@article {pmid40851072,
year = {2025},
author = {Zhang, L and Wang, S and Wong, MCS and Mok, CKP and Ching, JYL and Mak, JWY and Chen, C and Huo, B and Yan, S and Cheung, CP and Chiu, EOL and Fung, EYT and Cheong, PK and Chan, FKL and Ng, SC},
title = {The resident gut microbiome modulates the effect of synbiotics on the immunogenicity after SARS-COV-2 vaccination in elderly and diabetes patients.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {171},
pmid = {40851072},
issn = {2055-5008},
support = {COVID19F07//Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; COVID19F07//Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; COVID19F07//Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; COVID19F07//Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; NCI202346//New Cornerstone Science Foundation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Aged ; *Synbiotics/administration & dosage ; SARS-CoV-2/immunology ; Female ; Male ; *COVID-19/prevention & control/immunology ; *COVID-19 Vaccines/immunology/administration & dosage ; Feces/microbiology ; Bifidobacterium ; *Immunogenicity, Vaccine ; *Diabetes Mellitus/immunology/microbiology ; Vaccination ; BNT162 Vaccine/immunology ; Middle Aged ; Antibodies, Viral/blood ; },
abstract = {The study aims to tackle the seed and soil microbiome and mechanisms that contribute to the effect of synbiotics in enhancing immunogenicity after SARS-CoV-2 vaccination in elderly and diabetic patients. Among 369 subjects who received 3 months of SIM01, a gut microbiota-derived synbiotic formula of three Bifidobacterium strains (B. adolescentis, B. bididum, and B. longum) or a placebo after the SARS-CoV-2 vaccines (mRNA vaccine BNT162b2 (Pfizer-BioNTech) or the inactivated vaccine Sinovac-CoronaVac), we performed metagenomic sequencing in stool samples of 280 vaccinees collected at baseline and 3-month postvaccination and metabonomic sequencing in 276 vaccinees collected at baseline and 1-month postvaccination. The open niche of autochthonous gut microbiota (lower levels of Bifidobacterium and decreased functional potential for carbohydrate metabolism) was associated with enhancing SIM01-contained species. The enrichment of three bifidobacterial species after 3 months of SIM01 intervention (BABBBL_fc) was positively correlated with the level of neutralizing antibodies to the BNT162b2 vaccine at 6-month postvaccination. The fold change of benzoic acid was positively correlated with BABBBL_fc in the BNT162b2 vaccinees, which was also implicated with SARS-CoV-2 surrogate virus neutralization test (sVNT)% levels at 1-month postvaccination. Importantly, SIM01 strain engraftment assessed by StrainPhlAn (A metagenomic strain-level population genomics tool) was associated with a higher fold change of three bifidobacterial species and could be predicted based on the baseline gut microbiome. Therefore, the resident gut microbiome affected the SIM01 engraftment, which was associated with the immunogenicity of SARS-CoV-2 BNT162b2 vaccines.},
}

Humans
*Gastrointestinal Microbiome/immunology
Aged
*Synbiotics/administration & dosage
SARS-CoV-2/immunology
Female
Male
*COVID-19/prevention & control/immunology
*COVID-19 Vaccines/immunology/administration & dosage
Feces/microbiology
Bifidobacterium
*Immunogenicity, Vaccine
*Diabetes Mellitus/immunology/microbiology
Vaccination
BNT162 Vaccine/immunology
Middle Aged
Antibodies, Viral/blood

@article {pmid40851038,
year = {2025},
author = {Binyamin, D and Turjeman, S and Asulin, N and Schweitzer, R and Koren, O},
title = {The microbiome is associated with obesity-related metabolome signature in the process of aging.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {173},
pmid = {40851038},
issn = {2055-5008},
support = {Adams Fellowships program//Israel Academy of Sciences and Humanities/ ; },
mesh = {Animals ; Mice ; *Aging/metabolism ; Female ; *Metabolome ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Obesity/microbiology/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Germ-Free Life ; Lipid Metabolism ; },
abstract = {Aging involves changes in the gut microbiome impacting health and longevity; however, the roles of specific microbial metabolites remain understudied. Here, we examine the microbial contribution to the metabolic profile in aged mice. Fecal samples were collected from female Swiss-Webster mice raised conventionally (Conv) or germ free (GF), at 8 weeks (young) and 18 (aged) months of age, and the microbiome and metabolome were characterized. Significant differences were observed in bacterial composition and its predicted functional activity between young and aged mice. Interestingly, we found more age-related differences in metabolite abundances among Conv mice than GF mice, highlighting the contribution of the microbiome to aging. Moreover, microbiome-associated metabolites, predominantly lipids, were higher in aged mice, with linoleic acid metabolism enriched in this group. Our study underscores a microbiome-dependent component to age-related metabolic changes in mice, particularly in lipid-associated pathways, and contributes to the growing body of literature linking gut microbiota to host metabolism in aging.},
}

Animals
Mice
*Aging/metabolism
Female
*Metabolome
*Gastrointestinal Microbiome
Feces/microbiology
*Obesity/microbiology/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
Germ-Free Life
Lipid Metabolism

@article {pmid40851026,
year = {2025},
author = {Yan, F and Chen, S and Xia, X and Fan, Y and Yu, S and Zhang, X and Chen, X},
title = {Microbiome characteristics associated with lymph node metastasis in laryngeal squamous cell carcinoma.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {31123},
pmid = {40851026},
issn = {2045-2322},
support = {2022FY100800//Science & Technology Fundamental Resources Investigation Program/ ; 2021-I2M-1-023, 2023-I2M-C&T-B-005//CAMS Innovation Fund for Medical Sciences (CIFMS)/ ; 2022-PUMCH-B-094//National High Level Hospital Clinical Research Funding/ ; },
mesh = {Humans ; *Lymphatic Metastasis/pathology ; *Microbiota ; *Laryngeal Neoplasms/microbiology/pathology ; Male ; Female ; Middle Aged ; *Carcinoma, Squamous Cell/microbiology/pathology ; Aged ; Lymph Nodes/microbiology/pathology ; RNA, Ribosomal, 16S/genetics ; *Squamous Cell Carcinoma of Head and Neck/microbiology/pathology ; },
abstract = {Lymph node (LN) metastasis is a key prognostic factor in laryngeal squamous cell carcinoma (LSCC). Emerging evidence implicates the role of the microbiome in cancer progression. This study aimed to investigate the microbial features associated with lymph node metastasis in LSCC and their potential for patient stratification. Using 16 S rRNA gene sequencing, we characterized the microbiome of tumor tissues, adjacent normal tissues, lymph nodes, and oral rinses from 108 LSCC patients, including 36 with (LN+) and 72 without (LN-) cervical LN metastasis. Microbial functional potential was predicted using PICRUSt2. Based on repeated stratified 3 cross-validation, random forest models were used to identify metastasis-associated genera. Significant microbial differences were observed between LN + and LN- tumor tissues, with Ralstonia enriched in LN + tumors and Fusobacterium more abundant in LN- cases. All genera detected in lymph nodes were also found in tumor tissues. Functional predictions revealed enrichment of lipid biosynthesis, energy metabolism, and cell wall synthesis pathways in LN + patients, particularly in tumor and oral rinse samples, with low intra-group variability. Classifiers based on tumor, lymph node, and oral microbiota demonstrated the ability to distinguish LN + from LN- patients. The lymph node-derived classifier achieved an accuracy of 84.31% (95% confidence interval [CI]: 81.76% - 86.85%), followed by the tumor-based model (AUC = 84.11%, 95% CI: 81.75% - 86.46%) and oral rinse classifier (AUC = 79.88%, 95% CI: 77.09% - 83.11%). A tumor-specific 17 genera panel showed a discriminative efficacy of 84.11% (95% CI: 81.75% - 86.46%) in tumor tissues. These findings suggest that microbiome alterations may be associated with lymph node metastasis in LSCC. In addition, the oral microbiome showed potential as a non-invasive tool for occult lymph node metastasis detection. However, these results are preliminary and require validation in larger, independent cohorts.},
}

Humans
*Lymphatic Metastasis/pathology
*Microbiota
*Laryngeal Neoplasms/microbiology/pathology
Male
Female
Middle Aged
*Carcinoma, Squamous Cell/microbiology/pathology
Aged
Lymph Nodes/microbiology/pathology
RNA, Ribosomal, 16S/genetics
*Squamous Cell Carcinoma of Head and Neck/microbiology/pathology

@article {pmid40851019,
year = {2025},
author = {El-Maradny, YA and Abouakkada, AS and Abbass, AAG and Abaza, AF and El-Fakharany, EM},
title = {Prebiotic properties and antioxidant effect of crude extracts and polysaccharides from Agaricus bisporus and Pleurotus ostreatus mushrooms.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {31113},
pmid = {40851019},
issn = {2045-2322},
mesh = {*Agaricus/chemistry ; *Pleurotus/chemistry ; *Prebiotics ; *Antioxidants/pharmacology/chemistry ; *Polysaccharides/pharmacology/chemistry ; *Complex Mixtures/pharmacology/chemistry ; Probiotics ; Lactobacillus acidophilus ; },
abstract = {Modifying the gut microbiome, also known as bacteriotherapy, is a key strategy that uses probiotics, prebiotics, or synbiotics to reduce inflammation and fight infection and colonization by pathogenic bacteria. Various food sources, particularly those rich in Lactobacillus species, are well-recognized for their probiotic properties. Edible mushrooms are rich with their nutrient-dense composition, including carbohydrates, proteins, fibers, minerals, vitamins, and lipids, which stand out as a promising bio-source for several biological uses. In this study, four probiotic strains were isolated and identified from food samples: Lactobacillus acidophilus (L. acidophilus), L. pentosus, L. plantarum, and L. paracasei. Then the prebiotic and antioxidant properties of crude and polysaccharide extracts were assessed from two edible mushrooms, Agaricus bisporus (brown) and Pleurotus ostreatus (oyster). Using the phenol-sulfuric acid method, the ethanol extract of P. ostreatus exhibited the highest yields of total carbohydrates and reducing sugars (6.14 and 3.15 mg/mL, respectively). Among the mushroom extracts, the polysaccharide from A. bisporus demonstrated the strongest radical scavenging activity (93.73%), with a half-maximal effective concentration (EC50) of 0.19 mg/mL, measured using the 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging method. The prebiotic properties of the mushroom extracts were evaluated by their ability to promote probiotic growth and inhibit pathogenic bacteria. The polysaccharide extracts from A. bisporus and P. ostreatus significantly stimulated the growth of L. paracasei (1.99 and 2.04 nm, respectively). Additionally, the cell-free supernatant from L. acidophilus cultured with the A. bisporus polysaccharide extract exhibited the highest antimicrobial activity, producing a 36.33 mm inhibition zone against the pathogen L. monocytogenes. These findings demonstrate that polysaccharides from A. bisporus and P. ostreatus are promising candidates for functional food development. These extracts offer a multifaceted approach to promoting gut health and reducing oxidative stress through selectively stimulating beneficial Lactobacillus species while inhibiting the growth of pathogens and exerting significant antioxidant effects.},
}

*Agaricus/chemistry
*Pleurotus/chemistry
*Prebiotics
*Antioxidants/pharmacology/chemistry
*Polysaccharides/pharmacology/chemistry
*Complex Mixtures/pharmacology/chemistry
Probiotics
Lactobacillus acidophilus

@article {pmid40850975,
year = {2025},
author = {Yeo, LF and Lee, AWY and Tee, PYE and Chin, JSF and Lee, BKB and Lim, J and Teo, SH and Pan, JW},
title = {Characterization of intra-tumoral microbiota from transcriptomic sequencing of Asian breast cancer.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {31147},
pmid = {40850975},
issn = {2045-2322},
mesh = {Humans ; *Breast Neoplasms/microbiology/genetics/pathology/immunology ; Female ; *Microbiota/genetics ; *Transcriptome ; Middle Aged ; Tumor Microenvironment/genetics/immunology ; Malaysia ; Asian People/genetics ; Gene Expression Profiling ; Adult ; Aged ; },
abstract = {The human microbiome has garnered significant interest in recent years as an important driver of human health and disease. Likewise, it has been suggested that the intra-tumoral microbiome may be associated with specific features of cancer such as tumour progression and metastasis. However, additional research is needed to validate these findings in diverse populations. In this study, we characterized the intra-tumoral microbiota of 883 Malaysian breast cancer patients using transcriptomic data from bulk tumours and investigated their association with clinical variables and immune scores. We found that the tumour microbiome was not associated with breast cancer molecular subtype, cancer stage, tumour grade, or patient age, but was weakly associated with immune scores. We also found that the tumour microbiome was associated with immune scores in our cohort using random forest models, suggesting the possibility of an interaction between the tumour microbiome and the tumour immune microenvironment in Asian breast cancer.},
}

Humans
*Breast Neoplasms/microbiology/genetics/pathology/immunology
Female
*Microbiota/genetics
*Transcriptome
Middle Aged
Tumor Microenvironment/genetics/immunology
Malaysia
Asian People/genetics
Gene Expression Profiling
Adult
Aged

@article {pmid40850684,
year = {2025},
author = {Lei, G and Han, Z and Wang, X and Malacrinò, A and Kang, T and Zhang, D and Zhang, J and Zhang, Z and Wu, H},
title = {Synthetic microbial communities rescues strawberry from soil-borne disease by enhancing soil functional microbial abundance and multifunctionality.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.08.040},
pmid = {40850684},
issn = {2090-1224},
abstract = {INTRODUCTION: Synthetic microbial communities (SynCom) contribute to mitigating soil-borne crop diseases while enhancing both crop quality and yield. However, relatively little research has been done on the intricate regulatory mechanisms of SynCom on the suppression of soil-borne diseases.

OBJECTIVES: We aimed to elucidate the dynamic regulatory mechanisms and legacy effects of a SynCom on the composition of soil functional microorganisms, soil multifunctionality and crucial functions, and the suppression of soil-borne diseases.

METHODS: We conducted an extensive series of experiments to assess the effect of a SynCom on the changes in the rhizosphere functional microorganisms and soil functions (e.g., multifunctionality, functionality of C, N, and P cycling) across six successive generations of strawberry in consecutive monoculture soils by employing amplicon metagenomics and transcriptome sequencing.

RESULTS: Our results showed that the SynCom increased the aboveground fresh biomass of strawberry by 31-70.3% and the fruit biomass by 171.39-280.71%, and decreased the Fusarium oxysporum abundance by 17.91-49.51% compared to the consecutive monoculture. The SynCom significantly enhanced the soil C cycling and P cycling function, and soil multifunctionality (SMF). SynCom treatment significantly increased the Shannon diversity index and relative abundances of potentially beneficial bacteria and consumer protistan communities, while exerted a significant inhibitory effect on the Shannon diversity index and relative abundances of fungal pathogen. SEM result showed that SynCom significantly affected SMF by influencing soil nutrients, the abundance and diversity of functional microbial community. Our result also showed that the SynCom established the positive legacy effects on the abundance of rhizosphere soil beneficial bacteria, strawberry biomass and plant disease resistance-associated pathways (phenylpropanoid biosynthesis pathway, alpha-linolenic acid metabolism pathway), and negative effect on the abundance of pathogenic F. oxysporum under the 7th generation of strawberry cropping.

CONCLUSION: Collectively, our study demonstrated the effectiveness of employing SynCom in mitigating soil-borne Fusarium oxysporum diseases by enhancing soil functional microbial abundance and soil multifunctionality.},
}

@article {pmid40850681,
year = {2025},
author = {Wei, Z and Gao, G and He, Q and Kwok, LY and Sun, Z},
title = {The gut-tumor connection: the role of microbiota in cancer progression and treatment strategies.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.08.038},
pmid = {40850681},
issn = {2090-1224},
abstract = {BACKGROUND: The tumor microenvironment (TME) has become a critical focus in the diagnosis and treatment of cancer. The involvement of the microbiome in tumor initiation and progression underscores its potential as a promising biomarker and therapeutic target. Furthermore, microorganisms in the gut and other ecological niches play pivotal roles in shaping cancer immune surveillance and modulating responses to immunotherapy, acting as key mediators connecting gut health to cancer progression. Thus, investigating the intricate interplay between the TME and gut microbiota could offer valuable insights to advance personalized cancer therapies.

AIM OF REVIEW: This comprehensive review explores the complex interactions between the gut microbiota, tumor-associated microbiota, and TME, examining their origins, diversity, connections, and therapeutic implications. We investigate the potential for gut microbiota to translocate to tumors, where they may directly impact the TME and influence cancer progression. We compile the current knowledge on the diversity of intratumoral microbiota across various cancer types and its effects on cellular, immune, and spatial heterogeneity within the TME. Furthermore, we assess the efficacy of various methods for characterizing and identifying intratumoral microbiome, emphasizing their importance in understanding their composition and function in the TME. We also explore the therapeutic potential of modulating the gut microbiota, highlighting strategies such as dietary interventions, fecal microbiota transplantation, probiotics, prebiotics, and synthetic biology approaches. We then address the challenges and future directions in this emerging field, emphasizing the need for standardized protocols, advanced sequencing technologies, and refined animal models to enhance our understanding of microbiota-cancer interactions. In conclusion, the gut microbiota represents a promising therapeutic target for cancer treatment. Harnessing the power of gut microbial modulation could lead to novel combinatorial strategies that improve clinical outcomes for cancer patients. Nevertheless, further research is essential to surmount existing challenges and translate these insights into impactful, personalized cancer therapies.},
}

@article {pmid40850636,
year = {2025},
author = {Płoszka, Z and Nowak, KH and Tischer, M and Michalik, A and Kolasa, MR and Łukasik, P},
title = {Dissecting multitrophic interactions: The relationships among Entomophthora, their dipteran hosts, and associated bacteria.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108425},
doi = {10.1016/j.jip.2025.108425},
pmid = {40850636},
issn = {1096-0805},
abstract = {Interactions with microorganisms across the parasite-mutualist continuum shape the biology of insects at all levels - from individual traits to populations to communities. However, the understanding of pathogens infecting non-model insect species in natural ecosystems, or their interactions with other insect-associated microorganisms, is fragmentary. Here, we tested a conceptually novel approach - the simultaneous sequencing of insect, fungal, and bacterial marker gene amplicons - as a means of dissecting interactions among entomopathogenic fungi in the genus Entomophthora and their dipteran hosts in South Greenland. We aimed to describe the taxonomic diversity of Entomophthora, their dipteran hosts, and the bacterial diversity within a set of field-collected dead insects exhibiting signs of Entomophthora infection. Across nine collected dipteran species, we identified multiple Entomophthora genotypes, with strong but not perfect patterns of host-specificity across the five targeted marker regions. Additionally, we found consistent differences in bacterial community composition among fungus-killed fly species and sampling sites. Our results substantially expand the knowledge of Entomopthora diversity and host associations while providing the very first insights into associated bacteria and their potential roles. We also conclude that multi-target amplicon sequencing can be a powerful tool for addressing broad questions about biological interactions in diverse natural communities.},
}

@article {pmid40850628,
year = {2025},
author = {Horrocks, V and Hind, CK and Sutton, JM and Tribe, RM and Mason, AJ},
title = {Metabolism of Lactobacillus and Gardnerella vaginalis in vaginal defined media.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {102991},
doi = {10.1016/j.anaerobe.2025.102991},
pmid = {40850628},
issn = {1095-8274},
abstract = {OBJECTIVES: This study evaluates how well a vaginal defined medium (VDM) replicates the in vivo metabolic behaviour of key vaginal microbiota members - Lactobacillus crispatus, L. jensenii, and diverse Gardnerella vaginalis isolates - compared to brain heart infusion (BHI) medium.

METHODS: We used [1]H NMR spectroscopy to characterise metabolic profiles during in vitro growth of Lactobacillus and Gardnerella species in VDM and BHI. Differences in metabolite production, growth, acidification, and carbohydrate utilisation were assessed.

RESULTS: Both L. crispatus and L. jensenii grow well in VDM, produce substantially more lactate than in BHI, and acidify the culture more strongly - better reflecting the low pH environment of Lactobacillus-dominant vaginal microbiota. In contrast, G. vaginalis grows less robustly in VDM than in BHI, though key metabolic traits such as the Bifidobacterium shunt and mixed acid fermentation (evidenced by formate production) are preserved. Notably, neither genus consume available glucose, yet still ferment carbohydrates, suggesting a metabolic preference for glycogen over glucose. Evidence of glucose release further indicates glycogen breakdown in culture.

CONCLUSIONS: VDM more accurately models the metabolic activity and environmental effects of vaginal Lactobacillus species than BHI, particularly in terms of acidification and lactate production. Although G. vaginalis growth is limited in VDM, its characteristic metabolic pathways remain evident. These findings underscore the value of VDM in modelling key metabolic features of the vaginal microbiota, especially under conditions where Lactobacillus dominate or Gardnerella is prevalent.},
}

@article {pmid40850579,
year = {2025},
author = {Chen, P and Yu, K and Yang, K and Zhang, D and Li, P and He, Y},
title = {Indole-3-acetic acid-mediated root exudates as potential inhibitors of antibiotic resistance genes in the rhizosphere microbiome: Mechanistic insights into microbial community assembly and resistome dissemination.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133191},
doi = {10.1016/j.biortech.2025.133191},
pmid = {40850579},
issn = {1873-2976},
abstract = {Although the threat of antibiotic resistance genes (ARGs) in agriculture to human health has raised concerns, there is still a lack of effective and environmentally friendly measures to mitigate antibiotic resistance. Indole-3-acetic acid (IAA) and root exudates are environmentally friendly natural substances. However, the development of technologies harnessing their potential to suppress agricultural ARGs remains unexplored. Here, IAA-mediated key root exudates, N-acetylserotonin and N-methyltryptamine, were found to effectively reduce ARGs in rhizosphere soil. They affected microbial community assembly and further shaped ARGs profiles. Additionally, they inhibited antibiotic-resistant bacteria, potentially suppressing the vertical transfer of ARGs. More importantly, N-acetylserotonin and N-methyltryptamine inhibited ARGs conjugative transfer through suppressing pili assembly and homologous recombination. Overall, IAA-mediated root exudates reduce ARGs in rhizosphere soil by influencing microbial community assembly and inhibiting ARGs transfer. This study provides inspiration for the development of technologies related to plant auxins and root exudates to reduce ARGs in agriculture.},
}

@article {pmid40850461,
year = {2025},
author = {Wang, H and Lim, JJ and Gu, H and Xia, Z and Cui, JY},
title = {Cadmium-induced gut dysbiosis precedes the onset of hippocampus-dependent learning and memory deficits in mice.},
journal = {Toxicology},
volume = {},
number = {},
pages = {154265},
doi = {10.1016/j.tox.2025.154265},
pmid = {40850461},
issn = {1879-3185},
abstract = {Cadmium (Cd) is a heavy metal recognized as a neurotoxicant, but the detailed mechanisms contributing to its neurotoxicity remain to be fully elucidated. The gut-brain axis-a bidirectional communication pathway between the gut microbiome and the central nervous system-has been implicated in various neurological disorders. Since Cd targets the gut microbiome, it is important to investigate whether this axis contributes to Cd-induced neurotoxicity. In this study, adult male mice were exposed to environmentally relevant levels of Cd (3mg/L) via drinking water for nine weeks. Cognitive function was assessed throughout the exposure period, and fecal samples were collected biweekly to track changes in the gut microbiome. We found that Cd exposure caused gut dysbiosis before the onset of cognitive deficits, with specific bacterial species correlating with impaired cognition. RNA sequencing revealed alterations in the expression of genes involved in cognition and neuroinflammation in the hippocampus. Additionally, Cd exposure reduced the expression of genes related to intestinal barrier integrity, increased levels of inflammatory cytokines, and altered the levels of neuroactive microbial metabolites. These findings suggest a critical role for the gut-brain axis in mediating Cd neurotoxicity and highlight the gut microbiome as a potential target for therapeutic strategies to prevent or mitigate Cd-induced cognitive decline.},
}

@article {pmid40850390,
year = {2025},
author = {Pang, Y and Thomas, ZO and Ayanruoh, LD and Enriquez, GH and Chrisman, LP and Hooper, MJ and Stagaman, E and McCool, M and Achmar No Advanced Degree, D and Rahman No Advanced Degree, S and Seed, PC and Budunova, IV and Green, SJ and Guitart, J and Burns, MB and Zhou, XA},
title = {Skin microbiota differs between Black and White patients with cutaneous T-cell lymphoma.},
journal = {Journal of the American Academy of Dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaad.2025.08.049},
pmid = {40850390},
issn = {1097-6787},
}

@article {pmid40850168,
year = {2025},
author = {Tomassini, L and Goracci, V and Onofri, M and Gambelunghe, C and Fedeli, P and Vanni, N and Guarino, M and Scendoni, R and Lancia, M},
title = {Microbial succession after death: genomic and culture-based insights from external sampling sites in forensic science.},
journal = {Legal medicine (Tokyo, Japan)},
volume = {78},
number = {},
pages = {102685},
doi = {10.1016/j.legalmed.2025.102685},
pmid = {40850168},
issn = {1873-4162},
abstract = {BACKGROUND: Post-mortem microbial communities (microbiota and microbiome) have emerged as promising tools for forensic investigations, particularly in estimating the post-mortem interval (PMI). However, experimental variability in sampling protocols, analytical methods, and reporting standards has limited the comparability and reproducibility of findings across studies.

METHODS: A systematic review was conducted in accordance with PRISMA guidelines to evaluate the current literature on human post-mortem microbiota and microbiome. Inclusion criteria focused on studies that examined microbial communities in human cadavers using culture-based techniques, next-generation sequencing (NGS), or both. Data were extracted regarding sample types, microbial targets, analytical methods, decomposition stages, insect activity, and study objectives.

RESULTS: A total of 24 studies were included, revealing substantial heterogeneity in methodological approaches. NGS techniques dominated recent literature, targeting bacterial 16S rRNA gene sequences to characterize microbial succession during decomposition. While some studies have shown promising correlations between microbial taxa and PMI, the inconsistent use of controls and variable decomposition conditions impeded cross-study comparisons. Culture-based approaches were generally limited to early investigations and provided narrower taxonomic resolution.

CONCLUSIONS: Despite encouraging results, the forensic application of post-mortem microbiome and microbiota remains hindered by methodological inconsistencies and a lack of standardization. Establishing unified protocols and adopting interdisciplinary approaches will be essential for validating microbial signatures as reliable forensic tools.},
}

@article {pmid40850119,
year = {2025},
author = {Ellwood, KM and Kramer, AE and Dutta, A},
title = {Age-driven changes in the layer hen reproductive microbiome are associated with lay performance.},
journal = {Poultry science},
volume = {104},
number = {11},
pages = {105703},
doi = {10.1016/j.psj.2025.105703},
pmid = {40850119},
issn = {1525-3171},
abstract = {Eggs are a globally important food source and integral to optimal poultry production. Understanding the microbial ecology of the hen reproductive tract is essential for improving both food safety and reproductive efficiency. While the oviduct has been shown to harbor a continuous microbial community, this study is the first to demonstrate the presence of microbiota on the hen ovary surface, suggesting that the ovary is an extension of the oviductal microbial continuum. In this study, the ovarian and oviductal microbiomes of white-leghorn hens from mid-lay (high laying) and post-lay (lower laying) cohorts were analyzed. Using 16S rRNA sequencing, we identified significant shifts in reproductive tract microbiota between 9- and 18-month-old hens, coinciding with changes in lay performance. Several differentially abundant genera, including Acinetobacter, Ligilactobacillus, Bacillus, and Akkermansia, are known to modulate steroid hormone metabolism, with age-related abundance changes suggesting potential effects on hormone-driven reproductive processes. Other genera such as Ruminococcus_torques_group, Mucispirillum, and Fusobacterium-not traditionally associated with reproductive hormone pathways-may influence laying efficiency through their roles in mucin degradation, immune modulation, and inflammation. Notably, Turicibacter, newly identified on the ovary, increased with age and negatively correlated with lay performance, raising questions about its role in bile acid metabolism and stress response within the hen reproductive tract. Collectively, these findings highlight the ovary as an active microbial niche influenced by age and suggest that both hormone-associated and mucosal-interactive microbes contribute to lay dynamics. This work opens new avenues for probiotic strategies targeting key genera to support hen fertility and egg production across the productive lifespan.},
}

@article {pmid40850001,
year = {2025},
author = {Huang, X and Hu, L and Sun, W and Shao, Z and Ma, W and Yuan, Q and Liu, J and Wu, D and Cheng, L and Li, H},
title = {Integrative analysis of gut microbiome and serum metabolomics explores the therapeutic mechanism of tongfeng qingxiao prescription in treating gouty arthritis.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {266},
number = {},
pages = {117121},
doi = {10.1016/j.jpba.2025.117121},
pmid = {40850001},
issn = {1873-264X},
abstract = {Gouty arthritis (GA), a metabolic inflammatory disorder, shows increasing global prevalence, especially in China. Conventional GA treatments often cause adverse reactions, necessitating alternative therapies. Tongfeng Qingxiao Prescription (TFQXP) demonstrates clinical efficacy in GA, though its mechanisms remain unclear. This research explored TFQXP's effects in GA rats using gut microbiome and serum metabolomics analyses. Sprague-Dawley rats (n = 36) were randomly divided into six groups: control, model, TFQXP low-dose, medium-dose, high-dose, and positive groups. GA was induced in all groups except the control group and confirmed via gait analysis and infrared thermal imaging. Inflammation was assessed by measuring ankle joint edema. Histopathology evaluated colon and ankle joint tissues, while transmission electron microscopy examined intestinal epithelium. Mucin 2 expression was analyzed via immunohistochemistry. Synovial TLRs/MyD88/NF-κB pathway components were evaluated using western blotting and qRT-PCR. Gut microbiota structure was assessed via 16S rDNA sequencing, while serum metabolites were analyzed using non-targeted metabolomics. Multi-omics correlation analyses explored gut microbiota-serum metabolite relationships. TFQXP appears to mitigate GA-induced synovial and cartilage damage by suppressing the TLRs/MyD88/NF-κB signaling pathway, resulting in downregulation of pro-inflammatory mediators. Furthermore, TFQXP promoted intestinal barrier repair, alleviated dysbiosis, and ameliorated metabolic pathway dysregulation. Thus, TFQXP may exert therapeutic effects on GA by modulating the "gut-joint" axis.},
}

@article {pmid40849910,
year = {2025},
author = {Weis, AM and Bauer, KM and Tang, WW and Stephen-Victor, E and Bell, R and Brown, DG and Ekiz, HA and Tran, V and Klag, KA and Swanson, EA and Barrios, L and Harwood, M and Hill, JH and Ost, KS and Gigic, B and Schneider, M and Ose, J and Hardikar, S and Toriola, AT and Shibata, D and Li, CI and Figueiredo, JC and Byrd, DA and Siegel, EM and Arnolds, K and Lozupone, C and Ulrich, CM and O'Connell, RM and Stephens, WZ and Round, JL},
title = {A capsular polysaccharide from a healthy human microbiota member activates a Lag-3-NK cell axis to restrain colon cancer and augment immunotherapy.},
journal = {Cell reports},
volume = {44},
number = {9},
pages = {116172},
doi = {10.1016/j.celrep.2025.116172},
pmid = {40849910},
issn = {2211-1247},
abstract = {Colorectal cancer (CRC) is increasing globally, making identification of preventative measures necessary. Transplantation of the microbiota from CRC and non-CRC patients into mice demonstrates that non-diseased individuals possess organisms that reduce tumor formation and highlights Bacteriodes uniformis as protective. B. uniformis is reduced in humans with CRC, and proactive treatment with B. uniformis slows tumor growth in mice. Natural killer (NK) cells, but not T cells, are required for B. uniformis-mediated protection. CRC is recalcitrant to immunotherapies; however, addition of B. uniformis restores response to α-CTLA-4 treatment in an NK cell-dependent manner. We report that high Lag-3 expression is associated with greater survival in CRC patients and that B. uniformis-mediated protection is reliant on Lag-3 in innate cells. Induction of NK cell activity and reduced tumor growth is dependent on a specific B. uniformis capsular polysaccharide. Thus, healthy individuals possess tumor suppressor microbes that prevent cancer development and can be harnessed therapeutically.},
}

@article {pmid40849761,
year = {2025},
author = {Mahima, and Mazumder, A and Pentela, B},
title = {Future Directions in Anxiolytic Therapy: A Comprehensive Review of Novel Targets and Strategies.},
journal = {Current neurovascular research},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115672026394052250808075022},
pmid = {40849761},
issn = {1875-5739},
abstract = {BACKGROUND: With 301 million cases worldwide, anxiety disorders represent a serious public health concern. Many people endure ongoing distress while receiving several treatments because of the drawbacks of traditional therapy, such as adverse effects, dependence, and inconsistent efficacy. This emphasizes the absolute need for novel treatment approaches.

OBJECTIVE: This review examines emerging pharmacological and non-pharmacological strategies for anxiety disorders, assessing existing and developing therapeutic options while examining the drawbacks of conventional therapies.

METHODS: A comprehensive literature review was carried out using the NIH, PubMed, and Google Scholar databases. Studies from 2020-2025 were given priority in the inclusion criteria, with a few supporting references from earlier years. Personalized medicine, combination therapy, non-pharmacological interventions, and novel anxiolytic targets, etc., were among the keywords used.

RESULTS: Conventional therapies, including benzodiazepines, SSRIs, and SNRIs, are still the major choices, but they have significant disadvantages. The protein kinase pathway, endocannabinoid and orexin systems, NK1R antagonists, and microbiome modulation are examples of emerging targets. Emerging strategies that show preliminary promise include digital therapeutics, gene therapy, optogenetics, personalized medicine, combination therapy, herbal therapy, and peptide-based medicines (e.g., NPY, NPS, oxytocin analogs, CRF, vasopressin, and melanocortin receptor antagonist). Several of these approaches modulate key neural circuits, such as the involvement of the amygdala-prefrontal cortex axis, via the HPA axis, and biomarker-informed personalization, among others; yet many remain in early-phase or preclinical investigation. However, limited comparative data exist between these novel strategies and standard therapies, underlining the need for rigorous head-to-head evaluations.

CONCLUSION: Advances in molecular neuroscience and precision medicine offer potential alternatives to conventional treatments. However, most emerging therapies require further clinical validation, large-scale trials, and translational refinement before they can be integrated into realworld decision-making for anxiety disorders.},
}

@article {pmid40849659,
year = {2025},
author = {Wang, H and Niu, X and Jin, Z and Zhang, S and Fan, R and Xiao, H and Hu, SS},
title = {Immunotherapy resistance in non-small cell lung cancer: from mechanisms to therapeutic opportunities.},
journal = {Journal of experimental & clinical cancer research : CR},
volume = {44},
number = {1},
pages = {250},
pmid = {40849659},
issn = {1756-9966},
support = {2024ZZ2027//Shanghai Municipal Health Commission Medical New Technology Research and Transformation Seed Program/ ; YG2025LC10//Fundamental Research Funds for the Central Universities of Interdisciplinary Program of Shanghai Jiao Tong University/ ; TMSK-2024-116//Translational Medicine National Major Science and Technology Infrastructure/ ; GWVI-11.2-XD40//Shanghai Municipal Medical and Health Outstanding Academic Leader Program/ ; 2024ZY01013//Guiding grants from the Central Government for Supporting the Development of the Local Science and Technology/ ; 2024ZY01013//Guiding grants from the Central Government for Supporting the Development of the Local Science and Technology/ ; 2024ZY01013//Guiding grants from the Central Government for Supporting the Development of the Local Science and Technology/ ; },
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/therapy/immunology/pathology/drug therapy ; *Immunotherapy/methods ; *Lung Neoplasms/immunology/therapy/pathology/drug therapy ; *Drug Resistance, Neoplasm ; Tumor Microenvironment ; Animals ; },
abstract = {This review provides a comprehensive synthesis of current knowledge on immunotherapy resistance in non-small cell lung cancer (NSCLC), a disease that accounts for approximately 85% of all lung cancer cases and remains the leading cause of cancer-related death worldwide. Although immune checkpoint inhibitors (ICIs) have significantly improved survival for a subset of patients with advanced NSCLC, over 70% of cases ultimately exhibit primary or acquired resistance, underscoring the urgent need to understand the underlying mechanisms. The review categorizes resistance into tumor-intrinsic and tumor-extrinsic processes and provides an in-depth mechanistic analysis of how factors such as tumor antigen loss, impaired antigen presentation, cGAS-STING pathway dysregulation, metabolic reprogramming in tumor microenvironment (TME), immune cell exhaustion, and microbiomes collectively contribute to immune escape. In parallel, the influence of the lung and gut microbiome on shaping immunotherapy responses is discussed, with emphasis on microbial dysbiosis, immunosuppressive metabolite production, and TME remodeling. Therapeutic strategies to overcome resistance are also discussed, including combination approaches involving chemotherapy, radiotherapy, and antiangiogenic agents, as well as epigenetic modulators (HDAC and BET inhibitors). Moreover, the review explores bispecific antibodies, antibody-drug conjugates, and small-molecule agents that enhance T cell function or disrupt immunosuppressive signaling networks. By integrating insights from preclinical models and clinical trials, the review underscores the necessity of biomarker-guided patient stratification, combination immunotherapy approaches, and interventions that restore tumor immunogenicity. It concludes that a multipronged therapeutic strategy, one that addresses both immune evasion and TME-induced suppression, holds the greatest promise for improving response durability and advancing personalized immunotherapy for NSCLC.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/therapy/immunology/pathology/drug therapy
*Immunotherapy/methods
*Lung Neoplasms/immunology/therapy/pathology/drug therapy
*Drug Resistance, Neoplasm
Tumor Microenvironment
Animals

@article {pmid40849632,
year = {2025},
author = {Jang, S and Lee, EJ and Park, S and Lim, H and Ahn, B and Huh, Y and Koh, H and Park, YR},
title = {Spatial host-microbiome profiling demonstrates bacterial-associated host transcriptional alterations in pediatric ileal Crohn's disease.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {189},
pmid = {40849632},
issn = {2049-2618},
abstract = {BACKGROUND: Crohn's disease (CD) is a chronic inflammatory bowel disease involving complex relationships between the gut microbiome and host immune system. However, the spatial relationships between tissue-resident bacteria and host cells in CD pathogenesis remain poorly understood. We developed a spatial host-microbiome profiling approach to simultaneously detect host transcriptomics and bacterial species at high taxonomic resolution in pediatric ileal CD tissues.

RESULTS: In this prospective case-control study, we analyzed 14 terminal ileal tissue samples from six pediatric patients with ileal CD and two controls. Spatial host-microbiome sequencing, combined spatial transcriptomics and in-situ polyadenylation, and bulk shotgun metagenome sequencing were performed. We developed a comprehensive bioinformatics pipeline to identify bacterial species and analyze host-microbiome interactions at cellular resolution, resulting in 13,876 analyzed cells. Our approach revealed increased bacterial abundance in CD tissues compared with controls. The extent of bacterial infiltration at diagnosis correlated with disease prognosis and severity of endoscopic findings. We identified 16 potentially beneficial and nine pathogenic microbiome members in ileal CD, including several newly discovered risk-modulating bacterial species. Cell-type-specific host gene expression analysis revealed transcriptome alterations related to bacterial defense mechanisms in the presence of various bacterial species.

CONCLUSIONS: Our spatial host-microbiome profiling approach enables simultaneous species-level identification of bacteria and host transcriptomics. It reveals the intricate interactions between host cells and bacteria, providing cellular-level insights into CD pathogenesis. Our approach offers a powerful tool for investigating host-microbiome interactions in various microbiome-associated diseases to direct new strategies for microbiome-based therapeutics and prognostic markers. Video Abstract.},
}

@article {pmid40849417,
year = {2025},
author = {Chen, D and Sun, L and Wan, L and Chen, Z and Peng, L and Peng, J and Ouyang, R and Long, X and Du, K and Dong, X and Wu, X and Xiao, X and He, R and Qiu, R and Tang, B and Jiang, H},
title = {Alterations of the skin microbiome in multiple system atrophy: a pilot study.},
journal = {NPJ Parkinson's disease},
volume = {11},
number = {1},
pages = {257},
pmid = {40849417},
issn = {2373-8057},
support = {2024JJ6493//Natural Science Foundation of Hunan Province/ ; 2024JJ6638//Natural Science Foundation of Hunan Province/ ; 2024JJ3050//Natural Science Foundation of Hunan Province/ ; 82301628//National Natural Science Foundation of China/ ; 82371272//National Natural Science Foundation of China/ ; 82401496//National Natural Science Foundation of China/ ; 82171254//National Natural Science Foundation of China/ ; 2022RC1027//Science and Technology Innovation Program of Hunan Province/ ; GZB20230870//Postdoctoral Fellowship Program of CPSF/ ; 2024M753690//China Postdoctoral Science Foundation/ ; 2021YFA0805200//National Key Research and Development Program of China/ ; R2023047//Major Scientific Research Project for High-level Health Talent in Hunan Province/ ; 2023SK2084//Furong Lab Research Project/ ; 2023QYJC010//Central South University Research Program of Advanced Interdisciplinary Study/ ; },
abstract = {Multiple system atrophy (MSA) alters skin physiology, potentially impacting skin microbiota. This pilot study investigated whether skin microbiota differs in MSA and whether these differences relate to disease severity. Using 16S rRNA sequencing of cervical and axillary sites in MSA, Parkinson's disease, and controls, we identified distinct microbial patterns among groups. These patterns allowed cohort classification and showed strong associations with clinical symptoms, suggesting disease-related microbial alterations in MSA.},
}

@article {pmid40849229,
year = {2025},
author = {Tanabe, N and Matsumoto, H},
title = {From mucus plugging to airway dilatation in chronic airway diseases: A perspective on the contribution of the airway microbiome and inflammation.},
journal = {Allergology international : official journal of the Japanese Society of Allergology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.alit.2025.07.003},
pmid = {40849229},
issn = {1440-1592},
abstract = {Airway mucus plugs are the main pathological and computed tomography (CT) findings that affect clinical outcomes in patients with asthma, chronic obstructive pulmonary disease (COPD), and asthma-COPD overlap. Despite the introduction of biologics targeting type 2 inflammation, mucus plug removal remains challenging and understanding its pathogenesis is critical for improved management. In eosinophilic airways, elevated MUC5AC and eosinophil-derived molecules (galectin-10 and extracellular traps) cause highly viscoelastic plugs detectable as high-density regions on ultra-high-resolution CT. In neutrophilic airways, where phylum Proteobacteria and genus Haemophilus are predominant, excessive neutrophil elastase impairs mucociliary clearance, induces neutrophil extracellular traps (NETs), and promotes mucus overproduction. Since mucus plugs could be reservoirs for bacterial colonization, an altered airway microbiome and airway inflammation may be associated with mucus plugging. Phylum Firmicutes and genus Streptococcus are positively and genus Fusobacterium is negatively associated with mucus plugging in severe eosinophilic inflammation. Anaerobic commensals produce short-chain fatty acids, which suppress eosinophilic inflammation. In moderate eosinophilic inflammation, anaerobic commensals may be replaced by pathogenic bacteria of the phylum Proteobacteria and genus Haemophilus, which triggers severe neutrophilic inflammation and exacerbates mucus plugging. Finally, in eosinophilic inflammation, mucus plugs containing aggregated eosinophils may induce mechanical dilation of the airways. In contrast, the presence of mucus plugs in a neutrophilic milieu may reflect severe inflammation characterized by excessive neutrophil extracellular traps and degenerative tissue remodeling, which is consistent with the pathological features of bronchiectasis. This review provides clues regarding how inflammation and microbiome alterations interact with mucus plugging in chronic airway disease.},
}

@article {pmid40849086,
year = {2025},
author = {Gattuso, JJ and Kong, G and Bezcioglu, B and Lu, D and Ekwudo, M and Wilson, C and Gubert, C and Hannan, AJ and Renoir, T},
title = {Chronic psilocybin administration increases sociability and alters the gut microbiome in male wild-type mice but not in a preclinical model of obsessive-compulsive disorder.},
journal = {Neuropharmacology},
volume = {},
number = {},
pages = {110648},
doi = {10.1016/j.neuropharm.2025.110648},
pmid = {40849086},
issn = {1873-7064},
abstract = {Psilocybin, a serotonergic compound that produces psychedelic effects primarily through activation of the 5-HT2A receptor, has shown promise in treating neuropsychiatric conditions, including obsessive-compulsive disorder (OCD). However, the effects of chronic psilocybin administration on gut function, microbiota, and behavioural phenotypes remain understudied. The present study investigated the impact of chronic psilocybin (0.1 mg/kg and 1 mg/kg, oral gavage) on gut and behavioural measures in wild-type (WT) and SAPAP3 knockout (KO) mice, a model of OCD-like phenotypes. We present novel evidence that SAPAP3 KO mice exhibit social deficits, and that chronic psilocybin increases sociability in male WT mice. Although no therapeutic effects were observed at either dose on anxiety-, compulsive-, or depressive-like behaviour, chronic psilocybin also did not induce psychosis-like behaviours. A dose-dependent effect of psilocybin was observed on gut motility. While chronic administration did not significantly affect overall gut microbiome diversity, reductions in Lactobacillus murinus, Lactobacillus animalis and Alistipes dispar were observed in male WT, but not female, mice. Integrative analysis revealed that a microbial cluster, comprising Lactobacillus and Alistipes species, correlated with locomotion, head twitch response and gut motility, effectively differentiating psilocybin-treated mice from vehicle controls. This suggests a potential host-microbiome feedback mechanism regulating host serotonin signalling, linked to central and peripheral 5-HT2A receptor activation. Additionally, separate microbial clusters were associated with startle response and sociability, indicating that psilocybin may engage distinct neural pathways to mediate these behaviours. These findings highlight the importance of considering the microbiome and sex in future psychedelic research and open new avenues for exploring the microbiota-gut-brain axis as a target for future therapeutic strategies.},
}

@article {pmid40848905,
year = {2025},
author = {Yang, J and Shi, J and Xu, W and Mu, J and Chang, Y and Zhang, X and Wang, X},
title = {Effects of Modified Xuanbai Chengqi Decoction Against Secondary Streptococcus pneumoniae Infection Following Influenza Virus Infection: A Multi-Omics Analysis.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {120458},
doi = {10.1016/j.jep.2025.120458},
pmid = {40848905},
issn = {1872-7573},
abstract = {The Modified Xuanbai Chengqi Decoction (XBCQ), derived from the classical formula "Xuanbai Chengqi Decoction," is a traditional Chinese herbal preparation. Traditional Chinese Medicine (TCM) is crucial for influenza management. Our previous studies have demonstrated the therapeutic effects of XBCQ on pulmonary and intestinal injuries induced by influenza A virus (IAV)/Streptococcus pneumoniae (SPN) co-infection, although the underlying gut-lung axis mechanisms remain to be further elucidated.

AIM OF THE STUDY: We hypothesize that XBCQ ameliorates secondary SPN infection by modulating the gut-lung axis through microbiota-metabolite-immune interactions, and we will evaluate its protective effects and mechanistic basis against IAV-induced secondary SPN infection through integrated multi-omics analyses (gut microbiota and metabolomics).

MATERIALS AND METHODS: Chemical profiling of XBCQ was performed using ultra-high-performance liquid chromatography coupled with quadrupole-Orbitrap high-resolution mass spectrometry (UHPLC-Q-Orbitrap-HRMS). A sequential infection model was established by intranasal inoculation of IAV followed by SPN to mimic post-influenza secondary bacterial infection. Therapeutic efficacy was validated through quantification of viral/bacterial loads, histopathological analysis, inflammatory cytokines, and intestinal tight junction (TJ) proteins, demonstrating XBCQ's protective effects on both pulmonary and colonic tissues. 16s RNA sequencing and metabonomics were used to evaluate the mechanism of XBCQ intervention in secondary bacterial infection after influenza.

RESULTS: UHPLC-Q-Orbitrap-HRMS analysis identified 60 bioactive components in XBCQ, including sucrose, adenosine, guanosine, and mulberroside A. XBCQ reduced SPN burden by 81.9%, restored gut microbiota balance, and modulated host metabolic profiles. Correlation analysis revealed that the microbiota altered by XBCQ was significantly associated with pharmacodynamic indicators and metabolites, further confirming the reliability of these findings.

CONCLUSIONS: XBCQ prevents SPN superinfection following IAV infection by modulating the microbiota-gut-lung axis. These findings provide a potential scientific basis for the clinical application of XBCQ, offering prospective guidance for preventing bacterial pneumonia during influenza seasons.},
}

@article {pmid40848874,
year = {2025},
author = {Fonnes, S and Mollerup, S and Paulsen, SJ and Petersen, AM and Holzknecht, BJ and Westh, H and Rosenberg, J},
title = {A prospective cohort study of the rectal microbiome in patients with suspected appendicitis.},
journal = {Clinics and research in hepatology and gastroenterology},
volume = {},
number = {},
pages = {102675},
doi = {10.1016/j.clinre.2025.102675},
pmid = {40848874},
issn = {2210-741X},
abstract = {PURPOSE: Diagnosing appendicitis is difficult. An infectious origin has been proposed, therefore signals from the microbiome could be a potential diagnostic measure. The aim was to evaluate the diagnostic potential of the rectal microbiome in patients with suspected appendicitis.

METHODS: We included adult Danish patients with suspected appendicitis undergoing appendectomy in a prospective, observational cohort study. Patients were first grouped as patients with and without appendicitis according to histopathological findings, and second, as having uncomplicated or complicated appendicitis according to the surgical report. Rectal swabs were analysed with shotgun metagenomics. The outcomes were alpha diversity, beta diversity, and differential abundance of bacteria.

RESULTS: Rectal swabs from 220 patients were analysed: 49 patients without appendicitis, 111 patients with uncomplicated and 60 patients with complicated appendicitis, respectively. Across all groups, both the alpha and beta diversity were similar. The relative abundance of bacterial genera and species was also similar across all groups. Thus, the three groups of patients had similar rectal microbiomes.

CONCLUSION: The rectal microbiome in adult patients with suspected appendicitis was similar and does not seem to have the potential to be used to diagnose neither appendicitis nor the severity of appendicitis preoperatively.

TRIAL REGISTRATION: NCT03349814 (clinicaltrials.gov).},
}

@article {pmid40848571,
year = {2025},
author = {Sang, S and Jiang, H and Gan, J and Ke, C},
title = {Microbial community dynamics across salinity gradients in coastal aquifers: Linking hydrogeochemical variability to prokaryotic diversity in a seawater-intruded aquifer of the Pearl River Delta, China.},
journal = {Marine environmental research},
volume = {211},
number = {},
pages = {107471},
doi = {10.1016/j.marenvres.2025.107471},
pmid = {40848571},
issn = {1879-0291},
abstract = {Coastal groundwater salinization driven by seawater intrusion creates dynamic salt-freshwater interfaces with steep biogeochemical gradients. While hydrological changes during seawater intrusion are well characterized, the linkage between hydrogeochemical variability and microbial community structure remains poorly resolved. Here, an integrated approach coupling V4-region 16S rRNA amplicon sequencing (Illumina) with geochemical profiling was employed to decipher prokaryotic diversity dynamics and environmental determinants in a Quaternary aquifer undergoing salinization, Pearl River Delta, China. Proteobacteria dominated bacterial communities across salinity gradients, whereas archaeal assemblages shifted from Thaumarchaeota-dominated freshwater zones to Methanobacteriota-enriched brackish/saline groundwater. High-salinity zones harbored anaerobic functional taxa, including sulfate-reducing Desulfovibrio and methanogenic Methanococcus, confirming active sulfate reduction and methanogenesis in the aquifer-processes critical to carbon and sulfur cycling in coastal groundwater systems. Microbial α-diversity correlated positively with salinity (total dissolved solids, TDS >1 g/L), despite non-linear community shifts along the intrusion path. Vector-based redundancy analysis identified TDS and total nitrogen (TN) as primary drivers of microbial assemblage restructuring (p < 0.01). Our results established salinity as a master regulator of groundwater microbiome composition and function, with direct implications for predicting biogeochemical feedbacks (e.g., methane emissions, sulfide mobilization) in coastal aquifers under climate-driven seawater intrusion. This mechanistic understanding of microbe-environment interactions supports optimized management of contaminated coastal groundwater resources facing salinization threats.},
}

@article {pmid40848430,
year = {2025},
author = {Vaithilingam, P and Seetharaman, B and Achudhan, AB and Mudgal, G and Vasantharekha, R},
title = {Chronic exposure to food additives: Monosodium glutamate and tartrazine dysregulate gut-brain axis in zebrafish model.},
journal = {The Science of the total environment},
volume = {998},
number = {},
pages = {180295},
doi = {10.1016/j.scitotenv.2025.180295},
pmid = {40848430},
issn = {1879-1026},
abstract = {The commonly used food additives to enhance color and flavor are Monosodium glutamate and Tartrazine. The effects of both were investigated on chronic exposure of over 30 days to adult zebrafish, in four groups: control, tartazine (31,844 ppm), monosodium glutamate (10.9 × 10[3] ppm), and a combined exposure group (monosodium glutamate+tartazine = 5450 ppm + 15,922 ppm), with 10 fish per group in triplicates. Neurobehavioral tests, acetylcholinesterase (AChE) activity, metabolic enzyme assays, and quantification of serotonin and cortisol levels were performed. DNA was extracted from zebrafish gut samples for gut microbiota analysis. Zebrafish exposed to monosodium glutamate and tartazine showed a statistically significant reduction in social interaction, mirror biting, and preference for familiar and novel objects. The combined exposure group showed increased anxiety, spent more time in light zones, and increased transition movements. Tartazine exposure elevated AChE activity and serotonin levels, and monosodium glutamate exposure increased cortisol. Disruptions in cortisol and serotonin levels, with increased AChE activity, were linked to stress, mood swings, memory deficits, and cognitive impairment. Gut microbiota analysis revealed a higher abundance of Actinobacteria, and increased Enterobacter indicates inflammation in the gut of treatment groups. Chronic consumption of monosodium glutamate and tartazine may disrupt metabolic processes, induce obesity, and impair cognitive functions, indicating potential health risks associated with these additives.},
}

@article {pmid40848419,
year = {2025},
author = {Jeong, SH and Jung, J and Park, YJ and Lee, SJ and Lee, SJ},
title = {The Influence of polycyclic aromatic hydrocarbons exposure on the gut microbiome composition and inflammatory responses.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {118910},
doi = {10.1016/j.ecoenv.2025.118910},
pmid = {40848419},
issn = {1090-2414},
abstract = {Particulate matter (PM) is recognized as a contributor to various gastrointestinal diseases, including inflammatory bowel disease. However, the specific impact of polycyclic aromatic hydrocarbons (PAHs), a major component of PM, on microbial community dynamics and immune regulation remains unexplored. In this study, we investigated the effects of PAHs on the inflammatory response of mouse intestinal tissues and microbiota composition using PAHs extracted from PM10 (PM10_PAHs). With increasing duration of exposure to PM10_PAHs, damage to the colonic mucosa and lung tissues was aggravated and the secretion of inflammatory cytokines increased. The composition of the gut microbiota was also significantly altered, with a decrease in Firmicutes and an increase in Bacteroidetes at the phylum level, along with an increase in Lactobacillus, Clostridium, and Romboutsia at the genus level. Notably, despite the cessation of PM10_PAHs administration and the recovery of gut microbial diversity, the microbiota composition and inflammatory cytokine levels did not return to pre-exposure conditions. These results suggest that exposure to PM can have lasting adverse health effects, such as inflammation induced by its main component, PAHs.},
}

@article {pmid40848192,
year = {2025},
author = {Parker, G and Russo, N},
title = {Antibiomania: An update.},
journal = {Australasian psychiatry : bulletin of Royal Australian and New Zealand College of Psychiatrists},
volume = {},
number = {},
pages = {10398562251370946},
doi = {10.1177/10398562251370946},
pmid = {40848192},
issn = {1440-1665},
abstract = {BackgroundAntibiomania, whereby an antibiotic induces a manic/hypomanic episode in those with or without a pre-existing bipolar condition, is a little-known phenomenon, diagnostically elusive, may be more prevalent than recognised and thus warrants the current overview.MethodRepresentative studies and clinical observations are noted.ResultsSeveral mechanistic issues are considered but with a weighting to the antibiotic causing gut dysbiosis and so activating gut-brain axis pathways that may induce manic/hypomanic episodes.ConclusionFuture studies should seek to determine the prevalence of antibiomania and whether differing antibiotics effect differential risks, while clinicians identifying such a potential linkage in a patient who has developed a first episode or recurrence of a manic/hypomanic episode should consider nuanced pre-emptive and management strategies in such instances.},
}

@article {pmid40848105,
year = {2025},
author = {Proskynitopoulos, PJ and Woltemate, S and Rhein, M and Böke, I and Molks, J and Schröder, S and Schneider, HU and Bleich, S and Frieling, H and Geffers, R and Glahn, A and Vital, M},
title = {The effect of alcohol withdrawal therapy on gut microbiota in alcohol use disorder and its link to inflammation and craving.},
journal = {Alcohol, clinical & experimental research},
volume = {},
number = {},
pages = {},
doi = {10.1111/acer.70128},
pmid = {40848105},
issn = {2993-7175},
support = {//Hetzler Foundation for Addiction Research and Prevention/ ; },
abstract = {BACKGROUND: Alcohol use disorder (AUD) is linked to changes in the function and composition of the human gut microbiome (GM). The GM affects inflammation by producing anti-inflammatory molecules such as short-chain fatty acids (SCFA), in particular butyrate, which are linked to appetite regulation, a mechanism involved in alcohol craving. This study investigates changes in GM composition and functional capacity to produce SCFA during alcohol withdrawal and their link to inflammation and craving.

METHODS: Sixty-three patients (mean age 48, SD = 12) with AUD were enrolled. We collected stool (n = 63) and blood (n = 48) during the first 48 h (timepoint A) of withdrawal therapy and between Days 10-14 (timepoint B). Microbiota were analyzed using shotgun metagenomics along with bacterial load determinations. TNF-α, IL-6, IL-8, and IL-10 were measured in plasma.

RESULTS: Bacterial diversity (species richness, Shannon Index) did not change significantly throughout withdrawal, while overall bacterial load increased. Abundances of several taxa changed, and the overall community composition during withdrawal was approaching those of healthy controls; the potential to synthesize butyrate, a key SCFA, increased. However, it remained at lower levels compared with controls. Both diversity parameters correlated with cell concentrations and the butyrate pathway at baseline. The latter was negatively associated with IL-6 at baseline. IL-8 and IL-10 levels decreased significantly during withdrawal, as did craving, which was linked to abundance alterations of six species and IL-8.

CONCLUSIONS: Alcohol withdrawal affected GM composition and increased concentration of the butyrate pathway along with overall bacterial load. Changes in bacterial composition and the butyrate production capacity demonstrate a shift toward healthier microbiota during withdrawal therapy. Changes in some species and IL-8 were linked to alcohol craving, replicating findings of previous studies. Our study adds new findings helping to understand the microbiome-gut-brain axis.},
}

@article {pmid40848087,
year = {2025},
author = {Shamsuzzaman, M and Dahal, RH and Choi, YJ and Kim, S and Kim, J},
title = {Segatella intestinalis sp. nov., and Parabacteroides caeci sp. nov., novel potential probiotics from the human gut microbiome.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {9},
pages = {136},
pmid = {40848087},
issn = {1572-9699},
mesh = {Humans ; Phylogeny ; *Gastrointestinal Microbiome ; *Probiotics/isolation & purification/classification ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Bacteroidetes/classification/isolation & purification/genetics/physiology ; Fatty Acids/analysis ; Base Composition ; DNA, Bacterial/genetics ; Republic of Korea ; Bacterial Typing Techniques ; },
abstract = {Two bacterial strains, B2-R-102[T] and W1-Q-101[T], were isolated from the feces of a healthy Korean individual. These strains were Gram-stain negative, anaerobic, and non-motile, growing optimally between 20 and 40 °C and at pH 5.5-8.0. Importantly, they survived at pH 2.0 and tolerated 0.3% bile salts and pepsin after a 4 h exposure. The strains demonstrated in vitro antioxidant activity, inhibiting DPPH radicals by 48.12 ± 1.45 and 70.80 ± 12.8%, respectively. Furthermore, they inhibited α-amylase activity by 46.52 ± 4.42 to 60.84 ± 2.20%, compared to 74.82 ± 0.76% inhibition by sitagliptin. In vitro, anti-inflammatory assays revealed 57.77 ± 3.15 to 62.39 ± 2.23% inhibition of albumin protein denaturation, comparable to aspirin 72 ± 2.39% inhibition. The abundant cellular fatty acids were C15:0, C16:0, iso-C15:0, C18:1ω9c, anteiso-C15:0 and iso-C17:0 3-OH. Neither strain exhibited haemolytic activity, and genomic analysis revealed no acquired antibiotic resistance or virulence genes. Phylogenetic analysis showed that B2-R-102[T] and W1-Q-101[T] belonged to the genera Segatella and Parabacteroides, with 96.9 and 97.7% 16S rRNA gene sequence similarities to Segatella copri CB7[T] and Parabacteroides goldsteinii DSM 19448[T], respectively. Furthermore, biosynthetic gene cluster analysis revealed the potential for antimicrobial thiopeptides, lanthipeptides, and non-ribosomal peptides (NRPs). In silico average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were below the thresholds to distinguish novel species. Based on phenotypic, genomic, and phylogenetic analysis, we propose the names Segatella intestinalis sp. nov. (type strain B2-R-102[T] = CGMCC 1.17963[T] = KCTC 25417[T]) and Parabacteroides caeci sp. nov. (type strain W1-Q-101[T] = KCTC 25456[T] = CGMCC 1.17991[T]).},
}

Humans
Phylogeny
*Gastrointestinal Microbiome
*Probiotics/isolation & purification/classification
RNA, Ribosomal, 16S/genetics
Feces/microbiology
*Bacteroidetes/classification/isolation & purification/genetics/physiology
Fatty Acids/analysis
Base Composition
DNA, Bacterial/genetics
Republic of Korea
Bacterial Typing Techniques

@article {pmid40847749,
year = {2025},
author = {Mu, C and Rho, JM and Shearer, J},
title = {The Interplay between the Gut and Ketogenic Diets in Health and Disease.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e04249},
doi = {10.1002/advs.202504249},
pmid = {40847749},
issn = {2198-3844},
support = {RGPIN-2018-04238//Natural Sciences and Engineering Research Council of Canada (JS)/ ; },
abstract = {The gut plays a central role in translating dietary signals into systemic health effects, making it a key mediator of the ketogenic diet (KD), a high fat, low carbohydrate regimen. This review synthesizes current knowledge on the interaction between the KD and the gut, emphasizing gut-mediated mechanisms as an interface between dietary interventions and systemic health outcomes, spanning gastrointestinal to neurological health. Topics address gut physiology (gut digestion and absorption, epithelial nutrient sensing, gut motility), intestinal immunity (covering innate, adaptive, and antiviral responses), and extracellular to intracellular processes (i.e. mitochondrial function, stem cell fate, and intestinal circadian rhythm). Special focus is given to the gut microbiome, including both bacterial and fungal communities and how the KD modulates them in conditions such as epilepsy, obesity, traumatic brain injury, and multiple sclerosis. Innovative methods for tailoring the KD, including the use of alternative formulations, ketone esters, and microbiome-focused interventions such as prebiotics and probiotics are examined. Strategies to maximize the diet's benefits while reducing potential side effects are considered. Together, these insights herein offer a comprehensive framework for understanding the interactions between the KD and the gut, a prerequisite for optimizing the overall health benefits of metabolism-based treatments.},
}

@article {pmid40847462,
year = {2025},
author = {Ma, H and Wang, M and Feng, Y and Zhang, W and Wang, W and Xie, Y and Kong, G and Feng, J and Wang, P and Wang, Q and Huang, X},
title = {Microbial profile of the appendix niche in acute appendicitis: a novel sampling approach.},
journal = {FEBS open bio},
volume = {},
number = {},
pages = {},
doi = {10.1002/2211-5463.70105},
pmid = {40847462},
issn = {2211-5463},
support = {GSWSKY2020-50//Gansu Provincial Health Commission, Provincial Health Industry Research Project/ ; 20240050058//Lanzhou University Student Innovation and Entrepreneurship Action Plan Project/ ; CY2023-QN-B17//Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University in 2023/ ; },
abstract = {Relatively little is known about the microbial variations within the human appendix niche. To overcome this knowledge gap, we employed endoscopic retrograde appendicitis treatment (ERAT) technology to collect microbial samples from the appendix lumen, followed by shotgun metagenomic sequencing on participants with acute appendicitis without antibiotic treatment. Compared to the cecum and terminal ileum, the appendix had a higher abundance at the genus level of Sphingobium, Leptotrichia and Oribacterium, as well as a significant increase in species-level abundance of oral bacteria, including Streptococcus sanguinis, Streptococcus australis, Streptococcus sp. A12, Leptotrichia sp. oral taxon 215, Veillonella dispar, Veillonella infantium and Oribacterium sinus. Pearson correlation analysis showed that bacterial species abundant in the appendix, such as Acinetobacter johnsonii, Sphingobium yanoikuyae and Agrobacterium tumefaciens, had negative correlations with the top five most abundant Gene Ontology (GO) categories (molecular function, biological process and cellular component). Conversely, species underrepresented in the appendix, including Mogibacterium diversum, Streptococcus sanguinis, Megasphaera micronuciformis and Actinomyces graevenitzii, had significant positive correlations with these GO categories. Our results show that ERAT technology can be used to improve sampling and microbiome profiling in the appendix. Furthermore, this in-depth microbial characterization could inform clinicians during antibiotic prescription. However, further large sample size studies are required to validate these results.},
}

@article {pmid40847238,
year = {2025},
author = {Zugman, M and Jaime-Casas, S and Zang, PD and Shah, K and Nguyen, CB},
title = {Immunotherapy in Renal Cell Carcinoma.},
journal = {Cancer treatment and research},
volume = {129},
number = {},
pages = {293-308},
pmid = {40847238},
issn = {0927-3042},
mesh = {Humans ; *Carcinoma, Renal Cell/therapy/immunology/drug therapy ; *Kidney Neoplasms/therapy/immunology/drug therapy/pathology ; *Immunotherapy/methods ; *Immune Checkpoint Inhibitors/therapeutic use ; },
abstract = {There have been tremendous advancements in immunotherapy approaches for patients with renal cell carcinoma (RCC) from the initial interleukin-2 era to the current immune checkpoint inhibitor (ICI) combinations. Several ICI-based therapies have greatly improved outcomes for patients with RCC with the potential for durable responses for a subset of patients. In this chapter, we review the data of key frontline ICI-based combinations for RCC in the metastatic setting and recent data on adjuvant immunotherapy. We also discuss recent data on the role of immunotherapy rechallenge following prior ICI treatment as well as emerging novel immunotherapy strategies with chimeric antigen receptor (CAR) T and gut microbiome interventions. Lastly, we highlight a multidisciplinary team-based approach for patients with RCC treated with ICI including management of immune-related adverse events as well as potential role of cytoreductive nephrectomy in an evolving treatment landscape.},
}

Humans
*Carcinoma, Renal Cell/therapy/immunology/drug therapy
*Kidney Neoplasms/therapy/immunology/drug therapy/pathology
*Immunotherapy/methods
*Immune Checkpoint Inhibitors/therapeutic use

@article {pmid40847229,
year = {2025},
author = {Duesberg, M and LeVee, A and Chang, H and Tsai, K and Crossman, B and Tadi, M and Xu, S and Wheeler, D and Kang, I},
title = {Breast Cancer Immunotherapy: A Team Science Approach.},
journal = {Cancer treatment and research},
volume = {129},
number = {},
pages = {67-82},
pmid = {40847229},
issn = {0927-3042},
mesh = {Humans ; Female ; *Immunotherapy/methods ; *Breast Neoplasms/therapy/immunology ; *Immune Checkpoint Inhibitors/therapeutic use ; *Triple Negative Breast Neoplasms/immunology/therapy/drug therapy ; },
abstract = {Immunotherapy has reshaped the treatment landscape of several malignancies, including breast cancer. While historically considered less immunogenic, breast cancer-particularly the triple-negative subtype (TNBC)-has demonstrated responsiveness to immune checkpoint inhibitors (ICIs). TNBC is characterized by higher tumor mutational burden, elevated PD-L1 expression, and increased tumor-infiltrating lymphocytes, making it a leading focus of immunotherapy development. In metastatic TNBC with PD-L1 expression, trials such as KEYNOTE-355 have shown improvements in progression-free and overall survival with the addition of the ICI, pembrolizumab to chemotherapy, leading to regulatory approval. In early-stage TNBC, KEYNOTE-522 established a neoadjuvant chemotherapy plus ICI as the standard of care for stage II and III tumors. This was based on improved pathologic complete response and event-free survival in this pivotal clinical trial regardless of PD-L1 expression. ICIs in other subtypes, such as HER2-positive and hormone receptor-positive/HER2-negative disease, remain under active investigation. Ongoing studies are also exploring novel strategies including dual immune checkpoint blockade, cellular therapies (e.g., CAR-T, TILs), cancer vaccines, and rational combinations with targeted agents and antibody-drug conjugates (ADCs). Biomarkers such as PD-L1, tumor mutational burden, immune gene signatures, and the gut microbiome are being evaluated to refine patient selection and predict response. Additionally, effective management of immune-related toxicities is critical, particularly in curative-intent settings. As the role of immunotherapy expands, a multidisciplinary, biomarker-driven approach will be essential to optimize outcomes and broaden its applicability across breast cancer subtypes.},
}

Humans
Female
*Immunotherapy/methods
*Breast Neoplasms/therapy/immunology
*Immune Checkpoint Inhibitors/therapeutic use
*Triple Negative Breast Neoplasms/immunology/therapy/drug therapy

@article {pmid40847065,
year = {2025},
author = {Al Masri, MT and Ali, AS and Vijayan, R and Muzaffar, SB and Al-Deeb, MA},
title = {Microbiome variation between male and female Hyalomma dromedarii ticks from camels in the UAE.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30990},
pmid = {40847065},
issn = {2045-2322},
support = {G00003718//United Arab Emirates University/ ; G00003718//United Arab Emirates University/ ; },
abstract = {Hyalomma dromedarii, a predominant camel tick species in the Arabian Peninsula, plays a significant role in pathogen transmission, yet its sex-specific microbiome composition remains poorly understood. This study analyzed the bacterial communities of male and female H. dromedarii ticks collected from camels across three locations in the United Arab Emirates: Al Khazna, Al Ja'ae, and Al Jabeeb. High throughput 16S rRNA gene sequencing revealed a total of 432,495 reads clustering into 848 operational taxonomic units, encompassing 20 phyla and 261 genera. Male ticks consistently exhibited higher microbial diversity and genus richness compared to females. Notably, Francisella dominated the female microbiome, accounting for over 90% of sequences in Al Ja'ae and Al Jabeeb, while males displayed a more balanced microbial profile, with genera such as Corynebacterium, Staphylococcus, and Trueperella being prevalent. Pearson's correlation and principal coordinate analyses (PCoA) indicated distinct sex-based microbial associations and clustering patterns. These findings underscore sex-associated disparities in the microbiome of H. dromedarii, suggesting potential implications for tick physiology and vector competence within the One Health framework.},
}

@article {pmid40847054,
year = {2025},
author = {Wagner, KS and Salasc, F and Marten, SM and Roth, O},
title = {Paternal microbiota manipulation influences offspring microbial colonization and development in a sex role-reversed pipefish.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30911},
pmid = {40847054},
issn = {2045-2322},
abstract = {Microbes are acquired through vertical and environmental horizontal transmission. Vertical transmission is directly linked to reproductive success and entails early transmission, facilitating coexistence of host and microbes over generations. The multiple potentially interacting routes of vertical transmission are challenging to be disentangled in conventional sex-role species, as they are mostly intermingled on the maternal side, i.e., through egg production, pregnancy, birth and postnatal care. The evolution of male pregnancy in syngnathids (pipefishes and seahorses) offers an opportunity to separate vertical microbial provisioning through the egg (maternal) from provisioning through pregnancy (paternal). We experimentally evaluated the existence and role of paternal vertical microbiota provisioning through male pregnancy on offspring development and microbial colonization. Male pipefish were exposed to antibiotics, and subsequently recolonized with bacteria of paternal, maternal, and environmental origin (spike treatment). After pregnancy, the microbiota of developing offspring was characterized using 16 S rRNA sequencing of the V3-V4 region. Paternal antibiotic and spike treatments influenced the microbial composition of the brood pouch and offspring microbiome development. Paternal spike treatment shortened pregnancy duration and enhanced offspring survival, underlining its beneficial effect for early life stages. Expanding on how distinct vertical microbial transmission routes shape the offspring microbiome will foster our understanding of holobiont function in health and disease.},
}

@article {pmid40846900,
year = {2025},
author = {Karta, J and Meyers, M and Rodriguez, F and Koncina, E and Gilson, C and Klein, E and Gabola, M and Benzarti, M and Pérez Escriva, P and Molina Tijeras, JA and Correia Tavares Bernardino, C and Ponath, F and Carpentier, A and Pujabet, MA and Schmoetten, M and Tsenkova, M and Saoud, P and Gaigneaux, A and Ternes, D and Alonso, L and Zügel, N and Willemssen, E and Koppes, P and Léonard, D and Casanova, LP and Haan, S and Mittelbronn, M and Meiser, J and Pozdeev, VI and Vogel, J and Nuciforo, PG and Wilmes, P and Letellier, E},
title = {Fusobacterium nucleatum interacts with cancer-associated fibroblasts to promote colorectal cancer.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {40846900},
issn = {1460-2075},
support = {CORE/C16/BM/11282028//Fonds National de la Recherche Luxembourg (FNR)/ ; CORE/C20/BM/14591557//Fonds National de la Recherche Luxembourg (FNR)/ ; CORE/C15/BM/10404093//Fonds National de la Recherche Luxembourg (FNR)/ ; PoC/18/12554295//Fonds National de la Recherche Luxembourg (FNR)/ ; AFR 17103240//Fonds National de la Recherche Luxembourg (FNR)/ ; CORE/C21/BM/15718879//Fonds National de la Recherche Luxembourg (FNR)/ ; PRIDE17/11823097//Fonds National de la Recherche Luxembourg (FNR)/ ; FNR matched funding scheme,MFP20/15251414/MelCol PFP//Fonds National de la Recherche Luxembourg (FNR)/ ; PRIDE21/16763386//Fonds National de la Recherche Luxembourg (FNR)/ ; Internal Research Project at the University of Luxembourg,MiDiCa//Université du Luxembourg (University of Luxembourg)/ ; Télévie,7.4565.21 and 7.6603.02//Fonds De La Recherche Scientifique - FNRS (FNRS)/ ; Télévie,7.4560.22//Fonds De La Recherche Scientifique - FNRS (FNRS)/ ; Télévie,7.4552.23//Fonds De La Recherche Scientifique - FNRS (FNRS)/ ; Fondation du Pélican de Mie and Pierre Hippert-Faber//Fondation de Luxembourg/ ; SFB 1583/1,Project number: 492620490,Subproject A09//Deutsche Forschungsgemeinschaft (DFG)/ ; C17937/A29070/CRUK_/Cancer Research UK/United Kingdom ; PI20/00889//Fondo de Investigaciones Sanitarias (FIS)/ ; MMADRILEÑA/PREMI/2020CCAA_NUCIFORO//Instituto de Salud Carlos III (ISCIII) and Fundación Mutua Madrileña/ ; P500PB_214405/SNSF_/Swiss National Science Foundation/Switzerland ; },
abstract = {Gut microbial species contribute to colorectal cancer (CRC) by interacting with tumor or immune cells, however if CRC-associated bacteria engage with stromal components of the tumor microenvironment remains unclear. Here, we report interaction between the CRC-associated bacterium Fusobacterium nucleatum and cancer-associated fibroblasts (CAFs), and show that F. nucleatum is present in the stromal compartment in murine CRC models in vivo and can attach to and invade CAFs. F. nucleatum-exposed CAFs exhibit a pronounced inflammatory-CAF (iCAF) phenotype, marked by elevated expression of established iCAF markers, secretion of pro-inflammatory cytokines such as CXCL1, IL-6 and IL-8, generation of reactive oxygen species (ROS), and an increased metabolic activity. In co-culture experiments, the interaction of cancer cells with F. nucleatum-stimulated CAFs enhances invasion, a finding further validated in vivo. Altogether, our results point to a role for the tumor microbiome in CRC progression by remodeling the tumor microenvironment through its influence on cancer-associated fibroblasts, suggesting novel therapeutic strategies for targeting CRC.},
}

@article {pmid40846880,
year = {2025},
author = {Kotrbová, L and Grabicová, K and Švecová, H and Staňová, AV and Petrlíková, M and Grabic, R and Kodešová, R and Chroňáková, A},
title = {The effect of WWTP products amendments on Phaseolus vulgaris rhizosphere and its ability to inactivate clarithromycin.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30950},
pmid = {40846880},
issn = {2045-2322},
support = {QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; 063/2023/P//Grantová agentura Jihočeské univerzity v Českých Budějovicích/ ; },
mesh = {*Rhizosphere ; *Phaseolus/microbiology/drug effects/growth & development ; *Clarithromycin/pharmacology/metabolism ; Soil Microbiology ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Wastewater/chemistry ; Phylogeny ; Microbiota/drug effects ; },
abstract = {With increasing efforts to reuse wastewater treatment plant (WWTP) products in agriculture, assessing their impact on soil-plant systems is crucial, while the effects of accompanying antibiotic residues on soil microbial communities have not yet been adequately studied. This study focuses on clarithromycin (CLR), highly present in wastewater, and investigates the CLR-degradation potential of plant-associated microorganisms. Phaseolus vulgaris plants were grown in raised beds filled with Haplic Cambisol and amended with or without WWTP products (treated wastewater, biosolid, or composted biosolid), as a source of CLR residues. The rhizosphere microbiomes after biosolid amendments was significantly enriched by Pseudomonadaceae as assessed by 16S rRNA metagenomics and cultures enriched by CLR revealed dominance of Proteobacteria. However, no degradation of CLR by microbial consortia or enrichment cultures was observed, suggesting the multiplication of CLR-resistant bacteria with other resistance mechanisms. Cultivation-based approach combined with antibiotic modulation assays and subsequent LC-MS analysis confirmed the complete CLR removal by seven phylogenetic groups of actinomycetes in vitro. The proportion of isolates indicated that the rhizosphere is a natural reservoir for CLR-inactivating microorganisms; however, the amendment of soils with WWTP products can significantly increase their abundance and diversity.},
}

*Rhizosphere
*Phaseolus/microbiology/drug effects/growth & development
*Clarithromycin/pharmacology/metabolism
Soil Microbiology
*Anti-Bacterial Agents/pharmacology
RNA, Ribosomal, 16S/genetics
*Wastewater/chemistry
Phylogeny
Microbiota/drug effects

@article {pmid40846855,
year = {2025},
author = {Zhang, M and Wang, X and Yao, H and Shen, Y and Teng, Y and Garber, PA and Pan, H and Li, M},
title = {Plasticity of the gut microbiome of golden snub-nosed monkeys (Rhinopithecus roxellana) in response to seasonal variation in diet.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {169},
pmid = {40846855},
issn = {2055-5008},
support = {32330015, 31821001//National Natural Science Foundation of China/ ; 32070404//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Seasons ; *Gastrointestinal Microbiome ; *Diet ; *Colobinae/microbiology ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; Feces/microbiology ; },
abstract = {The effects of seasonal fluctuations in food availability on gut microbiome composition, diversity, and function present significant challenges to animals with hard-to-digest diets. Here, we investigate seasonal variation the gut microbiome of wild golden snub-nosed monkeys (Rhinopithecus roxellana), a foregut fermenting primate, using metagenomics and metatranscriptomics data. We reconstructed 578 metagenome-assembled genomes (MAGs), 76.5% of which did not have exact matches in reference databases, highlighting the novelty of their gut microbiota. The gut microbiome of wild golden snub-nosed monkeys exhibited high diversity and enrichment in plant secondary compound metabolism during summer, while in winter it was enriched with enzymes that function in lichen polysaccharide degradation and Lachnospiraceae, which is important for energy balance. Captive monkeys on a consistent diet showed minimal seasonal variation in gut microbiome composition. Habitat changes also affected golden snub-nosed monkey microbiota community assembly and carbon cycling pathways. These findings underscore the gut microbiome's plasticity in meeting host dietary needs under varying environmental conditions.},
}

Animals
*Seasons
*Gastrointestinal Microbiome
*Diet
*Colobinae/microbiology
Metagenomics
*Bacteria/classification/genetics/isolation & purification
Metagenome
Feces/microbiology

@article {pmid40846748,
year = {2025},
author = {Ge, Y and Liu, L and Wu, L and Liu, X and Hao, Y and Wang, S and Xiong, Y and Yang, Z and Zhang, Z and Li, Q and Li, B and Wu, J and Ren, G and Jiang, Q},
title = {Impaired nutrient absorption, reduced bone mass and alterations in the gut microbiome contribute to postnatal growth retardation in a mouse model of MWS.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30890},
pmid = {40846748},
issn = {2045-2322},
support = {JCYJ-2023-04//Research Foundation of Capital Institute of Pediatrics/ ; CXYJ-2021-05//Research Foundation of Capital Institute of Pediatrics/ ; 82400215//National Natural Science Foundation of China/ ; 82370522, 82070532//National Natural Science Foundation of China/ ; PX2022054//Beijing Municipal Administration of Hospitals Incubating Program/ ; PX2020054//Beijing Municipal Administration of Hospitals Incubating Program/ ; 2021RU015//Research Unit of Minimally Invasive Pediatric Surgery on Diagnosis and Treatment, Chinese Academy of Medical Sciences/ ; CIP2024-0040//Beijing Finance Bureau/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; Disease Models, Animal ; Zinc Finger E-box Binding Homeobox 2/genetics/metabolism ; Dysbiosis ; Haploinsufficiency ; Bone and Bones/pathology ; *Intestinal Absorption ; *Nutrients/metabolism ; *Hirschsprung Disease/microbiology/genetics/metabolism/pathology ; Bone Density ; Male ; *Growth Disorders ; },
abstract = {Mowat‒Wilson syndrome (MWS), a rare genetic disorder caused by heterozygous loss-of-function mutations in ZEB2, is characterised by significant growth retardation with unclear mechanisms. In this study, we developed a Zeb2 haploinsufficient (Zeb2[+/-]) mouse model that recapitulates key features of MWS, including reduced body weight, impaired intestinal development and skeletal hypoplasia. RNA sequencing revealed significant downregulation of nutrient digestion and absorption pathways in the duodenum of Zeb2[+/-] mice, which was associated with reduced body fat and bone mass loss. Additionally, Zeb2[+/-] mice presented severe gut microbiota dysbiosis, as indicated by the depletion of beneficial Actinobacteria and Bifidobacterium and increases in the abundances of the proinflammatory Proteobacteria and Rikenella. These microbial shifts correlated with impaired intestinal development and key growth indicators. Our findings delineate a pathological cascade wherein Zeb2 haploinsufficiency disrupts nutrient absorption and bone homeostasis, while concomitant dysbiosis likely exacerbates intestinal dysfunction, collectively driving growth retardation. The model we developed can provide a platform for exploring therapeutic interventions targeting nutritional support and microbiome modulation in MWS.},
}

Animals
*Gastrointestinal Microbiome
Mice
Disease Models, Animal
Zinc Finger E-box Binding Homeobox 2/genetics/metabolism
Dysbiosis
Haploinsufficiency
Bone and Bones/pathology
*Intestinal Absorption
*Nutrients/metabolism
*Hirschsprung Disease/microbiology/genetics/metabolism/pathology
Bone Density
Male
*Growth Disorders

@article {pmid40846688,
year = {2025},
author = {Ding, SQ and Lei, Y and Zhao, ZM and Li, XY and Lang, JX and Zhang, JK and Li, YS and Zhang, CD and Dai, DQ},
title = {Crosstalk Between Microbiome and Ferroptosis in Diseases: From Mechanism to Therapy.},
journal = {Comprehensive Physiology},
volume = {15},
number = {4},
pages = {e70042},
doi = {10.1002/cph4.70042},
pmid = {40846688},
issn = {2040-4603},
support = {81972322//National Natural Science Foundation of China/ ; JYTMS20230108//Scientific Study Project for Institutes of Higher Learning, Ministry of Education, Liaoning Province/ ; RXXM202302//Young Backbone Talents of China Medical University/ ; 2023-MS-163//Liaoning Provincial Natural Science Foundation/ ; },
mesh = {*Ferroptosis/physiology ; Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; Iron/metabolism ; Dysbiosis/metabolism ; Reactive Oxygen Species/metabolism ; *Microbiota/physiology ; Lipid Peroxidation ; },
abstract = {The human microbiome is a unique organ and maintains host immunomodulation and nutrient metabolism. Structural and functional microbiome alterations are commonly known as dysbiosis, which is strongly associated with disease progression. Ferroptosis is a novel iron-dependent cell death mode characterized by intracellular iron accumulation, increased reactive oxygen species (ROS), and lipid peroxidation (LPO). Importantly, the complex crosstalk between the microbiome and ferroptosis in disease has attracted considerable research attention. The microbiome influences ferroptosis by regulating host iron homeostasis, mitochondrial metabolism, and LPO, among many other pathways. Thus, the in-depth analysis of microbiome-ferroptosis crosstalk and associated mechanisms could provide new strategies to treat human diseases. Therefore, understanding this crosstalk is critical. Here, we systematically explore the associations between gut microbiome and ferroptosis across multiple diseases. We show that the oral microbiome also influences disease progression by regulating ferroptosis. Furthermore, we provide a potential for certain disease therapies by targeting the crosstalk between the microbiome and ferroptosis.},
}

*Ferroptosis/physiology
Humans
*Gastrointestinal Microbiome/physiology
Animals
Iron/metabolism
Dysbiosis/metabolism
Reactive Oxygen Species/metabolism
*Microbiota/physiology
Lipid Peroxidation

@article {pmid40846661,
year = {2025},
author = {Qin, Q and Zhu, Y and Yang, L and Guo, R and Song, L and Wang, D and Li, W},
title = {Oral microbiome between patients with non-obstructive and obstructive hypertrophic cardiomyopathy.},
journal = {Chinese medical journal},
volume = {},
number = {},
pages = {},
pmid = {40846661},
issn = {2542-5641},
abstract = {BACKGROUND: The profile and clinical significance of the oral microbiome in patients with non-obstructive hypertrophic cardiomyopathy (noHCM) and obstructive hypertrophic cardiomyopathy (oHCM) remain unexplored. The objective of this study was to evaluate the difference of oral microbiome between noHCM and oHCM patients.

METHODS: This cross-sectional study enrolled 18 noHCM patients and 26 oHCM patients from Fuwai Hospital, Chinese Academy of Medical Sciences between 2020 and 2021. Clinical and periodontal evaluations were conducted, and subgingival plaque samples were collected. Metagenomic sequencing and subsequent microbial composition and functional analyses were performed.

RESULTS: Compared to oHCM patients, those with noHCM had higher systolic blood pressure (138.1 ± 18.8 mmHg vs. 124.2 ± 13.8 mmHg, P = 0.007), a larger body circumference (neck circumference: 39.2 ± 4.0 cm vs. 35.1 ± 3.7 cm, P = 0.001; waist circumference: 99.7 ± 10.5 cm vs. 92.2 ± 10.8 cm, P = 0.027; hip circumference: 102.5 ± 5.6 cm vs. 97.5 ± 9.1 cm, P = 0.030), a greater left ventricular end-diastolic diameter (46.6 ± 4.9 mm vs. 43.1 ± 4.9 mm, P = 0.026), and a lower left ventricular ejection fraction (64.1 ± 5.7 % vs. 68.5 ± 7.8%, P = 0.048). While overall biodiversity and general microbial composition were similar between the noHCM and oHCM groups, ten taxa displayed significant differences at the genus and species levels, with Porphyromonas gingivalis showing the highest abundance and greater enrichment in noHCM (relative abundance: 7.79535 vs. 4.87697, P = 0.043). Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis identified ten distinct pathways, with pathways related to energy and amino acid metabolism being enriched in oHCM patients, and those associated with genetic information processing less abundant in the oHCM group. Metabolic potential analysis revealed ten significantly altered metabolites primarily associated with amino sugar and nucleotide sugar metabolism, porphyrin metabolism, pentose and glucuronate interconversion, and lysine degradation.

CONCLUSIONS: The higher abundance of Porphyromonas gingivalis, which is known to impact cardiovascular health, in noHCM patients may partially account for clinical differences between the groups. Pathway enrichment and metabolic potential analyses suggest microbial functional shifts between noHCM and oHCM patients, potentially reflecting inherent metabolic changes in HCM.},
}

@article {pmid40846393,
year = {2025},
author = {McEwan, AG and Hosmer, J and Kappler, U},
title = {Molecular and cellular biology of bacterial lactate metabolism.},
journal = {Advances in microbial physiology},
volume = {87},
number = {},
pages = {299-355},
doi = {10.1016/bs.ampbs.2025.07.001},
pmid = {40846393},
issn = {2162-5468},
mesh = {*Lactic Acid/metabolism ; Humans ; *Bacteria/metabolism/genetics/enzymology ; Animals ; Gene Expression Regulation, Bacterial ; Bacterial Proteins/metabolism/genetics ; },
abstract = {Lactate is a key metabolite that is used as a carbon and energy source. It can also be generated as a metabolic end product, through reduction of pyruvate. Bacterial enzymes involved in lactate generation are classified as NAD[+]-dependent lactate dehydrogenases and are generally involved in production of lactate during fermentation, while NAD[+]-independent lactate dehydrogenases are involved in oxidation of lactate that is linked to reduction of quinone in respiratory or photosynthetic electron transport pathways, or in anaerobic lactate oxidation linked to electron bifurcation during heterotrophic growth. Enzymes specific for D-lactate, L-lactate or both stereoisomers exist and interconversion of D- and L- stereoisomers is catalyzed by a lactate racemase. Expression of operons encoding enzymes and transporters involved in lactate metabolism is regulated in several ways that can include sensing of the presence of L- or D- lactate by transcriptional regulators, control of gene expression through global regulators of carbon metabolism and regulators that respond to iron availability. Sensing of lactate also appears to be an important cue for changes in cell physiology and behavior and in some bacteria it has been shown to influence biofilm formation. Lactate plays a key role in the maintenance of human microbiomes in different niches and dysbiosis is often a result of an imbalance between lactate production and lactate consumption, which is linked to certain pathologies. Lactate is also an important carbon source for some bacterial pathogens and L-lactate has been shown to play a role in the pathogenesis in animal models of infection. Additionally, L-lactate produced by macrophages, neutrophils and epithelial cells may provide an important carbon source of the survival and growth of intracellular pathogens. Understanding of lactate metabolism at the biochemical, cellular and organismal/community level is of major importance in understanding and management of health and disease and in understanding environmental processes.},
}

*Lactic Acid/metabolism
Humans
*Bacteria/metabolism/genetics/enzymology
Animals
Gene Expression Regulation, Bacterial
Bacterial Proteins/metabolism/genetics

@article {pmid40846283,
year = {2025},
author = {Aumeran, C and Hamilton, L and Jamieson, L and Speake, E and Dancer, SJ},
title = {What is the viable microbiome of the healthcare toilet?.},
journal = {The Journal of hospital infection},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhin.2025.07.031},
pmid = {40846283},
issn = {1532-2939},
abstract = {BACKGROUND: Flushing water toilets in hospitals cater for staff, patients, including disabled and unisex facilities. The recent introduction of unisex toilets has highlighted potential microbiological risks between different bathroom facilities. This project sought to establish the cultivable microbiome in all types of healthcare toilet.

METHODS: Systematic sampling was performed using quantitative and qualitative microbiology within a multisite longitudinal study. Hand-touch sites, low sites (floors) and high sites (ceilings) in male/female staff and patient, unisex and disabled facilities were screened in three hospitals. Aerobic colony count (ACC) was determined alongside identification of key pathogens (Staphylococcus aureus, enterobacteriaceae, enterococci, Stenotrophomonas, Acinetobacter and fungi). Bacterial pathogens were tested for antimicrobial susceptibilities.

RESULTS: Expected environmental and skin flora were present at all sites. Bioburden was heaviest on floors, closely followed by ceilings. Hand-touch sites were cleanest (<2.5 cfu/cm[2]) in all toilets (p=0.003), with those in female toilets cleaner than male (p=0.008). Highest bioburden overall (>12 cfu/cm[2]) occurred in unisex toilets, followed by male toilets. Flora at high sites was almost identical to that on floors. Bacterial pathogens, including resistant bacteria, were concentrated on patient floors, with 80% isolated alongside ACC>2.5 cfu/cm[2]. Seven of eight Stenotrophomonas maltophilia were recovered from gender-neutral toilets. S. aureus predominated on floors and hand-touch sites in male staff and disabled toilets (p=0.02 and p<0.001, respectively).

CONCLUSION: Cleaning frequencies should be modelled against higher bioburden (unisex) and risk of pathogens (patient toilets). Similar flora on floors and ceilings suggested aerosolization during flushing. The data provides evidence to inform bathroom design, designation and decontamination practices.},
}

@article {pmid40846075,
year = {2025},
author = {Yusta, B and Wong, CK and Matthews, D and Koehler, JA and Baggio, LL and Bang, KWA and Drucker, DJ},
title = {GLP-1R signaling does not modify the severity of experimental graft versus host disease.},
journal = {Molecular metabolism},
volume = {},
number = {},
pages = {102235},
doi = {10.1016/j.molmet.2025.102235},
pmid = {40846075},
issn = {2212-8778},
abstract = {OBJECTIVE: Glucagon-like peptide-1 (GLP-1) reduces systemic and gut inflammation. Here we assessed whether gain or loss of GLP-1R signaling modifies the extent of gut injury and inflammation in experimental murine acute graft vs. host disease (aGvHD).

METHODS: Allogeneic hematopoietic cell transplantation (HCT) was performed using bone marrow and splenocytes from BALB/c donors to induce aGvHD in C57BL/6 recipients or vice versa. Chimerism was determined by flow cytometry analysis of immune cell compartments. Inflammation was assessed by histological scoring of gut mucosal damage and by measuring circulating cytokine levels. qPCR was used to quantify gene expression in small intestine immune cells and tissues. The gut microbiome was assessed by 16S rRNA sequencing.

RESULTS: Allogeneic chimerism was greater than 90% in peripheral blood and in the gut epithelial compartment. Levels of Glp1r mRNA transcripts were induced in the ileum of both vehicle- and semaglutide-treated allogeneic mice, reflecting that allogeneic T cells homing to the gut express a functional GLP-1R. Nevertheless, semaglutide did not attenuate the severity of systemic cytokine induction, gut injury or inflammation, or the extent of aGvHD in the gut mucosa. Loss of GLP-1R signaling in donor cells had limited effects on overall microbial diversity during acute GvHD, and semaglutide-treated mice exhibited modest changes in proportions of microbial species.

CONCLUSIONS: Although gut T cells express a functional GLP-1R, GLP-1R signaling has no meaningful impact on systemic or intestinal inflammation or microbiota composition in mice with experimental aGvHD, highlighting that the anti-inflammatory actions of GLP-1 medicines are highly context-dependent.},
}

@article {pmid40846055,
year = {2025},
author = {Nehme Marinho, M and Perdomo, MC and Souza Simões, B and Husnain, A and Arshad, U and Figueiredo, CC and Peixoto, PM and Monteiro, HF and Anderson, B and Santos, JEP},
title = {Impact of dietary supplementation of rumen native microbes on ruminal microbiome, ruminal fermentation, and total-tract digestibility in Holstein cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-26900},
pmid = {40846055},
issn = {1525-3198},
abstract = {Dietary microbial additives often benefit production performance in dairy cows. The objectives were to determine the effects of microbial additives on rumen microbial diversity, total-tract digestibility, incorporation of dietary N into milk N, and serum metabolites. One-hundred and 17 cows at 61 d postpartum (31-87 d) were blocked by parity group and pretreatment ECM yield. Within block, cows were randomly assigned to receive 100 g of corn meal containing no microbial additive (CON; n = 40), 100 g of corn meal containing 5 g of a mixture of Clostridium beijerinckii and Pichia kudriavzevii (G1; 4 × 10[7] cfu of C. beijerinckii and 1 × 10[9] cfu of P. kudriavzevii; n = 38), or 100 g of corn meal containing 5 g of a mixture of C. beijerinckii, P. kudriavzevii, Butyrivibrio fibrisolvens, and Ruminococcus bovis (G2; 4 × 10[7] cfu of C. beijerinckii, 1 × 10[9] cfu of P. kudriavzevii, 1 × 10[8] cfu of B. fibrisolvens, and 1 × 10[8] cfu of R. bovis; n = 39). Treatments were top-dressed for 140 d. Total-tract digestibility and rumen microbial composition were evaluated on d 61 and 124 of the experiment. Orthogonal contrasts compared the effect of microbial additive (MA) and the type of microbial additive (TMA). On experimental d 61, supplementing MA did not influence rumen microbial diversity, although cows fed G2 had a less diverse microbiome than those fed G1. On d 124, both MA and TMA reduced evenness, which resulted in lesser microbial α-diversity in cows supplemented with MA than those in CON. Minor differences were observed in rumen microbial β-diversity, except for multiparous cows on d 124 in which treatment tended to affect diversity because 16 amplicon sequence variant (ASV) groups representing phylogenetically related ASV differed among treatments. Two bacteria supplemented in G2, also native to the rumen, were identified, B. fibrisolvens and R. bovis, but treatment did not affect their abundance. Cows fed MA had increased total short-chain fatty acid concentration and partition of dietary N into milk N on d 61, but not on d 124. On d 61, feeding MA increased milk N secretion by 10 g/d (187 g/d vs. 193 g/d vs. 201 g/d), and incorporation of dietary N into milk N by 1.7 percentage units (CON = 30.8% vs. G1 = 31.2% vs. G2 = 33.7%). An interaction between TMA and parity affected the estimated microbial N production on d 124 because of the differences between G1 and G2 in primiparous cows (G1 = 302 g/d vs. G2 = 264 g/d). Type of MA affected digestibility on d 124, but the effect differed with parity. Feeding G1 increased digestibility of DM, OM, and CP in primiparous cows by 2.7, 2.8, and 4.7 percentage units, but not in multiparous cows. Collectively, supplementing diets of dairy cows with MA resulted in minor effects on the composition of the ruminal microbiota, total-tract digestibility, and use of dietary N. Present findings might not fully explain differences in production performance previously observed with the same MA added to the diet of cows.},
}

@article {pmid40845690,
year = {2025},
author = {Wang, Z and Sun, Y and Zhang, X and Wang, L and Song, D and Yu, J and Hu, X and Lin, W and Wei, R},
title = {Exploring potential therapeutic targets for myopia: Causal analysis and biological annotation with gut microbiota.},
journal = {Computational biology and chemistry},
volume = {120},
number = {Pt 1},
pages = {108634},
doi = {10.1016/j.compbiolchem.2025.108634},
pmid = {40845690},
issn = {1476-928X},
abstract = {PURPOSE: This study investigates the causal relationship between gut microbiota (GM) composition and myopia development through genetic instruments, aiming to identify specific microbial taxa with therapeutic potential and elucidate their underlying biological pathways.

METHODS: We performed bidirectional two-sample Mendelian randomization (MR) using summary statistics from GWAS of 473 GM taxa (n = 5959) and myopia (26,184 cases). Inverse variance weighted (IVW) and four complementary methods assessed causality (F-statistics>10), with sensitivity analyses to validate robustness. Biological annotation integrates protein-protein interaction networks and pathway enrichment to decode mechanisms.

RESULTS: Our inverse-variance weighted Mendelian randomization analysis identified 15 microbial features exhibiting causal associations with myopia (FDR < 0.05). Protective taxa included Family Dysgonomonadaceae (OR = 0.947, 95 % CI: 0.910-0.986) and species Megamonas funiformis (OR = 0.979, 0.964-0.995), while risk-associated taxa comprised Class Omnitrophota (OR = 1.144, 1.022-1.280) and species Bacillus velezensis (OR = 1.072, 1.017-1.129). Sensitivity analyses demonstrated robustness through nonsignificant heterogeneity (Q > 0.05), absence of horizontal pleiotropy (Egger intercept P > 0.1), and no influential outliers (MR-PRESSO P > 0.3). Host genetic variants were significantly enriched in PI3K-Akt (P = 9.4 ×10⁻⁵) and Ras signaling pathways (P = 3.7 ×10⁻³). Three hub genes (PIK3R1, KITLG, and IL2RB) may mediate scleral pathogenesis through TGF-β/Smad-regulated extracellular matrix degradation and dopaminergic deficiency via downregulation of tyrosine hydroxylase. Microbial metabolic interaction analyses revealed that Megamonas-derived short-chain fatty acids suppressed PI3K-Akt/HDAC signaling (β = -0.27 ± 0.08, P = 0.002). In contrast, the risk-associated taxon Prevotella massilia elevated oxidative stress markers via indole-3-acetate/AhR activation (β = 0.34 ± 0.12, P = 0.009).

CONCLUSION: This first MR-biological annotation study revealed a degree of congruence between microbiota-associated host genes and the PI3K-Akt/Ras-driven scleral-immune dysregulation in ocular signaling pathways. The findings of Megamonas-derived SCFAs as therapeutic targets provide a viable approach for addressing myopia through microbiome intervention.},
}

@article {pmid40845418,
year = {2025},
author = {Minari, TP and Pisani, LP},
title = {Skipping breakfast and its wide-ranging health consequences: A systematic review from multiple metabolic disruptions to socioeconomic factors.},
journal = {Nutrition research (New York, N.Y.)},
volume = {141},
number = {},
pages = {34-45},
doi = {10.1016/j.nutres.2025.07.006},
pmid = {40845418},
issn = {1879-0739},
abstract = {Skipping breakfast has been widely debated due to its potential health consequences across multiple domains. This systematic review evaluates literature from 2010 to 2025, analyzing 66 studies to assess its associations with obesity, diabetes, gut microbiome alterations, neurodegenerative diseases, cancer, sports performance, psychiatric disorders, cognitive health, and socioeconomic factors. The hypothesis suggests that breakfast omission is linked to various adverse health effects. Evidence highlights associations with obesity and weight gain due to altered hormonal responses influencing hunger and energy balance. Additionally, skipping breakfast negatively affects gut microbiota, contributing to systemic inflammation and metabolic dysfunction. Research suggests potential links to increased cancer risk through inflammatory pathways, while cognitive decline, mood disorders, and impaired athletic performance are also observed. Psychiatric disorders, including anxiety and depression, may be exacerbated by irregular meal patterns, influencing neurotransmitter regulation. Emerging studies indicate that breakfast consumption plays a role in bone mineral density, as prolonged fasting periods may affect calcium metabolism and skeletal health. Socioeconomic disparities impact breakfast consumption, affecting diet quality and overall health outcomes. While some individuals experience neutral or even beneficial effects, meal timing and caloric distribution play critical roles in metabolic and cardiovascular health. However, causality remains complex due to confounding factors like diet quality, physical activity, and socioeconomic status. Current studies face limitations, including small sample sizes and short intervention periods, requiring further research to refine conclusions and explore long-term mechanisms behind breakfast omission's health impacts.},
}

@article {pmid40845404,
year = {2025},
author = {Yang, Y and Duan, L and Ding, X and Yang, X and Yang, Y and Zhao, Z and Ma, Y and Li, R},
title = {Impact of Dental Caries and Odontogenic Infections on Henoch-Schönlein Purpura in Pediatric Patients.},
journal = {International dental journal},
volume = {75},
number = {5},
pages = {100959},
doi = {10.1016/j.identj.2025.100959},
pmid = {40845404},
issn = {1875-595X},
abstract = {OBJECTIVE: To investigate the impact of dental caries and odontogenic infections on pediatric patients with Henoch-Schönlein purpura (HSP), and to preliminarily explore the relationship between dental caries and the progression of HSP in these patients.

METHODS: From September 2021 to September 2022, 45 pediatric patients diagnosed with HSP at our hospital, were enrolled in this clinical study. The patients were divided into three groups: Group A (HSP without dental caries, n = 12), Group B (HSP with dental caries, n = 18), and Group C (HSP with dental caries receiving systematic treatment for dental caries, n = 15). Clinical indicators and the recurrence of HSP were monitored at a 3-month follow-up. Additionally, the 16S rDNA high-throughput sequencing technique was used to analyze changes in the composition and diversity of oral microbiota in the saliva and dental plaque of the patients.

RESULTS: Compared to discharge, Group B showed a significant increase in urinary protein (PRO) at the 3-month follow-up (P < .05), while Group C demonstrated a notable increase in red blood cell count (RBC) and hemoglobin (HGB), along with a significant decrease in red cell distribution width coefficient of variation (RDW-CV), monocyte count, and urinary white blood cell count (UWBC) (all P < .05). The oral microbiota composition across the three groups was largely similar. However, compared to HSP patients without dental caries, those with dental caries exhibited an increased abundance of Prevotella and Streptococcus mutans, along with a trend toward reduced oral microbiota diversity. After systematic treatment for dental caries, there was a significant increase in oral microbiota diversity as measured by the Shannon index (P < .05).

CONCLUSIONS: Oral examinations and early systematic dental treatments for pediatric patients with HSP can enhance oral microbiome diversity, mitigate the impact of odontogenic foci on systemic health, and may help reduce the recurrence rate of HSP and the risk of nephritis complications.},
}

@article {pmid40845016,
year = {2025},
author = {Choovanichvong, W and Supa-Amornkul, S and Rungraungrayabkul, D and Boonyapratheeprat, N and Meenetkum, S and Boongird, S and Chuengsaman, P and Kitiyakara, C and Sangkhamanee, SS},
title = {Salivary microbiome in peritoneal dialysis patients with and without sarcopenia: A pilot study.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0330767},
doi = {10.1371/journal.pone.0330767},
pmid = {40845016},
issn = {1932-6203},
mesh = {Humans ; *Saliva/microbiology ; Female ; Male ; *Sarcopenia/microbiology/complications ; *Microbiota/genetics ; Pilot Projects ; Middle Aged ; *Peritoneal Dialysis ; RNA, Ribosomal, 16S/genetics ; Aged ; *Kidney Failure, Chronic/microbiology/complications/therapy ; Bacteria/genetics/classification/isolation & purification ; Case-Control Studies ; Adult ; },
abstract = {PURPOSE: To investigate salivary microbiota composition in end-stage kidney disease (ESKD) patients with sarcopenia (SESKD), ESKD patients without sarcopenia (NSESKD), and individuals without chronic kidney disease (control group).

MATERIALS AND METHODS: Thirty-three participants were enrolled: 10 SESKD patients, 12 NSESKD patients, and 11 controls. Demographic data, oral examinations, and unstimulated saliva samples were collected. Salivary bacterial microbiomes were analyzed using high-throughput sequencing targeting the V3-V4 region of the bacterial 16S rRNA gene.

RESULTS: The overall bacterial abundance and distribution were significantly higher in the SESKD and NSESKD groups compared to the control group (p < 0.05), with no significant differences between the SESKD and NSESKD groups. ESKD, educational level, and muscle strength were significantly associated with variations in the salivary microbiome composition. Analysis of bacterial abundance revealed a shift in trends as the disease combined from control to NSESKD and SESKD group, respectively, across 7 genera: Actinobacillus, TM7x, Capnocytophaga, Neisseria, and Leptotrichia increased in abundance, while Actinomyces and Atopobium decreased. Linear discriminant analysis effect size (LEfSe) identified Leptotrichia as a potential biomarker for ESKD (both with and without sarcopenia).

CONCLUSION: ESKD condition impacted microbial composition, with minimal influence from sarcopenia. Specifically, Leptotrichia was notably higher in the ESKD group.},
}

Humans
*Saliva/microbiology
Female
Male
*Sarcopenia/microbiology/complications
*Microbiota/genetics
Pilot Projects
Middle Aged
*Peritoneal Dialysis
RNA, Ribosomal, 16S/genetics
Aged
*Kidney Failure, Chronic/microbiology/complications/therapy
Bacteria/genetics/classification/isolation & purification
Case-Control Studies
Adult

@article {pmid40845001,
year = {2025},
author = {Zhao, Y and Tan, X and Wang, T and Yuan, Y and Su, K and Shang, E and Xiao, Q and Guo, S and Su, S and Zhang, H and Duan, JA and Liu, P},
title = {Investigating the Trichosanthis Pericarpium - Trichosanthis Radix herbal pair's role in alleviating COPD through gut microbiota function, metabolomics analysis and cell validation experiment.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0330621},
doi = {10.1371/journal.pone.0330621},
pmid = {40845001},
issn = {1932-6203},
mesh = {*Pulmonary Disease, Chronic Obstructive/drug therapy/metabolism/microbiology ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Rats ; Metabolomics ; Male ; *Trichosanthes/chemistry ; Rats, Sprague-Dawley ; Humans ; Lung/metabolism/drug effects ; Disease Models, Animal ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The herbal pair of Trichosanthis Pericarpium - Trichosanthis Radix (TP-TR) is derived from the classic prescription Bei-Mu-Gua-Lou-San in Yixue Xinwu, which is commonly used to treat lung heat and cough. Both originate from Trichosanthes kirilowii Maxim, a medicinal plant known for its effects to clear heat, dissolve phlegm, promote salivation, and relieve dryness. However, the compatibility, pharmacological synergy and gut-lung axis regulation mechanisms of TP-TR remain unclear. This study innovatively explores the therapeutic effects and underlying mechanisms of TP-TR in COPD through microbiome and amino acid metabolism. A COPD rat model was established to evaluate the efficacy of TP-TR. The gut microbiota was analyzed with 16S rRNA sequencing, while the metabolites in serum and lung were analyzed by UPLC-MS/MS. Functional prediction of the microbiome and differential metabolite analysis were performed using KEGG/SMP. The LPS, CSE - induced cell model was used to validate the impact of TP-TR and its active components on amino acid metabolism. The results demonstrated that TP-TR significantly improved pulmonary function, alleviated inflammation, modulated gut microbiota composition (e.g., Lactobacillus, g_ Novosphingobium), and regulated metabolic disturbances in COPD rats. Notably, amino acid metabolic pathways were consistently enriched across microbiota function prediction and untargeted metabolomic analyses of serum and lung. Targeted metabolomics further confirmed alterations in amino acid levels. Moreover, TP-TR, along with cucurbitacin B, cynaroside, glutamine, guanine, and apigenin induced alterations in the amino acid content of model cells. These findings reveal a novel mechanism by which TP-TR ameliorates COPD through gut microbiota regulation and amino acid metabolism modulation along the gut-lung axis.},
}

*Pulmonary Disease, Chronic Obstructive/drug therapy/metabolism/microbiology
*Gastrointestinal Microbiome/drug effects
Animals
*Drugs, Chinese Herbal/pharmacology/therapeutic use
Rats
Metabolomics
Male
*Trichosanthes/chemistry
Rats, Sprague-Dawley
Humans
Lung/metabolism/drug effects
Disease Models, Animal
RNA, Ribosomal, 16S/genetics

@article {pmid40844740,
year = {2025},
author = {Wu, J and Zhang, X and Tan, Z and Jiao, J and Zhou, C},
title = {Microbiome-host co-oscillation patterns in shaping ruminal ecosystem from birth to puberty in a goat model.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40844740},
issn = {1869-1889},
abstract = {The maturation of the gastrointestinal tract and its interconnected microbial consortia in various ruminant species is essential for their survival and productivity, as this symbiotic group plays a key role in metabolizing phyto-derived feeds into bioavailable nutrients. The rumen mucosa serves as a crucial conduit for complex host-microbiota interplay, while scarce knowledge is available regarding their co-oscillation patterns from birth to puberty. Here, we characterized th overall interaction of five age groups, from 1-day-old to 90-day-old goats. The findings indicated that the composition of the mucosa-attached microbiota underwent significant changes, with Mannheimia, Porphyromonas and Streptococcus taking the lead as the dominant genera at day 1, Akkermansia muciniphila and Lactobacillus amylovorus dominated at day 10, and a mature microbiota characterized by Succiniclasticum ruminis, Ruminococcus albus, Succinivibrio dextrinosolvens, and Fibrobacter succinogenes until day 90. Additionally, the rumen mucosa underwent a three-phase temporal shift during early life, from digestive system to immune development, and finally to nutrient metabolism. Furthermore, the integration of mucosal microbiome and host gene expression profiles uncovered a phase-specific interaction between the microbial community and host epithelium, with the early phase emphasizing digestive and immune development and the later phase focusing on enhanced nutrient metabolism. Collectively, microbiome-host co-oscillation in the rumen mucosa shaped the ruminal ecosystem during early life.},
}

@article {pmid40844735,
year = {2025},
author = {Bhatt, P and Rajesh, P and Kukkar, D and Kim, KH},
title = {Metagenomic profiling of gut microbime: associating their role with the advancement of diabetic nephropathy.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {9},
pages = {135},
pmid = {40844735},
issn = {1572-9699},
support = {DST/WISE-PhD/LS/2023/73/G//Department of Science and Technology, Ministry of Science and Technology, India/ ; EMDR/SG/13/2023-0756//Indian Council of Medical Research/ ; 2021R1A3B1068304//Ministry of Science, ICT and Future Planning/ ; 2022R1A6C101A779//National Center for Inter-University Research Facilities, Seoul National University/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Diabetic Nephropathies/microbiology ; *Metagenomics/methods ; Diabetes Mellitus, Type 2/microbiology/complications ; Disease Progression ; },
abstract = {Emerging evidence suggests that alterations in the gut microbiome should play a critical role in the development and progression of type 2 diabetes and its complication such as diabetic nephropathy (DN). Nevertheless, a considerable gap remains in our understanding of the interconnection between DN pathogenesis and gut microbiota arrangement. In this context, this review highlights recent research on the connection between the intestinal microbiota and DN risk, with a particular focus on the role of microbial metabolites in disease development. It also highlights recent advancements in metagenomic analyses of gut microbial communities and their potential contribution to the progression of DN. Further, it describes the challenges associated with the metagenomics-based analysis of intestinal microbiota and the advancement of therapeutics for DN. An exploration of the surveyed literature reveals the lack of any definitive correlation between gut microbiota and DN transition, even when assessed in view of widespread geographical and ethnic diversity. Future research in this domain should be conducted to address various issues like increasing the number of participants, intake patient diversity, logistical difficulties, and racial disparities. A critical assessment of these parameters will help improve our understanding of the potential contribution of gut microbiota to the DN progression.},
}

*Gastrointestinal Microbiome/genetics
Humans
*Diabetic Nephropathies/microbiology
*Metagenomics/methods
Diabetes Mellitus, Type 2/microbiology/complications
Disease Progression

@article {pmid40844321,
year = {2025},
author = {Tanes, C and Li, Y and Falk, GW and Ginsberg, GG and Wang, KK and Iyer, PG and Lightdale, CJ and Del Portillo, A and Lagana, SM and Wang, TC and Rustgi, AK and Quante, M and Jin, Z and Wu, GD and Friedman, ES and Bittinger, K and Li, H and Abrams, JA},
title = {Increased reflux secondary bile acids are associated with changes to the microbiome and transcriptome in Barrett's esophagus.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2545420},
doi = {10.1080/19490976.2025.2545420},
pmid = {40844321},
issn = {1949-0984},
mesh = {Humans ; *Barrett Esophagus/microbiology/metabolism/pathology/genetics ; *Bile Acids and Salts/metabolism/analysis ; Male ; Female ; Middle Aged ; Aged ; Cross-Sectional Studies ; *Transcriptome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Gastrointestinal Microbiome ; *Gastroesophageal Reflux/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; Esophageal Neoplasms/microbiology ; Adenocarcinoma/microbiology ; },
abstract = {Bile acids are a major component of gastro-esophageal refluxate, thought to contribute to the development of Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC). As the microbiome shifts with EAC progression and bile acids influence bacterial composition, we examined these connections in a multi-center, cross-sectional study. We analyzed biospecimens from patients undergoing endoscopy using LC-MS to quantify bile acids in gastric aspirates, 16S rRNA sequencing for tissue microbiome profiling, and RNA sequencing on BE or cardia tissue. Among 153 patients (52 controls, 101 BE: 50 no dysplasia, 10 indefinite, 17 low-grade dysplasia, 17 high-grade dysplasia, and 7 EAC), we observed increased Streptococcus in BE tissue; dysplasia and EAC were associated with more Lactobacillus and decreased Actinomyces and other genera. Refluxate bile acids were mainly conjugated, indicating minimal bacterial metabolism, while BE patients had elevated secondary bile acid levels. Streptococcus correlated with upregulation of IL6, FGF2, and HGF, and decreased Actinomyces showed the most associations with gene expression, including the oxidative phosphorylation pathway. We identified two distinct BE gene expression clusters independent of histology, bile acid, or microbiome composition. These findings suggest bile acids shape the BE microbiome and associate with gene expression changes potentially relevant to EAC development.},
}

Humans
*Barrett Esophagus/microbiology/metabolism/pathology/genetics
*Bile Acids and Salts/metabolism/analysis
Male
Female
Middle Aged
Aged
Cross-Sectional Studies
*Transcriptome
*Bacteria/classification/genetics/isolation & purification/metabolism
*Gastrointestinal Microbiome
*Gastroesophageal Reflux/microbiology/metabolism
RNA, Ribosomal, 16S/genetics
Esophageal Neoplasms/microbiology
Adenocarcinoma/microbiology

@article {pmid40844032,
year = {2025},
author = {Perneel, M and Alexander, H and Hablützel, PI and Maere, S},
title = {A case for absolute gene expression estimates in microbiome studies using metatranscriptomics.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf188},
pmid = {40844032},
issn = {1751-7370},
abstract = {Metatranscriptomics is widely used to study the functional dynamics of microbial communities in their natural environment [1-6]. Changes in gene expression in microbial communities can be subdivided in two main categories: per capita changes at the cellular or organismal scale in response to developmental cues and environmental signals, and changes mediated by population dynamics and taxonomic shifts. In this perspective, we argue that understanding the effects of population dynamics on gene expression patterns benefits from the estimation of absolute transcript abundances, augmenting the relative expression measures that are commonly used. We use a recent study on the seasonal dynamics of metabolic activity and species turnover of microeukaryotic surface plankton in the southern North Sea as an example [7].},
}

@article {pmid40843723,
year = {2025},
author = {Fetarayani, D and Kahdina, M and Waitupu, A and Pratiwi, L and Ningtyas, MC and Adytia, GJ and Sutanto, H},
title = {Immunosenescence and the Geriatric Giants: Molecular Insights into Aging and Healthspan.},
journal = {Medical sciences (Basel, Switzerland)},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/medsci13030100},
pmid = {40843723},
issn = {2076-3271},
mesh = {Humans ; *Immunosenescence/immunology ; *Aging/immunology ; Immunity, Innate ; Geriatrics ; Aged ; },
abstract = {Aging is associated with complex immune dysfunction that contributes to the onset and progression of the "geriatric giants", including frailty, sarcopenia, cognitive decline, falls, and incontinence. Central to these conditions is immunosenescence, marked by thymic involution, the loss of naïve T cells, T-cell exhaustion, impaired B-cell class switch recombination, and increased autoreactivity. Concurrently, innate immunity deteriorates due to macrophage, neutrophil, and NK cell dysfunction, while chronic low-grade inflammation-or "inflammaging"-amplifies systemic decline. Key molecular pathways such as NF-κB, mTOR, and the NLRP3 inflammasome mediate immune aging, interacting with oxidative stress, mitochondrial dysfunction, and epigenetic modifications. These processes not only impair infection control and vaccine responsiveness but also promote tissue degeneration and multimorbidity. This review explores emerging interventions-ranging from senolytics and immunonutrition to microbiome-targeted therapies and exercise-that may restore immune homeostasis and extend healthspan. Despite advances, challenges remain in translating immunological insights into clinical strategies tailored to older adults. Standardization in microbiome trials and safety optimization in senolytic therapies are critical next steps. Integrating geroscience into clinical care could help to mitigate the burden of aging-related diseases by targeting fundamental drivers of immune dysfunction.},
}

Humans
*Immunosenescence/immunology
*Aging/immunology
Immunity, Innate
Geriatrics
Aged

@article {pmid40843619,
year = {2025},
author = {DE, A and Sahu, AK and Singh, VK},
title = {Bite size of Caenorhabditis elegans regulates feeding, satiety and development on a diet of live yeast.},
journal = {Journal of biosciences},
volume = {50},
number = {},
pages = {},
pmid = {40843619},
issn = {0973-7138},
mesh = {Animals ; *Caenorhabditis elegans/microbiology/physiology/growth & development ; Saccharomyces cerevisiae ; *Feeding Behavior/physiology ; Gastrointestinal Microbiome/physiology ; Larva/microbiology/growth & development/physiology ; Cryptococcus/pathogenicity ; Diet ; Escherichia coli ; Intestines/microbiology ; },
abstract = {In the wild, the nematode Caenorhabditis elegans primarily feeds on microbes, which are abundant in rotting vegetation. Studies show that several gram-positive and gram-negative bacterial populations predominantly constitute the C. elegans gut microbiome, but surprisingly lack any yeast species. To understand the lack of yeast in the intestine of C. elegans, we studied the behaviour of worms on pathogenic and non-pathogenic yeast diets. We show that C. elegans displays low satiety on a yeast diet of Cryptococcus neoformans, Cryptococcus laurentii or Saccharomyces cerevisiae. We find that the average size of cells of budding yeast is much larger than that of Escherichia coli, which constitute the laboratory diet of C. elegans. We have shown that yeast cells cause pharyngeal obstruction, diminished feeding, and lower level of neutral lipids in adult C. elegans. Using scanning electron microscopy, we show that the mouth size of C. elegans larvae is smaller than the average yeast cell. The larvae have no detectable yeast in their alimentary canal, and they undergo delayed development on a yeast diet. We propose that microbial cell size or bite size could be crucial factors in the regulation of feeding in C. elegans, and the composition of the microbiome in its intestine.},
}

Animals
*Caenorhabditis elegans/microbiology/physiology/growth & development
Saccharomyces cerevisiae
*Feeding Behavior/physiology
Gastrointestinal Microbiome/physiology
Larva/microbiology/growth & development/physiology
Cryptococcus/pathogenicity
Diet
Escherichia coli
Intestines/microbiology

@article {pmid40843233,
year = {2025},
author = {Nong, Y and Sugarman, J and York, JP and Levy-Hacham, O and Nadora, D and Mizrahi, R and Galati, A and Gallo, RL and Sivamani, RK},
title = {Impact of Microencapsulated Benzoyl Peroxide on the Skin Microbiome and Clinical Outcomes in Rosacea: An Update on a Randomized, Double-blind, Crossover, Vehicle-controlled Clinical Trial.},
journal = {The Journal of clinical and aesthetic dermatology},
volume = {18},
number = {8},
pages = {34-40},
pmid = {40843233},
issn = {1941-2789},
abstract = {OBJECTIVE: We sought to evaluate changes in skin microbiome biodiversity and correlation with rosacea improvement of microencapsulated benzoyl peroxide (E-BPO) versus vehicle cream in rosacea patients in a 12-week crossover study with a no-treatment period of four weeks (Week 16).

METHODS: This was a randomized, double-blind, single-center, crossover, vehicle-controlled evaluation of E-BPO on the skin microbiome in rosacea. Thirty-one participants had facial rosacea with global severity of 3 or 4 on the Investigator's Global Assessment (IGA) scale. Participants were randomly assigned to two groups. The E-BPO/vehicle group applied E-BPO for eight weeks, then vehicle for four weeks. The vehicle/E-BPO group applied vehicle for eight weeks, then E-BPO for four weeks. Clinical assessments were performed using IGA, inflammatory rosacea scale, and erythema scale. Determination of change in skin microbiome was based on facial swab sampling.

RESULTS: Shifts in the microbiome correlated with improvements in IGA, inflammatory rosacea, and erythema. At Week 8, similar bacterial species diversity profiles were observed among all participants. After crossover of the vehicle/E-BPO group at eight weeks to E-BPO, the relative abundance of Staphylococcus epidermidis was markedly lowered, and the relative abundance of Cutibacterium acnes was slightly increased. In the E-BPO/vehicle group, the relative abundance of S. epidermidis and C. acnes at Weeks 12 and 16 remained at the level observed at Week 8.

LIMITATIONS: The study had a short duration, which may not fully capture the long-term effects and durability of E-BPO in real-world clinical practice.

CONCLUSION: Even after withdrawal at 16 weeks, efficacy and shifts in the skin microbiome were maintained over the duration of the study period with demonstrated clinical improvement and a well-tolerated safety profile.},
}

@article {pmid40843200,
year = {2025},
author = {Zhao, Y and Li, X and Liu, Y and Wang, Q and Zhao, J and Pan, H and Chen, H and Liu, B and Qiao, W and Lin, L and Jin, Y and Chen, L},
title = {High-calcium milk improves osteoporosis in postmenopausal women by regulating intestinal flora and steroid hormone biosynthesis.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1607968},
pmid = {40843200},
issn = {2296-861X},
abstract = {BACKGROUND: Postmenopausal calcium loss increases osteoporosis risk in middle-aged and older women. While dairy products are a known calcium source that supports bone health, limited research addresses their specific effects on osteoporosis prevention in this population.

METHODS: A one-year randomized controlled trial recruited 97 postmenopausal women, randomly assigned to a high-calcium milk group (HCM, 51), consuming 400 mL nutrient-enriched fresh milk daily, or a control milk group (CM, 46), consuming 400 mL of regular fresh milk.

RESULTS: A one-year randomized controlled trial showed that the high-calcium milk group significantly increased lumbar spine bone mineral density (L1-4 BMD), slowed bone loss in the left hip and femoral neck, elevated serum phosphorus and 25-hydroxyvitamin D levels, and modulated the bone formation marker procollagen type I N-terminal propeptide compared with the regular milk group at 6 months. 16S ribosomal ribonucleic acid sequencing showed that high-calcium milk significantly altered the β-diversity of the intestinal flora, increasing the abundance of beneficial bacteria such as Bacteroides, Oscillibacter, and Subdoligranulum, while decreasing the abundance of Firmicutes and Weissella at 12 months. Metabolomics analysis revealed that high-calcium milk improved bone quality by modulating steroid hormone biosynthesis and arachidonic acid metabolic pathways, and that L1-4 BMD was positively correlated with Faecalibacterium spp. and adenine nucleotide.

CONCLUSIONS: Our study suggests that high-calcium milk can effectively delay postmenopausal osteoporosis by regulating intestinal flora and metabolic pathways, providing a new target for osteoporosis intervention.

ChiCTR2200064825 (https://www.chictr.org.cn/bin/home).},
}

@article {pmid40843192,
year = {2025},
author = {Zhou, X and Wang, S and Wang, X and Chen, X and Zhou, P and Ma, K and Zhang, P},
title = {Mechanisms of the effect of gut microbes on depression through the microbiota-gut-brain axis.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1634548},
pmid = {40843192},
issn = {2296-861X},
abstract = {Depression is a significant public health issue which exerts profound psychological and social impacts on both individuals and society. However, existing therapeutic strategies often exhibit limited efficacy. Accumulating evidence underscores the vital role of gut microbiota in the pathophysiology of depression through the microbiota-gut-brain (MGB) axis. This involves multiple mechanisms, including short-chain fatty acid (SCFA) metabolism, communication via the vagal nerve, regulation of the hypothalamic-pituitary-adrenal (HPA) axis, and immune-inflammatory interactions. This review provides a comprehensive review of the mechanisms through which gut microbiota influences depression via the MGB axis. It synthesizes recent achievements in this field and evaluates the potential of microbiome-targeted therapies for depression treatment. Furthermore, it outlines future research directions to establish a theoretical framework for novel therapeutic approaches and to foster the development of this area.},
}

@article {pmid40842975,
year = {2025},
author = {Tu, J and Yu, L and Zou, R and He, J and Qu, C},
title = {Influence of the gut microbiome on lymphoma treatment: current evidence and future therapeutic directions.},
journal = {Therapeutic advances in medical oncology},
volume = {17},
number = {},
pages = {17588359251363207},
pmid = {40842975},
issn = {1758-8340},
abstract = {The heterogeneity of lymphoma responses to various treatments remains a significant challenge in clinical practice. Emerging evidence implicates the potential role of the gut microbiome in lymphoma pathogenesis and progression. Advances in high-throughput sequencing and metabolomics have significantly enhanced our understanding of the complex interaction between the gut microbiome and lymphoma. Although causality requires further elucidation, the gut microbiome critically shapes host responses to traditional combined chemotherapy, hematopoietic stem cell transplantation, and targeted therapies, including chimeric antigen receptor T-cell therapy. Notably, the use of antibiotics, particularly broad-spectrum antibiotics, can alter the gut microbiome, thereby impacting treatment efficacy. Prudent antibiotic management should balance infection control with microbiome-dependent immune homeostasis. Strategies to restore gut microbial balance through a high-fiber diet, probiotics, prebiotics, fecal microbiota transplantation, and butyrate supplementation are critically important. Integrating microbiome-based therapies into lymphoma treatment could establish low-toxicity therapeutic paradigms for lymphoma patients.},
}

@article {pmid40842971,
year = {2025},
author = {Fukuyo, M and Takahashi, N and Hanada, K and Ishikawa, K and Venclovas, Č and Yahara, K and Yonezawa, H and Terabayashi, T and Katsura, Y and Osada, N and Kaneda, A and Camargo, MC and Rabkin, CS and Uchiyama, I and Osaki, T and Kobayashi, I},
title = {Helicobacter pylori base-excision restriction enzyme in stomach carcinogenesis.},
journal = {PNAS nexus},
volume = {4},
number = {8},
pages = {pgaf244},
pmid = {40842971},
issn = {2752-6542},
abstract = {Many recent lines of evidence from the human microbiome and other fields indicate bacterial involvement in various types of cancer. Helicobacter pylori has been recognized as the major cause of stomach cancer (gastric cancer), but the mechanism by which it destabilizes the human genome to cause cancer remains unclear. Our recent studies have identified a unique family of toxic restriction enzymes that excise a base (A: adenine) from their recognition sequence (5'-GTAC). At the resulting abasic sites (5'-GT_C), its inherent endonuclease activity or that of a separate endonuclease may yield atypical strand breaks that resist repair by ligation. Here, we present evidence demonstrating involvement of its H. pylori member, HpPabI, in stomach carcinogenesis: (i) Association of intact HpPabI gene with gastric cancer in the global H. pylori Genome Project and the open genomes; (ii) Frequent mutations at A in 5'-GTAC in the gastric cancer genomes as well as in H. pylori genomes; (iii) Its induction of chromosomal double-strand breaks in infected human cells and of mutagenesis in bacterial test systems. In addition, its unique regions that interact with DNA exhibit signs of diversifying selection. Our further analysis revealed similar oncogenic bacterium-restriction-enzyme pairs for other types of cancer. These results set another stage for cancer research and medicine around oncogenic restriction enzymes.},
}

@article {pmid40842939,
year = {2025},
author = {Han, X and Shortliffe, LD and Kambham, N},
title = {Impact of Fructose-Enhanced Solid and Soft Drink Diets on Metabolism, Physiology, and Gut Microbiome in Pregnant Rats.},
journal = {BioMed research international},
volume = {2025},
number = {},
pages = {6902453},
pmid = {40842939},
issn = {2314-6141},
mesh = {Animals ; Pregnancy ; Female ; *Fructose/pharmacology/adverse effects/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Rats ; Body Weight/drug effects ; Blood Glucose/metabolism ; Rats, Sprague-Dawley ; *Diet ; Blood Pressure/drug effects ; Insulin/blood ; },
abstract = {Introduction: High fructose consumption is linked to hypertension and metabolic disorders. We hypothesize fructose (solid and/or liquid) may further influence dietary patterns. To investigate potential effects, we compared eating behaviors, physiological and metabolic measures, and gut microbiome in pregnant rats fed solid or liquid fructose-enhanced (soft drink) diets to those fed standard chow. Methods: Pregnant rats were assigned to three dietary groups: (1) standard chow and water (CW), (2) standard chow and decarbonated soft drink (CS, decarbonated Sprite with 5.89% fructose w/v), and (3) 60% fructose chow and water (FW). Body weight, blood pressure, food and liquid intake, fasting blood glucose, plasma insulin, and lipid profiles were measured weekly. Fecal samples were collected before and during pregnancy. At euthanasia, livers and kidneys were analyzed for pathological changes. Results: Data from five rats per group were analyzed. The CS group showed nearly a twofold increase in fluid intake and urinary output at midpregnancy. Both solid and liquid fructose groups had increased carbohydrate calorie intake per kilogram of body weight, while protein and fat intake decreased. Although all rats showed pregnancy-related dyslipidemia, the FW group experienced a more pronounced increase. Pregnancy and the FW diet also led to distinct shifts in the fecal gut microbiome. Conclusions: This pregnant rat model highlights the impact of varying fructose diets during physiological stress. Pregnant rats on high-fructose diets (CS, FW) increased their carbohydrate intake at the expense of protein and fat intake when compared with pregnant rats on a routine diet. CS rats showed a marked increase in soft drink intake and urine. These findings have potential nutritional and health implications for pregnancy and long-term health and warrant further investigation and confirmation.},
}

Animals
Pregnancy
Female
*Fructose/pharmacology/adverse effects/administration & dosage
*Gastrointestinal Microbiome/drug effects
Rats
Body Weight/drug effects
Blood Glucose/metabolism
Rats, Sprague-Dawley
*Diet
Blood Pressure/drug effects
Insulin/blood

@article {pmid40842843,
year = {2025},
author = {Hei, J and Li, Y and Rui, R and Faisal, N and Peng, J and Wang, B and Wang, S and He, X},
title = {The cultivation of Panax notoginseng enhances the metabolites and microbial network complexity in the soil of Pinus armandii rather than Pinus kesiya.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1616266},
pmid = {40842843},
issn = {1664-302X},
abstract = {INTRODUCTION: The species of tree most appropriate for the cultivation of Sanqi in an understory environment is pine. Nevertheless, the precise type of pine that confers the greatest benefit to soil health during Sanqi cultivation has not been definitively established.

METHODS: Herein, four distinct land use configurations were established, including the Pinus armandii, Pinus kesiya, Sanqi-Pinus armandii (SPA), and Sanqi-Pinus kesiya (SPK) systems. High-throughput sequencing technology and metabolomics analysis were used to comparatively evaluate variations in bacterial and fungal community structures and soil metabolites between the SPA and SPK systems.

RESULTS AND DISCUSSION: After cultivating Sanqi, the content of total phosphorus, ammonium nitrogen, and total potassium as well as water content and soil pH were significantly increased in P. armandii soil. Moreover, the bacterial and fungal copy numbers, alpha- and beta-diversity, remained unchanged in the soil of P. armandii, but significantly decreased in the soil of P. kesiya following Sanqi planting. Moreover, Sanqi cultivation significant increased complexity of the microbial network in P. armandii rather than P. kesiya soil, while the network stability was maintained. Structural equation modeling indicated that soil enzymes, metabolites, and edaphic factors enhanced the complexity of the microbial network in P. armandii soil in SPA system. Additionally, the content of eight differentially accumulated metabolites (DAMs) was significantly increased in the rhizosphere and bulk soils of P. armandii. In conclusion, the cultivation of Sanqi benefits the microbiome and metabolites in P. armandii rather than P. kesiya soil, thus providing an important theoretical foundation for the sustainable development of Sanqi cultivation.},
}

@article {pmid40842836,
year = {2025},
author = {Bai, Q and Zhao, Z and Duan, Y and Cai, R and Chen, Y and Zhou, C and Tian, X and Yang, Y and Wu, H and Li, M and You, J and Song, Q and Dong, H and Liu, T},
title = {Enrichment of short-chain fatty acid-producing bacteria by pH-responsive sodium alginate and chitosan-encapsulated quercetin.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1594012},
pmid = {40842836},
issn = {1664-302X},
abstract = {INTRODUCTION: Conventional approaches to treat ulcerative colitis (UC) focus on suppressing excessive inflammation and immune responses. Nevertheless, these treatments fail to address gut dysbiosis or restore the intestinal mucosal barrier effectively. Regulating the intestinal microenvironment may be pivotal to more effective therapies for UC.

METHODS: Herein, oral colon-targeted microspheres, sodium alginate-chitosan-encapsulate quercetin (SA-Q-CS MPs), were developed. The stability and pH responsiveness of SA-Q-CS MPs were explored. Therapeutic effects were assessed in dextran sulfate sodium (DSS)-induced ulcerative colitis in female C57BL/6 mice via 16S ribosomal RNA (rRNA) gene sequencing, Disease Activity Index (DAI) scoring, colonic histopathology, inflammatory and antioxidant levels, and intestinal barrier function.

RESULTS AND DISCUSSION: SA-Q-CS MPs markedly enhanced the overall richness and diversity of the gut microbiota, enhancing the abundance of short-chain fatty acids (SCFAs)-producing bacteria, such as Bacteroidales, Lactobacillales, and Lachnospiraceae. These changes contributed to improved intestinal barrier function, better metabolic processes, and stronger defense mechanisms, thereby ameliorating UC induced by 3% dextran sulfate sodium (DSS) in C57BL/6J mice. Compared to the DSS group, the SA-Q-CS MPs treatment group showed significant improvements, with the Disease Activity Index (DAI) and histopathological scores reduced by more than 66.9%, pro-inflammatory factor levels decreased by 65%, antioxidant levels increased over sevenfold, and tight junction protein expression elevated by more than threefold. In conclusion, this investigation presents SA-Q-CS MPs as a promising strategy for restoring gut microbiome homeostasis and providing precise treatment for UC.},
}

@article {pmid40842830,
year = {2025},
author = {Rola, M and Coelho, MAG and Pruckner, C and Quiroga-Pérez, M and Stock, W and Baylina, N and Engelen, AH and Wägele, H and Serrão, EA and Frade, PR},
title = {Coral garden conservation and restoration: how host taxon and ex-situ maintenance affect the microbiome of soft and hard corals.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1605105},
pmid = {40842830},
issn = {1664-302X},
abstract = {Temperate coral gardens are dense coral formations, which support rich marine species diversity, enabling benthic-pelagic coupling. Over the past decades, coral gardens have been increasingly threatened by bottom fishing, oil and gas exploitation, and climate change. Microbiome research bears great potential for assisted resilience in targeted conservation and restoration approaches. Yet, fundamental parameters of the coral garden microbiome remain poorly understood. Here, we provide a first broad record of bacterial communities associated with NE Atlantic coral garden corals and their community changes as response to human maintenance in conservation research. Octocorals (10 species), scleractinians (2 species) and one black coral species, were opportunistically collected from fisheries bycatch at 60-480 m depth around Cape St. Vincent (SW Portugal). Metabarcoding of the 16S-rRNA gene using third-generation sequencing revealed a high microbial host-specificity in the wild-collected coral species analyzed, and supported the importance of bacterial families Endozoicomonadaceae (mean relative abundance ± SE; 28.3 ± 10.5%), Spirochaetaceae (8.2 ± 5.8%) and Spongiibacteraceae (4.6 ± 1.8%). Endozoicomonadaceae were particularly dominant in the octocoral order Malacalcyonacea (67.7 ± 14.5%). The low microbial alpha diversity and limited interspecies differences among the Malacalcyonacea species suggest a conserved microbiome within this group, as compared to orders Scleralcyonacea, Antipatharia, and Scleractinia. Microbial responses to ex-situ maintenance of two branching octocoral species, Eunicella verrucosa and Paramuricea cf. grayi (Order Malacalcyonacea), were investigated (1) over 45 days under standardized aquaria conditions in the research station (Ramalhete Marine Station, CCMAR) and (2) over long-term captivity in two public aquaria, Oceanário de Lisboa and Zoomarine. Eunicella verrucosa displayed a stronger microbial community shift to short-term captivity (45 days), in contrast to greater microbiome stability in P. cf. grayi. However, long-term captivity in public aquaria led to microbiome shifts in both species. The strong host specificity of microbial diversity and its response to maintenance indicate that conservation and restoration of coral gardens require taxon-specific strategies.},
}

@article {pmid40842827,
year = {2025},
author = {Veselovsky, V and Romanov, M and Zoruk, P and Larin, A and Babenko, V and Morozov, M and Strokach, A and Zakharevich, N and Khamidova, S and Danilova, A and Vatlin, A and Pavshintsev, V and Chenguang, F and Tsybizov, D and Mitkin, N and Galanova, O and Zakharenko, A and Golokhvast, K and Klimina, K},
title = {Comparative evaluation of sequencing platforms: Pacific Biosciences, Oxford Nanopore Technologies, and Illumina for 16S rRNA-based soil microbiome profiling.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1633360},
pmid = {40842827},
issn = {1664-302X},
abstract = {Soil microbiome profiling is crucial for understanding microbial diversity and its roles in ecosystem functioning and agricultural productivity. Recent advancements in high-throughput sequencing, particularly Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), offer long-read sequencing capabilities that enhance microbial community analysis. In this study, we performed a comparative evaluation of 16S rRNA gene sequencing using Illumina (V4 and V3-V4 regions), PacBio (full-length and trimmed V3-V4/V4 regions), and ONT (full-length) to assess bacterial diversity in soil microbiomes. We analyzed three distinct soil types and applied standardized bioinformatics pipelines tailored to each platform. To ensure comparability, sequencing depth was normalized across platforms (10,000, 20,000, 25,000, and 35,000 reads per sample). Our results demonstrated that ONT and PacBio provided comparable bacterial diversity assessments, with PacBio showing slightly higher efficiency in detecting low-abundance taxa. Despite differences in sequencing accuracy, ONT produced results that closely matched those of PacBio, suggesting that ONT's inherent sequencing errors do not significantly affect the interpretation of well-represented taxa. Our study demonstrated that, regardless of the sequencing technology used and the choice of the target region (full-length 16S rRNA gene or its regions), microbial community analysis ensures clear clustering of samples based on soil type. The only exception is the V4 region, where no soil-type clustering is observed (p = 0.79). These results provide a comprehensive evaluation of sequencing platform performance.},
}

@article {pmid40842817,
year = {2025},
author = {Jamali, AG and Ilyas, A and Wali Ahmed, F and Mansoor, A and Hassan, SZ and Singla, S and Singla, B and Kettaneh, K and Mim, RJ and Habib, M and Iqbal, AA},
title = {Association Between Diet Quality Linked to Gut Microbiota and Cardiovascular Risk Among South Asian Adults: A Cross-Sectional Study.},
journal = {Cureus},
volume = {17},
number = {7},
pages = {e88395},
pmid = {40842817},
issn = {2168-8184},
abstract = {Background Cardiovascular disease (CVD) is a significant public health issue worldwide that depends on various lifestyle and metabolic factors. Emerging research suggests that dietary patterns affecting the gut microbiota may influence cardiovascular risk. Nevertheless, not much research has been conducted on this relationship within South Asian communities. This study investigates the relationship between diet quality, as defined by patterns associated with gut microbiota in prior literature, and modifiable cardiovascular risk factors among South Asian adults. Methods This cross-sectional study was conducted from January to May 2025 in Pakistani community clinics and health centres. The study employed convenience sampling and recruited 385 South Asian adults. The participants were questioned using a structured questionnaire, and their demographic data, Global Diet Quality Questionnaire (GDQQ, Pakistan version), and INTERHEART Modifiable Risk Score (IHMRS) were obtained. Although gut microbiota was not directly assessed, diet quality was inferred to be linked with microbial changes based on previously validated dietary patterns in microbiome research. Both GDQQ and IHMRS have been validated in South Asian populations, with IHMRS demonstrating strong predictive performance (AUC > 0.75). Age categories used in the analysis included six groups: 18-24, 25-34, 35-44, 45-54, 55-64, and 65 years and older. The data were analysed using SPSS v.26, and associations between diet quality and cardiovascular risk were assessed using descriptive statistics, t-tests, analysis of variance (ANOVA), Pearson's correlation, and multivariable linear regression controlling for age, gender, physical activity, and comorbidities. Results Females had a significantly higher mean GDQQ score (M = 49.94, SD = 6.23) than males (M = 48.03, SD = 7.89), p < 0.001. Diet quality was inversely associated with cardiovascular risk (r = -0.827, p < 0.001). Multivariable regression confirmed that higher GDQQ scores were a strong independent predictor of lower IHMRS (β = -0.827, p < 0.001) after adjusting for key confounding variables. Significant relationships were also found between age and self-reported physical activity, as well as dietary quality and risk scores, using appropriate tests (t-tests, ANOVA, Pearson correlation). However, the use of convenience sampling may introduce selection bias and limit the generalizability of the results. Conclusion This study demonstrates an inverse correlation between diet quality, which is linked to gut microbiota based on previous evidence, and cardiovascular risk among South Asian adults. Older people had better diet quality, which was associated with reduced risk, whereas younger adults had a higher chance of poor diet and higher risks. These findings support the potential for culturally tailored dietary interventions targeting microbiome-related pathways to reduce the CVD burden in this region. However, the gut microbiota link is inferred, and further research involving direct microbiome assessment is warranted.},
}

@article {pmid40842787,
year = {2025},
author = {Patil, S and Mehdi, SS},
title = {The Gut-Brain Axis and Mental Health: How Diet Shapes Our Cognitive and Emotional Well-Being.},
journal = {Cureus},
volume = {17},
number = {7},
pages = {e88420},
pmid = {40842787},
issn = {2168-8184},
abstract = {The gut-brain axis (GBA) connects the gastrointestinal (GI) system and the central nervous system (CNS) in a two-way communication system that greatly impacts mental health and overall well-being. Dietary choices significantly influence the gut microbiome, thereby affecting emotional, cognitive, and neurological health. This review explores how specific dietary patterns, including high-fiber, plant-based, and Mediterranean diets (MD), enhance microbial diversity, decrease inflammation, and enhance gut-brain communication. It highlights the importance of probiotics, prebiotics, omega-3 fatty acids, and antioxidants in controlling gut microbiota, enhancing intestinal barrier function, and reducing systemic inflammation associated with anxiety, depression, and cognitive decline. The article covers practical methods for integrating dietary adjustments into personalized mental health treatment, while also addressing challenges such as individual microbiome variability and the need for long-term research. This review underscores the possibility of using nutritional interventions as a non-invasive and easily accessible way to promote mental health and resilience based on existing evidence. The methodology involved a comprehensive examination of existing literature exploring the GBA and its influence on mental health. We searched relevant databases, including PubMed and Google Scholar, using keywords such as "gut-brain axis," "microbiome," "diet," and "mental health." Peer-reviewed articles were selected based on their relevance to the relationship between dietary interventions and mental health outcomes, with a focus on studies exploring cognitive and emotional well-being.},
}

@article {pmid40842497,
year = {2025},
author = {Jiang, X and Wang, Y and Hua, Y and Tang, H and Li, H},
title = {Mechanisms of traditional Chinese medicine regulating polycystic ovary syndrome through gut microbiota: a review.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1610869},
pmid = {40842497},
issn = {1664-2392},
mesh = {Humans ; *Polycystic Ovary Syndrome/microbiology/therapy/drug therapy ; *Gastrointestinal Microbiome/drug effects/physiology ; Female ; *Medicine, Chinese Traditional/methods ; *Drugs, Chinese Herbal/therapeutic use ; Animals ; },
abstract = {Polycystic ovary syndrome (PCOS) is a prevalent endocrine disorder that adversely affects women's reproductive and metabolic health conditions. Recent studies have highlighted the significant contributory role of gut microbiota in the pathogenesis of PCOS, indicating a complex interplay between the microbiome and the syndrome's clinical manifestations. Given this connection, Traditional Chinese Medicine (TCM), a well-established therapeutic approach, has demonstrated potential efficacy in modulating gut microbiota and alleviating symptoms associated with PCOS. This review aims to summarize and analyze current research on the effects of TCM on gut microbiota in individuals with PCOS, exploring underlying mechanisms and relevant findings to provide insights for future clinical applications and improve understanding of TCM's role in managing PCOS.},
}

Humans
*Polycystic Ovary Syndrome/microbiology/therapy/drug therapy
*Gastrointestinal Microbiome/drug effects/physiology
Female
*Medicine, Chinese Traditional/methods
*Drugs, Chinese Herbal/therapeutic use
Animals

@article {pmid40842480,
year = {2025},
author = {McBeth, A and Miller, EA and Thompson, B and Hanaway, P and Thexton, A and Zwickey, H},
title = {Balancing Oxidative Stress: How the Gut Microbiome Supports Redox Homeostasis and Mitochondrial Health.},
journal = {Journal of restorative medicine},
volume = {15},
number = {1},
pages = {4-19},
pmid = {40842480},
issn = {2330-2941},
abstract = {The body's defense against oxidative stress is multilayered, involving a host of endogenous antioxidants and enzymes, as well as exogenous dietary factors that provide additional support. The gut microbiome's role is highlighted in its ability to produce antioxidative enzymes and metabolites, which contribute to maintaining redox balance. These antioxidant products of the gut microbiome support the structural integrity of the intestinal barrier and also play a protective role in mitochondrial health, thus influencing systemic physiological processes. The delicate interplay between oxidative processes and antioxidative defenses is known as redox homeostasis. This review discusses the critical role of redox biology in human health, exploring the essential equilibrium between oxidative stress and antioxidant mechanisms for cellular function and overall vitality. We explore the multifaceted causes of oxidative stress, from intrinsic factors like mitochondrial activity, inflammation, and immune responses to extrinsic influences such as environmental pollutants and dietary components.},
}

@article {pmid40842382,
year = {2025},
author = {Theys, C and Jorissen, S and Janssens, L and Tüzün, N and Decaestecker, E and Verheyen, J and Stoks, R},
title = {The gut microbiome shapes latitudinal differences in host immunity and pathogen load in a damselfly.},
journal = {The Journal of animal ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1365-2656.70119},
pmid = {40842382},
issn = {1365-2656},
support = {C16/17/002//KU Leuven/ ; G.095619//Fonds Wetenschappelijk Onderzoek/ ; G014423N//Fonds Wetenschappelijk Onderzoek/ ; },
abstract = {Latitudinal patterns in fitness-related traits within species are receiving increased attention as these inform how high-latitude populations may evolve in response to global warming. The underlying mechanisms for these latitudinal trait patterns remain poorly understood, and recently the gut microbiome has been suggested to be a potentially important proximate driver of these patterns. We investigated the novel idea of whether the gut microbiome drives latitudinal differences in immune function and pathogen load. To test this idea, we performed a reciprocal gut microbiome transplant between slow-paced, high-latitude (southern Sweden) and fast-paced, low-latitude (southern France) populations of Ischnura elegans damselflies. The transplants were conducted in the laboratory between high- and low-latitude larvae, at both a colder and warmer thermal regime, whereafter larvae were exposed to Escherichia coli, a widespread pathogenic bacterium in aquatic ecosystems. During the experiment, larval mortality, growth rate, phenoloxidase (PO) level (a measure of immune function), E. coli burden (a measure of pathogen load) and the gut microbiome diversity (α-diversity) and community compositions (β-diversity) were analysed. Exposure to the pathogen increased mortality, especially under warming. Our results confirmed latitude-associated thermal adaptation and a faster pace of life of the low-latitude larvae, which was associated with a lower immune function (lower activity of PO), consistent with previous findings and now showed this to be linked to a higher pathogen load (higher E. coli body burden). Moreover, our results provided the first experimental evidence that the gut microbiome causally contributed to latitudinal differences in the host's immune function and pathogen load. As latitudinal patterns in the microbiome are widespread, this may be an important yet ignored proximate driver of the latitudinal patterns in immune function and pathogen load.},
}

@article {pmid40842278,
year = {2025},
author = {Mukerebe, C and Cordeiro, AA and Aristide, C and Colombe, S and Bullington, BW and Kalluvya, S and van Dam, GJ and de Dood, CJ and Corstjens, PLAM and Maganga, JK and Changalucha, JM and Namkinga, LA and Makene, VA and Lee, MH and Downs, JA},
title = {Schistosome Infection is Associated with High-Risk Human Papillomavirus Persistence, Together with Altered Cervicovaginal Microbiota.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf447},
pmid = {40842278},
issn = {1537-6613},
abstract = {Schistosoma haematobium infection may impair female genital mucosal antiviral defense. We sought to determine whether women with S. haematobium infection had higher odds of high-risk human papillomavirus (HR-HPV) persistence, a pre-requisite to cervical cancer. We also examined cervicovaginal dysbiosis, which has been linked to HR-HPV persistence and schistosome infection. In 96 Tanzanian women with baseline and 9-12-month follow-up samples, we performed HPV genotyping, schistosome antigen quantification, and 16S rRNA sequencing. Both S. haematobium (Odds ratio (OR): 4.7 [1.3-16.5], p=0.017) and Gardnerella-dominant microbiome (p=0.049) were associated with HR-HPV persistence, suggesting these factors may contribute to high cervical cancer rates in Africa.},
}

@article {pmid40842228,
year = {2025},
author = {Claudel, JP and Ballanger, F and Auffret, N and Leccia, MT and Dréno, B},
title = {Obesity: A Modulator in Acne Management.},
journal = {Acta dermato-venereologica},
volume = {105},
number = {},
pages = {adv43945},
doi = {10.2340/actadv.v105.43945},
pmid = {40842228},
issn = {1651-2057},
mesh = {Humans ; *Acne Vulgaris/therapy/epidemiology/diagnosis ; *Obesity/epidemiology/therapy/diagnosis ; Risk Factors ; Adolescent ; Decision Trees ; },
abstract = {Acne vulgaris is an inflammatory and multifactorial skin disease involving the sebaceous gland and the skin microbiome. Different exposome factors, including hormonal and family factors, have been suggested to influence acne. Obesity is an increasingly observed condition worldwide, and is considered as a public health problem by the World Health Organization. Recently, a high body mass index has been identified as an acne severity risk factor in adolescents. A group of 5 dermatologists from different institutions and private practices from France involved in the research and clinical fields of acne -analysed recent literature on "obesity and acne" focusing on epidemiology, the pathogenesis of acne and obesity, as well as the management of acne in obese patients. The authors selected, prior to their discussion in November and December 2024 and again in March 2025, and discussed 52 articles concerning acne and obesity published since 2000 and available from the PubMed database. The authors agreed that, considering these common metabolic features, managing both acne and obesity in parallel and helping patients through a global approach including dermatological, endocrinal, psychological and nutrition, as well as lifestyle support is mandatory, and may allow for the improvement of both acne and obesity. Moreover, in order to allow dermatologists to manage acne in obese patients in the most efficient way, the authors developed and propose a decision tree. The authors consider that acne in obese patients is not a fatality, and taking care of acne should not be considered an isolated task in this specific patient population.},
}

Humans
*Acne Vulgaris/therapy/epidemiology/diagnosis
*Obesity/epidemiology/therapy/diagnosis
Risk Factors
Adolescent
Decision Trees

@article {pmid40842134,
year = {2025},
author = {Korten, NM and Thelen, AC and Voelz, C and Beyer, C and Seitz, J and Trinh, S and Blischke, L},
title = {Exploring the Link Between the Gut Microbiota and Epigenetic Factors in Anorexia Nervosa.},
journal = {Brain and behavior},
volume = {15},
number = {8},
pages = {e70733},
doi = {10.1002/brb3.70733},
pmid = {40842134},
issn = {2162-3279},
mesh = {*Anorexia Nervosa/microbiology/genetics/metabolism ; Humans ; *Gastrointestinal Microbiome/physiology ; *Epigenesis, Genetic/physiology ; Brain/metabolism ; Dysbiosis ; },
abstract = {OBJECTIVE: Anorexia nervosa (AN) is an often chronic eating disorder that involves genetic, neurohormonal, and epigenetic factors along with key contributions from the microbiota-gut-brain axis. However, interactions between these factors are poorly understood. Recent studies have emphasized the microbiota-gut-brain axis and epigenetic changes as potentially important contributors to AN. Exploring these interactions may improve understanding of the etiology and persistence of AN.

METHODS: Studies specifically addressing microbial-epigenetic interactions in AN remain limited. However, similar associations have been documented in related disorders such as obesity and depression, providing potential models for AN research.

RESULTS: Research in obesity has shown that dietary factors influence the composition of the gut microbiota and subsequent epigenetic modifications, affecting metabolic parameters and disease progression. Similarly, in depression, microbially produced metabolites influence brain function and epigenetic processes, contributing to neuropsychiatric symptoms. In AN, altered microbial composition may affect weight regulation and epigenetic patterns. Therapies targeting the microbiome, such as fecal microbiota transplantation, are under investigation for AN, highlighting the potential therapeutic utility of ameliorating microbial dysbiosis.

DISCUSSION: This article highlights the importance of investigating microbial-epigenetic interactions in AN. By drawing parallels with obesity and depression, we aim to deepen our understanding of AN mechanisms and ultimately improve patient outcomes.},
}

*Anorexia Nervosa/microbiology/genetics/metabolism
Humans
*Gastrointestinal Microbiome/physiology
*Epigenesis, Genetic/physiology
Brain/metabolism
Dysbiosis

@article {pmid40842068,
year = {2025},
author = {Azizah, N and Fadilah, F and Lestari, SW and Kadim, M and Sjatha, F and Oswari, H},
title = {Fecal microbiome profiles in infants with biliary atresia versus nonbiliary atresia cholestasis: a pilot study.},
journal = {Clinical and experimental pediatrics},
volume = {},
number = {},
pages = {},
doi = {10.3345/cep.2025.00563},
pmid = {40842068},
issn = {2713-4148},
abstract = {BACKGROUND: Cholestasis is characterized by disrupted bile flow and can lead to severe liver disease in newborns, of which biliary atresia (BA) is a common cause. The gut microbiome plays a crucial role in aggravating liver injury in BA and non-BA cholestasis. However, information is lacking regarding the differences in gut microbiome composition between patients with BA and non-BA cholestasis.

PURPOSE: This study aimed to assess the gut microbiome profile of infants with BA versus those with non-BA cholestasis and healthy controls in an Indonesian population.

METHODS: We investigated the changes in the microbial composition of fecal samples from 12 infants with BA and 8 with non-BA cholestasis and compared them with those of 8 age-matched healthy controls (HCs). Fecal DNA from all the participants was subjected to 16S rRNA amplicon sequencing.

RESULTS: The fecal microbiome at the phylum level differed between the BA and non-BA cholestasis groups with increased Proteobacteria and decreased Firmicutes. At the genus level, the BA group was enriched with Bacteroides, unclassified Enterobacteriaceae, and Dialister (P<0.05), whereas the non-BA group was enriched with Klebsiella, Chryseobacterium, Acinetobacter, and Pseudomonas (P<0.05). Parabacteroides, unclassified Lachnospiraceae, Actinomyces, Anaerococcus, Clostridium innocuum group, Collinsella, Gemella, and Peptostreptococcaceae (P<0.05) were more enriched in the HC than in the other 2 groups. Detected cytomegalovirus in fecal samples was associated with significant microbial shifts, including increased Lactobacillus, decreased Escherichia-Shigella, and altered Faith's phylogenetic diversity, highlighting its potential role in gut microbiome modulation. Microbial alterations in patients with BA versus non-BA cholestasis were significantly correlated with liver function indicators.

CONCLUSION: The BA and non-BA groups showed specific genus enrichment, highlighting the urgent need to identify potential treatments to inhibit the progression of liver injury in infants with cholestasis.},
}

@article {pmid40842040,
year = {2025},
author = {Prioux, C and Ferrier-Pagès, C and Lamarca, T and Allemand, D and Tignat-Perrier, R},
title = {Heatwave-driven persistent microbes threaten the resilience of Mediterranean coral holobionts.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {107},
pmid = {40842040},
issn = {2524-6372},
abstract = {BACKGROUND: The climate crisis poses a serious threat to octocorals in the Mediterranean Sea as marine heatwaves (MHWs) not only impair coral metabolism but also disrupt the complex symbiosis between the coral host and its microbiome. Since octocorals are the foundation species of the Mediterranean animal forests, understanding their resilience, i.e. ability to recover and survive to MHWs, is crucial to predict their viability under future climatic conditions. Using amplification of 16 S and 18 S rRNA genes for metabarcoding and qPCR analyses to follow the changes in bacterial microbiome and eukaryome as well as host response under stress and recovery conditions, this study provides the first comprehensive assessment of the resilience of an iconic Mediterranean octocoral (the red coral Corallium rubrum) to a mild (19 °C) and more severe (23 °C) heat stress.

RESULTS: The results of this work indicate a stress response of the host to elevated temperatures, even under mild temperature. The eukaryome was highly sensitive to heat stress and underwent rapid structural changes among the dominant microeukaryotes. In contrast, the relative and absolute abundance of the major bacterial symbionts remained stable throughout the stress. However, heat stress led to a significant increase in the abundance of some taxa such as Vibrionaceae that persisted after a week of recovery.

CONCLUSIONS: While the host recovered from the stress, and the microbiome largely returned to its original composition during recovery, the results highlight the persistent presence of some taxa that might compromise the short-term resilience of octocoral holobionts. This study provides new information on how octocoral holobionts respond to MHWs in the Mediterranean Sea. This knowledge is crucial for the development of effective, science-based strategies for coral protection and restauration.},
}

@article {pmid40841983,
year = {2025},
author = {Grant, ML and Petri, RM and Baecklund, TM and Wilson, GA and Kyle, CJ},
title = {Subspecific variation in gut microbiota of North American bison in a sympatric setting reveals differentially abundant taxa.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {89},
pmid = {40841983},
issn = {2524-4671},
support = {RGPIN-2023-04503//Natural Sciences and Engineering Research Council of Canada/ ; },
}

@article {pmid40841980,
year = {2025},
author = {Reyes, SM and Allen, DL and Williams, JE and McGuire, MA and McGuire, MK and Rasmussen, KM and Hay, AG},
title = {Pumping and hygiene practices are associated with bacterial load and microbial composition in human milk expressed at home.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {947},
pmid = {40841980},
issn = {1479-5876},
support = {T32-DK007158/DK/NIDDK NIH HHS/United States ; NYC-399346//USDA/Hatch/ ; P30 GM103324/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Milk, Human/microbiology ; Female ; *Hygiene ; *Bacterial Load ; Adult ; *Breast Milk Expression ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Young Adult ; },
abstract = {BACKGROUND: Human milk (HM) harbors a unique microbiome that contributes to the development of the infant gastrointestinal microbiome and influences long-term health outcomes. While pumping and bottle-feeding HM are increasingly common, doing so may introduce exogenous bacteria, altering this microbial community. The extent to which real-world pumping and hygiene practices alter the HM microbial community remains inadequately characterized.

METHODS: We conducted a secondary analysis of 104 paired milk samples from 52 healthy women to investigate the associations between at-home pump hygiene practices and the HM microbiota. We compared samples expressed with personal equipment, allowing women to follow their typical practices, noting variations in breast pump types (closed- vs. open-systems), pre-pumping handwashing, and collection kit cleaning practices (OWN). Milk was also expressed with hospital-grade pump with new, commercially sterilized equipment kits under study-controlled conditions (STER) to serve as a control representing each woman's own unaltered milk microbiota. Microbiota composition was characterized using aerobic culture and 16S rRNA gene sequencing.

RESULTS: Among OWN milk samples, personal breast pump type had little impact on the HM microbiota. Pre-pumping handwashing, practiced by only 22% of participants, was associated with lower bacterial counts. Compared to samples expressed with handwashed kits, those expressed using home-sterilized kits yielded fewer total and gram-negative bacterial counts, and lower relative abundances of Proteobacteria. The microbiota of OWN milk samples expressed with home-sterilized kits more closely resembled STER samples even in the absence of pre-pumping handwashing (R[2] = 0.36; P < 0.001).

CONCLUSIONS: At-home hygiene practices, particularly collection kit cleaning methods, substantially influence the HM microbiota. Home sterilization of collection kits may minimize changes to the HM microbiota during expression. These findings support evidence-based recommendations for hygienic pumping practices and underscore the need for further research on the health implications (if any) of pumping-dependent variations in the HM microbiota on infant health.},
}

Humans
*Milk, Human/microbiology
Female
*Hygiene
*Bacterial Load
Adult
*Breast Milk Expression
Microbiota
RNA, Ribosomal, 16S/genetics
Bacteria/genetics
Young Adult

@article {pmid40744276,
year = {2025},
author = {Cassir, N and Ghani, R and Biehl, LM and Graells, T and Kuijper, EJ and Mullish, BH and Marchesi, JR and Benech, N and , },
title = {Nonantimicrobial therapies for recurrent urinary tract infection in women: is there a place for faecal microbiota transfer?.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2025.07.022},
pmid = {40744276},
issn = {1469-0691},
abstract = {BACKGROUND: Recurrent urinary tract infection (rUTI) is a common condition, affecting approximately one-third of women after an initial UTI. It significantly impacts health care costs and patients' quality of life. The relationship between the pathophysiology of UTI and the gut and vaginal microbiota is recognized as a contributing factor to rUTI in women. As antibiotic resistance among uropathogens continues to increase, there is a clear need to develop novel therapeutic interventions. Faecal microbiota transfer (FMT) is a potent nonantimicrobial strategy for modulating the gut microbiota; however, its clinical relevance in the context of rUTI is unclear.

OBJECTIVES: This narrative review aimed to summarize the current evidence on the use of FMT for the treatment of rUTI, focusing on women, excluding those with mechanical dysfunctions such as urinary incontinence, neurogenic bladder, and bladder cancer, compared with other nonantimicrobial interventions. We also discussed the pathophysiology and epidemiology of rUTI to identify patients for whom microbiota-targeting therapies may be the most effective.

CONTENT: Periurethral colonization and migration to the bladder of uropathogens that inhabit the gut and vagina have been linked to the aetiology of UTI in women, particularly in patients with multidrug-resistant organisms. FMT appears to be a promising approach for preventing the clinical development of rUTI, although prospective data remain limited. In contrast, other reported nonantimicrobial strategies targeting the gut and urogenital microbiota have shown variable significant clinical efficacy. Prospective randomized controlled clinical trials are then needed to further confirm a potential therapeutic benefit, optimize the FMT procedure, and better assess its cost-effectiveness.},
}

@article {pmid40841806,
year = {2025},
author = {Morsy, Y and Shafie, NS and , and Amer, M},
title = {Integrative analysis of gut microbiota and metabolic pathways reveals key microbial and metabolomic alterations in diabetes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30686},
pmid = {40841806},
issn = {2045-2322},
abstract = {Type 2 diabetes mellitus (T2DM) is increasingly recognized as a condition influenced by gut microbiota composition and associated metabolic pathways. This study investigated the differences in gut microbial diversity, composition, and metabolomic profiles between diabetic and control individuals. Using 16 S rRNA gene sequencing and metabolomic analyses, we observed significantly higher microbial diversity and evenness in the diabetic group, with distinct clustering patterns as revealed by Principal Coordinate Analysis (PCoA). Taxonomic profiling demonstrated an increased relative abundance of Bacteroidaceae and Lachnospiraceae in the diabetic group, while Streptococcaceae was more prevalent in the control group. LEfSe analysis identified key microbial taxa such as Bacteroides, Blautia, and Lachnospiraceae_FCS020_group enriched in diabetic individuals, suggesting a role in metabolic dysregulation. Metabolomic pathway enrichment analysis revealed significant differences in pathways related to fatty acid metabolism, glucose homeostasis, bile acid metabolism, and amino acid biosynthesis in diabetic individuals. Enriching fatty acid elongation and β-oxidation pathways, alongside disrupted glucose metabolism, indicate profound metabolic changes associated with diabetes. Bile acid metabolism and branched-chain amino acid (BCAA) pathways were also elevated, linking these metabolites to the observed gut microbiota shifts. These findings suggest that diabetes is associated with significant alterations in the gut microbiome's composition and function, leading to disruptions in critical metabolic pathways. This study provides insights into potential microbial biomarkers and therapeutic targets for improving metabolic health in diabetic patients.},
}

@article {pmid40841760,
year = {2025},
author = {Copeland, DC and Mott, BM and Kortenkamp, OL and Erickson, RJ and Allen, NO and Anderson, KE},
title = {Image-based honey bee larval viral and bacterial diagnosis using machine learning.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30717},
pmid = {40841760},
issn = {2045-2322},
support = {2021-67013-33555//AFRI-NIFA/ ; 2021-67013-33555//AFRI-NIFA/ ; 2021-67013-33555//AFRI-NIFA/ ; 2021-67013-33555//AFRI-NIFA/ ; 2021-67013-33555//AFRI-NIFA/ ; 2021-67013-33555//AFRI-NIFA/ ; 2022-21000-021-00D//Agricultural Research Service/ ; 2022-21000-021-00D//Agricultural Research Service/ ; 2022-21000-021-00D//Agricultural Research Service/ ; 2022-21000-021-00D//Agricultural Research Service/ ; 2022-21000-021-00D//Agricultural Research Service/ ; 2022-21000-021-00D//Agricultural Research Service/ ; },
abstract = {Honey bees are essential pollinators of ecosystems and agriculture worldwide. With an estimated 50-80% of crops pollinated by honey bees, they generate approximately $20 billion annually in market value in the U.S. alone. However, commercial beekeepers often face an uphill battle, losing anywhere from 40 to 90% of their hives yearly, often by brood diseases caused by bacterial, viral, and fungal pathogens. Accurate diagnosis of brood diseases, especially distinguishing European Foulbrood (EFB) from viral infections with a superficial resemblance to EFB (EFB-like disease), remains challenging. Incorrect diagnoses often lead to prophylactic antibiotic treatment across entire apiaries, exacerbating antibiotic resistance, disrupting native gut microbiota, and increasing susceptibility to opportunistic pathogens. Correct field diagnosis of brood disease is challenging and requires years of experience to identify and differentiate various disease states according to subtle differences in larval symptomology. To explore the feasibility of an image-based AI diagnosis tool, we collaborated with apiary inspectors and researchers to generate a dataset of 2,759 honey bee larvae images from Michigan apiaries, molecularly verified through 16 S rRNA microbiome sequencing and qPCR viral screening. Our dataset included EFB cases and viral infections (ABPV, DWVA, and DWVB), which were augmented to 8,430 and 8,124 images, respectively. We leveraged transfer learning techniques, fine-tuning deep convolutional neural networks (ResNet-50v2, ResNet-101v2, InceptionResNet-v2) pre-trained on ImageNet to discriminate between EFB and viral infections. Our proof-of-concept models achieved 73-88% accuracy on the training/validation sets. When tested on an independent dataset from Illinois containing additional viral pathogens not present in training data, the models showed higher accuracy for EFB (72-88%) than viral infections (28-68%), highlighting both the promise and current limitations of this approach. Implementing AI-based diagnostic tools can reduce unnecessary antibiotic treatments and help maintain the microbiome integrity critical to colony health. However, expanding training datasets to include all major pathogens, healthy larvae, and diverse geographic regions will be essential for developing field-ready diagnostic tools.},
}

@article {pmid40841691,
year = {2025},
author = {Yau, PT and Taketani, RG and Bonnin, JM and Stewart, H and Thompson, CMA and Clark, IM and Mauchline, TH and Malone, JG and Ryan, MJ and Jones, S and Holden, N},
title = {Introducing the UK Crop Microbiome Cryobank data resource, AgMicrobiomeBase, with case studies and methods on metabarcoding analyses.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {108},
pmid = {40841691},
issn = {2524-6372},
support = {BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {BACKGROUND: Here, we describe AgMicrobiomeBase as an output of the UK Crop Microbiome Cryobank (UKCMCB) project, including details of the underlying meta-barcode sequence-based methods and three microbiome analysis case studies. The UKCMCB links genomic datasets and associated soil metadata with a cryobank collection of samples, for six economically significant crops: fava bean (Vicia faba), oil seed rape (Brassica napus), spring barley (Hordeum vulgare), spring oats (Avena sativa), spring wheat (Triticum aestivum) and sugar beet (Beta vulgaris). The crops were grown in nine agricultural soils from the UK, representing three major soil texture classes. The UKCMCB is a scalable sequence-based data catalogue linked to a cryo-preserved sample collection.

RESULTS: The focus of this paper is the amplicon sequencing, associated bioinformatics workflows, and development of the project data catalogue. Short-read amplicon sequencing (16 S rRNA gene and ITS region) was implemented to describe the rhizosphere and bulk soil communities, for the multiple crop-soil combinations. Three case studies illustrate how different biological questions in phytobiome research can be addressed using this data resource. The three case studies illustrate how to (1) determine the impact of soil texture and location on microbiome composition, (2) determine a core microbiome for a single crop across different soil types, and (3) analyse a single genus, Fusarium within a single crop microbiome. The UKCMCB data catalogue AgMicroBiomeBase (https://agmicrobiomebase.org/data) links the sequence-based data with soil metadata and to cryopreserved samples.

CONCLUSIONS: The UKCMCB provides baseline data and resources to enable researchers to assess the impact of soil type, location and crop type variables on crop soil microbiomes. The resource can be used to address biological questions and cross-study comparisons. Development of the UKCMCB will continue with the addition of metagenome and bacterial isolate genomic sequence data and has the potential to integrate additional data types including microbial phenotypes and synthetic microbial communities.},
}

@article {pmid40841660,
year = {2025},
author = {Bayraktaroglu, I and Ortí-Casañ, N and Van Dam, D and De Deyn, PP and Eisel, ULM},
title = {Systemic inflammation as a central player in the initiation and development of Alzheimer's disease.},
journal = {Immunity & ageing : I & A},
volume = {22},
number = {1},
pages = {33},
pmid = {40841660},
issn = {1742-4933},
support = {WE.03-2021-05//Alzheimer Nederland/ ; WE.03-2021-05//Alzheimer Nederland/ ; },
abstract = {Alzheimer's disease (AD) is an age-related neurodegenerative disorder and the most common cause of dementia. While the amyloid cascade hypothesis has long dominated AD research, emerging evidence suggests that neuroinflammation may play a more central role in disease onset and progression. Increasingly, AD is recognized as a multifactorial disorder influenced by systemic inflammation and immune dysregulation, shifting focus toward peripheral immune mechanisms as potential contributors to neurodegeneration. This review explores the hypothesis that inflammaging, the age-related increase in pro-inflammatory mediators, combined with lifelong exposure to infections, injuries, metabolic changes, and chronic diseases, among others, may prime the immune system, amplifying neuroinflammation and influencing the progression and exacerbation of AD pathology. To this end, we examined how systemic immune disturbances, including chronic pain, post-operative cognitive dysfunction, viral and bacterial infections, gut microbiome dysregulation, and cardiovascular disease, may act as risk factors for AD. Overall, evidence suggests that modulating peripheral inflammation, accompanied by early diagnosis, could significantly reduce the risk of developing AD. Furthermore, we highlight key immune signaling pathways involved in both central and peripheral immune responses, such as the NLRP3 inflammasome and TREM2, which represent promising therapeutic targets for modulating inflammation while preserving protective immune functions. Strategies aimed at reducing systemic inflammation, identifying early biomarkers, and intervening before significant neurodegeneration occurs may provide novel approaches to delay or prevent AD onset. In conclusion, this review underscores the crucial role of systemic inflammation in AD pathogenesis and progression. By targeting peripheral immune dysfunction, we may advance our understanding of AD mechanisms and develop more effective therapeutic interventions to mitigate disease risk and progression.},
}

@article {pmid40841578,
year = {2025},
author = {Bassu, S and Eichelsbacher, S and Giunta, F and Motzo, R and Dawid, C and Gastl, M and Schloter, M and Scherf, KA and Hör, S and De Souza, YPA and Schulz, S and Stark, TD and Mohler, V and Asseng, S},
title = {Positive impact of hydroponics and artificial light on yield and quality of wheat.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30768},
pmid = {40841578},
issn = {2045-2322},
mesh = {*Triticum/growth & development/microbiology/metabolism ; *Hydroponics/methods ; Glutens/metabolism ; *Light ; Microbiota ; Gliadin/metabolism ; Soil/chemistry ; Sunlight ; Crops, Agricultural/growth & development ; Agriculture/methods ; },
abstract = {Growing crops in controlled-environment indoor farming systems offers new ways of producing high-yield, pesticide-free, environmental-friendly food. However, it replaces soil with hydroponics and the sun with LED lights. Compared with the field, wheat grown indoors showed a much higher yield potential and bread-making quality parameters. Many mineral concentrations were higher due to the unrestricted water supply and nutrients in hydroponics. However, concentrations declined with increasing yields. The microbiome richness inside the grains of wheat grown without soil indoors was still within the range of wheat grown in the field. However, taxa were different among cultivars and treatments. There were differences in the presence of undefined secondary metabolites between indoor and outdoor wheat and across the indoor experiments. Regardless of the growing environment, immunoreactive proteins were present. Indoor-grown wheat had a higher share of ω5-gliadins but lower shares of γ-gliadins and low-molecular-weight glutenin subunits, which may affect the gluten protein immunoreactive potential for individuals with wheat-related disorders (allergy and celiac disease). Growing wheat without soil and sunlight indoors can produce high-yielding, high-quality grains. However, the food quality and health aspects associated with gluten proteins might deteriorate with a further, theoretically possible, yield increase in a controlled growing environment.},
}

*Triticum/growth & development/microbiology/metabolism
*Hydroponics/methods
Glutens/metabolism
*Light
Microbiota
Gliadin/metabolism
Soil/chemistry
Sunlight
Crops, Agricultural/growth & development
Agriculture/methods

@article {pmid40841555,
year = {2025},
author = {Wang, T and Zhang, P and Anantharaman, K and Wang, H and Zhang, H and Zhang, M and Xu, J},
title = {Metagenomic analysis reveals how multiple stressors disrupt virus-host interactions in multi-trophic freshwater mesocosms.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7806},
pmid = {40841555},
issn = {2041-1723},
support = {42377469//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32001151//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Metagenomics/methods ; Microbiota/genetics ; Lakes/microbiology/virology ; *Fresh Water/microbiology/virology ; Ecosystem ; Metagenome ; *Viruses/genetics/classification ; *Bacteria/genetics/virology ; Pesticides ; *Host Microbial Interactions/genetics ; Stress, Physiological ; Climate Change ; },
abstract = {Virus-host interactions are vital to microbiome ecology and evolution, yet their responses to environmental stressors under global change remain poorly understood. We perform a 10-month outdoor mesocosm experiment simulating multi-trophic freshwater shallow lake ecosystems. Using a fully factorial design comprising eight treatments with six replicates each, we assess the individual and combined effects of climate warming, nutrient loading, and pesticide loading on DNA viral communities and their interactions with microbial hosts. Metagenomic sequencing recovers 12,359 viral OTUs and 1628 unique prokaryotic metagenome-assembled genomes. Our analysis shows that combined nutrient and pesticide loading causes significant disruption by synergistically reducing viral alpha diversity while altering beta diversity and predator-prey linkages. Stressors lead to the simplification of virus-bacteria cross-kingdom networks, with nutrient-pesticide combinations exerting the strongest influence, although warming impacts diminish in the presence of pesticides. Stressor-driven changes also affect the abundance and composition of viral auxiliary metabolic genes, leading to complex shifts in virus-mediated metabolic pathways under multiple stress conditions. These findings underscore the importance of understanding the regulatory role of viruses on microbial communities to effectively address the challenges posed by global change.},
}

*Metagenomics/methods
Microbiota/genetics
Lakes/microbiology/virology
*Fresh Water/microbiology/virology
Ecosystem
Metagenome
*Viruses/genetics/classification
*Bacteria/genetics/virology
Pesticides
*Host Microbial Interactions/genetics
Stress, Physiological
Climate Change

@article {pmid40841315,
year = {2025},
author = {Ho, E and Wong, CP and Bouranis, JA and Shannon, J and Zhang, Z},
title = {Cruciferous Vegetables, Bioactive Metabolites, and Microbiome for Breast Cancer Prevention.},
journal = {Annual review of nutrition},
volume = {45},
number = {1},
pages = {171-195},
doi = {10.1146/annurev-nutr-062222-024321},
pmid = {40841315},
issn = {1545-4312},
mesh = {Humans ; *Breast Neoplasms/prevention & control/microbiology ; Female ; *Vegetables/chemistry ; Isothiocyanates/pharmacology ; Sulfoxides ; *Gastrointestinal Microbiome ; Phytochemicals/pharmacology ; Indoles/pharmacology ; *Brassicaceae ; Anticarcinogenic Agents ; Glucosinolates/metabolism ; Animals ; Microbiota ; },
abstract = {Breast cancer is a heterogeneous disease with varying subtypes, prognoses, and treatment responses. Cruciferous vegetables have shown promise in reducing breast cancer risk. This review discusses (a) the efficacy of sulforaphane (SFN) and indole-3-carbinol (I3C)/3,3'-diindolylmethane (DIM) on breast cancer risk, prognosis, and treatment outcomes in recent human studies through 2024; (b) preclinical studies (2018-2024) that evaluate the efficacy and synergism of SFN, DIM, and other phytochemicals with conventional breast cancer treatments as promising combination therapy strategies for validation in future clinical trials; and (c) the role of the microbiome in breast cancer and the interaction between interindividual variations in gut microbiome and glucosinolate metabolism that could modify the benefits of cruciferous vegetable consumption and breast cancer treatment efficacy. Integrating cruciferous vegetables and their bioactive compounds in light of an individual's microbiome profile as a complementary approach alongside standard treatments is a promising strategy in breast cancer care.},
}

Humans
*Breast Neoplasms/prevention & control/microbiology
Female
*Vegetables/chemistry
Isothiocyanates/pharmacology
Sulfoxides
*Gastrointestinal Microbiome
Phytochemicals/pharmacology
Indoles/pharmacology
*Brassicaceae
Anticarcinogenic Agents
Glucosinolates/metabolism
Animals
Microbiota

@article {pmid40841147,
year = {2025},
author = {Richardson, H and Alferes De Lima Headley, D and Clarke, C and Veluchamy, A and Rauchhaus, P and Pollock, J and Pembridge, T and Cassidy, D and Keir, HR and Finch, S and Hussain, F and Band, M and Smith, A and Patel, M and Paracha, M and Choudhury, G and Dhasmana, D and Chaudhuri, R and Short, PM and Chalmers, JD},
title = {The effect of different inhaled corticosteroid and long-acting bronchodilator combinations on the airway microbiome in patients with severe chronic obstructive pulmonary disease: A randomized trial (MUSIC).},
journal = {The European respiratory journal},
volume = {},
number = {},
pages = {},
doi = {10.1183/13993003.00287-2025},
pmid = {40841147},
issn = {1399-3003},
abstract = {INTRODUCTION: The microbiome is associated with exacerbation risk, quality of life and mortality in COPD. Inhaled corticosteroid (ICS) treatment has been reported to alter the microbiome through modulating host defence. How ICS alters the microbiome and whether effects are equal between different ICS preparations is debated. The aim of the MUSIC trial was to investigate whether commonly used ICS therapies have different effects on the airway microbiome in COPD.

METHODS: Multicentre randomized controlled trial. After a four-week washout period during which they withdrew from ICS, patients with COPD (FEV1 <50% predicted at baseline and/or a history of 2 or more exacerbations per year) were randomized to one of 4 treatments (budesonide/formoterol 400/12 mcg, fluticasone/salmeterol 500 mcg, fluticasone/salmeterol 250 mcg or aclidinium/formoterol 340/12 mcg, twice daily). Patients were followed-up for 3 months with monthly induced sputum, oropharyngeal and nasopharyngeal swabs for bacterial load and 16S rRNA sequencing to characterise the microbiome. Inflammatory markers were measured in sputum and blood. The primary outcome was bacterial load in oropharyngeal swabs comparing budesonide/formoterol versus fluticasone/salmeterol 500, with sputum bacterial load the key secondary endpoint.

RESULTS: 122 participants started the washout period. ICS withdrawal was poorly tolerated, 61 participants withdrew before randomization with 45 experiencing an exacerbation. 61 patients were randomized. No statistically significant differences were observed for the primary comparison of budesonide/formoterol versus fluticasone/salmeterol 500 in oropharyngeal bacterial load. There was however a significant increase in sputum bacterial load with fluticasone/salmeterol 500 compared to budesonide/formoterol by month 3. This difference was not seen with fluticasone/salmeterol 250. No significant differences in microbiome alpha diversity were observed over time. Adverse events were similar between the groups.

CONCLUSION: Fluticasone/salmeterol 500 increased sputum but not upper airway bacterial loads. ICS withdrawal was poorly tolerated in severe COPD.},
}

@article {pmid40841038,
year = {2025},
author = {Tang, Z and Zhang, Y and Shangguan, H and Xie, A and Xu, X and Jiang, Y and Breed, MF and Sun, X},
title = {Urban organic manure application enhances antibiotic resistance gene diversity and potential human pathogen abundance in invasive giant African snails.},
journal = {Journal of environmental sciences (China)},
volume = {158},
number = {},
pages = {610-620},
doi = {10.1016/j.jes.2025.02.028},
pmid = {40841038},
issn = {1001-0742},
mesh = {Animals ; *Manure ; *Drug Resistance, Microbial/genetics ; *Snails/microbiology ; Humans ; Introduced Species ; Gastrointestinal Microbiome ; Soil Microbiology ; Environmental Monitoring ; RNA, Ribosomal, 16S ; Feces/microbiology ; },
abstract = {The giant African snail (Achatina fulica) is an invasive species served as potential vectors for antibiotic resistance genes (ARGs) and potential human bacterial pathogens. Currently, urban green spaces receive extensive organic manure additions as part of their management, may intensify the biological contamination potential of these snail vectors, thereby increasing the risk of biological pollution in green spaces. However, the specific impacts of this practice on the microbial ecology of these invasive species remain poorly understood. Here, we investigated the effects of organic manure application on the gut microbiome of giant African snails, focusing on ARGs, bacterial community structure, and potential human bacterial pathogens. Microcosm experiments compared snail gut microbiomes in different treatments (Soil: soil samples collected after manure amendment, before any snail exposure. Feces: fecal samples collected from snails that lived on manure-amended soil. Control: fecal samples collected from snails that lived on unamended soil) using 16S rRNA high-throughput sequencing and metagenomic analysis. Our results show that manure application significantly altered gut bacterial community structure and increased ARG diversity by enriching specific high-risk ARGs (such as sul1 and sul2 in the Feces group increased by 2.89 and 2.43 times, respectively, compared to the Control group), and the introduction of eight novel ARG subtypes, despite decreasing overall ARG abundance. Moreover, the relative abundance of potential human pathogens, particularly Pseudomonadaceae, was greatly increased by manure application. These findings reveal that organic manure application in urban green spaces can potentially enhances their role as reservoirs and vectors of ARGs and human pathogens.},
}

Animals
*Manure
*Drug Resistance, Microbial/genetics
*Snails/microbiology
Humans
Introduced Species
Gastrointestinal Microbiome
Soil Microbiology
Environmental Monitoring
RNA, Ribosomal, 16S
Feces/microbiology

@article {pmid40841030,
year = {2025},
author = {Nie, E and He, P and Zhang, H and Lü, F},
title = {Genome-centric metagenomic analysis unveils the influence of temperature on the microbiome in anaerobic digestion.},
journal = {Journal of environmental sciences (China)},
volume = {158},
number = {},
pages = {516-526},
doi = {10.1016/j.jes.2024.10.007},
pmid = {40841030},
issn = {1001-0742},
mesh = {Anaerobiosis ; *Microbiota ; Metagenomics ; *Temperature ; *Metagenome ; Archaea/genetics ; Bacteria/genetics ; },
abstract = {Temperature plays a crucial role in shaping microbial ecosystems during anaerobic digestion. However, the specific microbial communities and their functions across a wide temperature range still remain elusive. This study employed a genome-centric metagenomic approach to explore microbial metabolic pathways and synergistic networks at temperatures of 35, 44, 53, 55, and 65 °C. A total of 84 metagenome assembled genomes (MAGs) were assembled, with over 65 % of these MAGs corresponding to novel bacterial and archaeal species (including Firmicutes, Chloroflexota, Bacteroidia and Methanobacteriota), greatly enhancing our current comprehension anaerobic digestion process. Notably, functional annotation identified that 44_bin.2 (Methanothrix_A sp. 001602645) harbors enzymes associated with hydrogenotrophic metabolism. Additionally, this microorganism exhibited diverse metabolic capabilities at 44 °C, a temperature commonly employed in industrial practice yet less explored in bench studies. Consequently, it implies a promising potential for conducting anaerobic digestion at a moderate thermophilic temperature, as opposed to the conventional mesophilic range. The microorganism exhibited a variety of metabolic capabilities at 44 °C, a temperature frequently employed in industrial applications but underexplored in laboratory investigations. The findings suggest that anaerobic digestion carried out at moderate thermophilic temperatures may have a higher potential for methane production.},
}

Anaerobiosis
*Microbiota
Metagenomics
*Temperature
*Metagenome
Archaea/genetics
Bacteria/genetics

@article {pmid40840836,
year = {2025},
author = {Young, ME and Khanna, V and Metcalfe, M and Rameshkumar, N and Harington, S and Li, LH and Doost, JS and Taegtmeyer, H and Martino, TA},
title = {A brief history of circadian time in the heart.},
journal = {Journal of molecular and cellular cardiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.yjmcc.2025.08.005},
pmid = {40840836},
issn = {1095-8584},
abstract = {This review tracks the discovery of circadian biology in cardiovascular science, starting with early clinical observations of daily changes in heart rate, blood pressure, and cardiovascular events. These patterns suggested that time of day matters, but it was not until the past two decades that the mechanisms and knowledge translation of these rhythms were uncovered. We describe the heart's intrinsic circadian properties and importantly how this leads to regulation of cardiac gene and protein expression, neuroendocrine and vascular rhythms, metabolism, cellular electrophysiology, and cell signaling pathways. Next, we explore emerging themes, including the impact of circadian timing on ischemic injury, cardiac aging, and trends in circadian desynchrony, sex, and interorgan crosstalk. Building on these discoveries, circadian medicine is beginning to reshape clinical care including timing of surgery, chronotherapies, biomarkers, ICU design, novel molecular drugs targeting the circadian clock, the role of the microbiome and time restricted eating, the new field of rest, and the concept of One Health and applications to veterinary medicine. Looking ahead we address new frontiers such as epigenetics, gene editing, and spaceflight. Together, these advances offer a roadmap for how circadian rhythms can be harnessed to improve cardiovascular health and disease outcomes, supporting longer and healthier lives.},
}

@article {pmid40840821,
year = {2025},
author = {Shah, AH and Armstrong, HK and Mittal, I and Reimer, A and Kunutsor, SK and Ducas, RA and Alizadeh, K and Tam, JW and Ravandi, A and Dhingra, S},
title = {IMpact of therapY using coleSevelam treatment reducing bile acids in patients with fonTan cIrCulation (MYSTIC): Rationale and Study Design.},
journal = {American heart journal},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ahj.2025.08.011},
pmid = {40840821},
issn = {1097-6744},
abstract = {RATIONALE: Patients with a Fontan circulation suffer from progressive multiorgan dysfunction, yet central biochemical drivers remain poorly defined. Our recent work exploring metabolomic analyses have identified markedly elevated circulating bile acids (BAs) in adult Fontan patients compared with healthy controls. Elevated BAs, especially secondary and hydrophobic ones produced by the gut microbiome were found to correlate with worse exercise capacity, greater frailty, and impaired hemodynamics.

PRIMARY HYPOTHESIS: Bile acid accumulation may contribute to Fontan pathophysiology. Colesevelam, a non-absorbed bile acid sequestrant, offers a potential targeted therapy to reduce BA levels and interrupt this disease pathway.

DESIGN: The MYSTIC trial is a prospective, randomized, double-blind, placebo-controlled cross-over pilot study in 25 adult Fontan patients (with 25 age- and sex-matched healthy controls for baseline comparisons) to evaluate the safety, tolerability, and efficacy of colesevelam in lowering plasma BA levels. Primary outcomes include safety/tolerability and change in total plasma BA levels. Secondary outcomes include changes in non-invasive hemodynamics, gut microbiome composition, fecal bile acid excretion, and biochemical profiles.

SITES: Single center. Estimated enrollment: 25 patients and 25 healthy subjects. Enrollment dates: September 2025 - August 2027 Trial Registration: NCT06197763 This manuscript describes the rationale and design of the MYSTIC study, which to our knowledge is the first interventional trial targeting a Fontan-specific metabolic derangement. The results will inform the feasibility of BA sequestration therapy in Fontan patients and guide future larger studies aimed at improving outcomes in this growing high-risk population.},
}

@article {pmid40840819,
year = {2025},
author = {Chao, NN and Zhang, L},
title = {Elucidating cellular origins and TME dynamic evolution in NSCLC through multi-omics technologies.},
journal = {Biochimica et biophysica acta. Reviews on cancer},
volume = {},
number = {},
pages = {189425},
doi = {10.1016/j.bbcan.2025.189425},
pmid = {40840819},
issn = {1879-2561},
abstract = {Non-small cell lung cancer (NSCLC) is a leading cause of cancer mortality. Despite progress in targeted therapies and immunotherapy, resistance driven by tumor heterogeneity and dynamic tumor microenvironment (TME) remodeling persists. Multi-omics (single-cell/spatial transcriptomics) reveals lung adenocarcinoma (LUAD) origins in alveolar type 2 (AT2) cells and lineage plasticity via SOX2/WNT/YAP pathways driving aggressive subtypes. The TME, a dynamic ecosystem of immune cells and fibroblasts, evolves through immune-editing phases and cancer-associated fibroblasts (CAF)/tumor-associated macrophage (TAM) crosstalk to foster immunosuppression. Multi-omics identifies key immune subsets (CXCL13[+]CD8[+]T cells, M1/M2 macrophages) and antigen-presenting cancer-associated fibroblasts (apCAFs) as therapeutic targets. Emerging strategies targeting lineage plasticity, TME reprogramming, and microbiome modulation may overcome immune checkpoint blockade (ICB)/tyrosine kinase inhibitor (TKI) resistance. Challenges in spatiotemporal heterogeneity resolution call for artificial intelligence (AI)-driven TME modeling to guide precision interventions. This review highlights multi-omics in bridging NSCLC evolution with clinical translation for personalized therapies.},
}

@article {pmid40840698,
year = {2025},
author = {Muñoz-Laiton, P and Hernandez-Valencia, JC and Isaza, JP and Correa, MM},
title = {Metatranscriptomic profiling of the bacterial and fungal microbiota of field-collected Anopheles darlingi from Colombia: Community composition and functional insights.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107795},
doi = {10.1016/j.actatropica.2025.107795},
pmid = {40840698},
issn = {1873-6254},
abstract = {Mosquitoes harbor diverse microorganisms that can influence host biology. While microbiota research in Anopheles has primarily focused on the metabarcoding approach, knowledge regarding the transcriptionally active microbiota and its functional roles in the host remains limited. This study aimed to characterize the transcriptionally active bacterial and fungal microbiota in field-collected Anopheles darlingi, a primary malaria vector in the Neotropics, and in addition, to explore its functional profile. Mosquitoes were collected in malaria-endemic regions of Colombia. Total RNA was extracted from pooled specimens to prepare cDNA libraries and sequenced by Illumina NovaSeq 6000. Results on microbiota composition showed predominance of bacterial (65%) over fungal reads (35%). The most abundant bacterial families included Enterobacteriaceae, Pseudomonadaceae, Acetobacteraceae and Moraxellaceae; the dominant genera were Halopseudomonas, Acinetobacter, Klebsiella, Escherichia and Asaia. In the fungal microbiota composition predominated Aspergillaceae and Hypoxylaceae, primarily represented by Aspergillus and Hypoxylon. Functional analysis showed transcripts encoding an MFS family transporter - an arabinose efflux permease, an ABC-type branched-chain amino acid transport system, diaminopimelate decarboxylase and O-succinylbenzoic acid-CoA ligase (MenE). These transcripts were associated with functional categories related to carbohydrate transport and metabolism, as well as the transport and biosynthesis of essential amino acids and vitamins. These findings offer valuable insights into the microbiota-mosquito dynamic and establish a foundation for further research into the role of microbiota in mosquito biology.},
}

@article {pmid40840675,
year = {2025},
author = {Choi, J and Jo, JY and Lee, J and Son, JE and Kim, SY and Lee, HE and Seong, YJ and Heo, K and Kim, Y and Park, MS and Byun, S},
title = {Lactobacillus salivarius HHuMin-U attenuates vulvovaginal candidiasis via vaginal epithelial immune enhancement mediated by NF-κB activation.},
journal = {New biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.nbt.2025.08.003},
pmid = {40840675},
issn = {1876-4347},
abstract = {Vulvovaginal candidiasis (VVC), primarily caused by Candida albicans infection, is one of the most common diseases among women and leads to various symptoms that adversely impact quality of life. VVC is conventionally treated with antifungal agents, but the high recurrence rates and the risk of inducing vaginal microbiome dysbiosis pose major concerns in effective treatment. Probiotics with immune-enhancing properties can be an effective strategy by strengthening mucosal immunity and reducing susceptibility to infection. Herein, this study investigates the therapeutic potential of Lactobacillus salivarius HHuMin-U (HMU) as a probiotic agent for treating VVC. Phenotype screening identified HMU as a top candidate with antifungal activity against C. albicans. HMU significantly upregulated immunomodulatory factors such as antimicrobial peptides, cytokines, and chemokines in human vaginal epithelial cells, which can strengthen the antifungal immune system. In an animal study, administration of HMU in a mouse VVC model significantly decreased the fungal burden and protected the mice from vaginal infection. Additionally, cellular infection models revealed that HMU reduced fungal adhesion and the cytolytic activity of C. albicans, while conditioned media from HMU-treated epithelial cells inhibited fungal growth. Transcriptomic analysis revealed that HMU treatment enriched gene sets related to epithelial barrier integrity, innate immune responses mediated by epithelial cells, and immune cell regulation. Mechanistically, the NF-κB pathway emerged as a key mediator of these responses. Collectively, HMU inhibits VVC by enhancing epithelial immunity and thus could be considered as a probiotic agent for the prevention and treatment of VVC.},
}

@article {pmid40840669,
year = {2025},
author = {Menikdiwela, KR and Lenis, M and Storch, J},
title = {The Use of Organoid Cultures in Advancing Nutrition Research.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {100489},
doi = {10.1016/j.advnut.2025.100489},
pmid = {40840669},
issn = {2156-5376},
abstract = {The importance of food and nutrients in human health and chronic disease progression has been appreciated for centuries. Crucial developments enabling understanding of the complex interactions between dietary patterns and health were made in the 20th century, owing in part to improvements in in vitro cell culture methods. Such two-dimensional (2D) cell lines remain extensively used to study the molecular mechanisms through which nutrients regulate cellular homeostasis. Nevertheless, they do not recapitulate the in vivo environment, and the complexity associated with tissues and organs, which invariably contain multiple cell types. Thus, findings from 2D cell cultures may not be directly applicable or representative of the in vivo situation. By contrast, organoids are three-dimensional (3D) tissue structures capable of mimicking structural, functional, and multicellular features of an intact organ, and are becoming increasingly used to carry out in-depth cell and molecular level studies. In particular, the use of intestinal organoids in food and nutrition research is expanding in recent years due to the greater suitability of organoids relative to 2D cultures for investigating nutrient uptake, transport, metabolism, and host-microbiome interactions. In the present review we summarize the emerging role and contributions of organoids, with emphasis on intestinal organoids, in nutrition research and intestinal health. We further highlight current limitations of organoid cultures and discuss potential future strategies to improve the use of organoids as a preferred model for investigations in the nutritional sciences.},
}

@article {pmid40840600,
year = {2025},
author = {Minaei, E and Joyce, P and Wade, SJ and Brownlee, C and Penney, C and Ranson, M and Aghmesheh, M and Sluyter, R and Vine-Perrow, KL},
title = {Gut microbial diversity is preserved through localised chemo-immunotherapy delivery in a KPC mouse model of pancreatic cancer.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {114143},
doi = {10.1016/j.jconrel.2025.114143},
pmid = {40840600},
issn = {1873-4995},
abstract = {Systemic chemotherapy and immunotherapy can disrupt gut microbial homeostasis, contributing to inflammation, treatment-related toxicity, and diminished anti-tumour immunity in pancreatic ductal adenocarcinoma (PDAC). Here, we evaluated whether localised delivery of chemo-immunotherapy via biodegradable implants could mitigate these adverse effects and preserve gut microbiota integrity. Using a syngeneic KPC mouse model of PDAC, we compared systemic versus implant-based delivery of gemcitabine/nab-paclitaxel and anti-CD40/anti-PD1 antibodies. 16S rRNA sequencing of faecal samples revealed that systemic chemo-immunotherapy significantly reduced alpha diversity, depleted immunoregulatory species (e.g. Akkermansia muciniphila, Bifidobacterium longum), and enriched pathobionts (Escherichia coli, Clostridium septicum), accompanied by elevated intestinal pro-inflammatory cytokines. In contrast, localised delivery preserved microbial diversity, maintained beneficial taxa and suppressed inflammatory cytokine levels. Further, high-dose localised chemotherapy promoted M1 macrophage polarisation while preserving microbiota more effectively than even low-dose systemic regimens. This is the first study to demonstrate that spatial control of drug exposure via localised delivery can protect the gut microbiome and modulate systemic immunity in PDAC. These findings subsequently provide proof-of-concept that implant-based approaches can enhance tolerability and efficacy of chemo-immunotherapy by minimising microbiome disruption.},
}

@article {pmid40840439,
year = {2025},
author = {He, X and Gao, Y and Zhang, Y and Yang, Z and Wang, C and Ma, Q and Lei, P and Yu, L and Fan, Y and Liu, R and Wang, W and Zhang, J and Ma, X and Zhu, F},
title = {Distinct Gut Microbial Signatures and Diminished Anti-Inflammatory Effect of Short-Chain Fatty Acids in Schizophrenia With Immune Activation.},
journal = {Schizophrenia bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1093/schbul/sbaf110},
pmid = {40840439},
issn = {1745-1701},
support = {82171505//National Natural Science Foundation of China/ ; 82230044//National Natural Science Foundation of China/ ; 82022023//National Natural Science Foundation of China/ ; 82271572//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND AND HYPOTHESIS: A subset of patients with schizophrenia (SCZ) exhibit subclinical immune activation. However, the gut microbial features of this subgroup and their interplay with the immune function remain poorly understood. This study aimed to identify the gut microbiome signature of immune-activated SCZ and elucidate the role of short-chain fatty acids (SCFAs) in the gut-immune crosstalk.

STUDY DESIGN: In this study, 297 patients with SCZ and 301 healthy controls (HCs) were assessed for 4 serum immune mediators. Immune-activated subgroups were classified based on these biomarkers. Fecal metagenomic sequencing, SCFA metabolomics, and in vitro peripheral blood mononuclear cells (PBMCs) stimulation experiments were performed to analyze the microbial composition, SCFA levels, and immune responses.

STUDY RESULTS: We found that 46.5% of the patients with SCZ exhibited elevated immune activation biomarker levels, which displayed unique bacterial signatures. Microbiome-based machine learning classifiers demonstrated robustness in SCZ and immune activation classification. Notably, microbial species abundance, functional metagenomics, and SCFA levels have confirmed an elevated capacity for SCFA production in patients with immune activation. Furthermore, in vitro PBMC stimulation experiments revealed a diminished anti-inflammatory effect of SCFAs in immune-activated patients when exposed to lipopolysaccharide-induced inflammation.

CONCLUSIONS: This study delineates the gut microbiome and SCFA metabolic profiles of immune-activated SCZ patients, revealing an association between gut microbiota dysbiosis, enhanced SCFA production capacity, and diminished anti-inflammatory effect of SCFA. These findings provide new insights into the underlying mechanisms and potential targeted treatments for SCZ patients with immune activation.},
}

@article {pmid40840314,
year = {2025},
author = {Botero, J and Cnockaert, M and Zhang, Y and Peeters, C and Vandamme, P},
title = {Carnimonas bestiolae sp. nov. and Cernens ardua gen. nov., sp. nov.: new halotolerant bacteria from the invasive solitary bee Megachile sculpturalis.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {5},
pages = {126648},
doi = {10.1016/j.syapm.2025.126648},
pmid = {40840314},
issn = {1618-0984},
abstract = {Fifteen isolates from gut samples of the invasive solitary bee Megachile sculpturalis remained unidentified after matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. Phylogenomic and overall genome relatedness indices analyses of five representative isolates demonstrated that 14 isolates represented a novel Carnimonas species for which we propose the name Carnimonas bestiolae sp. nov., with LMG 33810[T] as the type strain. A single isolate represented a distinct lineage within the Halomonadaceae family with the genera Carnimonas and Halotalea as nearest neighbor taxa and is classified as Cernens ardua gen. nov., sp. nov., with LMG 33818[T] as the type strain. Comparative genomic analysis and physiological characterization revealed functional differences between C. bestiolae, Ce. ardua and established Carnimonas and Halotalea species in central metabolism, fatty acid metabolism, and osmoregulatory pathways, the latter being consistent with adaptation to a saline environment. A reanalysis of previously published insect microbiome studies in which Carnimonas was reported, revealed 16S rRNA amplicon sequence variants with >99 % identity to C. bestiolae LMG 33810[T] 16S rRNA in gut samples of Megachile sculpturalis, Anthidium florentinum, and the psyllid Leptynoptera sulfurea. In contrast, 16S rRNA amplicon sequence variants corresponding to Ce. ardua were rarely detected and only at low relative abundances, suggesting a transient association with the insect gut.},
}

@article {pmid40840119,
year = {2025},
author = {Maldonado-Barrueco, A and Almazán-Garate, E and Armijo-Suárez, O and Iniesta-Pérez, S and Sanz-González, C and Álvarez-López, C and Cacho-Calvo, J and Quiles-Melero, I},
title = {Detection of bacterial vaginosis-associated bacteria and outcomes during clinical gynaecological conditions using qPCR: A retrospective cohort study.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {4},
pages = {117065},
doi = {10.1016/j.diagmicrobio.2025.117065},
pmid = {40840119},
issn = {1879-0070},
abstract = {Endometriosis, chronic endometritis (CE), unexplained infertility (UI), and recurrent pregnancy loss (RPL) are gynecological conditions frequently associated with inflammation and alterations in the endometrial microbiome. The presence of bacterial vaginosis-associated bacteria (BVAB) and the expression of CD138 may influence clinical outcomes. We evaluate the relationship between endometrial BVAB detection via qPCR, CD138 marker expression, prior antibiotic treatment, and the number of miscarriages. A retrospective single-center cohort study was conducted on 86 women with endometriosis, CE, UI, and/or RPL. Endometrial samples were collected and analysed using the Allplex™ Bacterial Vaginosis Plus qPCR assay (Seegene[Ⓡ]). Demographic data, CD138 expression, antibiotic usage, and miscarriage history were recorded and statistically analysed. CD138 expression was positive in 44.2% of cases. BVAB were detected in 31.4% of patients, with Lactobacillus spp. (median Log10 copies/reaction 1.56) and G. vaginalis (median Log10 copies/reaction 0.81) being the most common. A significant inverse association was found between CD138 positivity and BVAB detection (p < 0.05, OR = 0.31), suggesting reduced BVAB presence in inflamed endometria. No significant association was found between BVAB detection and prior antibiotic therapy or number of miscarriages. A significant correlation was found between negative BVAB qPCR results and positive CD138 expression, indicating a potential link between endometrial inflammation and microbiome alterations. However, antibiotic treatment did not significantly impact BVAB presence, and no association was found with miscarriage frequency. Further studies using vaginal swabs, healthy controls, and microbiome next-generation sequencing are needed to clarify these associations.},
}