@article {pmid40866789,
year = {2025},
author = {Kusakabe, S and Kurashige, R and Fukushima, K and Shimizu, K and Yoshihara, T and Motooka, D and Nakamura, S and Kurashige, M and Nakata, K and Hino, A and Kasahara, H and Ueda, T and Fujita, J and Hosen, N and Takehara, T and Oda, J},
title = {Fecal microbiota transplantation for Crohn's disease-like intestinal lesions arising after allogeneic stem cell transplantation.},
journal = {International journal of hematology},
volume = {},
number = {},
pages = {},
pmid = {40866789},
issn = {1865-3774},
abstract = {Several cases of inflammatory bowel disease (or similar gastrointestinal lesions) arising after allogeneic hematopoietic stem cell transplantation have been reported, but the effect of intestinal dysbiosis on development of these lesions remains unclear. We performed fecal microbiota transplantation (FMT) and 16S rRNA microbiome analysis in a patient who developed Crohn's disease-like lesions after allogeneic transplantation. A 62-year-old woman underwent haploidentical stem cell transplantation from her daughter to treat double-hit lymphoma relapsed after chimeric antigen receptor T-cell therapy, and achieved remission without developing acute graft-versus-host disease. Eight months later, she developed Crohn's disease-like intestinal lesions after cytomegalovirus enteritis. Her condition did not improve with the conventional treatment, so she underwent FMT from her daughter as part of a clinical trial. Diarrhea gradually improved, and follow-up endoscopy 4 months after the FMT showed ulcer healing and scarring. The 16S rRNA analysis revealed a reduction in the relative abundance of the Enterococcus genus after FMT, suggesting that dysbiosis may have contributed to lesion development. The patient is currently on a regular diet, with no symptom recurrence, and the primary disease remains in remission. Although this outcome suggests that FMT is effective, careful patient selection is required to reduce the risk of FMT-associated sepsis.},
}

@article {pmid40866540,
year = {2025},
author = {Liu, L and Wang, H and Guo, S and Liu, S and Du, Y and Wang, L and He, D and Mo, X and Zhang, H and Cheng, Q and Xiao, R and Xie, P},
title = {The emerging role of the gut microbiome in depression: implications for precision medicine.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {40866540},
issn = {1476-5578},
support = {82201683//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82401814//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82401789//National Natural Science Foundation of China (National Science Foundation of China)/ ; CSTB2024NSCQ-MSX0649//Natural Science Foundation of Chongqing (Natural Science Foundation of Chongqing Municipality)/ ; },
abstract = {Major depressive disorder is a debilitating mental illness that seriously endangers human health. Its pathogenesis is highly complex, and traditional treatments face substantial challenges. A growing body of preclinical and clinical findings highlight the important role of the gut microbiome in the pathogenesis of depression and its potential as a diagnostic and therapeutic target. A deeper understanding of how the gut microbiome regulates depression will greatly enhance its clinical application, improve diagnostic and treatment strategies, and pave the way for microbiota-based precision medicine for depression. In this review, we summarize the depression-associated compositional and functional microbial alterations, delineate their mechanistic contributions to disease pathogenesis, and evaluate their potentiality as novel diagnostic biomarkers and treatment targets. Finally, we consider the future potential of utilizing the gut microbiome to advance precision medicine approaches for depression.},
}

@article {pmid40866335,
year = {2025},
author = {Camacho, E and Dong, Y and Chrissian, C and Cordero, RJB and Saraiva, RG and Anglero-Rodriguez, Y and Smith, DFQ and Jacobs, E and Hartshorn, I and Patiño-Medina, JA and DePasquale, M and Dziedzic, A and Jedlicka, A and Smith, B and Mlambo, G and Tripathi, A and Broderick, NA and Stark, RE and Dimopoulos, G and Casadevall, A},
title = {Dietary L-3,4-dihydroxyphenylalanine (L-DOPA) augments cuticular melanization in Anopheles mosquitos reducing their lifespan and malaria burden.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8011},
pmid = {40866335},
issn = {2041-1723},
abstract = {L-3,4-dihydroxyphenylalanine (L-DOPA), a naturally occurring tyrosine derivative, is prevalent in environments that include mosquito habitats, potentially serving as part of their diet. Given its role as a precursor for melanin synthesis we investigate the effect of dietary L-DOPA on mosquito physiology and immunity to Plasmodium falciparum and Cryptococcus neoformans infection. Dietary L-DOPA is incorporated into mosquito melanin via a non-canonical pathway and has a profound transcriptional effect associated with enhanced immunity, increased pigmentation, and reduced lifespan. Increased melanization results in an enhanced capacity to absorb electromagnetic radiation that affects mosquito temperatures. Bacteria in the mosquito microbiome act as sources of dopamine, a substrate for melanization. Our results illustrate how an environmentally abundant amino acid analogue can affect mosquito physiology and suggest its potential usefulness as an environmentally friendly vector control agent to reduce malaria transmission, warranting further research and field studies.},
}

@article {pmid40866318,
year = {2025},
author = {Inoue, N and Shibata, T and Sawada, R and Yamanishi, Y},
title = {Human Microbiome-Based Prediction of Health Effects of Foods via Machine Learning.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c06318},
pmid = {40866318},
issn = {1520-5118},
abstract = {Food absorption is dependent on the activities of internal microorganisms. When exploring food functionality, considering the food compounds and their metabolites produced by microbial metabolism is crucial. In this study, we developed a machine learning method to predict food functionalities using microorganism and metabolic data. The prediction was performed on the chemical properties of 70,478 constituent compounds and 24,255 metabolites and their interactions with target proteins in disease-related pathways. This identified potential functional associations between 941 foods and 83 diseases, providing insights into the mechanisms involved, particularly those related to microorganisms. The effects of microorganism-mediated foods on diseases can be categorized based on food type. For example, the microorganisms associated with diseases within each food category indicated the potential involvement of the Bacteroidetes phylum in dyslipidemia and the Firmicutes phylum in Parkinson's disease. This method could aid in identifying disease-associated microorganisms, identifying prebiotic foods, and highlighting the potential of food interventions in the preventive medicine field. Furthermore, this approach is expected to be useful for elucidating novel mechanisms of food-disease interactions mediated by microbial metabolites.},
}

@article {pmid40865967,
year = {2025},
author = {Jee, JJ and Park, S and Kim, J and Lee, H and Koh, H and Koo, BN},
title = {Bacterial extracellular vesicle as a predictive biomarker for postoperative delirium status after spinal surgery: a prospective cohort study.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000003024},
pmid = {40865967},
issn = {1743-9159},
abstract = {BACKGROUND: Prognostic factors significantly associated with postoperative delirium (POD) have been reported discordantly, possibly due to heterogeneous cohorts. Here, bacteria extracellular vesicles (BEVs) were introduced to predict the POD status of a unique patient cohort.

METHODS: One hundred twenty-eight patients who underwent spinal surgery participated in this prospective cohort study. Significant preoperative factors (i.e., baseline characteristics, and sequences of 16s rRNA genes from bloods and stools) between patients with and without delirium were subjected to random forest classifiers for prediction model, and potential metabolites that regulate the POD were inferred in silico.

RESULTS: No significant differences were found between patients with and without delirium in terms of demographics, anthropometrics, intervention history or preoperative cognitive function scores, except for circulating BEVs; delirium group had less diverse BEVs dominated with EVs from Gammaproteobacteria, whereas more diverse BEVs enriched with EVs from Bacilli and Alphaproteobacteria were significantly associated with non-delirium. Compared to that with baseline characteristics or gut microbiome, prediction model using random forest classifier with the significant BEVs yielded the lowest error rate of 21.59%, and was validated with an independent data set, resulting in 80% accuracy. Moreover, EVs from Moraxellaceae and Acinetobacter showed the highest probabilities of prediction of the POD despite their low relative abundance, indicating the most significant prognostic markers for the POD. As the inference of a potential metabolites that regulate the POD, succinate and enterobacterial common antigens delivered from BEV cargo were expected to participate in pathogenic events, whereas S-methyl-5'-thioadenosine, 2-oxoglutarate, pyruvate, acetate and butyrate may play a neuroprotective role in the POD.

CONCLUSIONS: The profile of circulating preoperative BEVs is the key prognostic factor for distinguishing POD in elderly surgical patients with controlled baseline conditions. Metabolites of defensive and offensive mechanisms inferred from BEVs will be essential for developing next-generation POD prevention strategies.},
}

@article {pmid40865917,
year = {2025},
author = {Xu, YN and Pu, M and Raut, J and Du, Y and Qiu, Q and Hermanson, K and Xu, Y and Doraiswamy, C and Chu, CC},
title = {Skin microbiome as a signature of premature ageing appearance: Manipulation through by use of topical products.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjd/ljaf098},
pmid = {40865917},
issn = {1365-2133},
abstract = {BACKGROUND/OBJECTIVES: Perceived facial age and chronological age can show strong discrepancy due to differential magnification of age-related features, such as wrinkles or hyperpigmented spots, that affects overall ageing appearance. The perceived skin age of an individual can hence vary significantly from the chronological age depending on environmental or lifestyle factors. Whilst age-related changes of the skin microbiome have been characterized between healthy adults at younger vs older chronological age, the inter-relationship between skin microbiome and physiological appearance of ageing remains to be elucidated. In a first ever study we compared the microbiome features of healthy adult female within a similar chronological age rage (40-50 years old) but exhibiting distinct (premature vs delayed) ageing (PA vs DA) features of wrinkle.

METHODS: PA and DA participants were defined based on historical VISIA CR® images. 30 PA and 35 DA volunteers were recruited following informed consent and independent ethics approval. PA volunteers were given a marketed product to use twice daily for four weeks. Skin brightness, elasticity, hydration, and barrier functions were measured at baseline and 4 weeks after product use. Facial microbiome samples were collected from upper cheeks using a cup scrub technique. The microbial DNAs were extracted and sequenced at the variable region (V1-V2) of the 16S rDNA gene for bacterial classification and analysis.

RESULTS/CONCLUSION: We revealed significant changes of the skin microbiome between PA and DA participants, with an increased abundance of Acinetobacter. By employing network theory to characterize polymicrobial interactions, we found that microbial community network of PA was more fragile and less resilient than that of DA. Topical use of a marketed skincare product could improve age-related skin physiology of premature ageing while modulating the microbiome features, showing a clear shift in the skin microbiome composition and community structure towards signatures closer to the delayed agers. Our findings unraveled the potential role of skin microbiome in accelerated ageing appearance and lay the foundation for future development of microbiome-based anti-ageing intervention strategy.},
}

@article {pmid40865713,
year = {2025},
author = {Ho, KD and Wang, M and Ho, KR and Tong, WM and Tonetti, MS and Leung, WK},
title = {Papilla preservation flap surgery and endoscope-assisted subgingival debridement for Step 3 therapy: A 12-month pilot study on subgingival microbial community dynamics in deep periodontal pockets.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {106058},
doi = {10.1016/j.jdent.2025.106058},
pmid = {40865713},
issn = {1879-176X},
abstract = {OBJECTIVES: This study aimed to assess subgingival microbial changes following papilla preservation flap surgery (PPFS) or endoscope-assisted subgingival debridement (EASD) in patients with residual periodontal intrabony defects requiring Step 3 therapy.

METHODS: Nineteen periodontitis participants requiring Step 3 periodontal therapy were randomly allocated to either the PPFS (n = 11) or EASD (n = 8) treatment group and were conveniently sampled. Subgingival plaque samples were collected at baseline, days 3, 7, 14, and months 1, 3, 6, 9, and 12 post-treatment. DNA extraction and 16S rRNA sequencing were used to analyze microbial communities through bioinformatics tools, assessing diversity and differential abundance.

RESULTS: Both treatments were effective, with no significant difference in clinical outcomes. Pocket resolution was achieved in 100% of PPFS sites and 87.5% of EASD sites. The overall microbiome composition was similar between groups. However, microbial diversity dynamics differed: PPFS exhibited stable shifts over time (PERMANOVA, p = 0.004), whereas EASD showed more variability in species richness and abundance, indicating less predictable microbial reorganization (Procrustes, p = 0.030). Notably, Fusobacterium nucleatum subsp. vincentii/Fretibacterium fastidiosum and Treponema socranskii were significantly associated with bleeding on probing/probing pocket depth, respectively (p<0.05).

CONCLUSIONS: Both PPFS and EASD effectively treat residual intrabony defects, with PPFS showing more consistent microbial modulation. This 12-month pilot study offers new insights into the changes in microbiota following surgical and minimally invasive periodontal therapies, highlighting potential microbial biomarkers associated with clinical outcomes.

CLINICAL SIGNIFICANCE: This 12-month study, for the first time, profiled the subgingival microbiota over the management of residual intrabony defects using either PPFS or EASD in Step 3 therapy. The study also revealed possible associations between specific microbes and clinical parameters during the post-operative period, which warranted further investigation.},
}

@article {pmid40865652,
year = {2025},
author = {Li, M and Deng, K and Zheng, R and Li, Y and Xiang, L and Cheng, J and Wang, Y and Kuang, S and Huang, S and Lv, Z},
title = {Mechanism of Bao Gan Ning Decoction in attenuating hepatic fibrosis via modulation of the gut microbiome and PPAR/CYP7A1-mediated bile acid metabolism.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {120488},
doi = {10.1016/j.jep.2025.120488},
pmid = {40865652},
issn = {1872-7573},
abstract = {Timely intervention in hepatic fibrosis (HF) is imperative to reduce mortality associated with cirrhosis and prevent progression to hepatocellular carcinoma. Bao Gan Ning Decoction (BGN), a Traditional Chinese Medicine formula, demonstrates therapeutic efficacy against HF. However, its mechanism of action remains incompletely defined.

AIM OF THE STUDY: To elucidate the mechanistic role of BGN in attenuating HF through modulation of specific gut microbiota taxa and bile acid (BA) metabolism.

MATERIALS AND METHODS: HF was induced in mice using CCl4. Gut microbiota composition was analysed using 16S rRNA gene sequencing. Hepatic BA profiles were quantified using LC-MS/MS, targeting 53 specific BA in negative ion mode through multiple reaction monitoring. Complementary histopathological, molecular, and functional analyses were performed.

RESULTS: The findings indicate that BGN mediates remodelling of the gut microbiota by enriching probiotic taxa (Lactobacillus, Bifidobacterium) and depleting pathobionts. Furthermore, BGN attenuates fibrosis by increasing anti-fibrotic BA levels (e.g., ursodeoxycholic acid) while reducing hepatotoxic BA; it activates the PPARα/CYP7A1 signalling axis to upregulate hepatointestinal BA transporters (Slc10a1/NTCP, ABCB11/BSEP, OSTα/β, Slc10a2/ASBT).

CONCLUSIONS: BGN alleviates HF through gut microbiota-dependent restoration of BA homeostasis and activation of the PPARα/CYP7A1 pathway. This study provides novel mechanistic insights into BGN's anti-fibrotic activities, positioning it as a microbiota-modulating therapeutic candidate for HF management.},
}

@article {pmid40865517,
year = {2025},
author = {Chen, J and Gao, Y and Chen, Y and Wang, Q and Zhang, Y and Huang, Y and Xian, X and Zhou, D and Zhou, H and Liu, R and Zou, Y and Zhang, W},
title = {Identification and validation of intratumoral microbiome associated with sensitization to immune checkpoint inhibitors.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102306},
doi = {10.1016/j.xcrm.2025.102306},
pmid = {40865517},
issn = {2666-3791},
abstract = {As a part of the commensal microbiome, the regulatory role of the intratumoral microbiome in tumor immunity is gradually revealed. However, the relationship between the intratumoral microbiome and the efficacy of immune checkpoint inhibitors (ICIs) clinical treatment remains unclear. Here, we collect RNA sequencing (RNA-seq) data and clinical information from publicly available ICIs therapy cohorts. By developing an improved bioinformatics pipeline to identify the intratumoral microbiome and performing a comprehensive association analysis, we find that the intratumoral microbiome is associated with response to ICIs and characteristics of the tumor microenvironment (TME). In vivo experiments demonstrate that intratumoral injection of Burkholderia cepacia, Priestia megaterium, or Corynebacterium kroppenstedtii, which were selected from our analysis results, would synergize with anti-PD-1 therapy to inhibit tumor growth and enhance antitumor immunity. Our findings highlight the essential role of the intratumoral microbiome in the clinical effectiveness differences of ICIs, suggesting its potential in future ICIs combination therapy.},
}

@article {pmid40865433,
year = {2025},
author = {Yu, BS and Park, Y and Park, S and Cho, JW and Han, K},
title = {Control system for soil microbes detrimental to trees using metabolites derived from algal bloom-causing microorganisms.},
journal = {The Science of the total environment},
volume = {999},
number = {},
pages = {180359},
doi = {10.1016/j.scitotenv.2025.180359},
pmid = {40865433},
issn = {1879-1026},
abstract = {Algal blooms, primarily caused by cyanobacteria such as Microcystis aeruginosa, disrupt aquatic ecosystems while also holding potential as a source of bioactive compounds. This study investigated microbial and metabolite changes during the occurrence and mitigation stages of algal blooms based on samples collected from Daecheong Lake in July (algal bloom season) and September (mitigation season) 2024. Using 16S rRNA sequencing, LC/MS-QTOF, and GC/MS, we identified a dynamic shift in microbial communities, with M. aeruginosa dominating during blooms and Flavobacterium fontis increasing post-mitigation. The metabolomic analysis highlighted unique fatty acid profiles, including linoleic acid and gamma-linolenic acid, which showed antimicrobial activity, particularly against plant pathogens such as Bacillus cereus. Algal supernatants significantly enhanced seed germination in crops like Cucumis sativus and Cucurbita moschata, attributed to growth-promoting metabolites such as stigmatellin Y, palmitic acid methyl ester, and phytohormone precursors. However, higher concentrations exhibited inhibitory effects, suggesting the need for optimal dosing. Antimicrobial assays revealed moderate inhibition of pathogens, indicating potential for natural biocontrol applications. This study highlights the dual role of algal blooms as both ecological challenges and valuable resources, laying the groundwork for their utilization in sustainable agriculture, biotechnology, and the development of natural antimicrobials. In particular, the potential of algae-derived substances to promote plant growth and inhibit pathogens has been confirmed through experimental analysis, providing a scientific basis for future practical applications in related fields. Based on this, further research is essential to improve extraction methods, evaluate ecological impacts, and expand production scale for practical application.},
}

@article {pmid40865404,
year = {2025},
author = {Zhong, Y and Zhang, D and Ding, F and Zhang, H and Guo, Y and Huang, Q and Liu, G and Zhang, X and Weng, S},
title = {Intratumoral microbiota-driven macrophage reprogramming in pancreatic cancer via Blautia metabolite 6-hydroxyhexanoic acid.},
journal = {International immunopharmacology},
volume = {164},
number = {},
pages = {115421},
doi = {10.1016/j.intimp.2025.115421},
pmid = {40865404},
issn = {1878-1705},
abstract = {Pancreatic ductal adenocarcinoma (PDAC) exhibits a particularly immunosuppressive microenvironment, which contributes to its poor prognosis and resistance to conventional therapies. Recent studies have highlighted the microbiome as a dynamic regulator of anti-tumor immunity, ultimately contributing to tumor suppression. The tumor microenvironment is increasingly recognized as a dynamic ecosystem where the microbiome plays a pivotal role in shaping immune responses. Therefore, it is crucial to explore the specific biological processes by which intratumoral microbiome suppresses tumor growth and enhances antitumor immunity. In this study, we identified a significant enrichment of Blautia genus in pancreatic cancer patients with favorable prognosis and revealed its role in modulating macrophage phenotypes within the tumor immune microenvironment. Targeted metabolomics and proteomics uncovered the regulatory correlation between its metabolite, 6-hydroxyhexanoic acid (6-HHA), and tumor-associated macrophages (TAMs) within the tumor microenvironment. Through cellular interventions and animal experiments, we demonstrated via flow cytometry and immunofluorescence imaging that 6-HHA facilitates the phenotypic transition of macrophages from M2 to M1, thereby exerting antitumor effects. RNA-seq analysis elucidated the mechanistic underpinnings by which 6-HHA induces M1 polarization through activation of the JAK1-STAT1 signaling pathway in TAMs. Finally, the addition of a JAK1-STAT1 pathway inhibitor in both in vitro and in vivo experiments attenuated the M1 repolarization effect of 6-HHA, suggesting that the JAK1-STAT1 signaling pathway plays a crucial role in mediating this process. Taken together, Blautia and its metabolite 6-HHA potentiate antitumor immunity through activation of TAMs, which establishes a novel microbiota-targeted therapeutic paradigm for cancer intervention.},
}

@article {pmid40865224,
year = {2025},
author = {Xu, M and Pan, D and Yi, J and Zheng, Y and Zeng, G and Lin, J and Song, Y and Sun, D and Chen, J},
title = {Gut-brain axis dysfunction mediates neurotoxicity of embryonic p-phenylenediamine exposure in zebrafish.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139650},
doi = {10.1016/j.jhazmat.2025.139650},
pmid = {40865224},
issn = {1873-3336},
abstract = {P-phenylenediamine antioxidants (PPDs) are widely used in the rubber industry and are increasingly recognized as environmental contaminants, raising concerns about their potential risks to wildlife and human health. Our present study investigated the neurotoxicity of embryonic exposure to a sublethal concentration (0.05 mg/L) of three PPDs (CPPD, IPPD and 77PD) in zebrafish. Our results showed that PPDs impaired the fish growth and induced distinct behavioral alterations. Specifically, CPPD exposure induced hyperactivity, aggression and social deficit. IPPD caused hyperactivity and loose shoaling behavior. And 77PD led to social deficits and reduced social cohesion. Examination of head tissues indicated elevated oxidative stress markers, altered antioxidant enzyme activities, increased neurotransmitter levels and abnormality of neural markers (Gfap/Olig2) using transgenic zebrafish. Histopathological analyses revealed marked intestinal damage including villus structural distortion and reduced mucus secretion. Integrated head-transcriptome and gut-microbiome analyses elucidated compound-specific molecular mechanisms. CPPD and IPPD significantly affected ocular lens development and visual perception pathways, whereas CPPD and 77PD notably disrupted olfactory sensory signaling and G protein-coupled receptor pathways. 16S rDNA sequence indicated PPDs-induced intestinal flora disorder by changing the composition and structure of intestinal flora, where the decreased Firmicutes to Bacteroidetes ratio may account for the fish growth suppression. Dual-omics integration revealed regulatory interactions between brain metabolic genes and gut microbiota, corroborating elevated gut lysozyme activity and increased inflammatory markers (TGFβ, IL6). These gut disturbances were linked to head gene dysregulations (muc5.3, or109 and apip). Additional antibiotic metronidazole (MTZ) treatment alleviated PPDs-induced zebrafish behavioral changes and suppressed the gut-brain stress response indicators. Our findings demonstrate that embryonic PPD exposure induces neurotoxicity mediated through gut-brain axis disruption, providing critical insights into the ecological risks of PPD pollutants.},
}

@article {pmid40865051,
year = {2025},
author = {Zheng, Z and Yuan, F and Li, J and Zhu, X and Jia, R and Wei, J and Jia, F and Hou, X and Zhang, Z and Wang, Y and Ma, Y and Jia, W and Zhao, L},
title = {Gut Microbiota-Mediated Bile Acid Metabolism Regulates Colorectal Cancer Liver Metastasis by Altering Neutrophil Recruitment.},
journal = {Cancer research},
volume = {},
number = {},
pages = {},
doi = {10.1158/0008-5472.CAN-24-4425},
pmid = {40865051},
issn = {1538-7445},
abstract = {The gut microbiome is frequently dysregulated in colorectal cancer (CRC). Gut microbiota can modify bile acids (BAs), which is a group of metabolites that have been linked to tumorigenesis and progression. Here, we observed a significant deficiency in gut bacteria with bile salt hydrolase (BSH) activity in patients with liver metastatic CRC (CRLM). These patients exhibited elevated levels of conjugated primary BAs (CPBAs) and decreased levels of unconjugated BAs (UBAs) in their circulation. The changes in bacterial BSH activity and CPBA levels were more pronounced in male CRLM patients. Microbial manipulation in mouse CRC models to create a BSH-deficient state increased CPBAs, reduced UBAs, and promoted liver metastasis. Specifically, taurocholic acid (TCA), a CPBA, promoted CRLM through a neutrophil-dependent mechanism. TCA upregulated TIMP1 in CRC cells, which in turn stimulated CXCL5/CXCR2-mediated neutrophil recruitment and CRLM. Alternatively, unconjugated primary and secondary BAs counteracted neutrophil migration induced by TCA in vitro and abolished TCA-promoted neutrophil recruitment and liver metastasis in vivo. Together, these findings elucidate a mechanistic role of the dysregulated gut microbiota-BA axis in CRLM, suggesting that manipulating the balance between conjugated and unconjugated BAs could be a potential therapeutic strategy to suppress CRC metastasis.},
}

@article {pmid40864791,
year = {2025},
author = {Pelc, A and Fic, W and Typrowicz, T and Polak-Szczybyło, E},
title = {Physiological Mechanisms of and Therapeutic Approaches to the Gut Microbiome and Low-Grade Inflammation in Obesity.},
journal = {Current issues in molecular biology},
volume = {47},
number = {8},
pages = {},
doi = {10.3390/cimb47080637},
pmid = {40864791},
issn = {1467-3045},
abstract = {Obesity is a growing global health challenge, closely linked to chronic low-grade inflammation. This persistent, low-intensity immune response contributes to the development of metabolic, cardiovascular, and cancer-related diseases. A key player in this process is the gut microbiota. Dysbiosis, an imbalance in gut bacterial composition, disrupts metabolic function, weakens the intestinal barrier, and promotes the production of pro-inflammatory cytokines. In people with obesity, gut microbial diversity is reduced, and the ratio of beneficial to harmful bacteria shifts, affecting lipid metabolism and immune balance. Short-chain fatty acids, produced by gut bacteria, help maintain gut integrity and reduce inflammation. Butyrate, a major SCFA, also improves insulin sensitivity and may support obesity treatment. Diet plays a central role in shaping the gut microbiome. Western diets tend to promote dysbiosis and inflammation, while Mediterranean-style diets encourage the growth of beneficial bacteria. Targeted modulation of the microbiota through diet, probiotics, or medication emerges as a promising strategy for preventing and managing obesity.},
}

@article {pmid40864773,
year = {2025},
author = {Guan, T and Yang, X and Hong, C and Zhang, Z and Xiao, P and Yang, Y and Zhang, C and He, Z},
title = {The Extract of Periplaneta americana (L.) Promotes Hair Regrowth in Mice with Alopecia by Regulating the FOXO/PI3K/AKT Signaling Pathway and Skin Microbiota.},
journal = {Current issues in molecular biology},
volume = {47},
number = {8},
pages = {},
doi = {10.3390/cimb47080619},
pmid = {40864773},
issn = {1467-3045},
support = {82060747//Peiyun Xiao/ ; },
abstract = {Alopecia, a prevalent dermatological disorder affecting over half of the global population, is strongly associated with psychological distress. Extracts from Periplaneta americana (L. PA), a medicinal insect resource, exhibit pharmacological activities (e.g., antioxidant, anti-inflammatory, microcirculation improvement) that align with core therapeutic targets for alopecia. This study aimed to systematically investigate the efficacy and mechanisms of PA extracts in promoting hair regeneration. A strategy combining network pharmacology prediction and in vivo experiments was adopted. The efficacy of a Periplaneta americana extract was validated by evaluating hair regrowth status and skin pathological staining in C57BL/6J mice. Transcriptomics, metabolomics, RT-qPCR, and 16s rRNA techniques were integrated to dissect the underlying mechanisms of its hair-growth-promoting effects. PA-011 significantly promoted hair regeneration in depilated mice via multiple mechanisms: enhanced skin superoxide dismutase activity and upregulated vascular endothelial growth factor expression; modulated FOXO/PI3K/AKT signaling pathway and restored skin microbiota homeostasis; and accelerated transition of hair follicles from the telogen to anagen phase. PA-011 exerts hair-promoting effects through synergistic modulation of FOXO/PI3K/AKT signaling and the skin microbiome. As a novel therapeutic candidate, it warrants further systematic investigation for clinical translation.},
}

@article {pmid40864733,
year = {2025},
author = {Lee, JY and Kim, H},
title = {p53 Protein Stability Plays a Crucial Role in NaB-Mediated Apoptosis in Colorectal Cancer Cells.},
journal = {Current issues in molecular biology},
volume = {47},
number = {8},
pages = {},
doi = {10.3390/cimb47080579},
pmid = {40864733},
issn = {1467-3045},
abstract = {Colorectal cancer (CRC) is associated with factors such as an unhealthy diet, physical inactivity, obesity, diabetes, and chronic inflammatory conditions like inflammatory bowel disease (IBD), as well as TP53 mutations, which are observed in a broad spectrum of CRC. Additionally, alteration in the composition of the gut microbiome community and metabolism plays a significant role in the development of colorectal cancer and its therapeutic effects. It is well known that treatment with sodium butyrate (NaB), an intestinal microbial metabolite, can induce apoptosis by activating histone deacetylase (HDAC) in cancer cells. Therefore, this study examined the relationship between NaB-induced apoptosis and p53 protein level in colorectal cancer cells. Treatment with NaB triggered cell death in the HCT116 cell line. Furthermore, a notable elevation in p53 protein level was detected following treatment with a high concentration of NaB, compared to both the control group and the low concentration NaB. Furthermore, apoptotic cell death was diminished in a p53-deficient cell line (HCT 116 p53[-/-]) and p53 protein expression was more stabilized. Although p53 mRNA expression was not affected, acetylation of p53 protein was clearly observed by high concentration NaB treatment. To demonstrate the relationship between p53 acetylation and cell death, HT29 cells were treated with a high concentration of NaB. In HT29 cells with a mutation in the p53 gene, increased cell viability, overproduction p53 protein, and hyperacetylation of p53 were observed compared to the control. The results of this study suggest that p53 protein expression plays an important role in the effectiveness of therapy utilizing gut microbiota metabolites.},
}

@article {pmid40864614,
year = {2025},
author = {Felten, V and Turck, JL and Unterer, S and Favrot, C and Suchodolski, J and Fischer, NM and Rostaher, A},
title = {An insight into the gut microbiota of healthy and allergic West Highland Whiter Terrier dogs.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0328100},
doi = {10.1371/journal.pone.0328100},
pmid = {40864614},
issn = {1932-6203},
abstract = {Canine atopic dermatitis (cAD) is a multifactorial, genetically predisposed inflammatory skin disease, with a high prevalence in many different dog breeds, with certain breeds being particularly affected, like the West Highland White Terrier (WHWT). While gut microbiome alterations are linked to allergic diseases in humans and some dog breeds, this relationship has never been investigated in WHWT dogs. This study aimed to compare the gut microbiome of allergic and healthy WHWT dogs to explore its role in cAD. Fecal samples from 21 WHWT dogs (12 allergic, 9 healthy) were analyzed using DNA shotgun sequencing and qPCR assays. No significant differences were observed in alpha or beta diversity, and no significant abundance of bacterial taxa was identified between allergic and healthy dogs. The Dysbiosis Index (DI) did not differ between the allergic (median -4.2, range -6.6 to 1.3) and healthy group. However, a moderate negative correlation was found between the relative abundance of E. coli and pruritus severity. These findings indicate that while the gut microbiome overall may not significantly contribute to cAD pathogenesis in WHWT dogs, some species like E. coli may be associated with clinical symptoms. Further studies are needed to investigate this relationship and to explore the role of genetics and the gut microbiota across different breeds with a larger number of dogs and with multi-omics approaches.},
}

@article {pmid40864582,
year = {2025},
author = {Jeong, K and Moon, SJ and Rachim, VP and Song, Y and Cho, YM and Park, SM},
title = {Enhanced Post-Prandial Glycemic Response Prediction in Type 2 Diabetes with Microbiome Data and Deep Learning.},
journal = {IEEE journal of biomedical and health informatics},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/JBHI.2025.3602827},
pmid = {40864582},
issn = {2168-2208},
abstract = {Nutritional intervention can improve glycemic control for type 2 diabetes mellitus (T2DM), and thus accurately predicting post-prandial glycemic responses (PPGRs) to each meal is essential. PPGRs can vary significantly between individuals, even when consuming the same foods, due to the diverse and complex nature of individual characteristics. However, to date, system-scale studies investigating the variability of PPGRs in people living with T2DM are scarce. This research collected meal logs, continuous glucose monitoring records, clinicodemographic profiles, and gut microbiota data comprising over 2,000 real-life meals across 88 individuals with T2DM, revealing causal relationships in the diet-microbiome-PPGR interplay. Furthermore, we developed a multimodal deep learning predictive PPGR model that integrates heterogeneous input data. The proposed model achieves R of 0.62 and 0.66 for 2- and 4-h PPGR prediction, respectively, significantly surpassing the perfor-mance of the carbohydrate single predictor and state-of-the-art machine learning algorithms. This model substantially improved the prediction in the subgroup of low responders to carbohydrates, a traditionally challenging population for accurate prediction using carbohydrate-based methods. This advancement empowers personalized PPGR prediction, laying the foundation for precision nutrition and better glycemic management for individuals with T2DM.},
}

@article {pmid40864418,
year = {2025},
author = {Bai, X and Xu, L and Wang, K and Chen, L and Bai, T and Li, P and Chu, W and Song, C},
title = {Effects of Three Microbiome-Based Therapies on Loperamide-Induced Constipation in Mice by Restoring Intestinal Motility and Modulating the Intestinal Microbiota.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40864418},
issn = {1867-1314},
support = {M-2022193//Traditional Chinese Medicine Technology Project of Shandong Province/ ; 2019GSF108249//Key Technology Research and Development Program of Shandong Province/ ; },
abstract = {Constipation is a common gastrointestinal disorder, often associated with dysbiosis of the intestinal microecology. The treatments for constipation are various, and microbiome-based therapies provide supplementary or alternative options for its management. This study compared the therapeutic effects of three microbiome-based therapies, including probiotics, prebiotics, and traditional Chinese medicine (TCM), with the agonist mosapride on loperamide-induced constipation in mice, focusing on their restorative effects on intestinal motility and intestinal microecology. The results showed that mosapride had the most significant improvement in gut motility and key motility hormones, and also significantly restored gut microbiota. Probiotics significantly improved the levels of the motility hormones motilin (MTL) and substance P (SP) and significantly altered the composition of the microbiota. TCM significantly increased gut motility and was most effective in improving gut microbiota composition and short-chain fatty acid (SCFA) content. Inulin, on the other hand, had the least effect on defecation phenotype, intestinal motility, and restoration of intestinal microecology. Overall, this preclinical study in mice provides experimental insights into the therapeutic efficacy and potential mechanisms of these methods, which may contribute to the appropriate selection of candidate therapies for human constipation subtypes characterized by motility-microbiota axis dysfunction. In addition, the research highlights the critical importance of gut microbiota and their metabolites in the treatment of constipation and their potential as therapeutic indicators.},
}

@article {pmid40864369,
year = {2025},
author = {Kumar, A and Raj, A and Chaman Lal, K and Puja, },
title = {Intratumoral Microbe Correlated with Expression of DNA Methylation Genes in Hepatocellular Carcinoma.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {40864369},
issn = {1573-2568},
}

@article {pmid40863928,
year = {2025},
author = {Li, B and Zhang, Y and Du, J and Liu, C and Zhou, G and Li, M and Yan, Z},
title = {Application of Multi-Omics Techniques in Aquatic Ecotoxicology: A Review.},
journal = {Toxics},
volume = {13},
number = {8},
pages = {},
pmid = {40863928},
issn = {2305-6304},
support = {No. 42277271//National Natural Science Foundation of China/ ; ZR2022QD147//Shandong Provincial Natural Science Foundation/ ; },
abstract = {Traditional ecotoxicology primarily investigates pollutant toxicity through physiological, biochemical, and single-molecular indicators. However, the limited data obtained through this approach constrain its application in the mechanistic analysis of pollutant toxicity. Omics technologies have emerged as a major research focus in recent years, enabling the comprehensive and accurate analysis of biomolecular-level changes. The integration of multi-omics technologies can holistically reveal the molecular toxicity mechanisms of pollutants, representing a primary emphasis in current toxicological research. This paper introduces the fundamental concepts of genomics, transcriptomics, proteomics, and metabolomics, while reviewing recent advancements in integrated omics approaches within aquatic toxicology. Furthermore, it provides a reference framework for the implementation of multi-omics strategies in ecotoxicological investigations. While multi-omics integration enables the unprecedented reconstruction of pollutant-induced molecular cascades and earlier biomarker discovery (notably through microbiome-metabolome linkages), its full potential requires experimental designs, machine learning-enhanced data integration, and validation against traditional toxicological endpoints within environmentally relevant models.},
}

@article {pmid40863916,
year = {2025},
author = {Liu, Z and Cao, F and Qiayimaerdan, A and Aisikaer, N and Zunong, Z and Ma, X and Yu, Y},
title = {BDE-47 Disrupts Gut Microbiota and Exacerbates Prediabetic Conditions in Mice: Therapeutic Potential of Grape Exosomes and Antioxidants.},
journal = {Toxics},
volume = {13},
number = {8},
pages = {},
pmid = {40863916},
issn = {2305-6304},
support = {SKL-HIDCA-2022-19//State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia/ ; 82160605//the National Natural Science Foundation of China/ ; No//the "14th Five-Year Plan" Characteristic Discipline of Colleges and Universities in Xinjiang Uygur Autonomous Region-Public Health and Preventive Medicine./ ; },
abstract = {Background: BDE-47, a pervasive environmental pollutant detected in >90% of human serum samples, is increasingly linked to metabolic disorders. This study investigates the specific impact of BDE-47 exposure on the gut microbiota in prediabetic mice and evaluates the efficacy of therapeutic interventions in mitigating these effects. Objectives: To determine whether BDE-47 exposure induces diabetogenic dysbiosis in prediabetic mice and to assess whether dietary interventions, such as grape exosomes and an antioxidant cocktail, can restore a healthy microbiota composition and mitigate diabetes risk. Methods: In this study, a prediabetic mouse model was established in 54 male SPF-grade C57BL/6J mice through a combination of high-sugar and high-fat diet feeding with streptozotocin injection. Oral glucose tolerance tests (OGTT) were conducted on day 7 and day 21 post-modeling to assess the establishment of the model. The criteria for successful model induction were defined as fasting blood glucose levels below 7.8 mmol/L and 2 h postprandial glucose levels between 7.8 and 11.1 mmol/L. Following confirmation of model success, a 3 × 3 factorial design was applied to allocate the experimental animals into groups based on two independent factors: BDE-47 exposure and exosome intervention. The BDE-47 exposure factor consisted of three dose levels-none, high-dose, and medium-dose-while the exosome intervention factor included three modalities-none, Antioxidant Nutrients Intervention, and Grape Exosomes Intervention. Fresh fecal samples were collected from mice two days prior to sacrifice. Cecal contents and segments of the small intestine were collected and transferred into 1.5 mL cryotubes. All sequences were clustered into operational taxonomic units (OTUs) based on defined similarity thresholds. To compare means across multiple groups, a two-way analysis of variance (ANOVA) was employed. The significance level was predefined at α = 0.05, and p-values < 0.05 were considered statistically significant. Bar charts and line graphs were generated using GraphPad Prism version 9.0 software, while statistical analyses were performed using SPSS version 20.0 software. Results: The results of 16S rDNA sequencing analysis of the microbiome showed that there was no difference in the α diversity of the intestinal microbiota in each group of mice (p > 0.05), but there was a difference in the Beta diversity (p < 0.05). At the gate level, the abundances of Proteobacteria, Campylobacterota, Desulfobacterota, and Fusobacteriota in the medium-dose BDE-7 group were higher than those in the model control group (p < 0.05). The abundance of Patellar bacteria was lower than that of the model control group (p < 0.05). The abundances of Proteobacteria and Campylobacterota in the high-dose BDE-7 group were higher than those in the model control group (p < 0.05). The abundance of Planctomycetota and Patescibacteria was lower than that of the model control group (p < 0.05), while the abundance of Campylobacterota in the grape exosome group was higher than that of the model control group (p < 0.05). The abundance of Patescibacteria was lower than that of the model control group (p < 0.05), while the abundance of Firmicutes and Fusobacteriota in the antioxidant nutrient group was higher than that of the model control group (p < 0.05). However, the abundance of Verrucomicrobiota and Patescibacteria was lower than that of the model control group (p < 0.05). At the genus level, the abundances of Bacteroides and unclassified Lachnospiraceae in the high-dose BDE-7 group were higher than those in the model control group (p < 0.05). The abundance of Lachnospiraceae NK4A136_group and Lactobacillus was lower than that of the model control group (p < 0.05). The abundance of Veillonella and Helicobacter in the medium-dose BDE-7 group was higher than that in the model control group (p < 0.05), while the abundance of Lactobacillus was lower (p < 0.05). The abundance of genera such as Lentilactobacillus and Faecalibacterium in the grape exosome group was higher than that in the model control group (p < 0.05). The abundance of Alloprevotella and Bacteroides was lower than that of the model control group (p < 0.05). In the antioxidant nutrient group, the abundance of Lachnospiraceae and Hydrogenophaga was higher than that in the model control group (p < 0.05). However, the abundance of Akkermansia and Coriobacteriaceae UCG-002 was significantly lower than that of the model control group (p < 0.05). Conclusions: BDE-47 induces diabetogenic dysbiosis in prediabetic mice, which is reversible by dietary interventions. These findings suggest that microbiota-targeted strategies may effectively mitigate the diabetes risk associated with environmental pollutant exposure. Future studies should further explore the mechanisms underlying these microbiota changes and the long-term health benefits of such interventions.},
}

@article {pmid40863733,
year = {2025},
author = {Alaeddin, S and Ko, Y and Steiner-Lim, GZ and Jensen, SO and Roberts, TL and Ho, V},
title = {The Effect of Faecal Microbiota Transplantation on Cognitive Function in Cognitively Healthy Adults with Irritable Bowel Syndrome: Protocol for a Randomised, Placebo-Controlled, Double-Blinded Pilot Study.},
journal = {Methods and protocols},
volume = {8},
number = {4},
pages = {},
pmid = {40863733},
issn = {2409-9279},
abstract = {Faecal microbiota transplantation (FMT) is an emerging therapy for gastrointestinal and neurological disorders, acting via the microbiota-gut-brain axis. Altering gut microbial composition may influence cognitive function, but this has not been tested in cognitively healthy adults. This randomised, double-blinded, placebo-controlled pilot trial investigates whether FMT is feasible and improves cognition in adults with irritable bowel syndrome (IBS). Participants receive a single dose of FMT or placebo via rectal retention enema. Cognitive performance is the primary outcome, assessed using the Cambridge Neuropsychological Test Automated Battery (CANTAB). Secondary outcomes include IBS symptom severity and mood. Tertiary outcomes include microbiome composition and plasma biomarkers related to inflammation, short-chain fatty acids, and tryptophan metabolism. Outcomes are assessed at baseline and at one, three, six, and twelve months following treatment. We hypothesise that FMT will lead to greater improvements in cognitive performance than placebo, with benefits extending beyond practice effects, emerging at one month and persisting in the long term. The findings will contribute to evaluating the safety and efficacy of FMT and enhance our understanding of gut-brain interactions.},
}

@article {pmid40863567,
year = {2025},
author = {Venter, A and El-Kharoubi, AF and El-Kharoubi, M and Ghitea, EC and Ghitea, MC and Ghitea, TC and Venter, CF},
title = {Diet Therapy and Probiotics to Improve Sleep Apnea Risk and Quality of Life in Older Adults (>60 Years) with Metabolic Syndrome: A Study from Romania.},
journal = {Geriatrics (Basel, Switzerland)},
volume = {10},
number = {4},
pages = {},
pmid = {40863567},
issn = {2308-3417},
support = {410068//University of Oradea/ ; },
abstract = {Background: Metabolic syndrome (MetS) and obstructive sleep apnea (OSA) are prevalent and interrelated conditions in older adults, both contributing to decreased quality of life and increased health risks. Nutritional interventions, including dietary changes and probiotic supplementation, may offer effective non-pharmacological strategies to address these conditions. This study aimed to evaluate the impact of diet therapy alone and in combination with probiotics on quality of life and sleep apnea risk in older adults (>60 years) with MetS. Methods: In this controlled interventional study, 192 older adults with metabolic syndrome were assigned to one of three groups: control, diet therapy alone, or diet therapy plus probiotic supplementation. Participants were evaluated at baseline and after the intervention period using the SF-36 quality of life questionnaire and an apnea risk screening tool. Clinical and metabolic parameters, including BMI, HOMA index, and visceral fat, were also assessed. Results: Significant improvements in SF-36 scores were observed in both intervention groups compared to the control group (p < 0.05) (mean difference = -5.31, p = 0.016), with the diet + probiotics group showing the greatest enhancement. Participants who reduced their apnea risk also reported higher post-intervention SF-36 scores. The intervention led to reductions in visceral fat, inflammatory markers (CRP), and insulin resistance (HOMA index), which were correlated with improved quality of life. Conclusions: Integrated nutritional strategies, especially the combination of diet and probiotics, significantly improve quality of life and reduce apnea risk in older adults with metabolic syndrome. These findings support the use of personalized, non-pharmacological interventions targeting both metabolic health and sleep-related outcomes in geriatric populations.},
}

@article {pmid40863338,
year = {2025},
author = {Lang, T and Lipp, AM and Wechselberger, C},
title = {Xenobiotic Toxicants and Particulate Matter: Effects, Mechanisms, Impacts on Human Health, and Mitigation Strategies.},
journal = {Journal of xenobiotics},
volume = {15},
number = {4},
pages = {},
pmid = {40863338},
issn = {2039-4713},
support = {Impetus No. I-02-23//Johannes Kepler University of Linz/ ; },
abstract = {Particulate matter (PM), a complex mixture of solid particles and liquid droplets, originates from both natural sources, such as sand, pollen, and marine salts, and anthropogenic activities, including vehicle emissions and industrial processes. While PM itself is not inherently toxic in all its forms, it often acts as a carrier of xenobiotic toxicants, such as heavy metals and organic pollutants, which adhere to its surface. This combination can result in synergistic toxic effects, significantly enhancing the potential harm to biological systems. Due to its small size and composition, PM can penetrate deep into the respiratory tract, acting as a physical "shuttle" that facilitates the distribution and bioavailability of toxic substances to distant organs. The omnipresence of PM in the environment leads to unavoidable and constant exposure, contributing to increased morbidity and mortality rates, particularly among vulnerable populations like the elderly, children, and individuals with pre-existing health conditions. This exposure also imposes a substantial financial burden on healthcare systems, as treating PM-related illnesses requires significant medical resources and leads to higher healthcare costs. Addressing these challenges necessitates effective mitigation strategies, including reducing PM exposure, improving air quality, and exploring novel approaches such as AI-based exposure prediction and nutritional interventions to protect public health and minimize the adverse effects of PM pollution.},
}

@article {pmid40863336,
year = {2025},
author = {Gonçalves, M and Vale, N and Martins da Costa, P and Silva, P},
title = {Xenobiotics and Broiler Microbiota: Molecular Insights into Bacterial Antimicrobial Resistance and Food Safety Implications for Human Health.},
journal = {Journal of xenobiotics},
volume = {15},
number = {4},
pages = {},
pmid = {40863336},
issn = {2039-4713},
support = {Grant UID/05021/2023//Fundação para a Ciência e Tecnologia/ ; },
abstract = {Antibiotics have played an evolving role in poultry production, generally transitioning from widespread use to more precise and controlled applications. Despite this shift, the long-term consequences of earlier practices continue to affect current and future generations. This review aims to explore the multifaceted consequences of antibiotic use in poultry production, with particular emphasis on the growing challenge of antimicrobial resistance (AMR). Evidence demonstrates that antibiotic use affects the gut microbiome, often resulting in long-lasting decreased diversity and restructuring of the bacterial communities. Moreover, consequences extend to the surrounding environment, including the airborne microbiome, water systems, and poultry litter, where alterations in microbial communities tend to be more subtle, whereas changes in genetic elements related to resistance are often more pronounced (drift). The emergence and persistence of resistance in these environments facilitate the spread of resistance genes across ecological boundaries, contributing to the broader dissemination of AMR. These findings highlight the complex, interconnected nature of AMR, underscoring the urgent need for responses grounded in the One Health framework. Such approaches are essential for safeguarding both public and environmental health while maintaining sustainable poultry production practices.},
}

@article {pmid40863331,
year = {2025},
author = {Wei, J and Li, Y and Chen, Y and Lin, Q and Zhang, L},
title = {Spatial Gradient Effects of Metal Pollution: Assessing Ecological Risks Through the Lens of Fish Gut Microbiota.},
journal = {Journal of xenobiotics},
volume = {15},
number = {4},
pages = {},
pmid = {40863331},
issn = {2039-4713},
support = {NO. 2023AFB299//he Natural Science Foundation of Hubei Province/ ; Q20234403//the Hubei Provincial Department of Education Science Research Plan - Science and Technology Innovation Service Project/ ; NO. TMKJZ2404//the Open Topics of Fujian Key Laboratory of Special Aquatic Formula Feed/ ; },
abstract = {This comprehensive study investigates the spatial distribution of metals in surface water, their accumulation in fish tissues, and their impact on the gut microbiome dynamics of fish in the Qi River, Huanggang City, Hubei Province. Three distinct sampling regions were established: the mining area (A), the transition area (B), and the distant area (C). Our results revealed that metal concentrations were highest in the mining area and decreased with increasing distance from it. The bioaccumulation of metals in fish tissues followed the order of gut > brain > muscle, with some concentrations exceeding food safety standards. Analysis of the gut microbiota showed that Firmicutes and Proteobacteria dominated in the mining area, while Fusobacteriota were more prevalent in the distant area. Heavy metal pollution significantly altered the composition and network structure of the gut microbiota, reducing microbial associations and increasing negative correlations. These findings highlight the profound impact of heavy metal pollution on both fish health and the stability of their gut microbiota, underscoring the urgent need for effective pollution control measures to mitigate ecological risks and protect aquatic biodiversity. Future research should focus on long-term monitoring and exploring potential remediation strategies to restore the health of affected ecosystems.},
}

@article {pmid40863290,
year = {2025},
author = {Đapić, I and Aurer, A and Žučko, J and Mravak-Stipetić, M and Baranović Baričević, M and Pavelić, K and Ozer, F and Kraljević Pavelić, S},
title = {Enhancing Professional Periodontal Therapy with a Novel PMA-Zeolite Application: A Clinical Study on Periodontal Outcomes and Microbiological Changes.},
journal = {Journal of functional biomaterials},
volume = {16},
number = {8},
pages = {},
pmid = {40863290},
issn = {2079-4983},
support = {UNIZG 2021//University of Zagreb/ ; },
abstract = {Periodontitis is a chronic, multifactorial inflammatory disease characterized by the progressive destruction of the periodontal supporting tissues, including alveolar bone, potentially resulting in tooth loss. Etiopathogenesis involves a dysbiotic shift in the subgingival microbiota where the presence of pathogenic species such as Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, and Treponema denticola has been documented. This disbalance is combined with an inadequate host immune response, often exacerbated by other systemic comorbidities including diabetes mellitus and cardiovascular diseases. Conventional therapy typically comprises mechanical debridement and adjunctive local or systemic antimicrobials, but emerging antibiotic resistance highlights a need for alternative adjuvant therapeutic strategies. The present descriptive analysis of microbiome and clinical trends study evaluated the adjuvant effects of a clinoptilolite-based zeolite material, namely PMA-zeolite, with professional prophylaxis on clinical and microbiological parameters in patients with chronic periodontitis over a 10-week period. Clinical assessment revealed significant reductions in bleeding on probing (BoP) and periodontal pocket depth (PD), indicating improved inflammatory status. Microbiome profiling demonstrated a marked decrease in key periodontal pathogens, suggesting that PMA-zeolite can help rebalance the oral microbiome. These findings suggest that the combined therapy exhibits promising anti-inflammatory and antimicrobial properties, indicating its role in promoting microbial homeostasis and reducing periodontal inflammation. However, further investigation through larger, controlled clinical trials is needed to validate the efficacy of the therapy.},
}

@article {pmid40863224,
year = {2025},
author = {Neag, MA and Mitre, AO and Pomana, IG and Velescu, MA and Militaru, C and Nagy, G and Melincovici, CS},
title = {Host-Microbiome Interaction in the Intensive Care Unit.},
journal = {Diseases (Basel, Switzerland)},
volume = {13},
number = {8},
pages = {},
pmid = {40863224},
issn = {2079-9721},
abstract = {Critical illness profoundly disrupts the gut microbiota leading to a state of dysbiosis characterized by reduced microbial diversity and overrepresentation of pathogenic taxa such as Enterobacteriaceae and Proteobacteria. This dysbiotic shift compromises gut barrier integrity and modulates immune responses, contributing to systemic inflammation and increasing susceptibility to nosocomial infections and multi-organ dysfunction. Nutritional strategies in the ICU significantly influence the composition and function of the gut microbiota. Enteral nutrition supports the maintenance of microbial diversity and gut mucosal health, whereas parenteral nutrition is associated with mucosal atrophy and further microbial imbalance. Emerging interventions, including the administration of probiotics, prebiotics, synbiotics, and fermented products like kefir, show promise in restoring microbial equilibrium and improving patient outcomes. This review presents current evidence on the alterations of the gut microbiota in critically ill patients, explores the systemic consequences of dysbiosis, and evaluates the impact of nutritional and microbiota-targeted therapies in improving patient outcomes.},
}

@article {pmid40863168,
year = {2025},
author = {Buckley, AM and Zaidan, S and Sweet, MG and Ewin, DJ and Ratliff, JG and Alkazemi, A and Davis Birch, W and McAmis, AM and Neilson, AP},
title = {Choline Metabolism to the Proatherogenic Metabolite Trimethylamine Occurs Primarily in the Distal Colon Microbiome In Vitro.},
journal = {Metabolites},
volume = {15},
number = {8},
pages = {},
pmid = {40863168},
issn = {2218-1989},
support = {N/A/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; N/A//OIRC INFORM hub/ ; N/A/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; N/A//North Carolina Agricultural Research Service/ ; N/A//Applied Microbiology International/ ; N/A//Hatch program, USDA/ ; },
abstract = {BACKGROUND/OBJECTIVES: Gut microbial metabolism of choline and related quaternary amines to trimethylamine (TMA) is the first step in the production of trimethylamine N-oxide (TMAO), a circulating metabolite that contributes to the development of atherosclerosis and other forms of cardiovascular disease (CVD). No data exist on regional differences in TMA production within the colon due to difficulties studying gut regions in vivo. A better understanding of TMA production by gut microbiota is needed to develop strategies to limit TMA production in the gut and TMAO levels in circulation with the goal of reducing CVD risk.

METHODS: We employed our novel three-compartment MiGut in vitro model, which establishes three distinct microbial ecologies mimicking the proximal, mid, and distal colon, to study conversion of choline to TMA by human gut microbiota using isotopically labelled substrate.

RESULTS: Choline-d9 was almost completely converted to TMA-d9 in vessels 2-3 (mimicking the mid and distal colon) within 6-8 h, but little conversion occurred in vessel 1 (mimicking the proximal colon). Abundance of cutC, part of the cutC/D gene cluster responsible for choline conversion to TMA, was highest in vessel 1 vs. 2-3, suggesting that its expression or activity may be suppressed in the proximal colon. Another possibility is that the viability/activity of bacteria expressing cutC could be suppressed in the same region.

CONCLUSIONS: This novel finding suggests that while bacteria capable of converting choline to TMA exist throughout the colon, their activity may be different in distinct colon regions. The regional specificity of TMA production, if confirmed in vivo, has implications for both basic microbial ecology related to CVD and the development of strategies to control TMA and TMAO production, with the goal of lowering CVD risk. These findings warrant further study in vitro and in vivo.},
}

@article {pmid40863164,
year = {2025},
author = {Ning, W and Jiang, L and Yang, M and Lei, T and Liu, C and Zhao, F and Shu, P and Liu, Y},
title = {Metabolomic Profiling Reveals the Effects of Cu-Ag Nanoparticles on Tomato Bacterial Wilt.},
journal = {Metabolites},
volume = {15},
number = {8},
pages = {},
pmid = {40863164},
issn = {2218-1989},
abstract = {Background: The bacterial wilt of tomatoes, caused by Ralstonia solanacearum, is a soil-borne plant disease that causes substantial agricultural economic losses. Various nanoparticles have been utilized as antibacterial agents to mitigate pathogenic destructiveness and improve crop yields. However, there is a lack of in-depth research on how nanoparticles affect tomato metabolite levels to regulate the bacterial wilt of tomatoes. Methods: In this study, healthy and bacterial wilt-infected tomatoes were treated with Cu-Ag nanoparticles, and a metabolomics analysis was carried out. Results: The results showed that Cu-Ag nanoparticles had a significant prevention and control effect on the bacterial wilt of tomatoes. Metabolomic analysis revealed that the nanoparticles could significantly up-regulate the expression levels of terpenol lipids, organic acids, and organic oxygen compounds in diseased tomatoes, and enhance key metabolic pathways such as amino acid metabolism, carbohydrate metabolism, secondary metabolite metabolism, and lipid metabolism. These identified metabolites and pathways could regulate plant growth and defense against pathogens. Correlation analysis between the tomato microbiome and metabolites showed that most endophytic microorganisms and rhizospheric bacteria were positively correlated with fatty acyls groups and organic oxygen compounds. Conclusions: This study reveals that Cu-Ag nanoparticles can actively regulate the bacterial wilt of tomatoes by up-regulating the levels of lipid metabolism and organic oxygen compounds, providing an important theoretical basis for the application of nanoparticles in agriculture.},
}

@article {pmid40863149,
year = {2025},
author = {Harthoorn, LF and Heyse, J and Baudot, A and van Hengel, IAJ and Van den Abbeele, P},
title = {Galacto-Oligosaccharides Exert Bifidogenic Effects at Capsule-Compatible Ultra-Low Doses.},
journal = {Metabolites},
volume = {15},
number = {8},
pages = {},
pmid = {40863149},
issn = {2218-1989},
abstract = {BACKGROUND: Prebiotics are selectively used by host microorganisms to promote health. Because effective prebiotic doses (1.5-30 g/day) often require inconvenient delivery formats, this study aims to explore whether capsule-compatible doses of galacto-oligosaccharides (GOS) can effectively modulate the gut microbiome.

METHODS: The impact of Bimuno[®] GOS (Reading, UK) at 0.5, 0.75, 1.83, and 3.65 g on the adult gut microbiome was assessed using the ex vivo SIFR[®] technology (n = 8), a clinically validated, bioreactor-based technology.

RESULTS: The GOS were rapidly fermented and significantly increased beneficial Bifidobacterium species (B. adolescentis, B. bifidum, and B. longum), even at the lowest tested dose. In doing so, GOS strongly promoted SCFA production, particularly acetate (significant from 0.5 g) and butyrate (significant from 0.75 g). Gas production only mildly increased, likely as Bifidobacterium species do not produce gases. Based on the ability of the SIFR[®] technology to cultivate strictly anaerobic, hard-to-culture gut microbes, unlike in past in vitro studies, we elucidated that GOS also enriched specific Lachnospiraceae species. Besides Anaerobutyricum hallii, this included Bariatricus comes, Blautia species (B. massiliensis, Blautia_A, B. faecis), Oliverpabstia intestinalis, Mediterraneibacter faecis, and Fusicatenibacter species. Finally, GOS also promoted propionate (significant from 0.75 g), linked to increases in Phocaeicola vulgatus.

CONCLUSIONS: GOS displayed prebiotic potential at capsule-compatible doses, offering greater flexibility in nutritional product formulation and consumer convenience. Notably, the strong response at the lowest dose suggests effective microbiome modulation at lower levels than previously expected.},
}

@article {pmid40863144,
year = {2025},
author = {Joblin-Mills, A and Wu, ZE and Cooper, GJS and Sequeira-Bisson, IR and Miles-Chan, JL and McGill, AT and Poppitt, SD and Fraser, K},
title = {Site-Specific Trafficking of Lipid and Polar Metabolites in Adipose and Muscle Tissue Reveals the Impact of Bariatric Surgery-Induced Weight Loss: A 6-Month Follow-Up Study.},
journal = {Metabolites},
volume = {15},
number = {8},
pages = {},
pmid = {40863144},
issn = {2218-1989},
support = {3710040//New Zealand National Science Challenge High Value Nutrition/ ; },
abstract = {BACKGROUND: The causation of type 2 diabetes remains under debate, but evidence supports both abdominal lipid and ectopic lipid overspill into tissues including muscle as key. How these depots differentially alter cardiometabolic profile and change during body weight and fat loss is not known.

METHODS: Women with obesity scheduled to undergo bariatric surgery were assessed at baseline (BL, n = 28) and at 6-month follow-up (6m_FU, n = 26) after weight loss. Fasting plasma (Pla), subcutaneous thigh adipose (STA), subcutaneous abdominal adipose, (SAA), and thigh vastus lateralis muscle (VLM) samples were collected at BL through surgery and at 6m_FU using needle biopsy. An untargeted liquid chromatography mass spectrometry metabolomics platform was used. Pla and tissue-specific lipid and polar metabolite profiles were modelled as changes from BL and 6m_FU.

RESULTS: There was significant body weight (-24.5 kg) loss at 6m_FU (p < 0.05). BL vs. 6m_FU tissue metabolomics profiles showed the largest difference in lipid profiles in SAA tissue in response to surgery. Conversely, polar metabolites were more susceptible to change in STA and VLM. In Pla samples, both lipid and polar metabolite profiles showed significant differences between timepoints. Jaccard-Tanimoto coefficient t-tests identified a sub-group of gut microbiome and dietary-derived omega-3-fatty-acid-containing lipid species and core energy metabolism and adipose catabolism-associated polar metabolites that are trafficked between sample types in response to bariatric surgery.

CONCLUSIONS: In this first report on channelling of lipids and polar metabolites to alternative tissues in bariatric-induced weight loss, adaptive shuttling of small molecules was identified, further promoting adipose processing and highlighting the dynamic and coordinated nature of post-surgical metabolic regulation.},
}

@article {pmid40863141,
year = {2025},
author = {Faraj, S and Joblin-Mills, A and Sequeira-Bisson, IR and Leiu, KH and Tung, T and Wallbank, JA and Fraser, K and Miles-Chan, JL and Poppitt, SD and Taylor, MW},
title = {Investigating Multi-Omic Signatures of Ethnicity and Dysglycaemia in Asian Chinese and European Caucasian Adults: Cross-Sectional Analysis of the TOFI_Asia Study at 4-Year Follow-Up.},
journal = {Metabolites},
volume = {15},
number = {8},
pages = {},
pmid = {40863141},
issn = {2218-1989},
support = {3710040, 3719728 & 3720614//New Zealand National Science Challenge High-Value Nutrition Programme/ ; },
abstract = {Background: Type 2 diabetes (T2D) is a global health epidemic with rising prevalence within Asian populations, particularly amongst individuals with high visceral adiposity and ectopic organ fat, the so-called Thin-Outside, Fat-Inside phenotype. Metabolomic and microbiome shifts may herald T2D onset, presenting potential biomarkers and mechanistic insight into metabolic dysregulation. However, multi-omics datasets across ethnicities remain limited. Methods: We performed cross-sectional multi-omics analyses on 171 adults (99 Asian Chinese, 72 European Caucasian) from the New Zealand-based TOFI_Asia cohort at 4-years follow-up. Paired plasma and faecal samples were analysed using untargeted metabolomic profiling (polar/lipid fractions) and shotgun metagenomic sequencing, respectively. Sparse multi-block partial least squares regression and discriminant analysis (DIABLO) unveiled signatures associated with ethnicity, glycaemic status, and sex. Results: Ethnicity-based DIABLO modelling achieved a balanced error rate of 0.22, correctly classifying 76.54% of test samples. Polar metabolites had the highest discriminatory power (AUC = 0.96), with trigonelline enriched in European Caucasians and carnitine in Asian Chinese. Lipid profiles highlighted ethnicity-specific signatures: Asian Chinese showed enrichment of polyunsaturated triglycerides (TG.16:0_18:2_22:6, TG.18:1_18:2_22:6) and ether-linked phospholipids, while European Caucasians exhibited higher levels of saturated species (TG.16:0_16:0_14:1, TG.15:0_15:0_17:1). The bacteria Bifidobacterium pseudocatenulatum, Erysipelatoclostridium ramosum, and Enterocloster bolteae characterised Asian Chinese participants, while Oscillibacter sp. and Clostridium innocuum characterised European Caucasians. Cross-omic correlations highlighted negative correlations of Phocaeicola vulgatus with amino acids (r = -0.84 to -0.76), while E. ramosum and C. innocuum positively correlated with long-chain triglycerides (r = 0.55-0.62). Conclusions: Ethnicity drove robust multi-omic differentiation, revealing distinctive metabolic and microbial profiles potentially underlying the differential T2D risk between Asian Chinese and European Caucasians.},
}

@article {pmid40863120,
year = {2025},
author = {Kan, H and Zhang, K and Mao, A and Geng, L},
title = {The Causal Role of the Gut Microbiota-Plasma Metabolome Axis in Myeloproliferative Neoplasm Pathogenesis: A Mendelian Randomization and Mediation Analysis.},
journal = {Metabolites},
volume = {15},
number = {8},
pages = {},
pmid = {40863120},
issn = {2218-1989},
support = {BK20241621//Natural Science Foundation of Jiangsu Province/ ; GZC20230981//Postdoctoral Fellowship Program of CPSF/ ; },
abstract = {BACKGROUND: Myeloproliferative neoplasms (MPN), a group of chronic hematologic neoplasms, are driven by inflammatory mechanisms that influence disease initiation and progression. Emerging evidence highlights the gut microbiome and plasma metabolome as pivotal immunomodulators, yet their causal roles in MPN pathogenesis remain uncharacterized.

METHODS: We conducted a two-sample Mendelian randomization (MR) analysis to systematically evaluate causal relationships between 196 gut microbial taxa, 526 plasma metabolites, and MPN risk. Instrumental variables were derived from genome-wide association studies (GWASs) of microbial/metabolite traits. Validation utilized 16S rRNA sequencing data from NCBI Bioproject PRJNA376506. Mediation and multivariable MR analyses elucidated metabolite-mediated pathways linking microbial taxa to MPN.

RESULTS: Our MR analysis revealed that 7 intestinal taxa and 17 plasma metabolites are causally linked to MPN. External validation confirmed the three taxa's differential abundance in MPN cohorts. Mediation analysis revealed two mediated relationships, of which succinylcarnitine mediated 14.5% of the effect, and lysine 27.9%, linking the Eubacterium xylanophilum group to MPN. Multivariate MR analysis showed that both succinylcarnitine (p = 0.004) and lysine (p = 0.040) had a significant causal effect on MPN.

CONCLUSIONS: This study identifies novel gut microbiota-metabolite axes driving MPN pathogenesis through immunometabolic mechanisms. The validated biomarkers provide potential therapeutic targets for modulating inflammation in myeloproliferative disorders.},
}

@article {pmid40863109,
year = {2025},
author = {El-Baz, N and Kyser, A and Mahmoud, MY and Farrell, CZ and Ginocchio, S and Frieboes, HB and Doster, RS},
title = {Modulation of group B Streptococcus infection and vaginal cell inflammatory signaling in vitro by Lactobacillus crispatus-loaded electrospun fibers.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0017025},
doi = {10.1128/iai.00170-25},
pmid = {40863109},
issn = {1098-5522},
abstract = {Vaginal colonization by Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a major risk factor for ascending infections, preterm birth, and neonatal sepsis. Current GBS prevention efforts include routine GBS perinatal screening and intrapartum antibiotic prophylaxis, which decrease the rate of early-onset neonatal sepsis, but have drawbacks that include impacting the infant's developing microbiome. Lactobacillus-dominant vaginal microbiomes provide protection against pathogens such as GBS, and using probiotics as an antibiotic-free approach to limit GBS colonization is of increasing interest. In this study, we investigated the ability of Lactobacillus crispatus-loaded electrospun fibers to deliver live L. crispatus cells in an in vitro vaginal epithelial cell model, modulate GBS infection establishment and persistence, and alter vaginal cell inflammatory signaling. Our data demonstrate that electrospun fibers deliver viable L. crispatus to the surface of vaginal epithelial cells and that L. crispatus modulates vaginal cell inflammatory signaling by decreasing inflammatory IL-8 release and increasing anti-inflammatory IL-1RA secretion during established GBS infection. Treatment of pre-established GBS infection with electrospun fibers with or without L. crispatus decreased GBS burden at 24 hours, suggesting L. crispatus-dependent and -independent anti-GBS activity, and L. crispatus elicited an anti-inflammatory response via IL-1RA release. Overall, the data highlight the potential of electrospun fibers as a feasible probiotic delivery platform with antibacterial activity against GBS and which provides commensal lactobacilli capable of modulating host-pathogen interactions and inflammatory signaling of the vaginal epithelium.},
}

@article {pmid40863075,
year = {2025},
author = {Zhao, ZZ and Shan, W and Sun, X and Cheng, T and Zhang, J and Chu, CH},
title = {Quorum-Quenching AHL-Lactonase Est816 Inhibits Polymicrobial Subgingival-Plaque-Derived Biofilm Formation.},
journal = {Dentistry journal},
volume = {13},
number = {8},
pages = {},
pmid = {40863075},
issn = {2304-6767},
support = {2022zhyx-C58//the Research Fund of Anhui Institute of translational medicine/ ; AHWJ2023A20161//Scientific Research Funding of Anhui Province Health Commission/ ; },
abstract = {Objectives: This study aimed to investigate the effects of the quorum-quenching enzyme N-acyl-homoserine lactone (AHL)-lactonase Est816 on biofilm formation in subgingival plaque microbiota from participants with advanced periodontitis. Methods: Subgingival plaque samples were collected from 30 adults with untreated Stage III or higher periodontitis and cultured anaerobically. Est816 was applied in vitro, with phosphate-buffered saline (PBS) serving as the control. Biofilm composition was analyzed via 16S rRNA sequencing, and alpha diversity metrics were assessed. Differential taxa abundance was assessed with the multivariate statistical software MaAsLin3. Biofilm morphology, biomass, and thickness were evaluated using scanning electron microscopy (SEM), crystal violet staining, and confocal laser scanning microscopy (CLSM). Results: Est816 significantly reduced microbial richness (Chao1 Index, p = 0.031), biofilm biomass (64% reduction, p < 0.001), and thickness (76% reduction, p < 0.001) compared to controls. SEM revealed fragmented biofilm architecture in Est816-treated samples. Conclusions: AHL-lactonase Est816 inhibited polymicrobial subgingival-plaque-derived biofilm formation while reducing species richness, phylogenetic diversity, and community evenness. These findings demonstrate Est816's potential as an adjunctive therapy for disrupting pathogenic biofilms in periodontitis.},
}

@article {pmid40862619,
year = {2025},
author = {McGuire, CM and Cinco, IR and Takahashi, D and Sauter, KA and Kirigiti, M and Messaoudi, I and Sacha, JB and Roberts, CT and Kievit, P},
title = {Impact of obesity on the gut microbiome and inflammatory markers during SIV infection and antiretroviral therapy.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0073325},
doi = {10.1128/spectrum.00733-25},
pmid = {40862619},
issn = {2165-0497},
abstract = {Dysbiosis and impaired gut barrier integrity contribute to chronic immune activation associated with both obesity and HIV infection. Given the increased incidence of obesity in people living with HIV, we explored the impact of obesity on the gut microbiome and microbial translocation (MT) biomarkers during HIV infection and antiretroviral therapy (ART). Lean and obese rhesus macaques were infected with simian immunodeficiency virus (SIV) and subsequently treated with ART. Obese animals exhibited higher initial MT and inflammation biomarkers that remained constant throughout the study, while lean animals exhibited significant increases in these biomarkers that approached levels observed in obese animals. Lean and obese animals exhibited similar observed amplicon sequence variants (ASVs) at baseline, with obese animals exhibiting reduced ASVs during acute SIV infection that rebounded after 39 weeks of ART treatment. Beta diversity differed between groups and was longitudinally altered in obese animals. Obese animals exhibited significant changes in differential abundance in four times as many bacterial genera compared to lean animals. Our finding that MT and inflammation biomarkers significantly changed in lean animals, while obese animals exhibited significant alterations in microbial diversity, suggests that microbiome changes and systemic inflammation may not directly correlate during SIV infection and ART.IMPORTANCEIn response to the obesity epidemic, the incidence of obesity at the time of HIV diagnosis has increased, but the impacts of pre-existing obesity throughout antiretroviral therapy (ART)-treated HIV infection remain underexplored. Both obesity and HIV infection have been associated with inflammatory and microbiome perturbations. Here, we utilized 16S rRNA amplicon sequencing and quantification of systemic inflammation markers to longitudinally characterize the fecal microbiome and systemic inflammation in lean and obese rhesus macaques throughout simian immunodeficiency virus (SIV) infection and ART. Lean animals exhibited marked increases in inflammatory markers corresponding with minimal gut microbiome perturbations throughout SIV infection and ART. In contrast, obese animals exhibited minimal inflammatory alterations corresponding with distinct differentially abundant fecal bacterial taxa throughout SIV infection and ART. Our results provide crucial insights into the interactions between pre-existing obesity, inflammation, and the gut microbiome that may aid in developing therapeutic strategies for obese individuals diagnosed with HIV.},
}

@article {pmid40862605,
year = {2025},
author = {Bhattacharya, D and Jiya, N and Mondal, S and Acharya, A and Chatterjee, A and Bakshi, U and Sharma, A and Ghosh, A},
title = {Bacterial diversity in the freshwater sponges of Sundarban and their potential role in biomonitoring toxic element pollution.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0214925},
doi = {10.1128/spectrum.02149-25},
pmid = {40862605},
issn = {2165-0497},
abstract = {Sponges serve as the natural cleaner in diverse aquatic ecosystems, harboring diverse microbial communities and forming a highly specialized holobiont. The present study provides the first insights into the bacterial communities associated with freshwater sponges of Sundarban, highlighting their distinct microbial community composition compared to the surrounding water using 16S rRNA gene-based metataxonomic analyses. The analysis encompassing six sponge species collected from Sagar Island and Ghoramara revealed distinct variations in microbial abundance and diversity compared to their ambient water, suggesting selective bacterial associations with the sponges. The sponge species displayed a varied abundance of bacterial taxa across different species and locations. Furthermore, significantly greater concentrations of potentially toxic elements (PTEs) were observed in sponges when compared with corresponding water samples, thereby suggesting the bioaccumulation capability of these sponges. Functional profiling of bacterial communities in sponge and water samples revealed enrichment of various metabolic pathways linked to metal ion transport and resistance, as well as antimicrobial resistance in the sponges, suggesting an adaptive response to environmental stressors. The abundance of diverse metal ion regulators and transporters underscores the ecologically significant function of sponge-associated bacterial communities in metal ion resistance, placing the sponges as promising bioindicators for monitoring polluted aquatic ecosystems.IMPORTANCEFreshwater sponges play an essential role as natural biofilters in aquatic ecosystems, effectively purifying water. These sponges harbor unique microbial communities, forming a holobiont that is key to their ecological function. This study offers new insights into the bacterial communities associated with freshwater sponges from the Sundarbans, a previously underexplored region. Using 16S rRNA gene-based metataxonomic analyses, we compared the bacterial diversity of six sponge species from Sagar Island and Ghoramara to that of surrounding water. Our results reveal distinct bacterial associations within sponges, different from the ambient water's microbial composition. Notably, sponge concentrations of potentially toxic elements (PTEs) were much higher than in the surrounding water, highlighting their bioaccumulation capacity. Functional profiling of sponge-associated bacteria revealed genes related to metal ion transport and antimicrobial resistance, suggesting adaptive responses to environmental stress. This research enhances our understanding of sponge microbiomes and their potential for bioremediation, particularly for removing heavy metals from polluted water.},
}

@article {pmid40862604,
year = {2025},
author = {Katz, LA and Leleu, M and Ani, G and Gawron, R and Cote-L'Heureux, A},
title = {Rethinking large-scale phylogenomics with EukPhylo v.1.0, a flexible toolkit to enable phylogeny-informed data curation and analyses of diverse eukaryotic lineages.},
journal = {mBio},
volume = {},
number = {},
pages = {e0177025},
doi = {10.1128/mbio.01770-25},
pmid = {40862604},
issn = {2150-7511},
abstract = {Eukaryotic diversity is largely microbial, with macroscopic lineages (plants, animals, and fungi) nesting among a plethora of diverse protists. Our understanding of the evolutionary relationships among eukaryotes is rapidly advancing through 'omics analyses, but phylogenomic analyses are challenging for microeukaryotes, particularly uncultivable lineages, as single-cell sequencing approaches generate a mixture of sequences from hosts, associated microbiomes, and contaminants. Moreover, many analyses of eukaryotic gene families and phylogenies rely on boutique data sets and methods that are challenging for other research groups to replicate. To address these challenges, we present EukPhylo v.1.0, a modular, user-friendly pipeline that enables effective data curation through phylogeny-informed contamination removal, estimation of homologous gene families (GFs), and generation of both multisequence alignments and gene trees. For the GF assignment, we provide the "Hook Database" of ~15,000 ancient GFs, which users can easily replace with a set of gene families of interest. We demonstrate the power of EukPhylo, including a suite of stand-alone utilities, through phylogenomic analyses of 500 conserved GFs sampled from 1,000 diverse species of eukaryotes, bacteria, and archaea. We show improvements in estimates of the eukaryotic tree of life, recovering clades that are well established in the literature, through successive rounds of curation using the EukPhylo contamination loop. The final trees corroborate numerous hypotheses in the literature (e.g., Opisthokonta, Rhizaria, Amoebozoa) while challenging others (e.g., CRuMs, Obazoa, Diaphoretickes). The flexibility and transparency of EukPhylo set new standards for curation of 'omics data for future studies.IMPORTANCEIlluminating the diversity of microbial lineages is essential for estimating the tree of life and characterizing principles of genome evolution. However, analyses of microbial eukaryotes (e.g., flagellates, amoebae) are complicated by both the paucity of reference genomes and the prevalence of contamination (e.g., by symbionts, microbiomes). EukPhylo v.1.0 enables taxon-rich analyses "on the fly" as users can choose optimal gene families for their focal taxa and then use replicable approaches to curate data in estimating both gene and species trees. With multiple entry points and curated data sets from up to 15,000 gene families from 1,000 taxa ready for use, EukPhylo provides a powerful launching point for researchers interested in the evolution of eukaryotes.},
}

@article {pmid40862315,
year = {2025},
author = {Zhou, P and Tian, L and Siddique, MS and Rashid, S and Graham, NJD and Yu, W},
title = {Microbes from Different Soil Regions Play Distinct Roles in the Processing of Aquatic Dissolved Organic Matter.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c05562},
pmid = {40862315},
issn = {1520-5851},
abstract = {Soil harbors abundant bacteria and viruses that can be delivered into water environments and alter aquatic ecology. However, the mechanisms by which the intruded soil microbes mediate the turnover of dissolved organic matter (DOM) in waters are unknown. Here, we prepared bacterial and phage-enriched inocula from the northern high-humic-composition (NHHS) and southern low-humic-composition (SLHS) soils in China, and investigated their roles in aquatic DOM transformation via microcosm experiments. The aquatic DOM was more rapidly degraded by the soil-derived microbes than the aquatic microbes. However, associated with the soil regions, phage-enriched inocula caused two different molecular transformation patterns. Unlike the NHHS soils, phage-enriched fractions from the SLHS soils can enhance the bacterial decomposition of DOM (especially many aromatic CHO and S-containing compounds), while inhibiting the accumulation of few aliphatic molecules with O/C < 0.5 and H/C > 1. Additionally, the potential effects of soil virus-enriched fractions on the microbial degradation of aquatic DOM can be largely predicted by the organic composition in soils. Our findings demonstrate the divergent and environment-associated roles of different soil microbial fractions in aquatic carbon cycling, which provide new insights into the biogeochemical consequences of soil microbiome transfer in the land-water continuum.},
}

@article {pmid40862158,
year = {2025},
author = {Han, X and Yang, J and Li, Q and Zhang, L and Li, Y and Gai, Y and Sang, Y and Zhang, Z},
title = {Organic fertilizer application rates affect rhizosphere microbial communities and yield optimization in potato (Solanum tuberosum L. V7).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1651178},
pmid = {40862158},
issn = {1664-302X},
abstract = {BACKGROUND: Organic fertilizers enhance sustainable agriculture by providing nutrients and supporting microbial communities. However, optimal application rates that maximize potato yield while maintaining rhizosphere microbial diversity remain poorly understood.

METHODS: Four organic fertilizer levels (0, 40, 60, and 80% nitrogen replacement) were tested on potato rhizosphere bacterial and fungal communities across three growth stages using high-throughput 16S rDNA and ITS sequencing.

RESULTS: Bacterial richness increased progressively with organic fertilizer rates (80% > 60% > 40% > 0), with principal coordinate analysis revealing distinct community separations and largest differentiation during tuber expansion under 80% treatment. Bacterial and fungal communities were dominated by Proteobacteria, Acidobacteriota, and Gemmatimonadota, and Ascomycota, Mortierellomycota, and Basidiomycota, respectively. T60 maintained optimal balance of beneficial rhizospheric microorganisms and delivers superior yield outcomes compared with other fertilization regime. Potato yield responded quadratically to organic fertilizer application, with optimal yield of 81,020 kg/ha at 51.25% organic fertilizer rate, while bacterial and fungal diversity correlated with yield.

CONCLUSION: Moderate organic fertilization (50-60% nitrogen replacement) optimizes both rhizosphere microbial diversity and potato productivity through enhanced nutrient cycling efficiency, providing a sustainable approach for potato production systems.},
}

@article {pmid40862145,
year = {2025},
author = {Howard-Stone, R and Gerwin, P and Capunitan, D and Driscoll, M and Jackson, E and Tran, TDB and Măndoiu, I and Oziolor, E},
title = {Cecal microbiome transplantation without antibiotic preconditioning standardizes murine microbiomes.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1632210},
pmid = {40862145},
issn = {1664-302X},
abstract = {INTRODUCTION: Translation of nonclinical findings from laboratory mice to the clinic may be confounded by un-controlled variance in bacterial gut content, as a driver of immune maturation and recruitment, as well as drug metabolism. Understanding and controlling for microbiome variation in animal experiments can lead to better reproducibility of animal findings, more translatable characterization of efficacy and toxicity end-points and time and cost savings associated with pharmaceutical development. Microbiome composition has been linked to failure of translation of drug responses.

METHODS: In an effort to test the stability of microbiome introduction, we compare various methods for establishing a well-characterized, stable bacterial community in laboratory mice via Cecal Microbiome Transplant (CMT) with and without antibiotic preconditioning.

RESULTS: We demonstrate a single CMT treatment protocol effectively treats outbred mouse populations with two different initial gut bacterial profiles, causing the populations to converge to a third, more wild-type bacterial genetic environment suitable for initiation of nonclinical studies. We show that ASV-based monitoring provides the highest resolution for identifying and tracking bacterial profile differences, which can be obscured at the species level. We find that antibiotic preconditioning reduces efficiency for uptake of CMT-specific strains. Instead, antibiotics introduce uncontrolled variance in the resulting microbiome composition.

CONCLUSIONS: We propose that CMT without antibiotic preconditioning provides increased control over host microbial composition, enabling expanded utility, accuracy, and relevance for nonclinical drug toxicity and therapeutic effect studies in laboratory mice, with minimal additional costs.},
}

@article {pmid40862144,
year = {2025},
author = {Yue, Z and Fan, Y and Shan, G and Chen, X},
title = {Oral microbiome contributions to metabolic syndrome pathogenesis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1630828},
pmid = {40862144},
issn = {1664-302X},
abstract = {Comprising over 700 bacterial species, the oral microbiome is the second most diverse microbial community in the human body after the gut microbiome. Currently, existing review literature suggests that gut microbiome events may play a significant role in the pathogenesis of metabolic syndrome, but the role of the oral microbiome in this disease has not yet been reviewed. The oral-gut microbiome axis refers to a bidirectional regulatory system that facilitates interaction between the oral cavity and the gut through microbial pathways. The microbiota from these two sites can migrate between each other via pathways such as swallowing and blood circulation, which may participate in disease development. In addition to the oral-gut axis, the oral microbiome itself may also influence disease pathogenesis. This review examines the potential contributions of the oral microbiome in the pathogenesis of metabolic syndrome, emphasizing its impact on insulin resistance, systemic inflammation and adipokine secretion. We explore therapeutic strategies targeting the oral microbiome which hold promise as future treatments for metabolic syndrome. Future research is needed to further elucidate the causal relationship between the oral microbiome and metabolic syndrome and to develop personalized microbiome-based therapies.},
}

@article {pmid40862137,
year = {2025},
author = {Yadav, A and Chen, M and Acharya, SM and Kim, G and Yang, Y and Zhao, TZ and Tsang, E and Chakraborty, R},
title = {A stable 15-member bacterial SynCom promotes Brachypodium growth under drought stress.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1649750},
pmid = {40862137},
issn = {1664-302X},
abstract = {INTRODUCTION: Rhizosphere microbiomes are known to drive soil nutrient cycling and influence plant fitness during adverse environmental conditions. Field-derived robust Synthetic Communities (SynComs) of microbes mimicking the diversity of rhizosphere microbiomes can greatly advance a deeper understanding of such processes. However, assembling stable, genetically tractable, reproducible, and scalable SynComs remains challenging.

METHODS: Here, we present a systematic approach using a combination of network analysis and cultivation-guided methods to construct a 15-member SynCom from the rhizobiome of Brachypodium distachyon. This SynCom incorporates diverse strains from five bacterial phyla. Genomic analysis of the individual strains was performed to reveal encoded plant growth-promoting traits, including genes for the synthesis of osmoprotectants (trehalose and betaine) and Na[+]/K[+] transporters, and some predicted traits were validated by laboratory phenotypic assays.

RESULTS: The SynCom demonstrates strong stability both in vitro and in planta. Most strains encoded multiple plant growth-promoting functions, and several of these were confirmed experimentally. The presence of osmoprotectant and ion transporter genes likely contributed to the observed resilience of Brachypodium to drought stress, where plants amended with the SynCom recovered better than those without. We further observed preferential colonization of SynCom strains around root tips under stress, likely due to active interactions between plant root metabolites and bacteria.

DISCUSSION: Our results demonstrate that trait-informed construction of synthetic communities can yield stable, functionally diverse consortia that enhance plant resilience under drought. Preferential colonization near root tips points to active, localized plant-microbe signaling as a component of stress-responsive recruitment. This stable SynCom provides a scalable platform for probing mechanisms of plant-microbe interaction and for developing microbiome-based strategies to improve soil and crop performance in variable environments.},
}

@article {pmid40862113,
year = {2025},
author = {Wang, W and Wang, L and Chen, J and Yang, X and Guo, Q and Zhang, Z and Liang, J and Gu, P and Shao, J},
title = {The gut microbiome: a vital link to hyperuricemia, gout and acute flares?.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1643566},
pmid = {40862113},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Hyperuricemia/microbiology ; *Gout/microbiology ; Male ; Middle Aged ; Female ; Adult ; Uric Acid/blood ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Aged ; Feces/microbiology ; Bacteria/genetics/classification ; },
abstract = {OBJECTIVES: To explore the associations between the gut microbiome and asymptomatic hyperuricemia, as well as acute gout flares.

METHODS: Forty-three Chinese participants were divided into healthy and hyperuricemic groups according to serum uric acid (SUA) levels. The hyperuricemia group were further separated into asymptomatic hyperuricemia (HUA) and gout patients on the basis of their clinical symptoms. In addition, the gout group was further divided into intercritical gout and acute gout groups on the basis of the claim of joint pain and relevant clinical parameters. 16S rRNA sequencing was used to evaluate the microbiome composition of all the groups.

RESULTS: A dramatic decreasing trend in microbial richness and diversity was observed in hyperuricemic patients compared with healthy controls. The same decreasing trend in microbial relative abundance was also observed. The butyrate-producing genera Faecalibacterium, Coprococcus and Enterococcus were markedly decreased in hyperuricemic patients. Moreover, opportunistic pathogens, such as the phylum Proteobacteria and genus Fusobacterium, were enriched in the hyperuricemia group. Furthermore, the gut microbiota of gout patients also exhibited significantly reduced microbial diversity compared with asymptomatic hyperuricemic patients, characterized by decreased richness of the genera Dialister, Ruminococcus, and Faecalibacterium. Greater differences in microbial richness and diversity can still be observed when gout flares occur. The abundances of Bacteroides and Lachnospira genera decreased in the acute gout stage.

CONCLUSION: Our study revealed that community richness and diversity change during the process of gout or HUA, especially during acute gout flares. Metagenomic species were significantly altered during different stages of hyperuricemia.},
}

Humans
*Gastrointestinal Microbiome
*Hyperuricemia/microbiology
*Gout/microbiology
Male
Middle Aged
Female
Adult
Uric Acid/blood
RNA, Ribosomal, 16S/genetics
Case-Control Studies
Aged
Feces/microbiology
Bacteria/genetics/classification

@article {pmid40861794,
year = {2025},
author = {Wang, B and Stephen, SJ and Cyphert, EL and Liu, C and Hernandez, CJ and Vashishth, D},
title = {Fecal microbiota transplantation in mice improves bone material properties through altered mineral quality.},
journal = {JBMR plus},
volume = {9},
number = {9},
pages = {ziaf115},
pmid = {40861794},
issn = {2473-4039},
abstract = {Disruptions of the composition of the gut microbiome are linked to impaired bone tissue strength. Fecal microbiota transplantation (FMT) is an established clinical therapy that can restore a healthy gut microbiome and reduce systemic inflammation. However, whether FMT from a healthy donor could rescue bone fragility is unknown. As induced inflammation causes mineralization defects, we hypothesize that manipulations of the gut microbiota alter bone fracture resilience through changes in mineral quality. Here, we altered the compositions of the gut microbiome in mice via antibiotics (ampicillin and neomycin) and FMT. Mice were allocated to 5 groups (M/F, N = 13-18/group): Unaltered, Continuous (dosed 4-24 wk), Initial (dosed 4-16 wk), Reconstituted (dosed 4-16 wk with subsequent FMT from age- and sex-matched mice with unaltered gut microbiota), and Delayed (dosed 16-24 wk). Fracture toughness testing and Raman spectroscopy were conducted on the femora. The maximum toughness was greater in the Reconstituted group (for females, p < .05 compared to Continuous, Unaltered, and Delayed groups; for males, p < .05 compared to groups with antibiotic dosing). The Reconstituted group showed lower type-B carbonate substitution in the bone mineral (all p < .01 for both sexes), and lower mineral-to-matrix ratio (all p < .01 for males, for females, p < .01 compared to Unaltered, Initial, and Delayed groups). In females, mineral crystallinity was higher in the Reconstituted group than those dosed with antibiotics (all p < .05). Serum inflammation marker TNF-α was positively correlated with type-B carbonate substitutions (ρ = 0.66), mineral-to-matrix ratio (ρ = 0.71), and carboxymethyl-lysine (CML) in bone matrix (ρ = 0.43). Enhanced bone maximum fracture toughness was associated with reduced type-B carbonate substitution (r = -0.45), decreased mineral-to-matrix ratio (r = -0.40), increased mineral crystallinity (r = 0.33), and lower levels of bone CML (r = -0.49, all p < .01). These results suggest that the introduction of more beneficial gut microbiota can increase fracture resistance by modifying mineral composition and quality, likely through the reduction of systemic inflammation.},
}

@article {pmid40861490,
year = {2025},
author = {Huang, L and Ge, S and Yang, K and Duan, L and Gao, L and Li, YZ and Yi, YS},
title = {Effects of oral gavage with periodontal pathogens and plaque biofilm on gut microbiota ecology and intestinal tissue architecture in mice: a mechanistic study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1589055},
pmid = {40861490},
issn = {2235-2988},
mesh = {Animals ; *Biofilms/growth & development ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Male ; Mice ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; *Dental Plaque/microbiology ; Disease Models, Animal ; Bacteria/classification/genetics ; Fusobacterium nucleatum/physiology ; Porphyromonas gingivalis/physiology ; Feces/microbiology ; Cytokines/metabolism ; Colon/pathology/microbiology ; },
abstract = {OBJECTIVE: This study aimed to establish an in vitro model simulating periodontal biofilm architecture with three representative periodontal pathogens and evaluate its systemic impact through oral gavage administration in C57BL/6 mice. The findings provide mechanistic insights into the oral-gut axis dysbiosis, elucidating potential pathways linking periodontal inflammation to gastrointestinal pathophysiology.

METHODS: Fifty 7-week-old male C57BL/6 mice were randomized into five groups(n=10/group): control (H), F. nucleatum (F), P.gingivalis (P), S.sanguinis (S) and biofilm (BF, F.n + P.g + S.s) groups. Mice were gavaged twice weekly for 6 weeks with 1×10[9] CFU (F, P, BF groups) and 1×10[8] CFU (S group) of bacterial suspensions or PBS (H group). Post-intervention, fecal and colon tissues were collected for 16S rRNA sequencing, H&E staining, immunohistochemistry (Occludin expression), and qRT-PCR analysis of inflammatory markers(IL18, TNF-α, IL-1β, B220, F4/80, NOS2, ARG1).

RESULTS: A stable in vitro three-species biofilm model was successfully established to mimic the ecology of periodontal plaque. Gavage with F.n, P.g or the biofilm consortium (BF group) induced intestinal barrier disruption and elevated pro-inflammatory cytokines levels. PCR indicated a significant increase in the expression of IL-1β, TNF-α, B220, F4/80, and NOS2 in the P group (P < 0.001), while Arg-1 expression exhibited a significant decrease (P < 0.01). In the BF group, only TNF-α expression demonstrated a significant increase (P < 0.01). The expression of occludin is significantly reduced in the F/P/BF group, with the most pronounced decrease observed in the P group (P < 0.01). Gut microbiota alterations occurred in all groups. At the phylum level, the Firmicutes/Bacteroidetes (F/B) ratio increased in all three groups (F/P/BF group). Proteobacteria abundance rose substantially in the P group, while Desulfovibrio increased and Verrucomicrobia decreased in the F/P/BF and F/S groups, respectively. Genus-level analysis showed reduced Muribaculaceae in the F/P/BF group, alongside elevated pro-inflammatory bacteria (e.g., Enterococcus, Acinetobacter) and diminished beneficial bacteria (e.g., Bifidobacterium, Parabacteroides).

CONCLUSION: These findings demonstrate that periodontal pathogens induce gut barrier compromise through microbiome-driven immunomodulation, with P. gingivalis exhibiting predominant pro-inflammatory effects.},
}

Animals
*Biofilms/growth & development
*Gastrointestinal Microbiome
Mice, Inbred C57BL
Male
Mice
RNA, Ribosomal, 16S/genetics
Dysbiosis/microbiology
*Dental Plaque/microbiology
Disease Models, Animal
Bacteria/classification/genetics
Fusobacterium nucleatum/physiology
Porphyromonas gingivalis/physiology
Feces/microbiology
Cytokines/metabolism
Colon/pathology/microbiology

@article {pmid40861487,
year = {2025},
author = {Tao, W and Yu, Y and Tan, D and Huang, X and Huang, J and Lin, C and Yu, R},
title = {Microbiota and enteric nervous system crosstalk in diabetic gastroenteropathy: bridging mechanistic insights to microbiome-based therapies.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1603442},
pmid = {40861487},
issn = {2235-2988},
mesh = {Humans ; *Enteric Nervous System/physiopathology ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/microbiology ; Animals ; *Gastrointestinal Diseases/microbiology/therapy ; *Diabetes Complications/microbiology/therapy ; },
abstract = {Diabetes mellitus has emerged as a global public health crisis, with over half of patients experiencing gastrointestinal (GI) symptoms that exacerbate glucose fluctuations and impair quality of life. While prior research on the pathophysiology of diabetic gastroenteropathy (DGE) focused primarily on autonomic neuropathy, particularly involving the vagus nerve, recent studies have shifted toward the impairment of the enteric nervous system (ENS). As the largest autonomous neural network governing GI motility independent of central control, structural and functional abnormalities of the ENS constitute the fundamental pathological basis for DGE. This review first delineates gut microbial alterations in diabetes and mechanisms by which dysbiosis compromises the integrity of the ENS. Second, we analyze how microbiota-derived metabolites (short-chain fatty acids, bile acids, tryptophan), gut hormones (glucagon-like peptide-1, ghrelin), and neurotransmitters (acetylcholine, vasoactive intestinal peptide, nitric oxide) multitarget the ENS-collectively establishing the "microbiota-ENS axis" as the central hub for GI sensorimotor control. Finally, we provide an overview of preclinical and clinical evidence for microbiome-targeted therapies (probiotics, prebiotics, fecal microbiota transplantation) in alleviating DGE symptoms and repairing ENS while outlining translational challenges and future research priorities.},
}

Humans
*Enteric Nervous System/physiopathology
*Gastrointestinal Microbiome/physiology
Dysbiosis/microbiology
Animals
*Gastrointestinal Diseases/microbiology/therapy
*Diabetes Complications/microbiology/therapy

@article {pmid40861423,
year = {2025},
author = {Sudhakar, P and Van Steen, K and Mallick, AI and Arnauts, K},
title = {Editorial: Multi-scale systems: ecological approaches to investigate the role of the microbiota in different niches.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1665390},
pmid = {40861423},
issn = {2296-889X},
}

@article {pmid40861397,
year = {2025},
author = {Seki, M and Zhang, YZ and Imoto, S},
title = {Diffusion model for imputing time-series gut microbiome profiles using phylogenetic information and metadata integration.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf181},
pmid = {40861397},
issn = {2635-0041},
abstract = {MOTIVATION: The gut microbiota interacts closely with the host, playing crucial roles in maintaining health. Analysing time-series genomic data enables the investigation of dynamic microbiota changes. However, missing values create significant analytical challenges.

RESULTS: We propose a microbiome imputation framework based on a conditional score-based diffusion model, tailored to microbiome data by incorporating phylogenetic convolutional layers. Our method effectively reduces mean absolute error across various missing data ratios for both 16S rRNA and whole-genome shotgun profiles. The imputed datasets enhance downstream predictive tasks, achieving area under the curve scores that exceed or are comparable with those of the existing methods. To further improve the performance, we embedded host metadata into the model using a tabular encoding approach, which yielded additional improvements particularly under higher missing ratios. Our findings underscore the potential of the diffusion model for processing time-series microbiome data with missing values.

Related codes and dataset can be found at: https://github.com/misatoseki/metag_time_impute_phylo.git.},
}

@article {pmid40861113,
year = {2025},
author = {Toledo, LT and Polveiro, RC and Diamantino, CA and Simão, GMR and Pereira, CER and Costa, EF and Moreira, MAS and Marks, FS},
title = {Use of Subtherapeutic Tylvalosin Against Mycoplasma hyopneumoniae: Implications For Respiratory Microbiome Dysbiosis and Swine Lung Health.},
journal = {Transboundary and emerging diseases},
volume = {2025},
number = {},
pages = {8903237},
pmid = {40861113},
issn = {1865-1682},
mesh = {Animals ; *Mycoplasma hyopneumoniae/drug effects ; Swine ; *Tylosin/analogs & derivatives/administration & dosage/therapeutic use/pharmacology ; *Pneumonia of Swine, Mycoplasmal/drug therapy/microbiology ; Female ; *Microbiota/drug effects ; *Anti-Bacterial Agents/administration & dosage/therapeutic use ; *Dysbiosis/veterinary/microbiology ; Lung/microbiology/pathology ; RNA, Ribosomal, 16S ; },
abstract = {Enzootic pneumonia (EP) caused by Mycoplasma hyopneumoniae (M. hyopneumoniae) has a significant impact on swine production. Subtherapeutic exposures of tylvalosin in swine, often due to inconsistent dosing in feed or water, promote antimicrobial resistance. This study investigated the efficacy of 1.0625 mg/kg/day of tylvalosin administered for 7 days via feed to pigs experimentally infected with the UFV01 strain of M. hyopneumoniae and its impact on the respiratory microbiome. Thirty landrace x large white female piglets were divided into three groups: G1 (negative control, n = 2), G2 (infected, n = 14) and G3 (infected and treated, n = 14). Clinical signs, seroconversion, macroscopic and microscopic lung lesions and bacterial load were assessed. The respiratory microbiota of swine was analysed through 16S rRNA gene sequencing, followed by bioinformatics analyses. While G1 piglets remained healthy, G2 and G3 piglets developed lung lesions consistent with EP, although no significant difference was observed between these groups. Seroconversion was higher in G2 (90.9%) than in G3 (45.5%) at 35 days post-infection, suggesting modulation of the humoral immune response by tylvalosin. Microbiota analyses revealed a significant shift in post-infection composition, with infected pigs exhibiting reduced alpha diversity and distinct beta diversity compared to healthy pigs. M. hyopneumoniae dominated the respiratory microbiome of infected animals, drastically reducing the abundance of other taxa, notably Stenotrophomonas maltophilia. While tylvalosin treatment partially restored alpha diversity and shifted the microbiota composition towards the control group, it failed to eliminate M. hyopneumoniae. Variivorax, Ralstonia and Pseudomonas were identified as potential biomarkers for respiratory health and treatment response. These findings emphasise the complex relationship between M. hyopneumoniae infection, suboptimal tylvalosin dosage and resulting respiratory microbiome dysbiosis. Identifying and correcting the inappropriate use of antimicrobial dosages in clinical and preventive treatments, as well as promoting research focused on optimising dosage strategies and management practices, is essential for swine production and for reducing antimicrobial resistance. Moreover, maintaining a balanced microbiota may be a key factor in achieving healthier swine production, both in terms of animal welfare and food safety for consumers.},
}

Animals
*Mycoplasma hyopneumoniae/drug effects
Swine
*Tylosin/analogs & derivatives/administration & dosage/therapeutic use/pharmacology
*Pneumonia of Swine, Mycoplasmal/drug therapy/microbiology
Female
*Microbiota/drug effects
*Anti-Bacterial Agents/administration & dosage/therapeutic use
*Dysbiosis/veterinary/microbiology
Lung/microbiology/pathology
RNA, Ribosomal, 16S

@article {pmid40861091,
year = {2025},
author = {Mohammadi, A and Moini, A and Falsafi, S and Feizabadi, MM},
title = {Lactobacilli Deficiency in Infertile Women Seeking IVF in Arash Hospital: An Imbalance in the Genital Microbiome.},
journal = {Journal of family & reproductive health},
volume = {19},
number = {2},
pages = {122-127},
pmid = {40861091},
issn = {1735-8949},
abstract = {OBJECTIVE: It is estimated that infertility affects approximately 9-30% of couples in their reproductive age and microorganisms may play an important role in such genital system dysfunction. The aim of this study was to investigate the presence of lactobacilli, Gardnerella, Enterobacteriaceae, and streptococci in the vagina, cervix and endometrium of women who referred for infertility and the healthy women who referred for oocyte donation.

MATERIALS AND METHODS: The endometrial, cervical and vaginal swab specimens were collected three days after the end of menstruation and cultured to isolate lactobacilli. DNA form these specimens was extracted and subjected to quantitative real-time PCR to determine the frequency of the above bacteria. All uterine biopsy samples were tested for the presence of bacterial DNA by PCR method.

RESULTS: 94% of uterine biopsy samples contained bacterial DNA. The frequency of lactobacilli identified by real-time quantitative PCR in these two groups was 40% (endometrial samples), 70% (cervical samples), and 80% (vaginal samples), which differed from lactobacilli isolated by the culture method. The number of lactobacilli from cervical endometrium of healthy donors was higher than in the diseased group. There was a significant difference in the mean of Gardnerella bacteria in the cervix and endometrium and Streptococcus in the cervix (p<0.05).

CONCLUSION: Considering the decrease of lactobacilli and the increase of other bacteria, it is suggested to consider the composition and number of bacteria in the genital tract of asymptomatic infertile women as one of the possible causes of infertility.},
}

@article {pmid40860937,
year = {2025},
author = {Zhao, M and Li, X and Li, Y and Ma, L and Liu, Y and Wang, S and Tian, J and Liang, Y and Shen, C and Ma, X and Yu, D and Ma, L},
title = {Multi-Omics Profiling of the 42-Day Infant Gut as a Pilot Predictor of Atopic Dermatitis at One Year: A Birth Cohort Study in China.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {11205-11216},
pmid = {40860937},
issn = {1178-7031},
abstract = {BACKGROUND: Early-life gut microbiota and metabolism are increasingly linked to immune development and atopic diseases. However, predictive microbial and metabolic markers present during the neonatal period for later atopic dermatitis (AD) remain poorly defined. This study aimed to identify early-life gut microbiome and metabolite signatures associated with the development of AD by one year of age.

METHODS: We conducted a prospective birth cohort study in Beijing, China, enrolling 18 infants with fecal samples collected at 42 days of age. Infants were followed for one year and classified into AD (n = 6) or non-AD (n = 12) groups. Fecal samples underwent 16S rRNA gene sequencing and untargeted metabolomic profiling. Key microbial taxa, differential metabolites, and functional pathways were identified and integrated via multi-omics correlation analysis.

RESULTS: While overall microbial diversity was similar between groups, Staphylococcus was significantly less abundant in the AD group. Bifidobacterium and Lactobacillus showed strong correlations with lipid- and amino acid-related metabolites, including linoleic acid and N2-acetyl-L-ornithine. AD infants exhibited reduced levels of linoleic acid and choline phosphate. KEGG analysis revealed enrichment in linoleic acid metabolism, sphingolipid signaling, and AGE-RAGE signaling pathways. Integrated network analysis identified microbial-metabolite modules potentially involved in immune and barrier regulation.

CONCLUSION: Multi-omics profiling of the infant gut at 42 days identified microbial and metabolic features associated with later AD development. These findings support the gut-skin axis and suggest potential early-life biomarkers for predicting AD risk and informing targeted prevention strategies.},
}

@article {pmid40860916,
year = {2025},
author = {Zhang, C and Zhang, B and Li, Y and Kastelic, JP and Li, X and Tong, X and Yao, A and Xu, C and Han, B and Gao, J},
title = {Modified Huangqi Shengmai Yin enhances ruminal microbiome and metabolites activity in dairy cows with subclinical mastitis.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1631756},
pmid = {40860916},
issn = {2297-1769},
abstract = {INTRODUCTION: Bovine mastitis, especially subclinical mastitis (SCM), with minimal clinical signs, is detrimental due to its resistance to treatment, recurrence, and substantial economic impact on global dairy industry. The modified form of Huangqi Shengmai Yin (HSY), classical traditional herbal medicine renowned for its effects in antimicrobial and circulatory-enhancing and thus beneficial for subclinical mastitis, has been developed for treatment attempt of SCM, yet its therapeutic effect and mechanism remains unclear. This study aims to investigate the therapeutic effects of mHSY on SCM in cows, and elucidate its potential therapeutic mechanism.

METHODS: In this study, mHSY was given orally to cows with SCM. After a 3-day treatment regimen, the therapeutic effects were evaluated. 16S diversity sequencing and metabolomics were used to elucidate the therapeutic mechanism of HSY.

RESULTS: The SCM was significantly alleviated after the 3-day treatment with HSY. In cows infected with SCM, there were significant alterations in rumen fluid microbiota, particularly proportions of Enterobacter, Desulfovibrio, and Flavonifractor, implying a pivotal role for these bacteria in SCM. Furthermore, the therapeutic potential of HSY is linked to improving the proportion of beneficial bacteria (e.g., Succinivibrionaceae_UCG-001) and re-establishing a balanced ruminal bacterial profile. Modulation of fatty acid and amino acid metabolism, as evidenced by changes in metabolite profiles, is a critical aspect of SCM and can be markedly ameliorated with mHSY administration.

CONCLUSION: mHSY shows significant inhibitory effects on SCM, which may be attributed to regulating ruminal microbiota and metabolic pathways in vivo.},
}

@article {pmid40860758,
year = {2025},
author = {Tuoliu, D and Cheng, J and Xia, L and Wen, Z and Wang, M and Yang, W and Yang, Q},
title = {Bacterial microbiome and their assembly processing in two sympatric desert rodents (Dipus sagitta and Meriones meridianus) from different geographic sources.},
journal = {Current zoology},
volume = {71},
number = {4},
pages = {440-448},
pmid = {40860758},
issn = {1674-5507},
abstract = {The microbiome of mammals has profound effects on host fitness, but the process, which drives the assembly and shift of mammalian microbiome remains poorly understood. To explore the patterns of small mammal microbial communities across host species and geographical sites and measure the relative contributions of different processes in driving assembly patterns, 2 sympatric desert rodent species (Dipus sagitta and Meriones meridianus) were sampled from 2 geographically distant regions, which differed in the environment, followed by 16S rRNA gene sequencing. The microbiomes differed significantly between D. sagitta and M. meridianus, and linear mixed modeling (LMM) analysis revealed that microbial diversity was mostly affected by species rather than the environment. For each rodent species, the microbiome diversity and structure differed across geographical regions, with individuals from lower rainfall environments exhibiting greater diversity. The null modeling results suggested dispersal limitation and ecological drift rather than differential selective pressures acting on the microbiome. In addition, each group had a different core genus, suggesting that the taxonomic composition of the microbiome was shaped most strongly by stochastic processes. Our results suggest that variation in the microbiome between hosts, both within and among geographic rodent populations, is driven by bacterial dispersal and ecological drift rather than by differential selective pressures. These results elucidated the diversity patterns and assembly processes of bacterial microbiomes in small desert mammals. Deciphering the processes shaping the assembly of the microbial community is a premise for better understanding how the environment-host-microbe interactions of mammals are established and maintained, particularly in the context of increased environmental disturbances and global changes.},
}

@article {pmid40860667,
year = {2025},
author = {Singhakarn, C and Toonen, RJ and Work, TM},
title = {Gram staining reveals diverse bacterial associations in coral cell-associated microbial aggregates in the Pacific Ocean.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19867},
pmid = {40860667},
issn = {2167-8359},
mesh = {*Anthozoa/microbiology ; Animals ; Pacific Ocean ; *Gentian Violet ; *Bacteria/isolation & purification/classification ; *Phenazines ; Hawaii ; Staining and Labeling/methods ; },
abstract = {Cell-associated microbial aggregates (CAMAs) (also referred to as coral-associated microbial aggregates) have been observed in 24 coral species from the Pacific Ocean, and studies indicate most contain gram-negative bacilli from the genus Endozoicomonas. Here, we used histology with Gram staining to evaluate the morphology and distribution of CAMAs in six species of scleractinian corals from Hawaii and Palmyra. Within CAMAs, we observed the coexistence of bacteria with differing morphologies and Gram-staining properties both within and among coral species. Pocillopora and Acropora had mostly gram-negative bacilli, whereas gram-negative cocci dominated in Porites. Acropora had the highest abundance of gram-positive CAMAs. The anatomical distribution of CAMAs varied by coral species. CAMAs dominated in the tentacles of Pocillopora meandrina, Pocillopora grandis, and Porites evermanni, were mostly in the coenenchyme of Acropora cytherea, and were found equally between tentacles and coenenchyme in Porites compressa and Porites lobata. Tissue-layer distribution also varied, with CAMAs mainly in the epidermis of Pocillopora but in the gastrodermis of Porites and Acropora. The diversity of bacteria in CAMAs and their anatomic distribution in Pacific corals may be more complex than previously understood. This indicates other bacterial species, in addition to Endozoicomonas, are colonizing CAMAs in corals from the Pacific Ocean.},
}

*Anthozoa/microbiology
Animals
Pacific Ocean
*Gentian Violet
*Bacteria/isolation & purification/classification
*Phenazines
Hawaii
Staining and Labeling/methods

@article {pmid40860564,
year = {2025},
author = {Schokker, D and Stege, PB and Duhamel, M and Bekker, M and Timmerman, HM and Kar, SK and Smidt, H and Zoetendal, EG and van Overbeek, L and Meisner, A},
title = {Rationally designed microbial communities in agri-food production systems: from research to market.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf121},
pmid = {40860564},
issn = {2730-6151},
abstract = {Primary production needs to transition towards more sustainable systems that reduce environmental impact, mitigate climate change, and ensure healthy food production with limited use of chemical plant protection products, fertilizers, or antibiotics. Rationally designed microbial communities, or engineered microbial consortia, involve the intentional assembly of microorganisms that can underpin more sustainable primary production systems. Rationally designed microbial communities can for example, (i) enhance ecosystem resilience, (ii) improve bioremediation, (iii) enhance industrial processes, or (iv) prevent diseases. In the perspective, we discuss the route towards market applications with a focus on the methodology needed to rationally design microbial communities for applications in the agri-food production systems. Often in silico and in vitro approaches are considered as a continuous process that first consider the in silico genomic and then in vitro condition to develop microbial consortia. However, host-microbe interactions influence both the microbial community assembly and host phenotypes and need to be considered from an early stage when developing microbial communities. As such, we propose that the route towards market application(s) should, from a technical perspective include (i) the host of interest, (ii) a library of both slow and fast-growing species, and (iii) genomic information about functions present in the selected microbial consortia.},
}

@article {pmid40860479,
year = {2025},
author = {Panda, C and Kruse, R and Williams, K and Nance, B and Gudavalli, M and Pourafshar, S and Metzger, B and Komarnytsky, S},
title = {Metabolic reset purification program improves antioxidant balance and gut microbiome in individuals transitioning to a healthier diet.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1621709},
pmid = {40860479},
issn = {2296-861X},
abstract = {UNLABELLED: A healthy diet helps transition individuals towards numerous long-term metabolic benefits but is challenging to maintain. Supplementation with additional whole food-based concentrates and herbs may support this shift by enhancing metabolic resilience. This randomized, controlled, crossover study evaluated a 21-day purification program emphasizing plant foods and whole food supplementation on metabolic detoxification, oxidative stress, and gut microbiota composition. Participants followed a plant-based diet for 7 days, with lean proteins introduced from days 8-21. Whole food supplements rich in polyphenols, glucosinolates, and prebiotic fibers were included to support metabolic and gastrointestinal function. The intervention group exhibited 9% (p < 0.0001) reduction in ROS-associated oxidative stress compared to diet alone, suggesting enhanced redox balance. Additionally, the intervention group exhibited higher urinary creatinine levels, indicating enhanced kidney filtration efficiency (p = 0.03). Self-reported stress levels decreased by 36% (p = 0.049) in the intervention group, with a notable reduction in anxiety related to future uncertainty, demonstrating the psychological benefits of dietary supplementation. Gut microbiome analysis revealed a reduction in Proteobacteria, a phylum associated with chronic metabolic and inflammatory diseases, and beneficial increases in Ruminococcus gnavus, Lactobacillus zeae, and Roseburia faecis, which contribute to gut barrier integrity and butyrate production. These findings highlight the potential of whole food-based supplementation to enhance dietary transitions by reducing oxidative stress, supporting kidney function, alleviating psychological stress, and modulating gut microbiota composition.

CLINICAL TRIAL REGISTRATION: NCT05877365.},
}

@article {pmid40860434,
year = {2025},
author = {Liu, S and Zhuang, Y and Chen, T and Gao, D and Xiao, J and Wang, J and Li, J and Zhao, X and Peng, R and Guo, W and Wei, J and Sha, M and Wang, J and Ma, J and Ma, M and Li, M and Wang, W and Wang, YJ and Li, S and Cao, Z},
title = {Spatio-temporal characteristics of the gastrointestinal resistome in a cow-to-calf model and its environmental dissemination in a dairy production system.},
journal = {iMeta},
volume = {4},
number = {4},
pages = {e70047},
pmid = {40860434},
issn = {2770-596X},
abstract = {Microbiome and resistome transmission from mother to child, as well as from animal to environment, has been widely discussed in recent years. Dairy cows mainly provide milk and meat. However, in the dairy production system, the characteristics and transmission trends of resistome assembly and the microbiome in the gastrointestinal tract (GIT) remain unclear. In this study, we sequenced the GIT (rumen fluid and feces) microbiome of dairy cow populations from two provinces in China (136 cows and 36 calves), determined the characteristics of their resistome profiles and the distribution of antibiotics resistance genes (ARGs) across bacteria and further tracked the temporal dynamics of the resistome in offspring during early life using multi-omics technologies (16S ribosomal RNA [rRNA] sequencing, metagenome, and metatranscriptome). We characterized the GIT resistome in cows, distinguished by gut sites and regions. The abundance of ARGs in calves peaked within the first 3 days after birth, with Enterobacteriaceae as the dominant microbial host. As calves aged, resistome composition stabilized, and overall ARG abundance gradually decreased. Both diet and age influenced carbohydrate-active enzymes and ARG profiles. Resistance profiles in ecological niches (meconium, colostrum, soil, and wastewater) were unique, resembling maternal sources. Mobile genetic elements (MGEs), mainly found in soil and wastewater, played an important role in mediating these interactions. Multidrug resistance consistently emerged as the most significant form of resistance at the both the metagenome and metatranscriptome levels. Several antibiotic classes showed higher proportions at the RNA level than at the DNA level, indicating that even low-abundance gene groups can have a considerable influence through high expression. This study broadens our understanding of ARG dissemination in livestock production systems, providing a foundation for developing future preventive and control strategies.},
}

@article {pmid40860431,
year = {2025},
author = {Liu, Y and Yang, L and Meskini, M and Goel, A and Opperman, M and Shyamal, SS and Manaithiya, A and Xiao, M and Ni, R and An, Y and Zhang, M and Tian, Y and Zhou, S and Ye, Z and Zhuang, L and Li, L and Saraswat, I and Kar, A and Ali, SL and Ullah, S and Ali, SY and Kaushik, S and Tian, T and Jiao, M and Wang, S and Ghisleni, G and Armanni, A and Fumagalli, S and Wang, W and Cao, C and Carpena, M and Prieto, MA and Bruno, A and Jin, C and Hu, H and Zhang, Y and du Preez, I and Aspatwar, A and Zhang, L and Gong, W},
title = {Gut microbiota and tuberculosis.},
journal = {iMeta},
volume = {4},
number = {4},
pages = {e70054},
pmid = {40860431},
issn = {2770-596X},
abstract = {Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), remains a significant global health challenge. Recent advancements in gut microbiota (GM) research have shed light on the intricate relationship between GM and TB, suggesting that GM alterations may influence host susceptibility, disease progression, and response to antituberculosis drugs. This review systematically synthesizes and analyzes the current research progress on the relationship between GM and TB, focusing on six key aspects: (1) bidirectional effects between GM dynamics and TB progression; (2) the interaction between GM and anti-TB drugs; (3) GM and TB immune response; (4) GM as a potential target for diagnosis and treatment of TB; (5) multi-omics and artificial intelligence (AI) technologies in GM-TB research; (6) current challenges and future directions in GM-TB research. We highlight the bidirectional nature of the GM-TB interaction, where MTB infection can lead to GM dysbiosis, and changes can affect the host's immune response, contributing to TB onset and progression. Advanced molecular techniques, such as next-generation sequencing and metagenomics, along with AI, play pivotal roles in elucidating these complex interactions. Future research directions include investigating the relationship between GM and TB vaccine efficacy, exploring GM's potential in TB prevention, developing microbiome-based diagnostic and prognostic tools, and examining the role of GM in TB recurrence. By addressing these areas, we aim to provide a comprehensive perspective on the latest advancements in GM and TB research and offer insights for future studies and clinical applications. Ultimately, the development of novel microbiome-based strategies may offer new tools and insights for the effective control and management of TB, a disease that continues to pose a significant threat to public health.},
}

@article {pmid40860430,
year = {2025},
author = {Gao, M and Chen, S and Fan, H and Li, P and Liu, A and Li, D and Li, X and Hu, Y and Han, G and Guo, Y and Lv, Z},
title = {Soyasaponin and vertical microbial transmission: Maternal effect on the intestinal development and health of early chicks.},
journal = {iMeta},
volume = {4},
number = {4},
pages = {e70044},
pmid = {40860430},
issn = {2770-596X},
abstract = {Multiple factors, including genetics, nutrition, and health, influence the vertical transmission of microbiota from mothers to their offspring. Recent studies have shown that avian microbiota can be passed to the next generation via the eggshell and egg albumen. However, it remains unclear whether these microbial communities are regulated by nutrition and how they are associated with the host genotype. Chickens, with their controlled rearing conditions and stable genotypes, provide a promising model for investigating microbiome transmission in birds. This study aims to determine whether host genotype-associated bacteria are vertically transmitted between generations, and how maternal nutritional intervention with soyasaponin modulates this microbial transfer, thereby shaping chick intestinal development and informing effective nutritional strategies. We established a microbial vertical transmission model across various anatomical sites in breeder hens, chicken embryos, and chicks. Avian gut microbiota and reproductive tract microbiota can both be found in chicks at various developmental stages. Supplementing breeder hen diets with soyasaponin interacts with vertically transmitted Bifidobacterium adolescentis to produce γ-aminobutyric acid. This compound modulates offspring intestinal development through distinct mechanisms in chick epithelial cells, including the inhibition of LC3 and caspase3-associated autophagy and apoptosis pathways, as well as the promotion of proliferation and differentiation pathways mediated by LGR5 and Olfm4. Our study highlights that avian gut and reproductive tract microbiota are transmitted to chicks through the cloaca, with the yolk sac also being instrumental in this vertical transfer. The incorporation of soyasaponin in avian diets affects microbial transfer, providing a theoretical basis for studying maternal effects in poultry and formulating corresponding dietary strategies.},
}

@article {pmid40860388,
year = {2025},
author = {Shetty, P and Bhat, R and Padavu, S and Rai, P and Kumar, BK and Shetty, S},
title = {Molecular profiling of antibiotic resistance genes in acute and chronic irreversible pulpitis: A cross-sectional study.},
journal = {Journal of conservative dentistry and endodontics},
volume = {28},
number = {8},
pages = {814-820},
pmid = {40860388},
issn = {2950-4708},
abstract = {CONTEXT: Antimicrobial resistance represents a global health crisis, with the oral microbiome serving as a significant reservoir for resistance genes. Despite guidelines discouraging antibiotic use for irreversible pulpitis, empirical prescription remains common in endodontic practice. This study aimed to evaluate the prevalence of β-lactam and tetracycline resistance genes in acute and chronic irreversible pulpitis.

SUBJECTS AND METHODS: Pulp tissue samples were collected from 24 patients (12 acute and 12 chronic irreversible pulpitis) meeting strict inclusion criteria. Following DNA extraction, polymerase chain reaction amplification was performed to detect tetracycline resistance determinants (tetA and tetB) and β-lactamase genes (blaTEM and blaCTX). Amplicons were analyzed by gel electrophoresis.

RESULTS: Antibiotic resistance genes were detected in 54.2% of samples, with higher prevalence in acute (66.7%) versus chronic pulpitis (41.7%). The blaTEM gene was detected in 25.0% of samples from both acute and chronic cases, while tetA was more prevalent in acute (41.7%) than chronic pulpitis (16.7%). Co-occurrence of both resistance genes was observed exclusively in acute pulpitis (25.0%, P = 0.043). Sequence analysis confirmed the functionality of detected resistance genes with >98% homology to reference sequences.

CONCLUSION: The present analysis demonstrates the concerning prevalence of antibiotic resistance genes in pulpal infections, particularly in acute irreversible pulpitis. The higher prevalence of tetA and co-occurrence of multiple resistance genes in acute cases provide molecular evidence supporting clinical guidelines against routine antibiotic prescriptions for irreversible pulpitis. The findings reinforce the significance of implementing robust antibiotic stewardship protocols within endodontic practice and underscore the imperative for continuous surveillance of antimicrobial resistance patterns.},
}

@article {pmid40860377,
year = {2025},
author = {Bhate, M and Sharma, S},
title = {Standardization of extraction, identification, and characterization of an immunoglobulin Y antibody: A potential inhibitor of cariogenic and endodontic microbiome.},
journal = {Journal of conservative dentistry and endodontics},
volume = {28},
number = {8},
pages = {772-782},
pmid = {40860377},
issn = {2950-4708},
abstract = {AIM: This study aimed to formulate a protocol to isolate and characterize immunoglobulin Y (IgY) antibodies from chicken egg yolk and evaluate its potential in inhibiting Streptococcus mutans.

MATERIALS AND METHODS: Part A: IgY was extracted from fresh chicken egg yolk using a polyethylene glycol precipitation method. The isolated IgY was characterized using ultraviolet-visible (UV-Vis) spectroscopy to assess protein concentration and purity, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) for molecular weight confirmation, high-performance liquid chromatography (HPLC) for purity, and mass spectrometry for further protein analysis. Functional activity was evaluated using Western blotting and enzyme-linked immunosorbent assay (ELISA) to confirm antigen binding. PART B: antimicrobial testing: (i) minimum inhibitory concentration (MIC) assays: determining the lowest concentration of IgY that inhibits the growth of each pathogen and (ii) zone of inhibition tests: measuring the effectiveness of IgY in inhibiting pathogen growth on agar plates. The concentration of IgY 50 μl, and 100 μl was utilized against S. mutans, Enterococcus faecalis, and Candida albicans.

RESULTS: The UV-Vis spectroscopy results indicated a high concentration of IgY with minimal impurities. SDS-PAGE revealed a single band at approximately 180 kDa, corresponding to the expected molecular weight of IgY, with no significant contamination. HPLC analysis confirmed a pure IgY preparation with a single major peak. Mass spectrometry further validated the molecular weight of the IgY at ~180 kDa. Functional assays (western blotting and ELISA) demonstrated that the isolated IgY retained its ability to bind specifically to S. mutans, confirming its potential as an antimicrobial agent. MIC assays showed that IgY effectively inhibited the growth of endodontic pathogens at relatively low concentrations. The zone of inhibition for S. mutans group was as follows: positive control (PC) - 13 mm, test-50 μL - 11 mm, and test 100 μL - 20 mm; for E. faecalis - 50 μL - 14 mm, 50 μL - 15 mm, and PC - 15 mm; for C. albicans - 100 μL - 26 mm 100 μL - 24 mm and PC - 18 mm.

CONCLUSION: IgY antibodies isolated from chicken egg yolk were characterized as highly pure and functional, with a strong potential for use in inhibiting S. mutans - an established dental caries causative microorganism. The use of IgY could offer an effective, ethical, and cost-efficient alternative to mammalian antibodies in oral health treatments, particularly for targeting S. mutans, and can be a viable therapeutic tool in passive immunization, caries prevention, and caries inhibition. It also has inhibitory potential on E. faecalis and C. albicans and can be developed as a therapeutic agent in endodontic infections.},
}

@article {pmid40860250,
year = {2025},
author = {Tang, L and Bi, H and Lin, K and Chen, Y and Xian, H and Li, Y and Xie, H and Zheng, G and Wang, P and Chen, Y and Yang, B and Tan, Y and Song, Q and Wang, M and Li, G and Chang, J and Guan, Y and So, KF and Lu, C},
title = {The Skin-Brain Axis in Psoriasis and Depression: Roles of Inflammation, Hormones, Neuroendocrine Pathways, Neuropeptides, and the Microbiome.},
journal = {Psoriasis (Auckland, N.Z.)},
volume = {15},
number = {},
pages = {411-428},
pmid = {40860250},
issn = {2230-326X},
abstract = {Psoriasis, a common chronic inflammatory skin disease affecting approximately 2-3% of the global population, frequently co-occurs with depression. This highly prevalent comorbidity significantly impairs patients' quality of life. Despite the substantial physical and mental health burden imposed by psoriatic depression, the underlying pathophysiological mechanisms connecting psoriasis and depression remain poorly understood. In this review, we explored several pathological processes that may contribute to psoriasis-associated depression, including immune cells dysregulations, hormones imbalances, hypothalamic-pituitary-adrenal (HPA) axis dysfunctions, neuropeptides expression abnormalities, and gut dysbiosis. The primary purpose of this review was to present a comprehensive overview of the pathogenic mechanisms linking psoriasis and depression. These insights may guide trans-disciplinary interventions aimed at both skin and mood symptoms.},
}

@article {pmid40860241,
year = {2025},
author = {Zhao, F and Wang, L and Du, D and Zhao, H and Tian, G and Li, Y and Liu, Y and Wang, Z and Liu, D and Li, J and Ji, L and Zhao, H},
title = {Tumor microenvironment signatures enhances lung adenocarcinoma prognosis prediction: Implication of intratumoral microbiota.},
journal = {Microbial cell (Graz, Austria)},
volume = {12},
number = {},
pages = {182-194},
pmid = {40860241},
issn = {2311-2638},
abstract = {The interaction between intratumoral microbiome and the tumor microenvironment (TME) has furthered our understanding of tumor ecology. Yet, the implications of their interaction for lung cancer management remain unclear. In the current work, we collected host transcriptome samples and matched intratumoral microbiome samples, as well as detailed clinical metadata from The Cancer Genome Atlas (TCGA) of 478 patients with lung adenocarcinoma (LUAD). Utilizing the multiomics integration approach, we comprehensively investigated the crosstalk between the TME and intratumoral microbiome in patients with LUAD. First, we developed a prognostic model based on the TME signatures (TMEindex) that clearly distinguished clinical, survival, and response to immunotherapy of patients with LUAD. Additionally, we found profound differences in intratumoral microbiota signatures, including alpha- and beta-diversity, among patients with different survival risks based on the TME signatures. In depth, we detected that genera Luteibacter and Chryseobacterium were strongly negatively and positively associated with patients' survival risk, respectively, suggesting their opposing roles in cancer progression. Moreover, we developed a model that fused intratumoral microbial abundance information with TME signatures, called intratumoral microbiome-modified TMEindex (IMTMEindex), leading in predicting patient overall survival at 1-, 3-, and 5-years. Future clinical profiling of the specific intratumoral microbes in the TME could improve prognosis, inform immunotherapy, and facilitate the development of novel therapeutics for LUAD.},
}

@article {pmid40859950,
year = {2025},
author = {Uti, DE and Omang, WA and Alum, EU and Ugwu, OP and Wokoma, MA and Oplekwu, RI and Atangwho, IJ and Egbung, GE},
title = {Combined Hyaluronic Acid Nanobioconjugates Impair CD44-Signaling for Effective Treatment Against Obesity: A Review of Comparison with Other Actors.},
journal = {International journal of nanomedicine},
volume = {20},
number = {},
pages = {10101-10126},
pmid = {40859950},
issn = {1178-2013},
mesh = {*Hyaluronic Acid/chemistry/pharmacology ; *Hyaluronan Receptors/metabolism/antagonists & inhibitors ; Humans ; *Obesity/drug therapy/metabolism ; Animals ; *Nanoconjugates/chemistry/administration & dosage ; Signal Transduction/drug effects ; Drug Delivery Systems/methods ; Adipose Tissue/metabolism/drug effects ; Nanoparticles/chemistry ; },
abstract = {CD44, a key hyaluronic acid (HA) receptor, has emerged as a central mediator of adipose tissue inflammation, remodeling, and insulin resistance in obesity. Its overexpression in obese adipose depots promotes leukocyte infiltration, pro-inflammatory signaling, and extracellular matrix dysregulation processes that underlie metabolic dysfunction. This review explores the therapeutic relevance of targeting the HA-CD44 axis by synthesizing data primarily from preclinical studies, with emerging evidence from early clinical investigations. A narrative review methodology was employed to assess and compare therapeutic modalities, highlighting advances in molecular targeting, drug delivery systems, and metabolic interventions. We focus on two primary therapeutic classes: small molecules and nanobioconjugates. Small molecules, such as curcumin, metformin, and CD44 antagonists, offer systemic modulation and accessibility but are limited by their low tissue specificity and potential side effects. In contrast, HA-functionalized nanobioconjugates, including liposomes, PLGA nanoparticles, dendrimers, and exosomes, enable targeted delivery to adipose tissue, prolonged drug release, and reduced systemic toxicity. These nanosystems have demonstrated superior modulation of CD44 signaling, adipose inflammation, and glucose homeostasis in obesity models. Emerging strategies such as monoclonal antibodies, GLP-1 analogs, gene-editing tools (eg, CRISPR/Cas9), microbiome modulators, and brown adipose tissue (BAT) activators are also discussed. A comparative analysis indicates that nanobioconjugates offer the highest targeting precision, while small molecules remain advantageous in terms of cost and ease of administration. However, biologics and gene therapies face challenges related to delivery and scalability. Collectively, current evidence predominantly preclinical supports the HA-CD44 axis as a promising therapeutic target in obesity. Integrated approaches combining nanotechnology with molecular inhibitors and biologics could offer a multifaceted strategy for managing metabolic disease.},
}

*Hyaluronic Acid/chemistry/pharmacology
*Hyaluronan Receptors/metabolism/antagonists & inhibitors
Humans
*Obesity/drug therapy/metabolism
Animals
*Nanoconjugates/chemistry/administration & dosage
Signal Transduction/drug effects
Drug Delivery Systems/methods
Adipose Tissue/metabolism/drug effects
Nanoparticles/chemistry

@article {pmid40859872,
year = {2025},
author = {Bunka, L and Rozenberga, M and Silamiķelis, I and Saksis, R and Birzniece, L and Megnis, K and Fedulovs, A and Pahirko, L and Zaļizko, P and Krustiņš, E and Kloviņš, J and Sokolovska, J and Elbere, I},
title = {Dual-approach analysis of gut microbiome in patients with type 1 diabetes and diabetic kidney disease.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2531254},
pmid = {40859872},
issn = {1365-2060},
mesh = {Humans ; *Diabetes Mellitus, Type 1/microbiology/complications ; *Diabetic Nephropathies/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Feces/microbiology ; Adult ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Middle Aged ; Disease Progression ; Metagenomics/methods ; Biopsy ; Young Adult ; Bacteroides/isolation & purification/genetics ; },
abstract = {BACKGROUND: Type 1 diabetes (T1D) is a multifactorial autoimmune disease mediated by genetic, epigenetic, and environmental factors. Diabetic kidney disease (DKD) is a major complication of diabetes mellitus which affects 30-40% of T1D patients. Increasing evidence suggests the significant role of the microbiome in the progression of both T1D and DKD.

MATERIALS AND METHODS: Here we recruited 76 T1D patients and 22 healthy controls and combined data from sigmoid colon biopsy samples analysed with V3-V4 region amplification of 16S rRNA gene and shotgun metagenomics data obtained from faecal samples. Additionally, we compared T1D patients with and without progression of DKD.

RESULTS: We observed significant differences within both sample types at various taxonomic and functional levels. T1D patient microbiota detected using biopsy samples had a lower abundance of the Bacteroides genus when compared to healthy controls. Significantly, despite only a few taxonomic differences patients with and without DKD progression were vastly different at the functional pathway level within the faecal samples - we observed 2 and 61 enriched pathways in these groups. respectively, with several of these pathways linked to the mediation of renal function.

CONCLUSION: Altogether, we present novel data about microbial signatures relevant to T1D and DKD progression, which partly supports previous data and also presents possible tissue type or population-specific elements. DKD progression is characterized with significant differences within the functional level of the gut microbiome.},
}

Humans
*Diabetes Mellitus, Type 1/microbiology/complications
*Diabetic Nephropathies/microbiology
*Gastrointestinal Microbiome/genetics
Male
Female
Feces/microbiology
Adult
RNA, Ribosomal, 16S/genetics
Case-Control Studies
Middle Aged
Disease Progression
Metagenomics/methods
Biopsy
Young Adult
Bacteroides/isolation & purification/genetics

@article {pmid40859682,
year = {2025},
author = {Zhao, X and Cao, Y and Hu, J and Yue, Z and Liu, X and Deng, D},
title = {Hybrid Spike-Facilitated Capture and Biofilm Destruction Co-Enhances Ultrasound-Mediated Bactericidal Therapy.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.5c09843},
pmid = {40859682},
issn = {1936-086X},
abstract = {Bacterial pneumonia, a leading global cause of infectious disease-related mortality, faces critical challenges from antibiotic resistance and microbiome disruption associated with conventional therapies. Herein, inspired by the antibacterial microstructure of gecko skin, the study developed a tannic acid-modified Mn-ZnO hybrid microparticle (denoted as MZT) with a biomimetic cocklebur-inspired spine-like architecture, achieving synergistic modulation of surface morphology and chemical composition. The material demonstrates dual antimicrobial mechanisms: (i) the microspikes significantly enhance bacterial capture efficiency by leveraging polyphenol-mediated bacterial membrane interactions, enabling synergistic bacterial trapping and physical penetration for targeted antimicrobial action; (ii) a piezoelectricity-driven, acid-responsive reactive oxygen species catalytic system achieves pathogen-selective eradication under ultrasound activation without harming healthy tissues. Theoretical analyses revealed that surface piezoelectric fields enhance catalytic kinetics through charge redistribution. In vivo studies demonstrated precise pulmonary delivery via a nebulized system in Klebsiella pneumoniae-infected mice, exhibiting superior therapeutic efficacy. Cell viability assays and histopathological evaluations confirmed excellent biosafety at both cellular and organismal levels. This work establishes a bioinspired material design paradigm for targeted antimicrobial strategies with minimized resistance risks and microbiome preservation.},
}

@article {pmid40859431,
year = {2025},
author = {Thwaites, PA and Yao, CK and Maggo, J and Parker, FC and Halmos, EP and Burgell, RE and Muir, JG and So, D and Kalantar-Zadeh, K and Gearry, RB and Gibson, PR},
title = {Telemetric Assessment and Comparison of Regional Colonic Metabolic Activity in Ambulant Healthy Individuals Using pH and Gas-Sensing Wireless Motility Capsules.},
journal = {Alimentary pharmacology & therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1111/apt.70345},
pmid = {40859431},
issn = {1365-2036},
support = {//Crohn's and Colitis Australia/ ; //University of Otago/ ; //Atmo Biosciences/ ; GNT1190265//National Health and Medical Research Council/ ; },
abstract = {BACKGROUND: Ingestible wireless motility capsules enable locoregional quantification of luminal pH and concentrations of hydrogen and carbon dioxide in the human colon.

AIM: To evaluate these measures in the colon of healthy adults.

METHODS: Gas-sensing and pH-sensing wireless motility capsules were ingested tandemly and repeatedly over time. Measurements were analysed and compared in proximal and distal segments of the colon.

RESULTS: In paired datasets from 37 participants, colonic pH rose from a median 6.3 (IQR 5.8-6.9) proximally to 7.0 (6.6-7.2) distally (p < 0.001). Concentrations of carbon dioxide rose in nearly all participants from 12.7 (9.1-18.6) proximally to 18.8 (11.9-28.1) %.h/h distally (p < 0.001) with a positive correlation between proximal and distal colon (r = 0.76; p < 0.001). Hydrogen concentrations showed widely varied proximal-to-distal gradients with an increase in 69% of participants, but no correlation between proximal and distal colon measures. No significant correlations between colonic pH, hydrogen concentrations, and carbon dioxide concentrations were observed. Comparison of hydrogen and carbon dioxide concentrations between tandem gas-sensing capsules by Bland-Altman analysis (n = 24) showed minimal (< 1.2%) bias for both measures, and gas metrics on repeat ingestion were similar (n = 20). However, there was greater variance in the distal colon.

CONCLUSIONS: Both wireless motility capsules evaluate different yet complementary aspects of colonic fermentation. Carbon dioxide concentrations that most likely reflect overall microbial metabolic activity were consistently greater distally, while proximal-to-distal gradients in hydrogen concentrations varied, likely due to inter-subject variations in dietary carbohydrate and/or methanogenesis. Luminal pH poorly reflects carbohydrate fermentation in the distal colon.

TRIAL REGISTRATION: ACTRN12619001219178 and ACTRN12622000422729.},
}

@article {pmid40859402,
year = {2025},
author = {Diab, H and Langén, V and Yeo, LF and Salomaa, V and Havulinna, A and Lahti, L and Pärnänen, K and Knight, R and Jalkanen, S and Salmi, M and Niiranen, T and Palmu, J},
title = {Associations between gut microbiome and circulating cytokines: a cross-sectional analysis in the FINRISK 2002 population cohort.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {66},
doi = {10.1186/s13099-025-00742-z},
pmid = {40859402},
issn = {1757-4749},
support = {postdoctoral grant [348439]//Research Council of Finland/ ; },
abstract = {BACKGROUND: A growing body of evidence suggests a relationship between gut microbiome and circulating cytokines, yet there is still a lack of large-scale population-based studies investigating gut microbiome-cytokine associations. In this cross-sectional study, we aimed at investigating the associations of gut microbiome (exposure variable) with 45 cytokines and C-reactive protein (CRP) (outcome variables) in the population-based FINRISK 2002 cohort (N = 2,398). Our analyses focused mainly on gut microbiome alpha diversity, beta diversity, differentially abundant taxa, and predicted functions. All statistical models were adjusted for age, sex, BMI, diabetes, and smoking.

RESULTS: Using linear modeling, we identified an inverse association of the gut microbial alpha diversity (Shannon index) with CRP (β=-0.062 ± 0.019/standard deviation (SD), False Discovery Rate adjusted p-value (FDR-P) = 0.025), interleukin-8 (IL-8) (β=-0.066 ± 0.021/SD, FDR-P = 0.025), and interferon-γ-inducible protein 10 (IP-10) (β=-0.063 ± 0.02/SD, FDR-P = 0.025). For beta diversity, linear modeling revealed that the first axis of Principal Component Analysis (PCA) describing the most strongly varying parts of the microbial community composition across population was inversely associated with CRP (β=-0.071 ± 0.019/SD, FDR-P = 0.008) and the second axis was inversely associated with macrophage inflammatory protein-1β (MIP-1B) (β=-0.082 ± 0.021/SD, FDR-P = 0.008), and monokine induced by interferon-γ (MIG) (β=-0.071 ± 0.019/SD, FDR-P = 0.008). The majority of the top taxa contributing to the first and second PCA axes belonged to class Bacilli (7/10) and class Gammaproteobacteria (9/10), respectively. In addition to this, we detected 8 significant associations of specific gut microbiome taxa (species-level) with cytokines and CRP using linear models. The majority of significant taxa belonged to class Clostridia_258483 (5/8) and class Bacteroidia (2/8). We did not detect any significant associations between species-specific predicted MetaCyc pathways (using all prevalent pathways) and cytokines or CRP. When analysis was limited to pathways associated with significant species only, we observed a positive association between purine synthesis predicted pathways in B. thetaiotaomicron and CRP.

CONCLUSIONS: Taken together, these results show that CRP, MIP-1B, IL-8, and other cytokines are associated with gut microbial diversity and composition, as well as specific taxa. This could lay the groundwork for future experimental studies to assess the causality of these associations.},
}

@article {pmid40859385,
year = {2025},
author = {Zhang, Y and Allegre, L and Salipante, F and Morsli, M and Thubert, T and Lavigne, JP and Dunyach-Remy, C and de Tayrac, R},
title = {Impact of surgical field disinfection on vaginal microbiome in transvaginal urogynecological surgery: a prospective cohort study.},
journal = {Antimicrobial resistance and infection control},
volume = {14},
number = {1},
pages = {102},
pmid = {40859385},
issn = {2047-2994},
mesh = {Humans ; Female ; *Vagina/microbiology/surgery ; *Microbiota/drug effects ; Prospective Studies ; Aged ; *Disinfection/methods ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Lactobacillus/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: The study aimed to assess the effects of vaginal disinfection and sterile draping on the composition and dynamics of the vaginal microbiota during vaginal surgery.

METHODS: A prospective cohort study was conducted involving post-menopausal patients undergoing vaginal urogynecological surgery. The vaginal microbiota was assessed by partial 16 S rRNA gene sequencing at three time points: before disinfection (V1); immediately after disinfection and sterile draping (V2); and one-hour post-disinfection (V3).

FINDINGS: In a cohort of 54 postmenopausal women (median age: 69.2 ± 7.6 years), with a mean operative time of 92.89 ± 45.92 min, native tissue prolapse repair was the most common urogynecological vaginal procedure performed (n = 47, 87%). The vaginal microbiota diversity was significantly increased after disinfection associated with reduced abundance of Lactobacillus and Bifidobacterium and increased Pseudomonas (p < 0.0001). Community state type (CST) I prevalence decreased notably from 20% at V1 to 6% at V3, primarily due to the disappearance of CST I-A, while CST IV prevalence rose from 31 to 44%, which was mainly secondary to an increase in CST IV-C (from 20 to 33%).

CONCLUSIONS: These findings highlight the impact of povidone-iodine on vaginal microbiota composition during vaginal urogynecological surgery. Disinfection significantly increased vaginal bacterial diversity and reducing Lactobacillus abundance. This observation requires further exploration in the context of development of optimized disinfection protocols aimed at preserving vaginal health during and after surgery.},
}

Humans
Female
*Vagina/microbiology/surgery
*Microbiota/drug effects
Prospective Studies
Aged
*Disinfection/methods
Middle Aged
RNA, Ribosomal, 16S/genetics
Lactobacillus/isolation & purification
Bacteria/classification/genetics/isolation & purification

@article {pmid40859368,
year = {2025},
author = {He, S and Lu, S and Yang, T and Ma, H and He, Y and Mi, J and Yue, K and Huang, Y and Song, L and Xiao, Y and Ren, Z},
title = {Bacteroides dorei RX2020-derived bile acid alleviates influenza virus infection through TGR5 signaling.},
journal = {Cell communication and signaling : CCS},
volume = {23},
number = {1},
pages = {382},
doi = {10.1186/s12964-025-02384-9},
pmid = {40859368},
issn = {1478-811X},
support = {2023YFC0871200//National Key Research and Development Program of China/ ; 33054//the National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/ ; },
mesh = {Animals ; *Bile Acids and Salts/metabolism/pharmacology ; *Receptors, G-Protein-Coupled/metabolism/genetics ; Mice ; *Orthomyxoviridae Infections/metabolism ; *Bacteroides/metabolism ; *Signal Transduction ; Humans ; Mice, Knockout ; Mice, Inbred C57BL ; Gastrointestinal Microbiome ; Male ; },
abstract = {BACKGROUND: The role of the gut microbiome in respiratory infections is increasingly recognized. We have found that a gut commensal strain, Bacteroides dorei RX2020 (B. dorei) previously isolated from healthy human fecal microbiota, alleviates influenza virus infection, but the underlying mechanisms remain elusive.

METHODS: To explore the mechanism by which B. dorei alleviates influenza, we administered it via gavage to influenza virus-infected mice. Gene knockout mice were then used to verify the underlying signaling pathways involved in the antiviral action of B. dorei. Metabolomics analysis was conducted to identify effective metabolites of B. dorei against influenza, followed by complementary verification to confirm these metabolites.

RESULTS: Metabolomics reveals that influenza virus infection significantly reduced the concentrations of secondary bile acid (BA) in feces at 7 post-infection (dpi). Oral administration of B. dorei increased bile salt hydrolase (BSH) activity and restored the BA metabolism, thereby protecting wild-type but not TGR5-deficient mice from influenza virus infection. B.dorei-mediated TGR5 activation inhibited influenza virus-induced lung inflammation via cAMP-PKA pathway. Supplementing exogenous Ursodeoxycholic acid (UDCA) and Hyodeoxycholic acid (HDCA), two metabolites changed dramatically after B. dorei treatment, reproduced the protective effect of B. dorei.

CONCLUSIONS: Overall, our work elucidates the protective efficacy of commensal microbes against influenza virus infection by modulating lung immunity and restoring BA metabolism, suggesting a potential strategy to intervene in distal infections by regulating gut microbial metabolism.},
}

Animals
*Bile Acids and Salts/metabolism/pharmacology
*Receptors, G-Protein-Coupled/metabolism/genetics
Mice
*Orthomyxoviridae Infections/metabolism
*Bacteroides/metabolism
*Signal Transduction
Humans
Mice, Knockout
Mice, Inbred C57BL
Gastrointestinal Microbiome
Male

@article {pmid40859350,
year = {2025},
author = {Klaes, S and White, C and Alvarez-Cohen, L and Adrian, L and Ding, C},
title = {De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {111},
pmid = {40859350},
issn = {2524-6372},
abstract = {BACKGROUND: Protein-based stable isotope probing (Protein-SIP) is a powerful approach that can directly link individual taxa to activity and substrate assimilation, elucidating metabolic pathways and trophic relationships within microbial communities. In Protein-SIP, peptides and corresponding taxa are identified by database matching, making database quality crucial for accurate analyses. For samples with unknown community composition, Protein-SIP typically employs either unrestricted reference databases or metagenome-derived databases. While (meta)genome-derived databases represent the gold standard, they may be incomplete and are typically resource-intensive to generate. In contrast, unrestricted reference databases can inflate the search space and require complex post-processing.

RESULTS: Here, we explore the feasibility of using de novo peptide sequencing to construct peptide databases directly from mass spectrometry raw data. We then use the mass spectrometric data from labeled cultures to quantify isotope incorporation into specific peptides. We benchmark our approach against the canonical approach in which a sample-matching (meta)genome-derived protein sequence database is used on three different datasets: (1) a proteome analysis from a defined microbial community containing [13]C-labeled Escherichia coli cells, (2) time-course data of an anammox-dominated continuous reactor after feeding with [13]C-labeled bicarbonate, and (3) a model of the human distal gut simulating a high-protein and high-fiber diet cultivated in either [2]H2O or H2[18]O. Our results show that de novo peptide databases are applicable to different isotopes, detecting similar amounts of labeled peptides compared to sample-matching (meta)genome-derived databases, and also identify labeled peptides missed by this canonical approach. Furthermore, we show that peptide-centric Protein-SIP allows up to species-level resolution and enables the assessment of activity related to individual biological processes. Finally, we provide access to our modular Python pipeline to assist the construction of de novo peptide databases and subsequent peptide-centric Protein-SIP data analysis (https://git.ufz.de/meb/denovo-sip).

CONCLUSIONS: De novo peptide databases enable Protein-SIP of microbial communities without prior knowledge of the composition and can be used complementarily to (meta)genome-derived databases or as a standalone alternative in exploratory or resource-limited settings.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40793-025-00767-6.},
}

@article {pmid40859345,
year = {2025},
author = {Wu, J and Wang, T and Yu, B},
title = {Changes in intestinal bacterial characteristics during hospitalization in the NICU in very low birth weight infants.},
journal = {Italian journal of pediatrics},
volume = {51},
number = {1},
pages = {263},
pmid = {40859345},
issn = {1824-7288},
support = {No. 2022-B17//Ningbo key discipline Pediatrics/ ; No.2022020405//Ningbo Top Medical and Health Research Program/ ; PPXK2024-06//Ningbo Medical and Health Brand Discipline/ ; },
mesh = {Humans ; *Infant, Very Low Birth Weight ; *Gastrointestinal Microbiome ; Infant, Newborn ; Prospective Studies ; Female ; Male ; *Intensive Care Units, Neonatal ; Infant, Premature ; Feces/microbiology ; Hospitalization ; Infant ; },
abstract = {BACKGROUND: The gut microbiota plays a crucial role in neonatal defense against pathogens, immune training, nutrient absorption, and postnatal disease development.

METHODS: We prospectively collected fecal samples from 58 very low birth weight infants and 34 preterm infants with birth weights > 1500 g during their first two postnatal months. Using 16SrRNA sequencing, we characterize the compositional dynamics of gut microbiota in very low birth weight infants during early postnatal development, and evaluate potential associations with clinical factors.

RESULTS: In the very low birth weight infants group (experimental group), a total of 45 bacterial phyla and 1,327 genera were identified. The top two dominant phyla were Proteobacteria (65.64%) and Firmicutes (29.64%), accounting for 95.28% collectively. Among the dominant phyla, the experimental group showed significantly higher levels of Bacteroidetes (P < 0.001) and Firmicutes (P = 0.018) compared to the control group, whereas Acidobacteria (P < 0.001), Proteobacteria (P < 0.001), Fusobacteria (P = 0.001), Chloroflexi (P = 0.018), and Patescibacteria (P = 0.006) were significantly lower. The top 10 dominant genera represented 91.9% of the total. At the genus level, the experimental group had significantly higher abundances of Klebsiella (P = 0.016), Streptococcus (P < 0.001), Corynebacterium_1 (P < 0.001), Clostridium_sensu_stricto_1 (P = 0.018), Clostridioides (P = 0.013), Staphylococcus (P < 0.001), and Lactobacillus (P = 0.001), while Escherichia_Shigella, Sphingomonas (P = 0.013), Veillonella (P = 0.037), Methylobacterium (P = 0.021), and Enterobacter (P = 0.029) were significantly lower compared to controls. Additionally, during the first 28 days after birth, the control group exhibited higher relative abundance of Bifidobacterium than the experimental group. Compared to preterm infants with birth weight > 1500 g, very low birth weight infants demonstrated more active intestinal metabolism. Within the very low birth weight infants, probiotic use, delivery mode, and premature rupture of membranes significantly influenced the relative abundances of Streptococcus, Clostridium_sensu_stricto_1, and Pseudomonas, respectively.

CONCLUSIONS: Very low birth weight infants exhibit distinct gut microbiota characteristics during their first two months of life. Factors including probiotic using, delivery mode, and premature rupture of membranes significantly influence specific bacterial populations. The gut microbiome represents a crucial influencing the health outcomes of very low birth weight infants.},
}

Humans
*Infant, Very Low Birth Weight
*Gastrointestinal Microbiome
Infant, Newborn
Prospective Studies
Female
Male
*Intensive Care Units, Neonatal
Infant, Premature
Feces/microbiology
Hospitalization
Infant

@article {pmid40859280,
year = {2025},
author = {Liu, M and Kochian, LV and Helgason, BL},
title = {The native soil microbiome is critical for early root-associated microbiota assembly and canola growth.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {112},
pmid = {40859280},
issn = {2524-6372},
support = {CARP.2019.24//Canola Agronomic Research Program/ ; RGPIN-2019-04158//Natural Sciences and Engineering Research Council of Canada/ ; },
}

@article {pmid40859157,
year = {2025},
author = {Gao, ZQ and Su, JW and Qin, Y and Ye, T and Cao, H and Yang, LH and Elsheikha, HM},
title = {Metagenomic analysis of vitamins B and K2 biosynthesis in chicken gut microbiota across laying periods.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {553},
pmid = {40859157},
issn = {1471-2180},
}

@article {pmid40858628,
year = {2025},
author = {Joshi, AA and Szafrański, SP and Steglich, M and Yang, I and Qu, T and Schaefer-Dreyer, P and Xiao, X and Behrens, W and Grischke, J and Häussler, S and Stiesch, M},
title = {Integrative microbiome- and metatranscriptome-based analyses reveal diagnostic biomarkers for peri-implantitis.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {175},
pmid = {40858628},
issn = {2055-5008},
support = {SFB/TRR-298-SIIRI - Project-ID 426335750//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Germany's Excellence Strategy - EXC 2155 - project number 390874280//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB/TRR-298-SIIRI - Project-ID 426335750//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB/TRR-298-SIIRI - Project-ID 426335750//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB/TRR-298-SIIRI - Project-ID 426335750//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Germany's Excellence Strategy - EXC 2155 - project number 390874280//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Peri-implantitis is a severe biofilm-associated infection affecting millions worldwide. This cross-sectional study aimed to identify taxonomic and functional biomarkers that reliably indicate peri-implantitis by utilizing paired data from full length 16S rRNA gene amplicon sequencing (full-16S) and metatranscriptomics (RNAseq) in 48 biofilm samples from 32 patients. Both full-16S and RNAseq analyses revealed significant differences between healthy and peri-implantitis samples, with a shift toward anaerobic Gram-negative bacteria in peri-implantitis. Metatranscriptomics identified enzymatic activities and metabolic pathways associated with peri-implantitis and uncovered complex peri-implant biofilm ecology related to amino acid metabolism. Integrating taxonomic and functional data enhanced predictive accuracy (AUC = 0.85) and revealed diagnostic biomarkers including health-associated Streptococcus and Rothia species and peri-implantitis-associated enzymes (urocanate hydratase, tripeptide aminopeptidase, NADH:ubiquinone reductase, phosphoenolpyruvate carboxykinase and polyribonucleotide nucleotidyltransferase). Thus, biofilm profiling at taxonomic and functional levels provides highly predictive disease biomarkers, laying the foundation for novel diagnostic and personalized treatment approaches for peri-implant disease.},
}

@article {pmid40858623,
year = {2025},
author = {Marsaux, B and d'Hoker, W and Moens, F and Van Elst, D and Minnebo, Y and Marzorati, M and Van de Wiele, T},
title = {Candida albicans colonization in the human colon correlates with a reduction in acetate- and butyrate-producing bacteria, as simulated using the M-SHIME® model.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {176},
doi = {10.1038/s41522-025-00803-w},
pmid = {40858623},
issn = {2055-5008},
support = {812969//European Union's Horizon 2020/ ; },
abstract = {Candida albicans is a common gut commensal, typically restricted by the resident microbiota. However, microbiome disruption can enable its outgrowth, increasing the risk of life-threatening candidiasis. Restoring key protective microbes offer a therapeutic strategy, though their identification remains challenging. Using the M-SHIME® model simulating the human proximal colon, we investigated C. albicans-bacteriome interactions under eubiotic and dysbiotic conditions. We assessed how clindamycin, ciprofloxacin, and metronidazole modulate C. albicans colonization and evaluated associated microbial and metabolic shifts. The effects were antibiotic- and donor-specific: clindamycin facilitated colonization, ciprofloxacin had no impact, and metronidazole showed variable outcomes. Engraftment did not correlate with total bacterial concentration or α-diversity, but with the loss of specific taxa, notably Lachnospiraceae and Bifidobacterium. These correlations were supported functionally by reductions in acetate and butyrate, suggesting a metabolic mechanism of fungal suppression. This study highlights the role of dysbiosis in C. albicans outgrowth and supports targeted microbiome restoration strategies.},
}

@article {pmid40858622,
year = {2025},
author = {Valentino, V and Magliulo, R and Balivo, A and Krysmann, AM and Calvanese, CM and Esposito, A and Sequino, G and Genovese, A and Porcellato, D and Ercolini, D and De Filippis, F},
title = {Microbiome profiling of Grana Padano and Parmigiano Reggiano cheeses reveals cheese-specific biomarkers, psychobiotic potential, and bioprotective activities.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {177},
pmid = {40858622},
issn = {2055-5008},
support = {IR0000033//NextGenerationEU/ ; CN_00000033//NextGenerationEU/ ; P2022X8A9M//Ministero dell'Università e della Ricerca/ ; },
abstract = {Grana Padano (GP), Trentingrana (TG), and Parmigiano Reggiano (PR) are among the finest Italian Protected Designation of Origin (PDO) cheeses. GP, TG, and PR undergo extensive proteolysis during ripening, where the microbiome metabolizes amino acids, producing flavour and bioactive molecules. We explored the microbiome, volatilome, and metaproteome of PDO GP (n = 42), TG (n = 18), and PR (n = 60). Findings revealed diverse microbial communities enriched in proteolytic microbes, associated with cheese-specific processing technology. Correlations between lactic acid bacteria strains and specific volatile compounds were identified in PR. Importantly, we identified genes involved in the production of neuroactive molecules, suggesting potential connections between cheeses consumption and mental health, along with genes related to bacteriocin biosynthesis, possibly enhancing cheese safety, shelf life, and process sustainability. This study provides novel insights into the functional attributes of long-ripened cheeses microbiome, highlighting their potential as sources of psychobiotics and bioprotective strains.},
}

@article {pmid40858544,
year = {2025},
author = {Zou, X and Cao, H and Hong, L and Suo, L and Wang, C and Chang, K and Ni, Y and Liu, B and Cao, B},
title = {Enrichment of Streptococcus oralis in respiratory microbiome enhance innate immunity and protects against influenza infection.},
journal = {Signal transduction and targeted therapy},
volume = {10},
number = {1},
pages = {272},
pmid = {40858544},
issn = {2059-3635},
abstract = {Respiratory microbial dysbiosis has been implicated in the occurrence and progression of community-acquired pneumonia (CAP). However, the dynamic variation in the respiratory microbiota and its interaction with the host response remain poorly understood. Here, we performed metagenomic analysis of respiratory and gut microbiota, along with blood transcriptomics, using longitudinally collected samples from 38 CAP patients. CAP patients presented disrupted sputum microbiota at the early, middle, and late stages of hospitalization. Microbial pathways involved in peptidoglycan biosynthesis and immune evasion, particularly contributed by the Streptococcus genus, were enriched in CAP patients. Additionally, several Streptococcus strains demonstrated correlation between respiratory and gut microbiota in CAP patients. By incorporating host response data, we revealed that Streptococcus oralis (SOR) was associated with host pathways involved in the innate immune response to infection, and this microbe‒host interaction was reproduced in a newly enrolled CAP cohort consisting of 22 patients with influenza infection. The host-SOR interaction was validated in a mouse model, where SOR demonstrated protective efficacy against influenza virus infection comparable to that of the well-established respiratory probiotic Lactobacillus rhamnosus GG. Preaspiration of SOR in mice significantly mitigated body weight loss, reduced lung inflammation, and lowered viral loads following influenza virus challenge. Host response profiling indicated that SOR priming activated a greater innate immune response at the early stage of infection and that this response resolved timely as the host began to recover. These findings suggest that respiratory commensals play an immune-protective role by inducing a timely innate immune response to prevent CAP progression.},
}

@article {pmid40858525,
year = {2025},
author = {Espinoza-Arrue, J and Arce, M and Endo, N and Hoare, A and Dutzan, N and Abusleme, L},
title = {Profiling the Bacterial Microbiome Across Peri-Implant Conditions.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.70024},
pmid = {40858525},
issn = {1600-051X},
support = {1231728//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; 1231350//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; 1251739//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; 2024-21240601//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; 2022-21221003//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; DE031213-01/DE/NIDCR NIH HHS/United States ; /NH/NIH HHS/United States ; },
abstract = {AIM: To comprehensively characterise the bacterial microbiome in peri-implant health, peri-implant mucositis and peri-implantitis.

MATERIALS AND METHODS: A re-analysis of raw microbiome data was performed from 15 studies, which were finally selected based on the availability of 16S rRNA sequencing. Reads were pre-processed using mothur and classified using the HOMD database. A total of 522 samples were analysed to evaluate diversity estimates and bacterial relative abundance, identifying discriminant features via LEfSe, while predictions of functional potential were obtained using PICRUSt2. Bacterial co-occurrence networks were constructed, and dysbiosis was measured by employing the subgingival microbiome dysbiosis index.

RESULTS: Peri-implantitis showed higher bacterial diversity compared to health and greater microbial richness than peri-mucositis. Each clinical condition displayed a distinct community structure and bacterial co-occurrence networks. The representative species in peri-implant health were Rothia aeria, R. dentocariosa and Veillonella parvula_dispar. Peri-mucositis is characterised by Leptotrichia hongkongensis, L. wadei and Fusobacterium nucleatum subsp. polymorphum, while peri-implantitis is defined by Porphyromonas gingivalis, F. nucleatum subsp. vincentii and Tannerella forsythia. Peri-implantitis exhibited enrichment in predicted microbial pathogenesis pathways and greater bacterial dysbiosis.

CONCLUSIONS: These results provide deeper insights into the peri-implant microbiome, identifying key bacterial species, functional processes and interactions that may be crucial to inflammation and destruction during peri-implant diseases.},
}

@article {pmid40858176,
year = {2025},
author = {Thorat, P and Dass, RS},
title = {An overview of production, characterization, and bioactive potentials of Aspergillus exopolysaccharides.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {147102},
doi = {10.1016/j.ijbiomac.2025.147102},
pmid = {40858176},
issn = {1879-0003},
abstract = {Exopolysaccharides (EPS) produced by Aspergillus have attracted considerable scientific interest due to their complex structural, chemical, biological, and functional properties. This article summarizes the literature published between 2011 and 2024, during which scientists extensively explored the production, structural characterization, and biological activities of Aspergillus-derived EPS (Asp-EPS). Various factors influence Asp-EPS biosynthesis, including nutrient composition, pH, temperature, and aeration conditions. Advanced analytical techniques, such as gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and fourier-transform infrared spectroscopy (FTIR), have been used to analyze their monosaccharide composition, functional groups, glycosidic linkages, and degree of branching. Asp-EPS demonstrate a wide range of bio-functional activities, including antimicrobial, antioxidant, anti-tumor, anticoagulant, immunomodulatory, gut microbiome-modulating effect, emulsifying, and flocculating properties. However, only a limited number of Aspergillus spp. have been extensively studied for their EPS-producing capabilities. Further research into the genetic, metabolic, and rheological properties, with deeper investigation into the mechanisms underlying their biological activities, could support the development of tailored applications in diverse areas, including functional foods, pharmaceuticals, biomaterials, and environmental biotechnology.},
}

@article {pmid40858074,
year = {2025},
author = {Ruiz-Castilla, FJ and Barbudo-Lunar, M and Gutiérrez, MC and Michán, C and Martín, MÁ and Alhama, J},
title = {Storage of Alperujo influences composting performance: Insights into gaseous emissions and functional metagenomics.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127015},
doi = {10.1016/j.jenvman.2025.127015},
pmid = {40858074},
issn = {1095-8630},
abstract = {Alperujo (AL), the primary by-product of olive oil extraction, poses a significant environmental challenge in the Mediterranean region. Understanding the AL composting process is essential for controlled aerobic revalorisation to obtain a stable and good quality organic amendment with the minimum environmental impact. Our approach assumes that full-scale pond storage duration modifies the degree of hydrolytic fermentation of AL, affecting the subsequent stages of the composting process. In this work, AL raw materials for composting were stored for 3 or 6 months. Subsequently, during pilot-scale composting, the loss of organic matter (OM) not only induced key changes in the solid mass but also in gaseous emissions, which decreased along with the storage time. Consequently, the initial C/N ratio decreased from 25.76 to 22.24, and composting yields relative to the AL initially mixed with a bulking agent (3/1, wt./wt.) were 76.4 % and 41.7 %, respectively. Phenolic compounds were effectively degraded throughout the composting process under both initial conditions, enhancing the potential value of the final products. Metagenomic analysis revealed differences in the raw material bacteriome, variations that also became evident throughout composting. The thermophilic stage fostered the selection of a range of thermotolerant microorganisms, many of them with lignocellulosic activity, which is essential for the decomposition of OM. Then, at the final mesophilic phase, a significant increase in bacterial diversity and metabolic activity was observed. This study contributes to better understand the functional role of the microbiome in AL composting, particularly regarding the bacterial community dynamics and gaseous emissions to the atmosphere.},
}

@article {pmid40857842,
year = {2025},
author = {Zhou, X and Wang, H and Liu, M and Yan, F and Du, X and Yang, S and Zhao, A},
title = {Microbiome and metabolome changes in laying hens induced by dietary epsilon-polylysine.},
journal = {Poultry science},
volume = {104},
number = {11},
pages = {105708},
doi = {10.1016/j.psj.2025.105708},
pmid = {40857842},
issn = {1525-3171},
abstract = {Epsilon-polylysine (ε-PL) is a natural antimicrobial peptide that has been broadly applied in the food industry as a preservative. The effects of ε-PL on the intestinal microbiota, animal metabolism, and its potential as a "new feed additive" require further exploration. In this study, ninety Hy-Line Brown laying hens were randomly divided into three groups. Egg-laying performance, egg quality, and liver parameters were measured; expression of gut barrier, immunity, and ferroptosis related genes in each intestinal segment were detected; microbiome and metabolomic analyses were performed. The results demonstrated that dietary ε-PL supplementation significantly increased average egg weight and egg quality (P < 0.05). It also markedly, ε-PL supplementation significantly increased the villus height to crypt depth ratio in the duodenum and ileum (P < 0.01), significantly reduced the mRNA levels of interleukin-1 beta (IL-1β) and interleukin-6 (IL-6), and elevated the mRNA levels of interleukin-10 (IL-10) and tumor necrosis factor-alpha (TNF-α) in the intestine (P < 0.05). Moreover, ε-PL inhibited intestinal mucosal ferroptosis (P < 0.05) and mitigated severe fatty liver development, as evidenced by a significantly reduction in hepatic malondialdehyde (MDA) content (P < 0.01). Microbiota analysis revealed that ε-PL supplementation significantly increased the abundance of Lactobacillus and Saccharimonadales; while decreasing the abundance of Anaerotruncus and Slackia in the cecal microbiota. Additionally, ε-PL supplementation enhanced the amino acid metabolism, lipid metabolism, the digestive system, arginine biosynthesis, tryptophan metabolism, bile secretion, and steroid hormone biosynthesis in the intestine, which might contribute to improved egg quality and intestinal absorptive capacity, as well as the inhibition of fatty liver formation. In summary, dietary ε-PL supplementation exerts multiple beneficial effects in laying hens, including enhancing egg quality, alleviate inflammation, boosting antioxidant capacity, improving intestinal morphology, modulating gut microbiota, and protecting liver health.},
}

@article {pmid40857503,
year = {2025},
author = {Yue, Y and Mao, Y and Read, TD and Fedirko, V and Satten, GA and Chen, X and Zhan, X and Hu, YJ},
title = {Integrative analysis of microbial 16S gene and shotgun metagenomic sequencing data improves statistical efficiency in testing differential abundance.},
journal = {Journal of the American Statistical Association},
volume = {},
number = {},
pages = {},
doi = {10.1080/01621459.2025.2516205},
pmid = {40857503},
issn = {0162-1459},
abstract = {The most widely used technologies for profiling microbial communities are 16S marker-gene sequencing and shotgun metagenomic sequencing. Surprisingly, many microbiome studies have performed both experiments on the same cohort of samples. The two sequencing datasets often reveal consistent patterns of microbial signatures, suggesting that an integrative analysis of both datasets could enhance the testing power for these signatures. However, differential experimental biases, partially overlapping samples, and uneven library sizes pose tremendous challenges when combining the two datasets. In this article, we introduce the first method of this kind, named Com-2seq, that combines the two datasets for testing differential abundance at the genus level as well as the community level while overcoming these difficulties. Our simulation studies demonstrate that Com-2seq substantially enhances statistical efficiency over analysis of a single dataset and outperforms two ad hoc approaches to integrative analysis. In analysis of real microbiome data, Com-2seq uncovered scientifically plausible findings, namely, the association of Butyrivibrio, Gemella and Ignavigranum with prediabetes status, which would have been missed by analyzing a single dataset. Butyrivibrio failed to reach the significance level in the analysis of each dataset despite showing a consistent trend; Gemella and Ignavigranum failed to produce adequate data in the 16S experiment.},
}

@article {pmid40857390,
year = {2025},
author = {Xia, JY and Komanduri, S and Keswani, RN and Rodrigues, TR and Sinha, J and Rengarajan, A and Tran, P and Hepler, C and Prindle, A and Aadam, AA},
title = {Integrating multi-omics in bile for biomarker discovery in cholangiocarcinoma.},
journal = {Hepatology communications},
volume = {9},
number = {9},
pages = {},
doi = {10.1097/HC9.0000000000000786},
pmid = {40857390},
issn = {2471-254X},
mesh = {Humans ; *Cholangiocarcinoma/diagnosis/metabolism/microbiology ; *Bile Duct Neoplasms/diagnosis/metabolism/microbiology ; *Bile/chemistry/microbiology/metabolism ; Metabolomics/methods ; Male ; Female ; Cholangiopancreatography, Endoscopic Retrograde ; *Biomarkers, Tumor/analysis ; Middle Aged ; Cholangitis, Sclerosing/complications ; Aged ; Sensitivity and Specificity ; Bile Acids and Salts/analysis ; Multiomics ; },
abstract = {BACKGROUND: Cholangiocarcinoma (CCA) is an aggressive cancer with a poor prognosis. Histopathology evaluation of brushings and biopsies obtained during endoscopic retrograde cholangiopancreatography (ERCP) currently remains the main method of diagnosis, which has limited sensitivity for malignancy detection. Our study aimed to identify human bile-derived biomarkers to improve CCA diagnosis. Bile samples were collected from patients during ERCP for primary sclerosing cholangitis, CCA, or benign biliary disease.

METHODS: Bile samples were collected from patients undergoing ERCP for biliary obstruction due to primary sclerosing cholangitis, newly identified malignant strictures concerning for CCA, or benign biliary disease. Using 16S sequencing, metabolomics, and bile acid quantification, we aimed to identify distinctive microbial and metabolite signatures associated with CCA.

RESULTS: Multi-omics analyses revealed distinct microbial and metabolite signatures associated with CCA. From these findings, we identified and validated microbial and metabolite markers capable of accurately detecting CCA with improved sensitivity and specificity for malignancy detection compared to current cytology-based methods.

CONCLUSIONS: These findings highlight the potential of multi-omics bile-based diagnostic panels to enhance endoscopic detection of biliary malignancies, offering a promising tool for evaluating indeterminate biliary strictures and advancing precision in ERCP diagnostics.},
}

Humans
*Cholangiocarcinoma/diagnosis/metabolism/microbiology
*Bile Duct Neoplasms/diagnosis/metabolism/microbiology
*Bile/chemistry/microbiology/metabolism
Metabolomics/methods
Male
Female
Cholangiopancreatography, Endoscopic Retrograde
*Biomarkers, Tumor/analysis
Middle Aged
Cholangitis, Sclerosing/complications
Aged
Sensitivity and Specificity
Bile Acids and Salts/analysis
Multiomics

@article {pmid40857311,
year = {2025},
author = {Xu, W and Jalomo-Khayrova, E and Gumerov, VM and Ross, PA and Köbel, TS and Schindler, D and Bange, G and Zhulin, IB and Sourjik, V},
title = {Specificities of chemosensory receptors in the human gut microbiota.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {35},
pages = {e2508950122},
doi = {10.1073/pnas.2508950122},
pmid = {40857311},
issn = {1091-6490},
support = {na//Max-Planck-Gesellschaft (MPG)/ ; LOEWE research cluster "Diffusible Signals"//Hessisches Ministerium für Wissenschaft und Kunst (Hessian Ministry for Science and Art)/ ; R35GM131760//HHS | National Institutes of Health (NIH)/ ; 464366151//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Ligands ; *Bacterial Proteins/metabolism/chemistry/genetics ; Chemotaxis ; Fatty Acids, Volatile/metabolism ; Uracil/metabolism ; },
abstract = {The human gut is rich in metabolites and harbors a complex microbial community, yet surprisingly little is known about the spectrum of chemical signals detected by the large variety of sensory receptors present in the gut microbiome. Here, we systematically mapped the ligand specificities of selected extracytoplasmic sensory domains from twenty members of the human gut microbiota, with a primary focus on the abundant and physiologically important class of Clostridia. Twenty-five metabolites from different chemical classes-including amino acids, nucleobase derivatives, amines, indole, and carboxylates-were identified as specific ligands for fifteen sensory domains from nine bacterial species, which represent all three major functional classes of transmembrane receptors: chemotaxis receptors, histidine kinases, and enzymatic sensors. We have further characterized the specificity and evolution of ligand binding to Cache superfamily sensors specific for lactate, dicarboxylic acids, and for uracil and short-chain fatty acids (SCFAs). Structural and biochemical analysis of the dCache sensor of uracil and SCFAs revealed that its two different ligand types bind at distinct sensory modules. Overall, combining experimental identification with computational analyses, we were able to assign ligands to approximately half of the Cache-type chemotaxis receptors found in the eleven gut commensal genomes from our set, with carboxylic acids representing the largest ligand class. Among these, the most commonly found ligand specificities were for lactate and formate, indicating a particular importance of these metabolites in the human gut microbiota and consistent with their observed growth-promoting effects on selected bacterial commensals.},
}

Humans
*Gastrointestinal Microbiome/physiology
Ligands
*Bacterial Proteins/metabolism/chemistry/genetics
Chemotaxis
Fatty Acids, Volatile/metabolism
Uracil/metabolism

@article {pmid40856929,
year = {2025},
author = {Yan, C and Chen, Y and Tian, Y and Hu, S and Wang, H and Zhang, X and Chu, Q and Huang, S and Sun, W},
title = {The emerging role of microbiota in lung cancer: a new perspective on lung cancer development and treatment.},
journal = {Cellular oncology (Dordrecht, Netherlands)},
volume = {},
number = {},
pages = {},
pmid = {40856929},
issn = {2211-3436},
support = {Y-2023AZMETQN-0066//Beijing Xisike Clinical Oncology Research Foundation/ ; 62131009//National Natural Science Foundation of China/ ; },
abstract = {Lung cancer remains the leading cause of cancer-related mortality worldwide, with limited treatment efficacy and frequent resistance to conventional therapies. Recent advances have uncovered the critical influence of the human microbiota-complex communities of bacteria, viruses, fungi, and other microorganisms-on lung cancer pathogenesis and therapeutic responses. This review synthesizes current knowledge on the compositional and functional roles of microbiota across multiple body sites, including the gut, lung, tumor microenvironment, circulation, and oral cavity, highlighting their contributions to tumor initiation, progression, metastasis, and immune regulation. We emphasize the bidirectional communication between microbial metabolites and host immune pathways, particularly the gut-lung axis, which modulates systemic and local antitumor immunity. Importantly, microbiota composition has been linked to differential responses and toxicities in chemotherapy, radiotherapy, targeted therapy, and immune checkpoint blockade. Microbiota-targeted interventions, such as probiotics, fecal microbiota transplantation, and selective antibiotics, show promising potential to enhance treatment efficacy and mitigate adverse effects. However, challenges remain in clinical translation due to interindividual microbiome variability, mechanistic complexities, and limited longitudinal data. Future research integrating multi-omics, microbial functional profiling, and controlled clinical trials is essential to harness the microbiome as a precision medicine tool in lung cancer management. This review provides a comprehensive overview of the emerging role of microbiota in lung cancer development and therapy, offering new perspectives for innovative therapeutic strategies.},
}

@article {pmid40856922,
year = {2025},
author = {Durairaj, K and Gajendran, B and Manivel, G and Gnanam, H and Vasudevan, SA and Seenivasan, SN and Pandian, S and Shanmugarajan, S and Vily-Petit, J and Mariappan, KT and Swaminathan, K and Ramasamy, S and Gilles, M and Velmurugan, G},
title = {Exposure to chlorpyrifos pesticide at a realistic dose modulates gut microbiome and induces non-obese associated diabetes.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11356-025-36888-1},
pmid = {40856922},
issn = {1614-7499},
support = {6303-3//Indo-French Centre for the Promotion of Advanced Research/ ; },
abstract = {During the last decade, there has been a significant rise in the incidence of diabetes particularly, in Asian and African countries. Although obesity is an established risk factor for diabetes, more than 50% of diabetes patients in Asian and African countries are non-obese, which is in contrast to the Western population. The pathophysiology of non-obese diabetes remains largely unexplored, and recent studies have highlighted the possible role of endocrine-disrupting chemicals and gut microbiota in the prevalence of non-obese type 2 diabetes. Among the endocrine-disrupting chemicals, chlorpyrifos, a widely used organophosphate insecticide, has been associated with the prevalence of non-obese associated type 2 diabetes. However, experiments on animal models have shown that CPF-induces obesity and lipogenesis, contributing to insulin resistance. Notably, all these animal experiments were conducted at doses not equivalent to human exposure levels. Therefore, this study aimed to investigate the impact of chronic exposure of CPF at a realistic dose in mice. C57/Bl6 mice were treated with CPF at 0.02 mg/kg body weight daily, which is equivalent to the daily exposure of humans based on theoretical maximum daily intake. After 120 days of treatment, the chlorpyrifos-treated group showed a significant increase in fasting blood glucose levels with no changes in body weight in comparison with untreated controls. 16S rDNA sequencing and metabolomics analyses revealed the role of gut microbiota in chlorpyrifos-induced hyperglycemia in mice. CPF disrupted gut microbial balance, with depletion of beneficial taxa (Lactobacillus, Akkermansia, Blautia, Bifidobacterium and Faecalibaculum) and enrichment of pathobionts (Oscillospiraceae_uncultured, Helicobacter, Colidextrobacter, Desulfovibrioceae_uncultured and Alistipes). Overall, this is the first animal study demonstrating the impact of exposure to chlorpyrifos at a realistic dose equivalent to human exposure that correlates with the observations from the human epidemiological studies.},
}

@article {pmid40856866,
year = {2025},
author = {Mensi, M and Scotti, E and Marchetti, S and Sordillo, A and Garzetti, G and Calza, S and Buijs, MJ and Zaura, E and Brandt, BW},
title = {Clinical and microbiological effectiveness of limosilactobacillus reuteri in supportive periodontal therapy: randomized clinical trial.},
journal = {Clinical oral investigations},
volume = {29},
number = {9},
pages = {422},
pmid = {40856866},
issn = {1436-3771},
mesh = {Humans ; *Limosilactobacillus reuteri ; *Probiotics/therapeutic use ; Male ; Female ; Adult ; Treatment Outcome ; Middle Aged ; Periodontal Index ; *Periodontitis/therapy/microbiology ; Biofilms ; },
abstract = {OBJECTIVES: The purpose of the present randomized clinical trial was to evaluate the clinical and microbiological effects of Limosilactobacillus reuteri probiotic therapy as an adjunct to Guided Biofilm Therapy (GBT) during supportive periodontal therapy (SPT) of patients with a history of stage III or IV and grade B or C periodontitis and residual pockets.

MATERIALS AND METHODS: Forty-four systemically healthy patients were selected. Complete periodontal assessment was performed including Pocket Probing Depth (PPD), Bleeding on Probing (BOP), Presence of supragingival plaque (PI), Clinical Attachment Loss (CAL) and Recession (REC). Two sites per patient with PPD ≥ 6 mm or PPD of 5 mm with BOP were selected in two different quadrants as test sites. A session of full-mouth debridement was provided at baseline (T0), and patients were randomized to receive a 3-weeks treatment with lozenges containing probiotic or placebo. Periodontal parameters were taken at baseline (T0), 3 months (T2), and 6 months (T3). Microbiological samples from the test sites were taken at baseline (T0), 3 weeks (T1), 3 months (T2), and 6 months (T3).

RESULTS: Forty patients completed the study. Both groups showed a significant decrease in PPD, BOP, CAL, and number/percentage of residual pockets compared to baseline. However, no inter-group differences were noted. The test group showed a lower percentage of BOP at sites with plaque at T2 and T3. The microbiological analysis detected minimal proportion of L. reuteri in the periodontal pockets. No significant inter-group differences were detected in the red complex at any observation time. The subgingival microbial dysbiosis index (SMDI) revealed a decrease in dysbiosis from T0 to T1, followed by a slight increase in dysbiosis towards T3 for both groups. However, no significant differences were noted between the groups.

CONCLUSION: In our cohort of patients, 3 weeks of bi-daily supplementation with lozenges containing L. reuteri in conjunction with a session of SPT did not provide any additional reduction in PPD or number/percentage of residual pockets and did not have a long-lasting effect on the subgingival biofilm microbial composition. However, patients receiving the probiotic had less bleeding at sites with plaque.

CLINICAL RELEVANCE: Whilst L. reuteri cannot be recommended as a standard adjunctive therapy in SPT, it can be considered to reduce BOP levels in patients with poor plaque control.},
}

Humans
*Limosilactobacillus reuteri
*Probiotics/therapeutic use
Male
Female
Adult
Treatment Outcome
Middle Aged
Periodontal Index
*Periodontitis/therapy/microbiology
Biofilms

@article {pmid40856522,
year = {2025},
author = {Hafez-Ghoran, S and Taktaz, F and Sang, S},
title = {Whole grains are not equal: the role of fiber structure and phytochemicals in health.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo02603b},
pmid = {40856522},
issn = {2042-650X},
abstract = {Precision nutrition seeks to optimize human health by tailoring dietary interventions to individual genetic, metabolic, microbial, and lifestyle profiles. In this context, whole grains (WGs) serve as ideal candidates, as their diverse fiber structures and grain-specific phytochemicals interact dynamically with host physiology and the gut microbiome. This review examines six widely consumed WGs: wheat (Triticum aestivum L.), rye (Secale cereale L.), oats (Avena sativa L.), barley (Hordeum vulgare L.), brown rice (Oryza sativa L.), and corn (Zea mays L.), focusing on their distinct dietary fiber and bioactive compounds. WGs should not be viewed as uniform fiber sources. The quantity, structural complexity, solubility, viscosity, and fermentability of fibers vary among different WGs, contributing to the distinct health benefits of each grain. Moreover, while these grains offer general nutritional benefits, each grain contains unique secondary metabolites. Key examples include alkylresorcinols (ARs) in wheat and rye, avenanthramides (AVAs) in oats, hordatines in barley, γ-oryzanols (γ-OZs) and tricin in rice, and polyamine-conjugated hydroxycinnamates (PACH) in corn. These grain-specific phytochemicals exert diverse pharmacodynamic effects across metabolic, inflammatory, and oxidative pathways. For instance, hordatines shows effects on cardiovascular and glycemic regulation; ARs, γ-OZs, and tricin support lipid homeostasis and colorectal cancer mitigation; AVAs possess anti-inflammatory and microbiota-modulating properties; and PACH contribute to antioxidant capacity. Such functional specificity positions WGs as strategic components in individualized nutrition frameworks, holding promise for disease prevention and health optimization within the paradigm of precision nutrition.},
}

@article {pmid40856313,
year = {2025},
author = {Klier, K and Mehrjerd, A and Fässler, D and Franck, M and Weihs, A and Budde, K and Bahls, M and Frost, F and Henning, AK and Heinken, A and Völzke, H and Dörr, M and Nauck, M and Grabe, HJ and Friedrich, N and Hertel, J},
title = {Integrating population-based metabolomics with computational microbiome modelling identifies methanol as a urinary biomarker for protective diet-microbiome-host interactions.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo00761e},
pmid = {40856313},
issn = {2042-650X},
abstract = {Background: Diet-microbiome interactions are core to human health, in particular through bacterial fibre degradation pathways. However, biomarkers reflective of these interactions are not well described. Methods: Using the population-based SHIP-START-0 cohort (n = 4017), we combined metabolome-wide screenings with elastic net machine learning models on 33 food items captured using a food frequency questionnaire (FFQ) and 43 targeted urine nuclear magnetic resonance (NMR) metabolites, identifying methanol as a marker of plant-derived food items. We utilised the independent SHIP-START-0 cohort for the replication of food-metabolite associations. Moreover, constraint-based microbiome community modelling using the Human Microbiome data (n = 149) was performed to predict and analyse the contribution of the microbiome to the human methanol pools through bacterial fibre degradation. Finally, we employed prospective survival analysis in the SHIP-START-0 cohort, testing urinary methanol on its predictive value for mortality. Results: Among 21 metabolites associated with 17 dietary FFQ variables after correction for multiple testing, urinary methanol emerged as the top hit for a range of plant-derived food items. In line with this, constraint-based community modelling demonstrated that gut microbiomes can produce methanol via pectin degradation with the genera Bacteroides (68.9%) and Faecalibacterium (20.6%) being primarily responsible. Moreover, microbial methanol production capacity was a marker of high microbiome diversity. Finally, prospective survival analysis in SHIP-START-0 revealed that higher urinary methanol is associated with lower all-cause mortality in fully adjusted Cox regressions. Conclusion: Integrating population-based metabolomics and computational microbiome modelling identified urinary methanol as a promising biomarker for protective diet-microbiome interactions linked to microbial pectin degradation.},
}

@article {pmid40856198,
year = {2025},
author = {Ammar, T and Abdelhedi, F and Keskes, LA and Triki, CC},
title = {Gut Microbiota Composition and Modulation in Developmental and Epileptic Encephalopathies.},
journal = {The European journal of neuroscience},
volume = {62},
number = {4},
pages = {e70234},
doi = {10.1111/ejn.70234},
pmid = {40856198},
issn = {1460-9568},
abstract = {The gut microbiota (GM) is a rapidly evolving field of research that is increasingly explored in the context of various diseases. The complex interactions between the host and microbial communities play a crucial role in health and well-being. It is now understood that the GM communicates with nearly every human organ, including the central nervous system (CNS), through the microbiome-gut-brain (MGB) axis. Furthermore, accumulating evidence suggests that pathological shifts in the GM may lead to various neurological disorders, including epilepsy. While the link between epilepsy and the MGB axis is increasingly recognized, studies investigating the impact of GM alterations in developmental and epileptic encephalopathies (DEEs) remain limited. This review highlights recent clinical and preclinical studies examining the impact of GM composition on DEEs, with a focus on infantile epileptic spasms syndrome (IESS) and Dravet syndrome (DS). Further investigation into the relationship between GM dysbiosis and the progression of DEEs is crucial for developing potential therapeutic strategies aimed at modulating the GM to alleviate seizures.},
}

@article {pmid40856172,
year = {2025},
author = {de-Dios, T and Bonucci, B and Barbieri, R and Kushniarevich, A and D'Atanasio, E and Dittmar, JM and Cessford, C and Solnik, A and Robb, JE and Warinner, C and Oras, E and Scheib, CL},
title = {Bone adhered sediments as a source of target and environmental DNA and proteins.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf202},
pmid = {40856172},
issn = {1537-1719},
abstract = {In recent years, sediments from cave environments have provided invaluable insights into ancient hominids, as well as past fauna and flora. Unfortunately, locations with favourable conditions for ancient DNA (aDNA) preservation in sediments are scarce. In this study we analysed a set of samples obtained from sediments adhered to different human skeletal elements, originating from Neolithic to Medieval sites in England, and performed metagenomics and metaproteomics analysis. From them, we were able to reconstruct a partial human genome. The genetic profile of those human sequences matches the one recovered from the original skeletal element. Additionally, aDNA sequences matching the genomes of endogenous gut microbiome bacteria were identified. We also found the presence of genetic sequences corresponding to animals and plants. In particular we managed to retrieve the partial genome and proteome of a Black Rat (Rattus rattus), sharing close genetic affinities to other medieval Rattus rattus. Our results demonstrate that material usually discarded, as it is sediments adhering to human remains, can be used to get a glimpse of the environmental conditions at the time of the death of an individual.},
}

@article {pmid40855336,
year = {2025},
author = {Haro-Moreno, JM and Roda-Garcia, JJ and Molina-Pardines, C and López-Pérez, M},
title = {The hidden genetic reservoir: structural variants as drivers of marine microbial and viral microdiversity.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {110},
pmid = {40855336},
issn = {2524-6372},
support = {PRE2021-098122//Ministerio de Ciencia e Innovación/ ; PID2023-150293NB-I00//Ministerio de Economía y Competitividad/ ; },
abstract = {BACKGROUND: Intraspecific genetic diversity is fundamental to understanding microbial adaptation, evolution, and contributions to ecosystem stability. However, traditional short-read metagenomics often underrepresents this diversity, particularly structural variants (SVs), due to assembly limitations in complex natural populations. To overcome these constraints, we employed third-generation (long-read) metagenomics to investigate the eco-evolutionary role of SVs in microbial and viral marine populations. Our analysis focused on the cellular metagenome fraction (0.22–5 μm size range) across distinct ecological niches within the photic zone of the marine water column.

RESULTS: Insertions and deletions emerged as the predominant SVs in the marine microbiome, occurring at similar frequencies across genomes. These SVs were not only found within the core genome but also in the flexible genome, serving as a source of genetic variability within genomic islands. Insertions were significantly larger, reaching more than 2 Kb, in streamlined microbes such as Pelagibacter (SAR11 clade) or the archaeon Nitrosopumilus. In contrast, SVs in viral populations were smaller and more uniform in size (~ 430 bp). Functionally, SVs were enriched in genes linked to nutrient uptake, amino acid metabolism, and regulatory networks due to the presence of non-coding RNAs. These SVs often encompassed entire genes or operons, acting as an important reservoir of niche-specific diversity that supports the emergence of ecological lineages better adapted to environmental gradients, such as rhodopsin-containing subpopulations in shallower waters. In viruses, SV-driven genetic plasticity facilitated host range adaptation and the evolution of mechanisms modulating host metabolism. We identified long-term genetically stable populations of cyanophages and pelagiphages, wherein SVs represented the primary source of genomic diversification. Notably, certain subpopulations of pelagimyophages carry SVs encoding a pstS gene, which enhances host phosphate uptake and increases viral replication efficiency—a beneficial adaptation in phosphate-depleted environments such as the oligotrophic Mediterranean Sea.

CONCLUSIONS: By capturing SVs directly from natural populations, this study provides new insights into microbial evolution, phage-host interactions, and the broader implications of genomic plasticity for ecosystem resilience in marine environments. Furthermore, these results highlight the transformative potential of third-generation sequencing to unveil previously hidden layers of microbial and viral diversity.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40793-025-00773-8.},
}

@article {pmid40855911,
year = {2025},
author = {Wei, L and Wu, H and Wen, L and Chen, M and Cui, B and Wang, X and Wu, T and Cheng, Y},
title = {Rice protein peptides alleviate lipid accumulation via modulating liver metabolism and remodeling the gut microbiota in HFD-induced mice.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo01536g},
pmid = {40855911},
issn = {2042-650X},
abstract = {Hyperlipidemia is a significant risk factor for lipid metabolism disorder and gut health impairment. Rice protein peptides (RPs) have emerged as promising interventions for hyperlipidemia management, owing to their safety profile, bioavailability, and cost-effectiveness. However, comprehensive investigations into their anti-hyperlipidemic effects and underlying mechanisms remain insufficiently explored. This study aimed to investigate the efficacy of RPs in alleviating hyperlipidemia and hepatic lipid accumulation by lipidomic and microbiome analyses. Results revealed that RP administration significantly ameliorated lipid metabolism disorders by reducing fat accumulation, normalizing blood lipid levels, and inhibiting lipase activity. Additionally, RPs exhibited hepatoprotective effects by increasing antioxidant enzyme activity and decreasing pro-inflammatory cytokines. Lipidomic analysis further revealed that RPs altered lipid metabolic patterns, identifying 10 differentially regulated lipid species that may serve as potential biomarkers for hyperlipidemia. Furthermore, RP supplements significantly regulated the mRNA levels of gene expression (HMGR, SREBP2, CYP7A1, LDLR, PPARα, PPARγ, FAS, and ACS) involved in hepatic lipid metabolism. Metagenomic analysis demonstrated that RPs reversed gut microbiota dysbiosis by reducing the Firmicutes/Bacteroidetes ratio and increasing the abundance of beneficial genera such as Akkermansia, Muribaculaceae, Clostridia_UCG-014, and Blautia. Furthermore, RP intervention significantly elevated fecal short-chain fatty acid (SCFA) content, particularly butyrate, isobutyrate, and isovalerate, suggesting a link between microbial modulation and metabolic improvement. These findings suggested RPs as an effective strategy for improving lipid metabolism and the gut microbiota composition, offering a promising dietary intervention for hyperlipidemia management.},
}

@article {pmid40855409,
year = {2025},
author = {Graeber, E and Tysha, A and Nisar, A and Wind, D and Mendling, W and Finzer, P and Dilthey, A},
title = {Shallow shotgun metagenomic sequencing of vaginal microbiomes with the Oxford Nanopore technology enables the reliable determination of vaginal community state types and broad community structures.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {544},
pmid = {40855409},
issn = {1471-2180},
abstract = {BACKGROUND: The vaginal microbiome plays an important role in female health; it is associated with reproductive success, susceptibility to sexually transmitted infections, and, importantly, the most prevalent vaginal condition in reproduction-age women, bacterial vaginosis (BV). Traditionally, 16S rRNA gene sequencing-based approaches have been used to characterize the composition of vaginal microbiomes, but shallow shotgun metagenomic sequencing (SMS) approaches, in particular when implemented with the Oxford Nanopore Technologies, have important potential advantages with respect to cost effectiveness, speed of data generation, and the availability of flexible multiplexing schemes.

RESULTS: Based on a study cohort of n = 52 women, of which 23 were diagnosed with BV, we evaluated the applicability of Nanopore-based SMS for the characterization of vaginal microbiomes in direct comparison to Illumina 16S-based sequencing. We observed perfect agreement between the two approaches with respect to detecting the dominance of individual samples by either Lactobacilli, vaginosis-associated, or other taxa; very high concordance (92%) with respect to community state type (CST) classification; and a high degree of concordance with respect to the overall clustering structures of the sequenced microbiomes. Comparing the inferred abundances of individual species in individual samples, we observed significant differences (Wilcoxon signed-rank test p < 0.05) between the two approaches for 12 of the 20 species most abundant in our cohort, indicating differences in the fine-scale characterization of vaginal microbiomes. Higher overall abundance of Gardnerella vaginalis, associated with an increased number of CST IV detections, in the Nanopore shallow SMS data indicated potentially increased sensitivity of this approach to dysbiotic states of the vaginal microbiome. Nanopore shallow SMS also enabled the methylation-based quantification of different human cell types in the characterized samples as well as the detection of non-prokaryotic species, including Lactobacillus phage and Candida albicans in study participants with microscopically detected Candida. One important potential limitation of the evaluated Nanopore-based SMS approach was marked variation in sequencing yields.

CONCLUSION: Our study demonstrated the successful application and potential advantages of Nanopore-based shallow SMS for the characterization of vaginal microbiomes and paves the way for its application in larger-scale research or diagnostic settings.},
}

@article {pmid40855353,
year = {2025},
author = {Mousa, AA and Zhang, H and Duan, H and Zhang, J and Mao, S},
title = {Correction: Metagenomic analysis reveals rumen microbiome enrichment and functional genes adjustment in carbohydrate metabolism induced by different sorting behavior in mid-lactation dairy cows.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {90},
pmid = {40855353},
issn = {2524-4671},
}

@article {pmid40854905,
year = {2025},
author = {Szczerbiak, P and Szydlowski, LM and Wydmański, W and Renfrew, PD and Leman, JK and Kosciolek, T},
title = {Large protein databases reveal structural complementarity and functional locality.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7925},
pmid = {40854905},
issn = {2041-1723},
support = {2023/05/Y/NZ2/00080//Narodowe Centrum Nauki (National Science Centre)/ ; 2023/05/Y/NZ2/00080//Narodowe Centrum Nauki (National Science Centre)/ ; 857533//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; MEiN/2023/DIR/3796//Ministerstwo Nauki i Szkolnictwa Wyższego (Ministry of Science and Higher Education)/ ; PN/01/0195/2022//Ministerstwo Nauki i Szkolnictwa Wyższego (Ministry of Science and Higher Education)/ ; },
abstract = {Recent breakthroughs in protein structure prediction have led to a surge in high-quality 3D models, highlighting the need for efficient computational solutions. In our work, we examine the structural clusters from the AlphaFold Protein Structure Database (AFDB), a high-quality subset of ESMAtlas, and the Microbiome Immunity Project (MIP). We create a single cohesive low-dimensional representation of the resulting protein space. We show that, while each database occupies distinct regions, they collectively exhibit significant overlap in their functional profiles. High-level biological functions tend to cluster in particular regions, revealing a shared functional landscape despite the diverse sources of data. By creating a representation of protein structure space, localizing functional annotations within this space, and providing an open-access web-server for exploration, this work offers insights for future research concerning protein sequence-structure-function relationships, enabling biological questions to be asked about taxonomic assignments, environmental factors, or functional specificity. This approach is generalizable, thus enabling further discovery beyond findings presented here.},
}