effects of strain KH-ZF1. These findings demonstrate that strain KH-ZF1 alters host resistance to infection by promoting bacterial substitution on the fish skin by producing fluviol C. Our study highlights a microbiota-mediated mechanism by which antimicrobial-producing bacteria can control infection through the fish epidermis, suggesting a potential microbiota-mediated approach for disease control in aquaculture.IMPORTANCEWe show that bacteria producing antibacterial substances, isolated from fish skin mucus, can inhibit percutaneous infections in aquatic environments. These bacteria effectively altered the skin mucus bacterial flora and suppressed pathogen growth. Fish skin acts as a barrier against infections, with its microorganisms being considered to play a crucial role in prevention. Our study highlighted the potential use of these specific microorganisms in the fish skin mucus as a novel fish disease control strategy. By targeting fish skin mucus bacteria that produce antimicrobial substances, we could develop a new approach to managing diseases in aquaculture, such as probiotics for fish skin. This research underscores the importance of studying fish epidermal microorganisms for innovative disease management.},
}

@article {pmid41165394,
year = {2025},
author = {Rozo-Lopez, P and Torres, V and Torres, J and Drolet, BS and Käfer, S and Parker, BJ},
title = {Heritable viral symbionts in the family Iflaviridae are widespread among aphids.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0160625},
doi = {10.1128/aem.01606-25},
pmid = {41165394},
issn = {1098-5336},
abstract = {UNLABELLED: Heritable microbes shape host phenotypes and serve as important drivers of evolution. While interactions between insects and bacterial symbionts have been extensively studied, the prevalence and evolution of insect-viral symbioses remain poorly understood. We discovered multiple new species of iflaviruses in aphids, an important model for research on symbiosis, and found these microbes to be widespread across aphid species. We show that iflaviruses are persistently maintained in asexual host lines without apparent fitness costs while being transmitted vertically from mothers to offspring. Using field data and phylogenetic evidence, we found that aphid iflaviruses move horizontally among host species, but laboratory experiments showed that horizontal transmission does not result in persistent infections. Using quantitative PCR and immunohistochemistry, we discovered that viral infections localize in the host fat bodies and developing embryos. Surprisingly, we also found viral infections inside bacteria-housing cells called bacteriocytes, along with a positive correlation between viral and bacterial symbiont density. Together, our work suggests that iflaviruses are widespread heritable symbionts in aphids.

IMPORTANCE: In recent years, the rise of metatranscriptome sequencing has led to the rapid discovery of novel viral sequences in insects. However, few studies have carefully investigated the dynamics of insect-virus interactions to produce a general understanding of viral symbiosis. Aphids are an important model for understanding the evolution and molecular basis of symbiosis, but whether viruses are forming persistent symbiotic relationships with aphids remains unclear. Here, we show that heritable iflaviruses are a widespread but previously unrecognized part of the aphid heritable microbiome. Aphid iflaviruses are transmitted alongside bacteria from mothers to offspring, potentially via specialized bacteriocytes that house symbiotic microbes. Our findings suggest that aphids establish persistent relationships with iflaviruses and are likely coevolving with these viral symbionts.},
}

@article {pmid41165341,
year = {2025},
author = {Gallardo-Cartagena, JA and German-Quiñones, DLG and Rosas-Benancio, FG and Tafur, KT and Velásquez-Velásquez, DR and Cabello, R and Konda, KA and Celum, C and Sanchez, JL},
title = {High Willingness to Use and Recommend Doxycycline Postexposure Prophylaxis for Bacterial STI Prevention in Peru.},
journal = {Sexually transmitted diseases},
volume = {},
number = {},
pages = {},
doi = {10.1097/OLQ.0000000000002268},
pmid = {41165341},
issn = {1537-4521},
abstract = {BACKGROUND: Bacterial sexually transmitted infections (STIs) remain prevalent among men who have sex with men (MSM) and transgender women (TGW) in Peru. Doxycycline postexposure prophylaxis (doxy-PEP) is a promising prevention strategy, but data from Latin America remain limited.

METHODS: We conducted two online surveys in Lima, Peru (September-October 2024). One assessed willingness to use doxy-PEP among MSM and TGW; the other assessed willingness to recommend doxy-PEP among healthcare providers (HCPs). Logistic regression evaluated correlates of high willingness.

RESULTS: Of 730 eligible MSM and TGW, 447 completed outcome measures. Overall, 82.1% expressed willingness to use doxy-PEP, 34.2% with high willingness. High willingness was associated with ≥5 anal sex partners in past three months (aOR 1.86; 95% CI 1.06-3.24), prior HIV preexposure prophylaxis (HIV-PrEP) use (aOR 2.56; 95% CI 1.40-4.71), living with HIV (aOR 2.74; 95% CI 1.44-5.24), and concern about needing a prescription (aOR 3.33; 95% CI 1.99-5.66). Concerns about side effects (aOR 0.55; 95% CI 0.31-0.98) and microbiome disruption (aOR 0.51; 95% CI 0.29-0.87) were negatively associated. Most participants preferred doxy-PEP over daily doxycycline (64.0% vs 28.6%). Among 132 HCPs, 54.5% were involved in HIV/STI care; 87.1% expressed willingness to recommend doxy-PEP, and 89.4% would do so if included in national guidelines. Limited diagnostic capacity and risk of unofficial use were most frequently endorsed concerns.

CONCLUSIONS: High willingness to use or recommend doxy-PEP was observed among clients and HCPs in Peru, providing evidence to guide integration into sexual health services in Latin America.},
}

@article {pmid41165334,
year = {2025},
author = {Horvath, M and Kang, HG and Wu, T-C and Aiken, E and Castaneda, DC and Akkurt, S and Marches, F and Anczuków, O and Palucka, K and Oh, J},
title = {Host-specific bacterial modulation of airway gene expression and alternative splicing.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0057725},
doi = {10.1128/msphere.00577-25},
pmid = {41165334},
issn = {2379-5042},
abstract = {The human microbiome varies extensively between individuals. While there are numerous studies investigating the effects of inter-individual differences on microbiome composition, there are few studies investigating inter-individual effects on microbial modulation of the host or host-specific effects. To address this knowledge gap, we colonized human bronchial epithelial air-liquid interface tissue cultures generated from six different adults with one of three phylogenetically diverse bacteria and compared how each microbe differentially modulated host gene expression in each of the six donors. Microbial treatment had the strongest effect on transcription, followed by donor-specific effects. Gene pathways differed markedly in their donor and microbe specificity; interferon expression was highly donor-dependent, while transcription of epithelial barrier and antibacterial innate immunity genes was predominantly microbially driven. Moreover, we evaluated whether microbial regulation of alternative splicing was modulated by the donor. Strikingly, we found significant nonredundant, donor-specific regulation of alternative splicing exclusively in the gram-positive commensal microbes. These findings highlight that microbial effects on the human airway epithelium are not only species-specific but also deeply individualized, underscoring the importance of the host context in shaping microbe-induced transcriptional and splicing responses.IMPORTANCEMicrobiota are integral regulators of host gene expression, utilizing diverse mechanisms that are shaped by the interplay between microbiome composition and inter-individual differences, i.e., host-specific factors. While previous studies have characterized inter-individual variation in microbiome composition and the effects of variable microbiome composition on the host, the extent to which host-specificity itself regulates host-microbe interactions remains poorly understood. In this study, we address this gap by characterizing changes in epithelial gene expression from six different human donors following colonization with one of three phylogenetically diverse bacteria. By systematically comparing donor-specific responses, we demonstrate that host specificity is a key determinant of the host transcriptional response to microbial colonization. Importantly, we demonstrate that the effects of host specificity are not uniform, but instead are dependent on the colonizing microbe. Our findings underscore the complexity of host-microbe relationships and establish host specificity as a significant factor shaping host-microbe interactions.},
}

@article {pmid41165314,
year = {2025},
author = {Nauwynck, W and Sakarika, M and Faust, K and Boon, N},
title = {Differential recovery of chain-elongating bacteria: comparing droplet, plating, and dilution-to-extinction methods.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0135625},
doi = {10.1128/msystems.01356-25},
pmid = {41165314},
issn = {2379-5077},
abstract = {Microbial chain elongation via reverse β-oxidation offers a more sustainable route to produce medium-chain fatty acids like caproate, commodity chemicals typically produced via (petro)chemical processes. Thermophilic anaerobic microbiomes allow production at a high rate and selectivity but remain poorly understood due to the limited cultivability of their members. To better access functional taxa from a thermophilic chain-elongating reactor community, we applied multiple isolation strategies: conventional anaerobic plating, dilution-to-extinction (DTE), droplet-based microfluidics, and fluorescence-activated cell sorting (FACS). We evaluated the taxonomic range and cultivation success of each method using 16S rRNA gene sequencing. Each method yielded a distinct subset of microbial taxa. While Clostridium acetireducens-related strains were consistently isolated across all strategies, key thermophilic chain elongators (e.g., Thermocaproicibacter melissae-like organisms) only appeared in DTE. Droplet microfluidics enriched the most unique taxa in total, mostly rare taxa, including Caproicibacter and Thermoanaerobacterium spp. Plating yielded the lowest diversity, recovering only dominant taxa. FACS-based approaches failed to yield isolates, likely due to stress during processing. Comparing droplet-based isolation to DTE revealed critical insights: although droplets offer higher throughput, which intrinsically increases the chance of capturing rare taxa, not all DTE-cultivated organisms grew in droplets. This suggests additional contributing factors (apart from an increased throughput), such as encapsulation stress and droplet-specific microenvironments. These findings clarify the advantages and limitations of droplet cultivation strategies, allowing a more informed application of these techniques to access the so-called "microbial dark matter."IMPORTANCEMany environmentally and industrially relevant microbes remain uncultured, limiting our ability to understand and use them. This is especially true in thermophilic anaerobic microbiomes, which are promising systems for producing sustainable chemicals from organic waste streams. In this study, we explored how different cultivation strategies influence which microbes can be isolated from a thermophilic chain-elongating reactor. By comparing traditional and novel methods, including droplet microfluidics, we showed that each method recovers a unique set of microbes. While droplet-based methods enable high sampling depth with minimal effort and excel at isolating rare microbes, we found that they also introduce clear biases, as certain organisms recovered by other methods did not grow in droplets. Our work highlights the importance of the cultivation method in isolation success and helps shine a light on the selective forces at play in droplet-based microbial isolation.},
}

@article {pmid41165307,
year = {2025},
author = {Wang, Y and Malmuthuge, N and Yao, J and Guan, LL},
title = {Revisiting cattle respiratory health: key roles of the gut-lung axis in the dynamics of respiratory tract pathobiome.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {},
number = {},
pages = {e0018025},
doi = {10.1128/mmbr.00180-25},
pmid = {41165307},
issn = {1098-5557},
abstract = {SUMMARYDespite the increasing preventative efforts (vaccines, hygiene, pre-conditioning), respiratory tract (RT) infections pose a significant challenge across mammalian species. Recently, there has been a greater emphasis on promoting healthy microbiome colonization to mitigate respiratory infection in humans and livestock species. In livestock animals, especially in cattle, RT microbiome research has mainly focused on characterizing the respiratory tract microbial community in healthy and sick animals, aiming to identify microbiota linked to disease or health status. However, this approach overlooked the dynamics of RT microbiome that comprises commensal opportunistic pathogens (an element of the pathobiome) contributing to the infection and disease pathogenesis. Moreover, there is a lack of attempts to evaluate the interactions among host immunity-microbiome-pathobiome during pathogenesis for the development of successful microbiome-based interventions to improve cattle respiratory health. Recent research has revealed new insights into the gut-lung axis (GLA) and the regulatory role of the gut microbiota in determining host susceptibility or resilience to respiratory infections. Therefore, this review aims to critically discuss the roles of RT microbiome (including pathobiome) and GLA in respiratory health, while elucidating the mechanisms driving the dynamic transition from a commensal state to pathogenic state during microbiome dysbiosis and immune dysregulation, and identifying microbiome targets for RT health improvement.},
}

@article {pmid41165062,
year = {2025},
author = {Senar, N and Zwinderman, AH and Hof, MH},
title = {Sparse Canonical Correlation Analysis for Multiple Measurements With Latent Trajectories.},
journal = {Biometrical journal. Biometrische Zeitschrift},
volume = {67},
number = {6},
pages = {e70090},
doi = {10.1002/bimj.70090},
pmid = {41165062},
issn = {1521-4036},
mesh = {*Biometry/methods ; Humans ; Correlation of Data ; Models, Statistical ; },
abstract = {Canonical correlation analysis (CCA) is a widely used multivariate method in omics research for integrating high-dimensional datasets. CCA identifies hidden links by deriving linear projections of observed features that maximally correlate datasets. An important requirement of standard CCA is that observations are independent of each other. As a result, it cannot properly deal with repeated measurements. Current CCA extensions dealing with these challenges either perform CCA on summarized data or estimate correlations for each measurement. While these techniques factor in the correlation between measurements, they are suboptimal for high-dimensional analysis and exploiting this data's longitudinal qualities. We propose a novel extension of sparse CCA that incorporates time dynamics at the latent variable level through longitudinal models. This approach addresses the correlation of repeated measurements while drawing latent paths, focusing on dynamics in the correlation structures. To aid interpretability and computational efficiency, we implement an ℓ 0 $\ell _0$ penalty to enforce fixed sparsity levels. We estimate these trajectories fitting longitudinal models to the low-dimensional latent variables, leveraging the clustered structure of high-dimensional datasets, thus exploring shared longitudinal latent mechanisms. Furthermore, modeling time in the latent space significantly reduces computational burden. We validate our model's performance using simulated data and show its real-world applicability with data from the Human Microbiome Project. This application highlights the model's ability to handle high-dimensional, sparsely, and irregularly observed data. Our CCA method for repeated measurements enables efficient estimation of canonical correlations across measurements for clustered data. Compared to existing methods, ours substantially reduces computational time in high-dimensional analyses as well as provides longitudinal trajectories that yield interpretable and insightful results.},
}

*Biometry/methods
Humans
Correlation of Data
Models, Statistical

@article {pmid41164979,
year = {2025},
author = {Zhang, M and Wang, R and Khan, RAA and Zhan, X and Ren, S and Jiang, H and Zheng, C and Wu, Y and Yang, F and Yu, X and Liu, T},
title = {Trichoderma asperellum FJ035 Restructure the Rhizosphere Microbiome to Control the Cucumber Fusarium Wilt.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70250},
pmid = {41164979},
issn = {1365-3040},
support = {//This study was supported by the PhD Scientific Research and Innovation Foundation of the Education Department of Hainan Province, the Joint Project of Sanya Yazhou Bay Science and Technology City, the Innovation Research Project of Graduate Students in Hainan Province, the Key Research and Development Program Project of Hainan Province, the Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture of Hainan University, and the National Natural Science Foundation of China./ ; },
abstract = {The rhizosphere microbial community serves as a protective barrier against soil-borne diseases. However, it is unclear how Trichoderma influences the rhizosphere microbial community to control cucumber Fusarium wilt (CFW). This study demonstrated that Trichoderma asperellum FJ035 effectively suppresses CFW under continuous cropping by altering the rhizosphere microbiome, as confirmed through microbiome transfer experiments. Amplicon sequencing combined with cultivation-based methods showed that T. asperellum FJ035 modifies the composition and abundance of cucumber rhizosphere microbial communities. Based on these findings, a synthetic consortium, TB11, was constructed containing T. asperellum FJ035 and 30 bacterial strains that effectively controlled CFW and promoted cucumber growth. We simplified this consortium to TB5, comprising six strains closely related to T. asperellum FJ035, with a 71.43% reduction in CFW and 54.69% increase in plant weight. Further investigation revealed that T. asperellum FJ035 promotes the colonisation of B5 in cucumber roots and forms a protective microbiota to resist Fusarium oxysporum infection. This study reported a novel mechanism by which T. asperellum FJ035 prevents and controls CFW by regulating native bacterial communities in the rhizosphere. Moreover, the construction of synthetic consortia is described as a sustainable strategy for healthy cucumber cultivation.},
}

@article {pmid41164885,
year = {2025},
author = {Hosseinkhani, F and Chevalier, C and Marizzoni, M and Park, R and Bos, S and Dunjko, AK and van Duijn, CM and Harms, AC and Frisoni, GB and Hankemeier, T},
title = {Plasma and feces multiomics unveil cognition-associated perturbations of chronic inflammatory pathways of the gut-microbiota-brain axis.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21},
number = {10},
pages = {e70844},
doi = {10.1002/alz.70844},
pmid = {41164885},
issn = {1552-5279},
support = {184.034.019//Dutch Research Council (NWO)/ ; 175.2019.032//Dutch Research Council (NWO)/ ; //Private Foundation of Geneva University Hospitals: A.P.R.A.-Association Suisse pour la Recherche sur la Maladie d'Alzheimer, Genève/ ; //Fondation Segré, Genève/ ; //Race Against Dementia Foundation, London, UK/ ; //Fondation Child Care, Genève/ ; //Fondation Edmond J. Safra, Genève/ ; //Fondation Minkoff, Genève/ ; //Fondazione Agusta, Lugano/ ; //McCall Macbain Foundation, Canada/ ; //Nicole et René Keller, Genève/ ; //Fondation AETAS, Genève/ ; //Clinical Research Center, University Hospital and Faculty of Medicine/ ; //Italian Ministry of Health (Ricerca Corrente)/ ; //Hôpitaux Universitaires de Genève/ ; 175.2019.032//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Feces/microbiology/chemistry ; Male ; Female ; *Dysbiosis/metabolism ; *Cognitive Dysfunction/metabolism/microbiology ; Aged ; *Inflammation/metabolism ; *Brain/metabolism ; Cytokines/blood ; Multiomics ; },
abstract = {INTRODUCTION: Gut-microbiota dysbiosis has been linked to cognitive decline. Given its role in metabolism, immunity, and environmental interactions, broader molecular signaling alterations are likely.

METHODS: We analyzed gut microbiota composition, plasma and fecal metabolites, and inflammatory cytokines across cognitive stages, from healthy controls to dementia.

RESULTS: Alpha diversity declined with increasing cognitive impairment severity. Short-chain fatty acid-producing Firmicutes and Bacteroidota decreased from 76% and 17% in controls to 59% and 11% in dementia, respectively. Proteobacteria (e.g., Escherichia-Shigella) rose from < 2% to 4%, and Verrucomicrobiota from 3% to 11%. Despite overall Firmicutes decline, Ruminococcus gnavus, a mucus-degrading species, increased in dementia. These shifts correlated with elevated plasma cytokines, suggesting a link between gut dysbiosis and systemic inflammation. Bacteria-associated metabolites, including bile acids, trimethylamine N-oxide, oxylipins, sugars, and fatty acids were significantly altered. Changes were seen as early as subjective cognitive decline.

DISCUSSION: Larger studies are needed to validate these findings and explore microbiome-based interventions.

HIGHLIGHTS: Examined gut microbiota, inflammation, and metabolic changes in cognitive impairment stages Early metabolic changes in feces detected before plasma alterations Observed shifts in gut microbiota and inflammation associated with cognitive decline Suggests potential for early biomarkers based on gut metabolites Calls for larger, longitudinal studies to validate findings.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Feces/microbiology/chemistry
Male
Female
*Dysbiosis/metabolism
*Cognitive Dysfunction/metabolism/microbiology
Aged
*Inflammation/metabolism
*Brain/metabolism
Cytokines/blood
Multiomics

@article {pmid41164876,
year = {2025},
author = {Chen, H and Lu, Z and Xiao, C and Wang, X and Xi, Y and Yan, Y and Zheng, JS and Chen, YM and Deng, K},
title = {Association Between Alternative Complement Pathway and Carotid Plaque and the Underlying Gut Microbial and Inflammatory Biomarkers: A Cohort Study.},
journal = {Arteriosclerosis, thrombosis, and vascular biology},
volume = {},
number = {},
pages = {},
doi = {10.1161/ATVBAHA.125.322968},
pmid = {41164876},
issn = {1524-4636},
abstract = {BACKGROUND: The alternative pathway (AP) plays a crucial role in triggering complement activation and promoting chronic inflammation. This study aims to investigate the longitudinal association between AP and atherosclerosis, and explore the potential role of gut microbiota and inflammatory factors in their association.

METHOD: This study was based on a 9-year prospective cohort of 3382 participants from Guangzhou, China (mean age±SD, 57.75±5.85 years; 68.8% female), with data on serum APACPs (AP-associated complement proteins) and carotid plaque (measured by ultrasound) repeatedly measured up to 3×. Baseline inflammatory markers were evaluated in 923 participants, and gut shotgun metagenome data were obtained from 1567 participants. Mendelian randomization analysis was performed using genome-wide significant genetic variants as instrumental variables to suggest potential causal associations.

RESULTS: Both longitudinal and prospective analyses consistently demonstrated positive associations between carotid plaque and 3 complement components: C3 (odds ratios [95% Cl] for the highest versus lowest quartiles, 1.36 [1.07-1.74] in longitudinal analysis and 1.29 [1.06-1.56] in prospective analysis), CFB (complement factor B; 1.36 [1.07-1.72] in longitudinal analysis and 1.39 [1.15-1.69] in prospective analysis), and CFH (complement factor H; 1.39 [1.10-1.76] in longitudinal analysis and 1.31 [1.07-1.61] in prospective analysis). Mendelian randomization analysis suggested a potential causal association between CFB and carotid plaque. Inflammatory factors (CRP [C-reactive protein] and IL-6 [interleukin-6]) and microbial species (Ruminococcus bromii, Roseburia hominis, Rothia mucilaginosa, Collinsella stercoris, Olsenella scatoligenes, and Bacteroides massiliensis) were significantly associated with both APACPs and carotid plaque (P<0.05). For example, butyrate-producing bacterium R bromii was inversely associated with CFB and carotid plaque (odds ratios [95% CI], 0.83 [0.79-0.88]) and may mediate the CFB-carotid plaque association (proportion mediated, 13.5%; P=0.005). Microbial risk score (weighted sum of selected microbial species; proportion mediated, 42.6%; P<0.001) and total immune factors (the sum of all inflammatory factors; proportion mediated, 19.0%; P=0.002) mediated the association between Total-APACPs (sum of standardized carotid plaque-related APACPs [C3, CFB, and CFH]) and carotid plaque.

CONCLUSIONS: Our study showed a negative association between the AP and carotid plaque in a longitudinal cohort. Gut microbiota and inflammatory biomarkers may provide mechanistic insights into the association between the AP and atherosclerosis. Our findings pave the way for the development of new therapeutic targets for atherosclerosis.},
}

@article {pmid41164761,
year = {2025},
author = {Su, D and Li, Q and Lai, X and Song, Y and Li, H and Ai, Z and Zhang, Q and Shao, W and Yang, M and Zhu, G},
title = {Correction: Sargassum pallidum reduces inflammation to exert antidepressant effect by regulating intestinal microbiome and ERK1/2/P38 signaling pathway.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1653830},
doi = {10.3389/fphar.2025.1653830},
pmid = {41164761},
issn = {1663-9812},
abstract = {[This corrects the article DOI: 10.3389/fphar.2024.1424834.].},
}

@article {pmid41164513,
year = {2025},
author = {Alsakr, A},
title = {Periodontal Diseases and Host Modulation Therapies.},
journal = {Journal of pharmacy & bioallied sciences},
volume = {17},
number = {Suppl 3},
pages = {S2052-S2054},
pmid = {41164513},
issn = {0976-4879},
abstract = {In periodontal diseases, bacteria and microbes serve as the primary pathogens that initiate the condition, while the host refers to the body that hosts these microorganisms. Host modulation therapy is a drug-based treatment that can be used along with systematic periodontal therapy to help the disease get better and stop tissue damage. There is a new way to treat periodontitis called "Host-Modulation Therapy" (HMT). It involves reducing the bacteria biofilm through daily good oral hygiene and regular scaling and root planing (SRP). Using host modulation therapies to lower inflammation, restore microbiome balance, and change the immune response of the host holds a lot of promise for better periodontal disease treatment. This review examines host modulation in treating and preventing periodontal diseases. The review encompasses a variety of studies that evaluate pharmaceutical agents, probiotics, and immunomodulatory methods.},
}

@article {pmid41164408,
year = {2025},
author = {Staab, S and Mayer, KI and Cárdenas, A and Peixoto, RS and Schreiber, F and Voolstra, CR},
title = {UniCor and UniCorP: a novel metric and hierarchical feature selection algorithm for microbial community analysis.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf174},
pmid = {41164408},
issn = {2730-6151},
abstract = {The rapid advancement of technologies and methods in the life sciences has significantly increased the availability of big data, presenting new challenges for its analysis. Microbiome datasets, in particular, are characterized by extensive feature sets with defined but complex hierarchical structures that are often overlooked or underutilized. Here we introduce a novel metric, UniCor, to identify UNIquely CORrelated eNtities (UNICORNs) in quantitative datasets associated with continuous target variables. These datasets may include microbiome community structures in relation to environmental factors (e.g., temperature, pH, salinity) or biotic variables (e.g., thermal tolerance, oxidative stress). The UniCor metric combines the uniqueness of a given feature within a dataset with its correlation to a target variable of interest. To further enhance its utility, we developed a propagation algorithm (UniCorP), which exploits inherent dataset hierarchies, such as taxonomic levels in microbiome datasets, by selecting and propagating features based on their UniCor metric. Using bacterial community datasets with hierarchical taxonomic annotations and various continuous environmental variables, we demonstrate the ability of the novel metric to reduce features and increase predictive performance in cross-validated Random Forest Regressions. After propagating features with UniCorP and enriching the hierarchical levels with UNICORNs, the predictive performance consistently outperformed control trials for taxonomic aggregation, even at the least granular hierarchical level, allowing a substantial reduction of the feature space. We also compared the metric to existing methods for feature aggregation, showing that it offers stable, competitive predictive performance and feature reduction, within a simple and adaptable framework.},
}

@article {pmid41164407,
year = {2025},
author = {Ma, P and Mu, W and Wang, Y and Liu, Y and Zou, Y and Lu, Z and Pang, S and Pan, H and Zhang, L and Chen, L and Yang, Y and Lin, X and Kuang, Z and Luo, W and Liu, G and Wang, S},
title = {Blastocystis load mediates the gut microbiome associations with within-host diversity of Blastocystis in non-human primates.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf170},
pmid = {41164407},
issn = {2730-6151},
abstract = {Blastocystis is a prevalent gut eukaryote intricately associated with the gut microbiota. This genetically diverse protozoan exhibits significant intra-host subtype heterogeneity, yet the implications of this diversity for the host gut microbiome remain poorly understood. Here, we investigated the interactions between Blastocystis and gut microbiota in non-human primates at the level of subtypes, using a comprehensive investigation of gut microbiota for Blastocystis carriers of captive Macaca fascicularis (discovery cohort, n = 100) and Macaca mulatta (validation cohort, n = 26). We identified highly prevalent intra-host co-occurrence patterns of Blastocystis SSU rRNA-based subtypes, primarily dominated by Subtype 1 (ST1) or ST3. These patterns were associated with compositional and structural variations in the gut microbiome but were not significantly influenced by host covariates such as sex, age, or BMI. Specifically, Ruminococcaceae-enterotype was enriched in the patterns dominated by ST1, whereas Limosilactobacillus-enterotype was predominantly identified in the patterns dominated by ST3. Variance partitioning and mediation analyses revealed that the absolute abundance of Blastocystis was a critical determinant in elucidating this microbiota association across subtype concurrent patterns. In vivo experiments in a new cohort (n = 11) demonstrated that lactic acid bacteria, enriched in the Limosilactobacillus-enterotype, were sufficient to reduce Blastocystis load. We validated the strong association between gut microbiome composition and Blastocystis load in M. mulatta, confirming that specific microbial features could quantitatively predict Blastocystis status in both species. These findings highlight the close links of the gut microbiome with within-host subtype diversity patterns and absolute abundance of Blastocystis.},
}

@article {pmid41164342,
year = {2025},
author = {Harris, NC and Hallam, J},
title = {Individual variation within parasite communities of endangered African lions.},
journal = {Royal Society open science},
volume = {12},
number = {10},
pages = {250501},
pmid = {41164342},
issn = {2054-5703},
abstract = {Prey depletion and human-wildlife conflict threaten the critically endangered West African populations of lion (Panthera leo leo), which occupy less than 1.1% of their historic range in West Africa. These threats may alter behaviour through prey selection and affect exposure to parasites to compromise their health. We extracted DNA from faecal samples collected in four national parks in Benin, Burkina Faso and Senegal to characterize haemoparasites, nemabiome and microbiome. We used microsatellite markers to differentiate individuals and five primer sets to complete molecular analyses. From 20 individuals (12 males and 8 females), we found significant differences in the species richness and composition for all parasite groups across host populations and individual lions. We detected haemoparasites, including Babesia and Sarcocystis species, along with Blechomonas, a kinetoplastid, all of which raise potential health concerns. The nemabiome was dominated by Ancylostoma species (hookworms) with additional detections of lungworms from the genera Oslerus and Troglostrongylus. Significant interactions were found between population-level microbiome richness and both nemabiome and haemoparasite diversity. Our study provides the first effort to determine the parasite diversity among West African lion populations using non-invasive metabarcoding. Our findings highlight metabarcoding as a powerful tool to assess spatial variation in health and parasite diversity metrics for an endangered apex predator.},
}

@article {pmid41164289,
year = {2025},
author = {Mishra, P and Logan, AC and Prescott, SL},
title = {Reimagining criminal accountability: microbial and omics perspectives in the evolution of legal responsibility.},
journal = {Journal of law and the biosciences},
volume = {12},
number = {2},
pages = {lsaf022},
doi = {10.1093/jlb/lsaf022},
pmid = {41164289},
issn = {2053-9711},
abstract = {Recent advances in microbiome science and omics technologies are reshaping our understanding of human behavior, suggesting that microbial communities significantly influence cognition, impulse control, and aggression. Emerging studies in neuromicrobiology, including fecal transplant studies, are pointing toward a causal role for gut microbes and their metabolites in human cognition and behavior. This essay introduces the legalome-a framework integrating microbial perspectives, including microbiome and omics sciences, into the courts and larger criminal justice system. We argue that the legalome is on a trajectory that will move the field of neurolaw forward, and challenge traditional doctrines of mens rea and culpability. Drawing on recent court decisions related to auto-brewery syndrome, and neuro-microbiological research, we examine how subtle biological processes influence behavior in ways overlooked by current legal standards. Recent findings raise questions about criminal intent, biological determinism, and equitable access to scientific defenses. At the same time, emergent research also suggests potential for microbiome-based rehabilitative interventions. Despite methodological challenges, we advocate for interdisciplinary collaboration to harmonize biological research with legal principles, creating a more nuanced framework for justice in the twenty-first century. The legalome provides concrete implementation protocols and assessment tools that demonstrate practical utility for courts, practitioners, and policymakers.},
}

@article {pmid41164228,
year = {2025},
author = {Wei, S and Yin, H and Hu, X and Chi, Y and Zhang, L and Zhang, B and Qian, K and Xu, W},
title = {Detection of antimicrobial peptides from fecal samples of FMT donors using deep learning.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1689589},
pmid = {41164228},
issn = {2297-1769},
abstract = {INTRODUCTION: Antimicrobial peptides (AMPs) represent a class of short peptides that are widely distributed in organisms and are regarded as an effective means to tackle bacterial resistance, potentially functioning as substitutes for onventional antibiotics.

METHODS: We employed metagenomics in combination with deep learning to mine AMPs from the 120 fecal microbiota transplantation (FMT) donor metagenome. Subsequently, a comprehensive analysis of the candidate AMPs was conducted through metaproteomic cross-validation, solubility analysis, cross-validation with other prediction tools, correlation analysis, and molecular dynamics simulations. Finally, four candidate AMPs were selected for chemical synthesis, and experimental validation identified two with broad-spectrum antimicrobial activity. Furthermore, molecular docking was utilized to further analyze the antimicrobial mechanisms of the candidate AMPs.

RESULTS: Our approach successfully predicted 2,820,488 potential AMPs. After a comprehensive analysis, four candidate AMPs were selected for synthesis, two of which exhibited broad-spectrum antimicrobial activity. Molecular docking provided further insight into the binding mechanisms of these peptides.

DISCUSSION: This study demonstrates the feasibility of discovering functional AMPs from the human fecal microbiome using computational and experimental approaches, highlights the potential of mining novel AMPs from the fecal microbiome, and provides new insights into the therapeutic mechanisms of FMT.},
}

@article {pmid41163934,
year = {2025},
author = {Jafari, M and Alipour, M and Zamani, S and Mohtasham Amiri, A and Pourabbas, P and Hasannejad-Bibalan, M},
title = {Probiotics as a Complementary Medicine in Neurologic Disorders.},
journal = {Health science reports},
volume = {8},
number = {11},
pages = {e71422},
pmid = {41163934},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: Today, neurological and neuropsychiatric disorders, including depression, anxiety, Parkinson's disease (PD), Alzheimer's disease (AS), autism spectrum disorder (ASD), and multiple sclerosis (MS), contribute significantly to global disability and healthcare burden. Most current treatment options only provide symptomatic relief and are limited by challenges such as drug resistance, systemic side effects, and poor blood-brain barrier permeability. The growing interest in the gut-brain axis has encouraged exploration of the gut microbiota as a potential therapeutic target. Probiotics-live microorganisms that may confer health benefits to the host-have been proposed to modulate the gut-brain axis through immune, metabolic, and neurochemical pathways.

METHODS: In this narrative review, a targeted search was performed across multiple databases to identify relevant articles, from which the key relationships and strategies were extracted. Then, we represented the findings to provide a comprehensive overview of the topic and highlight emerging trends and gaps in the literature.

RESULTS: Emerging preclinical and clinical studies suggest that specific probiotic strains can improve neurological symptoms by reducing neuroinflammation, supporting gut barrier integrity, and influencing neurotransmitter production. However, findings remain heterogeneous due to strain specificity, individual microbiome diversity, and methodological differences across studies. Preclinical and clinical studies suggest that specific probiotic strains can improve neurological symptoms by reducing neuroinflammation, enhancing gut barrier integrity, and influencing neurotransmitter production. Evidence supports their potential as adjunctive treatments for major neurological and neuropsychiatric disorders, including depression, anxiety, ASD, PD, AD, and MS, particularly in patients with gut dysbiosis or gastrointestinal comorbidities. However, findings remain heterogeneous due to strain specificity, individual microbiome variability, and methodological differences across studies.

CONCLUSION: This brief review summarizes the current evidence on the use of probiotics in neurological disorders, discusses potential mechanisms of action, and highlights safety considerations and limitations. Future directions include personalized probiotic therapies, large-scale randomized controlled trials, and integration with conventional neurological therapies. Overall, probiotics could be a low-risk, complementary option in the evolving field of neurotherapy, but more rigorous evidence is needed before definitive clinical recommendations can be made.},
}

@article {pmid41163826,
year = {2025},
author = {Alrahimi, JS and Ahmed, FA and Haneef, AA and Atar, D},
title = {Integrative Perspectives on Atherosclerosis: From Molecular Mechanisms to Therapeutic Approaches.},
journal = {Saudi journal of medicine & medical sciences},
volume = {13},
number = {4},
pages = {239-252},
pmid = {41163826},
issn = {2321-4856},
abstract = {Atherosclerosis, a leading cause of cardiovascular disease, is a complex, multifactorial disorder involving lipid accumulation, chronic inflammation, immune dysregulation, and metabolic disturbances. Recent advances highlight critical roles for the Stimulator of Interferon Genes (STING) pathway, macrophage immunometabolism (the metabolic reprogramming of immune cells), oxidative DNA damage, neutrophil heterogeneity, sex disparities, and interactions with the gut microbiome and non-coding RNAs (molecules that regulate gene expression without coding for proteins). This integrative review synthesizes current knowledge from molecular, immunological, and epidemiological perspectives to illuminate key mechanisms in atherogenesis. We critically examine emerging mechanistic insights, including STING-mediated inflammation and macrophage metabolic reprogramming, and their roles in plaque initiation and progression. The review further evaluates novel therapeutic approaches, ranging from established lipid-lowering agents (e.g., statins, PCSK9 inhibitors, inclisiran, and bempedoic acid) to anti-inflammatory strategies (e.g., IL-1β and IL-6 inhibitors) and potential STING-targeted interventions. By integrating recent discoveries across basic and clinical science, this review emphasizes the need for personalized, multi-targeted therapies addressing inflammation, metabolism, and immune signaling. We propose a research roadmap prioritizing translational studies that link molecular mechanisms to clinical outcomes, ultimately aiming to improve prevention and management of atherosclerotic cardiovascular disease.},
}

@article {pmid41163804,
year = {2025},
author = {Zhang, S and Zhang, K and Zheng, CX and Gao, YF and Deng, GR and Zhang, X and Yuan, Y and Jia, T and Tang, SY and He, GX and Gong, Z and Zhao, N and Ma, B and Tian, H and Zhang, H and Li, Z and Di-Wu, YC and Liu, YH and Kong, L and Ma, J and Jin, Y and Sui, BD},
title = {D-Mannose Alleviates Type 2 Diabetes and Rescues Multi-Organ Deteriorations by Controlling Release of Pathological Extracellular Vesicles.},
journal = {Exploration (Beijing, China)},
volume = {5},
number = {5},
pages = {20240133},
pmid = {41163804},
issn = {2766-2098},
abstract = {Type 2 diabetes (T2D) is a prevalent metabolic disease inducing alterations of multiple organ systems with currently no cure. Extracellular vesicles (EVs) have been increasingly noticed as one critical paracrine communicator inducing insulin resistance and metabolic disorders in T2D, but clinically available pharmaceuticals for controlling pathological EV release is lacking. Here, we discover that the natural monosaccharide D-mannose exists with an altered level in the db/db mouse T2D model. Intriguingly, oral administration of D-mannose with the drinking water safely ameliorates diabetic symptoms in db/db mice. D-mannose administration does not critically regulate the gut microbiome and circulatory T lymphocytes in treating T2D, while administrated D-mannose rapidly accumulates in the liver, alleviates hepatic steatosis and rescues insulin resistance. Regarding the mechanism, the T2D pathological EVs released by macrophages are targeted and reduced by D-mannose, which metabolically inhibits CD36 expression and restores function of hepatocytes. Importantly, by regulating macrophage EV release, D-mannose administration reveals extra-hepatic benefits and retards diabetic bone loss. Taken together, our findings unveil D-mannose as a candidate T2D therapeutic and highlight sugars governing intercellular EV crosstalk, paving an avenue for pharmaceutical T2D approaches with amelioration of multi-organ deteriorations.},
}

@article {pmid41163404,
year = {2025},
author = {Ricks, KD and Raglin, SS and Kent, AD},
title = {Signatures of local nitrogen adaptation in the Brachypodium distachyon root microbiome.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70684},
pmid = {41163404},
issn = {1469-8137},
support = {NREC 2021-2-360190-334//Illinois Nutrient Research and Education Council/ ; ILLU-875-637//National Institute of Food and Agriculture/ ; DE-SC0018420//Biological and Environmental Research/ ; },
abstract = {Plants associate with diverse microbiomes that impact their fitness, yet the contribution of the microbiome to plant adaptation is uncertain. As plant recruitment of its microbiome can be both highly variable and genetically determined, we hypothesized this recruitment process may be the result of adaptive evolution, and contributing to plant local adaptation. We investigated the evolution and adaptive benefit of plant-microbiome recruitment by characterizing the rhizosphere communities across a genotypic panel of Brachypodium distachyon in a common garden experiment. By linking microbial communities to their host genotype's historic environment, we identified signatures of selection on plant-microbiome recruitment. Plant-microbiome composition was significantly correlated with the host genotype's historic environment, with enrichment of microbial traits aligned to local resource conditions. For example, genotypes from low-nitrogen environments recruited communities enriched in nitrogen acquisition traits. In a complementary experiment evaluating plant nitrogen response, these same genotypes were well-adapted to low-nitrogen environments, contingent on the presence of key nitrogen-cycling microbes. These results suggest that local adaptation in plants may partially be mediated by recruitment of beneficial microbiomes. This perspective suggests that plant adaptation may be an emergent property of host-microbe interactions, where evolutionary responses favor traits that promote recruitment of locally beneficial microbiomes.},
}