@article {pmid40815990,
year = {2025},
author = {Li, P and Wu, Y and Bi, R and Cao, C and Hu, J and Chen, X and Luo, T and Wang, Z},
title = {Dietary Enterococcus faecium NCIMB 11181 supplementation mitigates intestinal and systemic inflammation induced by avian pathogenic Escherichia coli O78 infection in broiler chickens.},
journal = {Poultry science},
volume = {104},
number = {11},
pages = {105656},
doi = {10.1016/j.psj.2025.105656},
pmid = {40815990},
issn = {1525-3171},
abstract = {The development of non-antibiotic agents to control avian colibacillosis has become urgent work. Probiotics Enterococcus faecium strains are promising antibiotic alternatives to combat pathogen infection. This study investigated the protective efficacy and action mechanism of dietary probiotic Enterococcus faecium NCIMB 11181 (E. faecium 11181) supplementation on broilers infected with avian pathogenic Escherichia coli (APEC) O78 by measuring immune functions and intestinal microbiota. A total of 120 one-day-old male Arbor Acres broiler chicks were randomly assigned to a 2 × 2 factorial arrangement of treatments with two dietary E. faecium 11181 levels (0 or 2 × 10[8] CFU/kg of diet) and two disease challenge status (control or APEC O78 challenged). APEC infection model was induced via intra-tracheal inoculation of APEC O78 at 19 d of age. The results indicated that dietary E. faecium 11181 addition mitigated local and systemic inflammation caused by APEC O78 infection through decreasing spleen organ index and Escherichia coli (E. coli) counts (P < 0.05), intestinal cell apoptosis index (0.05 < P < 0.1); downregulating splenic NF-κB and IL-17 mRNA abundances as well as peripheral blood B lymphocytes proliferation activity (P < 0.05); upregulating the genes expression levels of antimicrobial peptides (β-defensin-1, -2, -4, -6 and -7), A20, Tollip, TGF-β2 and TGF-β3 genes in the spleen (P < 0.05); and increasing peripheral blood CD4+ T lymphocytes numbers (P < 0.05). Furthermore, E. faecium also improved intestinal microbial composition of the infected birds by enriching Alistipes, Faecalibacterium, and Lactobacillus, and reducing Helicobacter, Coprobacter, and Escherichia Shigella in the cecum of the infected chickens (P < 0.05). Collectively, our results suggested that dietary E. faecium 11181 addition could alleviate local and systemic inflammation induced by APEC O78 infection through inhibiting the over-activation of TLR-NF-κB signal pathway, inducing the expression of endogenous antimicrobial peptides, enhancing peripheral blood CD4+ T lymphocytes functions and improving gut microbiome.},
}

@article {pmid40815966,
year = {2025},
author = {Filip-Hutsch, K and Kwiecień, E and Czopowicz, M and Żabicka, D and Bednarek, M and Anusz, K and Olech, W and Demiaszkiewicz, AW and Rzewuska, M},
title = {Characterization of the bacterial ocular surface microbiota of European bison (Bison bonasus) and their association with infectious keratoconjunctivitis.},
journal = {Veterinary microbiology},
volume = {309},
number = {},
pages = {110682},
doi = {10.1016/j.vetmic.2025.110682},
pmid = {40815966},
issn = {1873-2542},
abstract = {Numerous cases of infectious keratoconjunctivitis (IKC) have been recently observed in European bison in Poland. The present study aimed to identify the ocular surface microbiota of European bison and determine if bacterial communities differed between animals with and without IKC. Ocular swabs were collected from the conjunctiva and cornea of 57 European bison with IKC and 30 healthy animals, from southern and northeastern Poland. Swabs were cultured on Columbia Agar and incubated. Bacterial isolates were identified using MALDI-TOF MS. In the eyes of European bison, 44 bacterial genera and 88 species were detected. The most common were opportunistic bacteria, including Acinetobacter spp., Pseudomonas spp., Aeromonas spp., Pantoea spp., Staphylococcus spp., Serratia spp., Enterococcus spp., and Lelliottia spp. The prevalence of bacteria of the genera Aeromonas, Serratia, and Lelliottia increased together with the severity of ocular changes. These genera were detected significantly more often in European bison with IKC compared to healthy animals, whereas bacteria of the genus Pantoea were identified more often in animals without ocular lesions. None of the isolated bacteria appeared to be a primary etiological agent of IKC in European bison. To the best of our knowledge, this is the first study describing ocular surface microbiota in European bison.},
}

@article {pmid40815909,
year = {2025},
author = {Browning, BD and Tomko, RL and Kirkland, AE and Visontay, R and Ferguson, PL and Alekseyenko, AV and Engevik, MA and Mewton, L and Squeglia, LM},
title = {Oral microbial profiles in young adults with cannabis use disorder.},
journal = {Drug and alcohol dependence},
volume = {275},
number = {},
pages = {112822},
doi = {10.1016/j.drugalcdep.2025.112822},
pmid = {40815909},
issn = {1879-0046},
abstract = {BACKGROUND: With increasing legalization and rising potency of cannabis products, cannabis use disorder (CUD) is a growing public health concern, particularly among young adults, who have the highest rates of CUD. While substance use is known to be associated with the oral microbiome, the impact of CUD remains understudied. Given the oral microbiome's role in overall health, identifying microbial signatures associated with CUD, relative to other substance use disorders (SUDs), may provide insight into its biological mechanisms and potential therapeutic targets.

METHODS: Saliva samples were collected from young adults (ages 18-25; N = 192) with CUD (n = 129) and non-CUD SUD (n = 63). The non-CUD SUD control group allowed for isolation of CUD-related associations in a population that often uses multiple substances. Using 16S rRNA gene sequencing, we examined alpha diversity, beta diversity, and taxa abundance between the groups and in relation to cannabis use patterns (frequency and amount; CUD group only), controlling for sequencing batch, age, sex, race, body mass index (BMI), and alcohol use.

RESULTS: Compared to the non-CUD SUD group, the CUD group exhibited significantly lower alpha diversity, distinct beta diversity, and differences in taxa abundance. Among those with CUD, greater cannabis use frequency was linked to lower diversity, while both frequency and amount were associated with higher abundances of strict anaerobes.

CONCLUSIONS: CUD is associated with specific alterations in the oral microbiome, including lower diversity and taxonomic shifts. Associations with cannabis use patterns underscore the relevance of frequent and heavy use. Future research should explore the functional implications of these findings for CUD-related outcomes.},
}

@article {pmid40815896,
year = {2025},
author = {Choi, W and Hong, J},
title = {Modulating the oral microbiome with dental biomaterials: A review of challenges, advances, and future perspectives.},
journal = {Biomaterials},
volume = {325},
number = {},
pages = {123610},
doi = {10.1016/j.biomaterials.2025.123610},
pmid = {40815896},
issn = {1878-5905},
abstract = {The oral microbiome plays a pivotal role in maintaining both oral and systemic health. Recent studies highlight the potential of dental biomaterials to modulate this complex microbial community. Because of the short retention time imposed by the dynamic oral environment, oral microbiome-modulating dental biomaterials require unique design considerations. This Review outlines recent advances in oral microbiome-modulating biomaterials, including probiotic delivery platforms, stem-cell transplantation, metal-ion-releasing hydrogels, antimicrobial and antioxidant materials, and enamel-mimicking membranes. These dental biomaterials selectively suppress pathogenic species such as Porphyromonas gingivalis while promoting commensal microbes. Bio-inspired design and artificial-intelligence-assisted material discovery are emerging as promising strategies. Ultimately, oral microbiome-modulating dental biomaterials can be leveraged to treat systemic diseases-including tumors and cardiovascular disorders-by promoting the saliva-mediated translocation of beneficial commensals. Integrating microbiology with materials science will be essential for personalized modulation of the oral microbiome and successful clinical translation.},
}

@article {pmid40815473,
year = {2025},
author = {Wang, W and Wang, W and Jiang, J and Bai, X and Chen, K and Zhang, X and Yang, J and Wu, D and Niu, B and Liu, G},
title = {Populus simonii × Populus nigra overexpressing PsnWRKY70 recruits phyllosphere bacterial strains that inhibit Alternaria alternata.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0176524},
doi = {10.1128/msystems.01765-24},
pmid = {40815473},
issn = {2379-5077},
abstract = {WRKY transcription factors have been implicated in the regulation of disease resistance associated with plant immune responses, which has crucial implications for defense responses against stress in plants. The role played by the PsnWRKY70 gene of Populus (Populus simonii × P. nigra) in triggering the mechanism between the phyllosphere microbiome and plant defense against foliar pathogens remains unclear. Molecular ecological network analysis demonstrated that the stability and complexity of the phyllosphere bacterial community of Populus were influenced by Alternaria alternata infection. Specifically, compared to the wild-type line, the PsnWRKY70-overexpressing (OE) line had a higher average clustering coefficient and modularity. Furthermore, metabolomic analysis revealed that 19 differential metabolites were significantly enriched in the leaves of the OE line. Among these metabolites, coumarin compounds, such as fraxetin-8-O-glucoside (fraxin) and scopoletin-7-O-glucoside (scopolin), significantly promoted the proliferation of the genera Methylobacterium and Achromobacter with resistance to A. alternata. Additionally, these genera also served as connectors in the molecular ecological network of the phyllosphere microbiome of the OE line. Thus, we concluded that the PsnWRKY70 gene enhanced the stability, complexity, and core taxa cooperation of the phyllosphere microbial network in Populus and regulated the biosynthesis of fraxin and scopolin to recruit beneficial bacteria controlling A. alternata infection. These findings provide valuable insights into the ability of resistant plant genotypes to drive the assembly of the phyllosphere microbiome, advancing our understanding of defense against pathogens using the biocontrol phyllosphere microbial community.IMPORTANCEPoplar leaf blight caused by Alternaria alternata, a common disease in Northeast China, can cause abnormal abscission of poplar leaves and even lead to plant death in severe cases. WRKY transcription factors have been implicated in the regulation of disease resistance associated with plant immune responses to secondary metabolism via a complicated gene network. However, little is known about how the metabolites regulated by the PsnWRKY70 gene trigger changes in the phyllosphere microbiome, leading to increased resistance to foliar pathogens. Here, the PsnWRKY70 overexpressing line of Populus (Populus simonii × P. nigra) exhibited increased coumarin synthesis in the leaves, triggering changes in microbial species central in phyllosphere microbial networks and leading to increased resistance to A. alternata infection. This study provides insights into the role of the PsnWRKY70 gene in triggering the resistance mechanism to A. alternata in Populus.},
}

@article {pmid40815468,
year = {2025},
author = {Gao, Y and Wang, D and Lu, T and Liu, K and Li, S and Kang, J and Sha, S and Xing, G and Cheng, L and Fan, S and Yang, W and Yan, Q and Ding, Y and Xu, D},
title = {Cross-cohort microbiome-wide study reveals consistent alterations in the gut bacteriome, but not the gut mycobiome, in patients with hypertension.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0065725},
doi = {10.1128/msystems.00657-25},
pmid = {40815468},
issn = {2379-5077},
abstract = {UNLABELLED: Hypertension, one of the most prevalent cardiovascular diseases, has been linked to the gut microbiota. However, there is a lack of well-defined, cross-population validated gut microbial signatures associated with hypertension, particularly at both the bacterial and fungal levels. To address this gap, we conducted a metagenome-wide analysis of fecal samples from 159 hypertensive patients and 101 healthy controls, using two publicly available data sets from the Beijing and Dalian regions. Our results showed that hypertensive patients exhibit a significant reduction in gut bacterial diversity, accompanied by substantial alterations in bacterial composition. A total of 61 bacterial species were identified with significantly different relative abundance between patients and controls across both regions (combined P < 0.05, q = 0.25). Hypertension-enriched species included Lachnospiraceae (Clostridium symbiosum, Enterocloster bolteae) and Clostridium sp. AT4, while Lachnospiraceae bacterium, Firmicutes bacterium, and Clostridium sp. AM49 4BH were significantly decreased in hypertensive patients. In contrast, no significant differences were observed in gut fungal diversity between hypertensive patients and healthy controls, and only minor differences in fungal composition were noted. Specifically, six fungal species were identified as potentially significant in the combined data set (P < 0.05, q = 0.73), but they only Blastomyces emzantsi c231 meet the same consistency across the two cohorts as the bacterial signatures. Furthermore, we developed classification models using gut bacterial and fungal signatures to distinguish hypertension patients from healthy controls. The bacterium-based models achieved area under the curves (AUCs) greater than 0.70 in cross-cohort classification and validation, while the fungus-based models only achieved AUCs between 0.55 and 0.57. In summary, our study identifies cross-cohort gut bacterial and fungal signatures associated with hypertension, suggesting that the gut bacteriome may serve as a more reliable target for hypertension intervention compared to the gut mycobiome.

IMPORTANCE: Hypertension (HTN) represents a global health burden affecting billions of individuals worldwide; however, the relationship between HTN and gut microbial ecosystems remains inadequately characterized. This study presents the first cross-cohort microbiome analysis revealing significant alterations in the gut bacteriome of HTN patients, with limited changes observed in the mycobiome. These findings highlight the critical role of the gut bacteriome in the pathogenesis of HTN and provide new microbial biomarkers for early diagnosis. Furthermore, the identification of bacterial species establishes a foundation for future intervention approaches, enhancing the applicability of microbiome research in cardiovascular health and opening new avenues for related studies in this field.},
}

@article {pmid40815467,
year = {2025},
author = {Wang, X and Liang, T and Liang, Z and Jiang, T and Chen, Y and Chen, T and Dong, B and Wu, Q and Gao, Y},
title = {Increased vaginal Gardnerella vaginalis abundance and reduced D-galactose metabolism are associated with preterm birth in older mothers with columnar ectopy in South China.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0082525},
doi = {10.1128/msystems.00825-25},
pmid = {40815467},
issn = {2379-5077},
abstract = {Advanced maternal age is associated with adverse pregnancy outcomes. However, the impact of changes in maternal physiology, biochemistry, vaginal microbiome, and its metabolites related to reproductive age on pregnancy outcomes is uncertain. Multi-omics were used to analyze vaginal samples collected from 195 pregnant women of different age groups to characterize the factors affecting the occurrence of adverse pregnancy outcomes in older mothers. Results showed that advanced maternal age is associated with a higher risk of premature birth. Furthermore, columnar ectopy may also contribute to premature birth. Moreover, older mothers with columnar ectopy exhibited vaginal microbiome dysbiosis, characterized by an increase in Gardnerella vaginalis and a reduction in Lactobacillus crispatus. Functional analysis of the microbiome revealed that disruptions in the vaginal microbiome might contribute to columnar ectopy by influencing carbohydrate metabolism in the host, such as galactose metabolism. Finally, galactose-degrading enzymes of L. crispatus were enriched in older mothers with non-columnar ectopies. In addition, G. vaginalis promoted the occurrence of columnar ectopy, whereas the dominance of galactosidase in L. crispatus was protective against columnar ectopy. Our findings demonstrate that L. crispatus is a target to prevent columnar ectopy or age-associated premature birth. G. vaginalis and galactose can be diagnostic markers for the occurrence of adverse pregnancy outcomes in older mothers.IMPORTANCEAdvanced maternal age poses a growing challenge to maternal health globally, yet the mechanisms linking age-related physiological changes to adverse pregnancy outcomes remain unclear. This study identifies vaginal microbiome dysbiosis, characterized by increased Gardnerella vaginalis and reduced Lactobacillus crispatus, as a critical mediator of age-associated preterm birth in mothers with columnar ectopy. By integrating multi-omics analyses, we reveal that disruptions in galactose metabolism driven by microbial shifts may contribute to columnar ectopy development. Notably, L. crispatus galactosidase activity emerges as a protective factor, while G. vaginalis and galactose accumulation serve as potential diagnostic markers. These findings provide actionable targets for microbiome-based interventions to mitigate age-related pregnancy complications, advancing personalized strategies for maternal care.},
}

@article {pmid40815466,
year = {2025},
author = {Bailey, C and Gwyther, P and Čaušević, S and Greene, BL and van der Meer, JR},
title = {Phosphite as an engineered niche for Pseudomonas veronii in a synthetic soil bacterial community.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0006125},
doi = {10.1128/msystems.00061-25},
pmid = {40815466},
issn = {2379-5077},
abstract = {Bioaugmentation, the process of soil restoration by introducing microorganisms capable of degrading pollutants, is a promising and cost-effective strategy for environmental remediation. Aromatic hydrocarbons, such as benzene, toluene, ethylbenzene, and p-xylene (BTEX), are highly toxic environmental contaminants that could be transformed to less harmful products through the inoculation of certain organisms capable of BTEX degradation. However, a barrier to successful bioaugmentation is the inoculant's failure to establish within the resident microbial community. In an effort to improve inoculant proliferation, we have investigated phosphite as a phosphorus source for selective nutrient supply. Phosphite is an inaccessible form of phosphorus to organisms that lack the capacity for phosphite oxidation to phosphate. We introduced a phosphite dehydrogenase-coding gene (ptxD) into the genome of the toluene-degrading bacterium Pseudomonas veronii 1YdBTEX2 to couple phosphite metabolism and aromatic hydrocarbon clearance. When inoculated in either soil matrix or liquid soil extract, P. veronii proliferates in a phosphite- and toluene-dependent manner in both growing and stable synthetic soil microbial communities, although the selective effects of phosphite and toluene were not additive in a carbon-limited context. Once toluene is metabolized, P. veronii abundance decays, and the microbial community recovers diversity and abundance resembling the uninoculated controls. Additional members of the microbial community were also enriched in the presence of phosphite, and genomic analysis suggests that these microorganisms utilize an alkaline phosphatase, phoV, for phosphite assimilation.IMPORTANCEBioaugmentation is a promising solution to soil contamination, but its practical application is limited due to poor inoculant establishment in the native soil community. This can often be attributed to low nutrient availability and resource competition with native microorganisms. We proposed the use of phosphite as a selective nutrient source to support the growth of a toluene-degrading bacterium, Pseudomonas veronii, in a model soil system. We engineered a strain of this organism that was capable of using phosphite as a phosphorus source and saw that phosphite application enhanced the abundance of the inoculant sixfold within a synthetic soil community. In this study, we present the first investigation of a phosphite selection system in the soil microbiome and characterize the environmental conditions in which it is effective. By demonstrating the potential of formulated nutritional niches in soil microbiome interventions, we provide significant insights into the field of microbiome engineering.},
}

@article {pmid40815428,
year = {2025},
author = {Bartosik, T},
title = {[The microbiome in diseases of the nose and paranasal sinuses].},
journal = {HNO},
volume = {},
number = {},
pages = {},
pmid = {40815428},
issn = {1433-0458},
abstract = {The nasal microbiome refers to the composition and diversity of bacterial communities residing in the nasal cavity. While the gut microbiome has been the primary focus of microbiome research in recent years, driven by advances in diagnostic technologies, increasing attention is now being directed toward microbial ecosystems in other regions of the body, including the respiratory tract. In general, a high and stable microbial diversity (α-diversity) is considered indicative of a "healthy" microbial community. Conversely, reduced bacterial diversity has been associated with clinical conditions, such as chronic rhinosinusitis (CRS); however, it remains unclear whether such microbial alterations are a cause or consequence of the disease, as current evidence does not yet allow for definitive conclusions. Interpreting existing studies on the nasal microbiome is challenging due to several factors: the low microbial biomass in the nasal cavity, the technical difficulty of accurately analyzing such samples, and the lack of standardized methodologies for sampling and data interpretation. These limitations contribute to the heterogeneity of current findings and highlight the need for consistent, guideline-based research protocols in this emerging field.},
}

@article {pmid40815427,
year = {2025},
author = {Patel, A and Jain, P and Ajazuddin, },
title = {Recent advances in the therapeutics and modes of action of a range of agents used to treat ulcerative colitis and related inflammatory conditions.},
journal = {Inflammopharmacology},
volume = {},
number = {},
pages = {},
pmid = {40815427},
issn = {1568-5608},
abstract = {Ulcerative colitis (UC) is a chronic, relapsing form of an inflammatory bowel disease characterized by epithelial barrier dysfunction, immune dysregulation, and gut microbiota imbalance. Despite advances in immunosuppressive and biologic therapy, shortcoming in barrier repair and long-term remission indicate that new treatments are required. The present study aimed to determine the contribution of protein-peptide complexes to the protection against the disruption of the barrier and colonic stress in UC. It seeks to review the mode of action, pharmacokinetic limitations, and therapeutic benefits that may be gained from using peptides as the intervention rather than using the conventional techniques. A literature review and synthesis of recent data on molecular pathophysiology, clinical pharmacology, and advances in drug delivery was performed. Mechanistic models of epithelial regeneration, immune cell targeting, and reconstitution of the microbiome were summarized. Protein-peptide complexes showed broad ranges of effect including epithelial healing, immunosuppression, and microbiota control. Improvement in the tight junction value and the epithelial proliferation by GLP-2 analogs and AMP conjugated the peptides. Combined decrease in pro-inflammatory cytokines (TNF-α, IL-13, IL-17) by cell-penetrating peptides and IL-pathway inhibitors was seen. Hybrid immunomodulatory peptides for immune promotion, regulation of inflammatory macrophage, and Th1-biased immunomodulation of naïve T cells were assessed. Gut-targeted nano-carrier and pH-responsive systems were shown to enhance bioavailability and site-specific delivery of peptide. Co-delivery of peptides and biologics resulted in enhanced clinical scores in preclinical UC models. Protein-peptide complexes are a potential class of bioactive molecules, which could tackle fundamental pathophysiological derangements in UC. Their accuracy to target, low systemic toxicity, and potential for mucosal healing place them among the next generation of therapeutics. On-going translational efforts should combine peptide engineering, nanotechnology, and patient stratification for maximum clinical impact in UC management.},
}

@article {pmid40815418,
year = {2025},
author = {Schott, EM and Charbonneau, MR and Kiel, DP and Bukata, S and Zuscik, MJ and Rosen, C and Ballok, A and Toledo, GV and Steels, E and Huntress, H and Rao, A and Ebelt, P and Travison, TG and Soto-Giron, MJ and Wolff, I and Easson, DD and Engelke, K and Vitetta, L},
title = {A randomized, double-blind, placebo-controlled clinical study to evaluate the efficacy of the synbiotic medical food, SBD111, for the clinical dietary management of bone loss in menopausal women.},
journal = {Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA},
volume = {},
number = {},
pages = {},
pmid = {40815418},
issn = {1433-2965},
abstract = {UNLABELLED: This 12-month study in 286 early postmenopausal women evaluated the efficacy and safety of SBD111, a synbiotic medical food, in reducing bone loss. SBD111 did not significantly reduce bone loss for the full cohort, but did produce evidence of reduced bone loss in women with osteopenia and BMI ≥ 30.

PURPOSE: To determine the efficacy of SBD111, a synbiotic medical food comprising probiotics and prebiotics, in reducing bone loss in women post-menopause, including prespecified subpopulations of women with osteopenia or elevated BMI.

METHODS: In this prospective, multicenter, double-blind, randomized, placebo-controlled clinical food trial (NCT05009875), 286 healthy, non-osteoporotic women between 1 and 6 years post-menopause were enrolled and consumed SBD111 (4.75 × 10[10] colony forming units) or placebo (maltodextrin) capsules twice daily for 12 months. The primary endpoint was change in areal BMD at the lumbar spine (LS). Secondary endpoints included change in areal BMD at the femoral neck (FN) and total hip (TH), trabecular volumetric BMD at the LS, markers of bone turnover and inflammation, and safety. Changes in gut microbiome composition were exploratory. The hypotheses being tested were formulated before data collection.

RESULTS: Two hundred eighty-six women [age 55 ± 3 years (mean ± standard deviation)] were enrolled, with 221 (77%) completing the study. For the primary outcome, SBD111 administration was not associated with significantly less bone loss in the LS after 12 months [0.15% (- 0.52%, 0.82%), mean effect size (95% CI) by linear mixed-effects regression]. However, SBD111 was associated with reduced BMD loss in the TH for women with BMI ≥ 30 [0.97% (0.015%, 1.925%)] and modestly reduced BMD loss in the FN for women with osteopenia [0.89% (- 0.277%, 2.051%)].

CONCLUSIONS: These findings indicate SBD111 did not significantly reduce BMD loss for the full cohort. However, the trial produced evidence that SBD111 reduced bone loss in women with osteopenia and BMI ≥ 30.},
}

@article {pmid40815346,
year = {2025},
author = {Davoody, S and Tayebi, Z and Sharif-Zak, M and Azizmohammad Looha, M and Mortezaei Ferizhandy, N and Sadeghi Mofrad, S and Houri, H},
title = {Assessing the role of Escherichia coli and Klebsiella pneumoniae in colorectal cancer oncogene expression: insights from microbial colonization phenotypes.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {828},
pmid = {40815346},
issn = {1573-4978},
abstract = {BACKGROUND: Colorectal cancer (CRC) remains a major global health burden, ranking as the third most prevalent malignancy and the second leading cause of cancer-related mortality. Its pathogenesis involves complex interactions between genetic, environmental, and lifestyle factors, with emerging evidence implicating the gut microbiome as a key contributor. Specific pathobionts, such as Escherichia coli and Klebsiella pneumoniae, have been linked to CRC progression due to their pro-inflammatory properties. This study investigated the association of E. coli and K. pneumoniae with CRC tissues and their influence on oncogenic gene expression, particularly within the TGF-β, Notch, Wnt/β-catenin, Rho GTPase, and EGFR/MAPK signaling pathways.

METHODS: Using both culture and molecular-based methods, we analyzed 100 CRC patient biopsies from Taleghani Hospital, Tehran (July 2021-May 2023), assessing bacterial presence and the expression of 19 CRC-associated genes. Adhesion and invasion capabilities of isolates were evaluated in Caco-2 cells.

RESULTS: While clinical parameters (e.g., age, survival, tumor stage) did not differ significantly between bacterial groups, gene expression analysis revealed elevated FOLH1 and MAP2K1 in adhesive-invasive K. pneumoniae isolates and increased FOLH1 in E. coli-positive samples. Tumor stage- and site-specific variations were observed, such as heightened ANXA3 expression in Stage I tumors harboring K. pneumoniae. Principal component analysis (PCA) demonstrated overlapping oncogenic profiles, suggesting complex, context-dependent microbial influences.

CONCLUSIONS: Our findings indicate that E. coli and K. pneumoniae may exert nuanced, tumor-specific effects on oncogenic pathways, potentially mediated more by chronic inflammation than direct gene dysregulation. Further studies employing single-cell RNA sequencing are warranted to elucidate these interactions and their translational potential for CRC diagnostics and therapeutics.},
}

@article {pmid40815158,
year = {2025},
author = {Berman, HL and McKenney, EA and Roche, CE and Michalski, S and Kwon, SH and Weichel, E and Matson, A and Nichols, LM and Alvarado, S and Horvath, JE and Dunn, RR},
title = {Cooking-class style fermentation as a context for co-created science and engagement.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0266024},
doi = {10.1128/spectrum.02660-24},
pmid = {40815158},
issn = {2165-0497},
abstract = {Fermented foods have been consumed for thousands of years and have been used as a model system to study community succession and other ecological questions. Additionally, cooking classes offer opportunities to learn about food preparation and history. In the present study, scientists and chefs delivered cooking-class style workshops in which participants learned the recipes of one of three fermented foods and the microbial ecology within these foods. Participants prepared jars of chow chow, kimchi, or kombucha to set up experiments to study microbial community succession and pH changes. The fermented foods were also used to test the following hypotheses: that increasing the number of substrates results in increased alpha diversity, and that phylogenetically diverse substrates will lead to greater beta diversity among microbial communities. Microbial communities contained lactic and acetic acid bacteria described previously in fermented foods, and indicator species were identified for cabbage and radish substrates in kimchi. Finally, we qualitatively comment on the experience of developing workshops with chefs and the use of participatory science in these experiments.IMPORTANCEThe present study demonstrates the utility of using fermented foods as an inexpensive and effective tool to investigate ecological phenomena and engage the public in microbiology and ecology through cooking-class style workshops. We also model a creative, interdisciplinary collaboration between scientists and chefs.},
}

@article {pmid40815148,
year = {2025},
author = {Sheikh, TMM and Yao, F and Liu, Z and Shafiq, M and Wu, J and Khalid, A and Xie, Q and Jiao, X and Shen, W},
title = {Integrated insights into gut microbiota and metabolomic landscape in breast cancer patients undergoing adjuvant endocrine therapy.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0087925},
doi = {10.1128/msystems.00879-25},
pmid = {40815148},
issn = {2379-5077},
abstract = {Gut microbiota and systemic metabolites are critical for breast cancer progression and therapeutic response. This study investigated gut microbiota and metabolic profiles of breast cancer patients before and after adjuvant endocrine therapy (AET). Using 16S rRNA sequencing and untargeted metabolomics, we identified significant disruptions in microbial diversity and metabolic pathways. Alpha diversity was reduced in pre-AET patients, with partial restoration observed post-AET. Key genera, such as Bifidobacterium and Coprococcus, were enriched in pre-AET patients, whereas Proteus and Methylobacterium were enriched in post-AET patients. Metabolomic analysis revealed significant reductions in the levels of vitamin B6 metabolites in both the pre-AET and post-AET groups compared to those in the healthy control (HC) group, indicating potential nutrient deficiencies or metabolic stress. Elevated cholesterol and estrogen metabolite levels in pre-AET patients reflect dysregulated lipid and hormone metabolism, with post-AET decreases in estrogen metabolites, confirming therapeutic efficacy. Correlation analysis revealed that Klebsiella_724518 was positively correlated with estrogen and vitamin B6 metabolites, whereas Proteus, Methylobacterium, Treponema_D, and Holdemanella were negatively correlated with cholesterol. Receiver operating characteristic (ROC) curve analysis identified estriol (area under the curve [AUC] = 1.000) as a strong diagnostic biomarker for distinguishing HCs from pre-AET patients, whereas cholesterol (AUC = 0.880) and estradiol-17β (AUC = 0.870) were highly effective in monitoring the therapeutic response to AET. This study highlights the role of gut microbiota and its metabolic byproducts in breast cancer development and treatment outcomes. It also reveals promising microbial and metabolite signatures for non-invasive cancer detection, tracking progression, and monitoring treatment response.IMPORTANCEBreast cancer progression and treatment response remain challenging to predict and monitor effectively. Our findings demonstrate the dual role of the gut microbiota and its metabolic products in influencing both. Strong correlations between specific microbial taxa and key metabolites provide new mechanistic insights into the influence of gut microbes on therapeutic outcomes during endocrine therapy. Importantly, we identified high-performance biomarkers, with estriol showing perfect diagnostic accuracy (AUC = 1.000) and cholesterol effectively monitoring treatment response (AUC = 0.880), highlighting their potential for non-invasive clinical applications. This study provides a foundation for applying gut microbiome research to develop clinical tools that could improve breast cancer management.},
}

@article {pmid40815145,
year = {2025},
author = {Scaglioni, M},
title = {Race by other names: critiquing population categories in microbiome research.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0021625},
doi = {10.1128/msystems.00216-25},
pmid = {40815145},
issn = {2379-5077},
abstract = {This minireview analyzes the social science literature on how categories of human difference are conceptualized and deployed in microbiome science, particularly in research conducted in Global South contexts. Through a systematic review of 180 microbiome studies (2014-2025) and analysis of social science critiques, it demonstrates how seemingly neutral terms like "population," "lifestyle," and "traditional" often imply racial meanings that echo colonial scientific frameworks. While microbiome science rarely uses explicit racial terminology, it frequently employs comparative frameworks that create hierarchical distinctions between Western and non-Western populations. The minireview argues that these categorizations stem not just from colonial legacies but from the comparative nature of scientific knowledge production itself. It traces the evolution of racial thinking in science from post-World War II genetics through contemporary microbiome research, showing how even as scientists reject biological racial determinism, race persists as an analytical category through various proxies. It concludes by examining recent efforts to develop more nuanced approaches to human categorization in microbiome science and calls for deeper integration of social science perspectives to avoid reproducing problematic categorizations while ensuring ethical and equitable research practices.},
}

@article {pmid40815091,
year = {2025},
author = {Garcia-Pichel, F and Farias, J and Fernandes, V and Roush, D and Swenson, TL and Kosina, SM and Northen, TR and Cao, H and Jaunin, S and Kandel, R and Gaxiola, R},
title = {Swift microbiome-mediated phenotype transfer from transgenic plants.},
journal = {Journal of environmental quality},
volume = {},
number = {},
pages = {},
doi = {10.1002/jeq2.70070},
pmid = {40815091},
issn = {1537-2537},
abstract = {The expression of an organism's genes determines its own characteristics in any given environment. In this study, we demonstrate that the phenotypic traits of genetically modified transgenic Arabidopsis thaliana plants, designed for nutrient efficiency and enhanced yield, can be naturally and readily transferred to neighboring wild-type plants. Our findings reveal that the transgenic plants significantly influence the populational, compositional, and functional traits of their root-associated microbiome (RAM), resulting in a larger population, with distinct composition and high functional potential compared to wild-type plants, regardless of soil type. This phenomenon appears to stem from altered metabolite exudation patterns, which enhance root recruitment. Notably, the RAM plays a dual role: it not only contributes to the robust phenotype of the transgenic plants but also facilitates the transfer of these traits to adjacent wild-type plants. Upon transplanting wild-type plants into the presence of transgenics, we observed the induction of transgenic-like phenotypes. Metagenomic and compositional analyses indicate that this transfer is linked to an increase in 2,3-butanediol (2,3-BD) fermenting bacteria. Furthermore, exposure to 2,3-BD alone was sufficient to elicit transgenic phenotypes in wild-type plants. These results suggest that factors external to plant tissues, such as root-associated bacteria and their volatile metabolic products, play a crucial role in the transferability of plant phenotypes to neighboring plants. Our findings underscore the importance of evaluating microbiome interactions in the context of transgenic organisms and open new avenues for alternative agricultural practices that may reduce reliance on genetic modification.},
}

@article {pmid40814739,
year = {2025},
author = {Nam, HM and Jeong, S and Sung, GY},
title = {Development of hair follicle spheroids with growth factor transfection and various cell combinations.},
journal = {Biomaterials science},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5bm00998g},
pmid = {40814739},
issn = {2047-4849},
abstract = {As the number of hair loss patients increases, research conducted on hair follicles and hair has recently become more active. However, most current hair follicle research models are limited in their ability to reproduce several key functions of the hair follicle microenvironment. To solve this problem, hair growth genes were injected into hair follicle cells, and long-term culture was performed for up to 90 days. DPCs (dermal papilla cells), KCs (keratinocytes), HUVECs (human umbilical vein endothelial cells) or HDMECs (human dermal microvascular endothelial cells), and FBs (fibroblasts) injected with hair follicle growth factors LEF1 and Wnt1 were mixed to produce spheroids, and the growth factor expression and growth behavior according to the type of cell and the presence or absence of transfection according to the culture period were analyzed using SEM, H&E staining, and IF imaging. As the culture period increased, the size of the spheroids increased, and the number decreased due to the association between spheroids; long fibers that appeared to be hair expression were observed. We also compared the differences between HUVECs and HDMECs, which have different phenotypes of vascular cells. In spheroids that did not contain FBs, the expression of HUVECs was more promoted, whereas in spheroids that contained FBs, the expression of HDMECs tended to be more promoted. These results are expected to contribute to dermatology and new drug development for the prevention of intractable skin diseases and hair loss using skin models with a microbiome environment in the future.},
}

@article {pmid40814727,
year = {2025},
author = {Lin, YW and Liu, MC and Lu, TJ and Ho, YY and Chen, TW and Yang, YJ},
title = {The Developmental Trajectory and Correlation of Human Milk Microbiota and Oligosaccharides in Taiwanese Lactating Mothers.},
journal = {Journal of food science},
volume = {90},
number = {8},
pages = {e70484},
doi = {10.1111/1750-3841.70484},
pmid = {40814727},
issn = {1750-3841},
support = {112-2327-B-006-007-//National Science and Technology Council/ ; 109-2327-B-006-001-;110-2327-B-006-007-;111-2327-B-006-006-//Ministry of Science and Technology, Taiwan/ ; },
abstract = {Human milk microbiota (HMM) and human milk oligosaccharides (HMOs) are crucial components of breast milk that influence infant health and development. This study provides long-term insights into the dynamic changes in HMM and HMOs and their interactions among Taiwanese lactating mothers. A cohort of 90 mothers with singleton, full-term infants contributed 319 breast milk samples across eight lactation stages over 52 weeks. HMOs were quantified using mass spectrometry, while milk microbiota composition was analyzed through 16S rRNA sequencing. Our findings reveal that HMO concentrations steadily declined from birth to 52 weeks postpartum. The most abundant HMO was 2'-fucosyllactose (2'-FL, 18.8%), followed by 3-fucosyllactose (3-FL, 16.5%). Notably, 2'-FL levels decreased over time, while 3-FL concentrations increased. Other HMOs exhibited a general downward trend throughout lactation. HMM composition also shifted dynamically, with significant variations in α-diversity and β-diversity across lactation stages. The predominant bacterial genera-Streptococcus, Pseudomonas, and Staphylococcus-showed distinct bimodal temporal patterns. Correlation analyses revealed that tetratose and sialylated HMOs were positively associated with Bacteroides abundance, while multiple HMOs negatively correlated with Streptococcus. These findings underscore the complex interactions between breast milk oligosaccharides and microbial communities, highlighting their potential implications for infant gut health. Further research is needed to explore the clinical significance of these transformations and their role in shaping the early-life microbiome. PRACTICAL APPLICATIONS: This study shows how breast milk changes over time, with certain sugars (HMOs) decreasing and others shifting, while beneficial bacteria also fluctuate. These changes may influence an infant's gut health and development. Understanding these patterns can help improve infant nutrition, guide breastfeeding recommendations, and support the design of better infant formulas or probiotics.},
}

@article {pmid40814555,
year = {2025},
author = {Wang, W and Xu, Y and Chu, Y and Zhang, H and Zhou, L and Zhu, H and Li, J and Zhang, Z and Cheng, J and Zhou, F and Yang, D and Xu, W and Peng, H},
title = {Lactobacillus-based probiotic cocktail inhibits colitis-associated cancer by altering intestinal metabolism.},
journal = {International journal of clinical and experimental pathology},
volume = {18},
number = {7},
pages = {317-334},
pmid = {40814555},
issn = {1936-2625},
abstract = {OBJECTIVE: Dysbiosis of intestinal microbiome is an important colorectal cancer (CRC) pathogenetic mechanism. Lactobacillus-based probiotic cocktail could inhibit colitis-associated cancer (CAC) by alleviating intestinal dysbiosis. The intestinal microbial metabolites have been linked with CRC etiology. However, the link between Lactobacillus-based probiotic cocktail and the alteration of intestinal metabolism and their functional mechanisms during CAC process is still poorly understood.

METHODS: For assessing protective effects of the probiotic cocktail, azomethanes/dextran sodium sulfate (AOM/DSS) induced CAC mice were pretreated with the probiotic cocktail. Colon of C57BL/6 mice were used to assess inflammation and tumorigenesis. Comparative analysis was performed for determining how the probiotic altered intestinal metabolism and gene expression. Meanwhile, intestinal microbiota alterations were analyzed. The concluding integrated analysis of intestinal metabolism and gene expression as well as intestinal microbiota was presented.

RESULTS: Pretreatment with the probiotic alleviated intestinal inflammation and limited the formation of tumors. Oncogenes were down-regulated and cancer suppressor genes were up-regulated after probiotic pretreatment. Pretreatment with the probiotic induced a rise of Lactobacillus-dominated genera and a reduction of potential pathogenic bacteria Parasutterella, Helicobacter and Muribaculum, and affected expression of intestinal metabolites that involved 37 metabolic pathways. Lactobacillus-associated intestinal metabolite variations involve five metabolic pathways - arginine and proline metabolism, histidine metabolism, pyrimidine metabolism, purine metabolism, and tyrosine metabolism.

CONCLUSIONS: Pretreatment with Lactobacillus-based probiotic cocktail protected mice from CAC by interfering with intestinal metabolites that affected the cancer suppressor genes and oncogenes' expression. Furthermore, Lactobacillus affected five metabolite pathways, which was important mechanism for probiotic anti-inflammatory and anti-tumorigenesis.},
}

@article {pmid40814028,
year = {2025},
author = {Mulindwa, J and Lujumba, I and Musiime, C and Namulondo, J and Kimuda, MP and Nyangiri, O and Cuu, G and Mwubaha, C and Tukwasibwe, S and Ssemaganda, A and Ssewanyana, I and Nerima, B and Baingana, R and Noyes, H and MacLeod, A and Matovu, E},
title = {High Schistosoma mansoni infection intensity is associated with distinct gut microbiota and low levels of systemic cytokines in children along the Albert-Nile, Northern Uganda.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {506},
pmid = {40814028},
issn = {1471-2180},
support = {MakRif3//Makerere University Research Innovation Fund (MakRif)/ ; MakRif3//Makerere University Research Innovation Fund (MakRif)/ ; H3A-18-004//H3Africa/ ; H3A-18-004//H3Africa/ ; H3A-18-004//H3Africa/ ; H3A-18-004//H3Africa/ ; H3A-18-004//H3Africa/ ; H3A-18-004//H3Africa/ ; H3A-18-004//H3Africa/ ; H3A-18-004//H3Africa/ ; },
abstract = {BACKGROUND: Schistosomiasis disease that affects millions of people in sub-Saharan Africa, with a range of impacts on both host immune responses and the gut microbiome. The gut microbiota plays a fundamental role in the host's nutrition, metabolism, protection against pathogens, and modulation of host immunity. Understanding the role of the gut microbiome in pathophysiology of Schistosoma mansoni infection and how it influences host immune response, is essential for developing a more comprehensive view of disease progression and potential therapeutic strategies.

METHODOLOGY: A cross-sectional study was carried out on 140 faecal samples collected from school children aged 10-15years residing in the schistosomiasis endemic hot spots of the Albert-Nile, Pakwach district, Northern Uganda. The samples were categorised by S. mansoni infection intensity based on the Kato Katz test. Faecal DNA was isolated, and microbiota composition was determined by 16 S rRNA V3-V4 sequencing. Plasma Th1/Th2 profiling of 13 cytokines was carried out on the Luminex platform and compared with respect to S. mansoni infection intensities.

RESULTS: The genera Phascolarctobaterium and Prevotella_7 were significantly enriched (padj < 0.05, LDA > 3.0) in the high S. mansoni infection intensity group whereas, Ruminobacter and Alloprevotella were enriched in the low infection intensity group. We observed significantly lower systemic Th1/Th2 cytokine levels between the high intensity infection and the control samples (padj < 0.05). Linear regression analysis using all cytokines as covariates showed that the genus Alloprevotella, Streptococcus, Gastranaerophilales and Ruminobacter were associated with systemic IL6 response.

CONCLUSION: There are alterations in the gut microbiota of S. mansoni infected children with distinct genera that discriminate the high and low infection intensity that could be potentially used as biomarkers. There is an association between the gut microbiota and systemic cytokine response whose mechanism in chronic disease pathophysiology needs to be further investigated.},
}

@article {pmid40813995,
year = {2025},
author = {Moraes, SM and Araújo, TT and Abuna, GF and Dionízio, A and Carvalho, TS and Reis, FN and Pardi, V and Murata, RM and Buzalaf, MAR},
title = {Impact of TiF4 Varnish on the Oral Biofilm Microbiome in High-Caries-Risk Patients.},
journal = {JDR clinical and translational research},
volume = {},
number = {},
pages = {23800844251348180},
doi = {10.1177/23800844251348180},
pmid = {40813995},
issn = {2380-0852},
abstract = {INTRODUCTION: Dental caries is a prevalent global disease, influenced by biofilm formation, dietary sugars, and host factors. Fixed orthodontic appliances increase the risk of noncavitated lesions, highlighting the need for effective prevention. Fluoride varnishes reduce demineralization and promote remineralization; however, their impact on the oral biofilm microbiome in high-caries-risk patients remains underexplored.

OBJECTIVE: To profile microbial biofilms involved in caries lesions after treatment with sodium fluoride (NaF) and titanium tetrafluoride (TiF4) varnishes using 16S rRNA sequencing of the oral biofilm microbiome.

METHODS: A randomized crossover study was conducted with 13 participants (12-18 y) with fixed orthodontic appliances and at least 1 active noncavitated lesion. Participants underwent 4 stages: G1 (nontreatment), G2 (professional prophylaxis; PP), G3 (PP + NaF varnish), and G4 (PP + TiF4 varnish). Clinical analyses (Nyvad and plaque indices) and supragingival biofilm sampling were performed. Bacterial DNA was extracted and amplified for 16S rRNA sequencing. Repeated-measures analysis of variance, Friedman/Wilcoxon with Bonferroni correction, Pearson chi-squared, and permutational multivariate analysis of variance tests were performed ( P < 0.05).

RESULTS: Shannon diversity (median, 25%-75%) values were as follows: G1 (6.25, 6.21-6.27), G2 (5.81, 5.77-5.83), G3 (5.63, 5.64-5.71), and G4 (5.76, 5.72-5.78). G2, G3, and G4 differed significantly from G1, with no difference among them ( P < 0.05). The most abundant genera were Veillonella (G1: 7.6%, G2: 10.6%, G3: 9.4%, G4: 5.7%), Corynebacterium (G1: 8.2%, G2: 7.3%, G3: 6.8%, G4: 10.4%), and Neisseria (G1: 4.0%, G2: 9.2%, G3: 9.6%, G4: 9.6%). Significant reductions were observed in the Prevotella/Haemophilus, Prevotella/Neisseria, and Prevotella/Rothia log-ratios compared with G1 ( P = 0.001). G2 reduced Prevotella/Haemophilus. G3 reduced Prevotella/Haemophilus and Prevotella/Neisseria. G4 reduced Prevotella relative to all 3 genera, indicating broader microbiome modulation.

CONCLUSION: PP, whether or not combined with fluoride varnishes, modified the biofilm microbiota. PP + TiF4 varnish affected a greater number of bacterial log-ratios associated with commensal-dysbiotic balance, although no significant differences were found between treatment groups.Knowledge Transfer Statement:The findings from this study can guide clinicians in selecting the most effective fluoride varnish for high-caries-risk patients. By understanding how sodium fluoride (NaF) and titanium tetrafluoride (TiF4) varnishes modulate the oral microbiome, clinicians can develop more targeted and effective prevention strategies. This knowledge has the potential to enhance patient outcomes by optimizing caries prevention during orthodontic treatment, allowing for more personalized and microbiome-focused approaches.},
}

@article {pmid40813994,
year = {2025},
author = {Chiu, SF and Huang, CY and Chen, CY and Hsu, WJ and Yeh, YM and Shih, YW and Chu, LJ and Lin, WN and Huang, KY},
title = {Interactions between bacterial vaginosis-associated microbiota and Trichomonas vaginalis modulate parasite-induced pathogenicity and host immune responses.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {346},
pmid = {40813994},
issn = {1756-3305},
support = {TPCH-112-14 ; TPCH-113-13//Taipei City Hospital/ ; 11301-62-040//Department of Health, Taipei City Government/ ; MOST 110-2320-B-016-011-MY3;NSTC 113-2320-B-016-006//National Science and Technology Council/ ; MND-MAB-D-112099; MND-MAB-D-113165//National Defense Medical Center/ ; },
abstract = {BACKGROUND: Trichomoniasis, caused by Trichomonas vaginalis (Tv), is the most common nonviral sexually transmitted infection (STI). Bacterial vaginosis (BV) is characterized by a reduction in health-associated Lactobacillus and an overgrowth of anaerobes. Both BV-associated bacteria (BVB) and Tv are linked to adverse gynecologic outcomes. Herein, we aimed to investigate whether interactions between vaginal bacterial species and Tv could modulate Tv pathogenicity and Tv-induced host immune responses.

METHODS: We established a co-culture system to evaluate the interaction between Tv and various vaginal bacteria, including Lactobacillus crispatus, Escherichia coli, Prevotella bivia, and Lactobacillus iners, in the context of polymicrobial infection in ectocervical cells (Ect1). The impact of the interactions between Tv and these bacterial species on Tv adhesion, Tv-induced cytotoxicity in Ect1 cells, and cytokine secretion were assessed. Additionally, the molecular mechanisms governing host inflammation following Tv-bacteria interactions were investigated.

RESULTS: Our in vitro model showed that specific BVB, particularly P. bivia, enhanced the expression of Tv ap65 gene and promoted Tv adhesion to host cells. Additionally, Tv pretreated with P. bivia increased cytotoxicity and upregulated IL-6, IL-8, CXCL1, and IP-10 secretion in Ect1 cells. Furthermore, Ect1 cells stimulated with Tv pretreated with P. bivia also activated the PI3K, ERK, and p38 MAPK pathways, triggering epithelial-mesenchymal transition (EMT) events. These results demonstrate that this potential pathobiont enhances Tv pathogenicity, highlighting the impact of the vaginal microbiome on host cells during Tv infection.

CONCLUSIONS: This study significantly advances our understanding of the complex host-bacteria-parasite interactions in the vaginal ecosystem.},
}

@article {pmid40813961,
year = {2025},
author = {Okalin, SS and Arslan, N and Demiray Gürbüz, E and Arayıcı, M and Kırca, ND and Ozel Demiralp, D and Dereli-Akdeniz, D and Akan, P and Ozkutuk, AA},
title = {The association between gut microbiota composition and cardiometabolic parameters in healthy adults.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {505},
pmid = {40813961},
issn = {1471-2180},
abstract = {BACKGROUND: The human gut microbiota comprises approximately 100 trillion microbial cells and produces a wide range of metabolites. Its composition is shaped by factors such as geography, dietary habits, and genetic background. Dysbiosis-an imbalance in this microbial ecosystem-has been associated with the development of metabolic diseases. This study aimed to characterize the gut microbiota composition in adults without diagnosed chronic diseases and assess its potential associations with cardiometabolic parameters.

METHODS: Volunteers over the age of 18 residing in Izmir province who met the inclusion criteria were enrolled in the study. Fecal and blood samples were collected from all participants. Bacterial DNA from fecal samples was extracted, and the full-length 16 S rRNA was amplified. Full-length 16 S rRNA PCR amplicons were sequenced using Oxford Nanopore Technologies. Taxonomic classification, Firmicutes/Bacteroidetes ratio, and Shannon index were determined using Massbiome Fecal Microbiome Analysis (Massive Bioinformatics, Türkiye). Dominant bacterial genera were also analyzed using the Epi2Me database. Blood samples were analyzed for metabolic health markers. Associations between bacterial taxa and blood-based metabolic parameters were examined statistically.

RESULTS: A total of 82 participants were included in the study. According to BMI, 34 (41.4%) of the participants were classified as having a healthy weight, 23 (28.1%) as overweight, and 25 (30.5%) as obese. Segatella (Prevotella) copri was identified as the dominant species in most participants (51%). Other dominant species included Ruminococcus torques (13%), Faecalibacterium prausnitzii (13%), Faecalitalea cylindroides (5%), Bacteroides uniformis (4%), and Phocaeicola vulgatus (3%). S. copri was identified as the dominant bacterial species in 45 participants (54.8%) according to the Epi2Me database. The Shannon index and Firmicutes/Bacteroidetes ratio varied among the three BMI groups. Both Lachnospira and Ruminococcus genera had a significant negative correlation with BMI, indicating that higher levels of BMI are associated with lower abundances of these genera. In the regression analysis, Lachnospira was found to be less abundant at higher HbA1c levels. HOMA-IR was found to be a significant predictor for the relative abundance of Vescimonas. Ruthenibacterium is found to be more abundant at higher HDL levels.

CONCLUSION: The dominant bacterial taxa differed from those reported in other populations, suggesting region-specific microbial profiles. Notably, specific gut microbial genera were associated with metabolic health indicators, including BMI, HbA1c, HOMA-IR, and HDL level. These findings underscore the potential role of gut microbiota in metabolic regulation and support the need for further region-specific research. This study is among the few in Türkiye focusing on healthy adults and contributes to the understanding of gut microbiota in relation to cardiometabolic parameters.},
}

@article {pmid40813885,
year = {2025},
author = {Yan, L and Wei, X and Zhong, F and Fu, L and Ru, H and Mo, X and Huang, M},
title = {Intratumoral microbial community profiling identifies clinicomolecular and prognostic subtypes of colorectal cancer liver metastasis.},
journal = {NPJ precision oncology},
volume = {9},
number = {1},
pages = {284},
pmid = {40813885},
issn = {2397-768X},
support = {2023GXNSFDA026032//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; 82160495//National Natural Science Foundation of China/ ; 2024GXNSFBA010083//Natural Science Foundation of Guangxi Zhuang Autonomous Region,China/ ; },
abstract = {Intratumoral microbiota are implicated in colorectal cancer liver metastasis (CRLM), but their relationships with clinical characteristics and prognosis remain to be explored. Using 5R 16S rRNA gene sequencing method, we analyzed the intratumoral microbiota of patients with colorectal cancer with and without liver metastasis. CRLM patients were classified into three intratumoral microbial community subtypes (IMCSs). These included IMCS1 (sugar metabolism-related liver metastasis with T cell activation, moderate proliferation and invasion, and median disease-free survival (mDFS) of 22 months), IMCS2 (protein metabolism-related liver metastasis with natural killer cell activation, high proliferation and invasion, and mDFS of 12 months), and IMCS3 (lipid metabolism-related liver metastasis with a pauci-immune phenotype, the highest level of proliferation and invasion, and mDFS of 10 months). Our study establishes intratumoral microbiome subtypes as a novel risk stratification strategy for CRLM, facilitating microbiota-directed therapeutic strategies with potential survival benefits.},
}

@article {pmid40813608,
year = {2025},
author = {Chun, SJ and Pack, IS and Kim, DY and Heo, JH and Nam, KH and Kim, CG},
title = {Ecological impacts of human thioredoxin expression and interspecific hybridization on the soybean rhizosphere microbiome: insights from ASV-level niche analysis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {29806},
pmid = {40813608},
issn = {2045-2322},
support = {NIE-A-2025-04//Ministry of the Environment, South Korea/ ; KGM1121511//Korea Research Institute of Bioscience and Biotechnology/ ; },
abstract = {Genetically modified (GM) soybean (Glycine max) expressing a human thioredoxin (trx) gene under the control of a seed-specific promoter has been developed for cosmetic applications, but its ecological effects remain poorly understood. We examined the rhizosphere microbiomes of GM soybean, wild soybean (Glycine soja), and F3 interspecific hybrids segregating for the transgene under low-input field conditions. Rhizosphere soil samples were collected at the vegetative and flowering stages, and microbial communities were analyzed via high-throughput sequencing of 16S rRNA and ITS regions. This study represents the first application of amplicon sequence variant (ASV)-level niche breadth analysis to evaluate the rhizosphere effects of a trx-expressing GM soybean. ASV-level analysis and ecological niche breadth classification revealed that genotype-specific microbial shifts were not apparent at relatively high taxonomic levels. Notably, several bacterial ASVs from the class Bacilli were more abundant in GM and homozygous plants at flowering. A fungal ASV from Tausonia also showed increased abundance in the GM lines. These findings highlight that genotype-driven microbial shifts can occur in a stage-specific manner and underscore the importance of fine-resolution microbial analyses in environmental risk assessment.},
}

@article {pmid40813488,
year = {2025},
author = {Ye, Q and Zhang, Z and Chen, T and Wu, L and Xu, K and Deng, T},
title = {Fecal gut microbiome alterations and its association with lactose intolerance in children with rotavirus infection-related diarrhea.},
journal = {European journal of pediatrics},
volume = {184},
number = {9},
pages = {553},
pmid = {40813488},
issn = {1432-1076},
support = {No. Y20210004//Wenzhou Municipal Science and Technology Bureau/ ; LQ23H160014//Natural Science Foundation of Zhejiang Province/ ; },
abstract = {UNLABELLED: Rotavirus (RV), a major cause of childhood diarrhea, damages intestinal epithelium and may induce lactose intolerance in some patients. Increasing studies have emphasized the importance of dysregulated gut microbiome community in diseases. In this study, fecal samples from rotavirus-infected children (n = 48) and healthy controls (n = 29) were analyzed based on 16S rRNA gene sequencing and clinical data. The rotavirus-infected group was further stratified by lactose tolerance status to investigate the distinctive features of the gut microbial communities. Our study verified a shift in gut microbiome constitution and abundance between the feces of healthy donors and rotavirus infection children. Notably, Agathobacter, Streptococcus, Veillonella, and Roseburia were significantly increased in rotavirus infection patients, while the relative abundance of the Ruminococcus gnavus group was decreased. Analyses of alpha diversity unveiled significant differences in the abundance of gut microbiota between rotavirus infection patients with or without lactose intolerance. In particular, the abundance of Parasutterella, Lachnospiraceae NK4A136 group, Morganella, and Veillonellaceae unclassified decreased significantly in rotavirus infection patients with lactose intolerance. Further, PLR, an inflammatory hematological ratio, was significantly elevated in rotavirus infection patients with lactose intolerance.

CONCLUSION: Overall, our study indicated the characteristic of change in diversity, taxonomy, and function of gut microbiota between rotavirus infection and healthy control in children, revealing the existence of dysbiosis in rotavirus infection. Further, our analysis identified the compositional uniqueness of gut microbiota between rotavirus infection patients with or without lactose intolerance, highlighting the diversity and taxonomy in gut microbiome and association with inflammatory state.

WHAT IS KNOWN: • Rotavirus causing diarrhea in children worldwide, causing damage to the intestinal epithelium and lactose intolerance-related diarrhea in children.

WHAT IS NEW: • Results demonstrated the characteristic changes of gut microbiome in rotavirus-infected children and further investigated the different gut microbiome composition between rotavirus infection-related lactose intolerance and lactose tolerance patients. • Further, the relationship between gut microbiome and inflammatory hematological ratios was explored.},
}

@article {pmid40813371,
year = {2025},
author = {Kiu, R and Darby, EM and Alcon-Giner, C and Acuna-Gonzalez, A and Camargo, A and Lamberte, LE and Phillips, S and Sim, K and Shaw, AG and Clarke, P and van Schaik, W and Kroll, JS and Hall, LJ},
title = {Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7569},
pmid = {40813371},
issn = {2041-1723},
support = {100974/C/13/Z//Wellcome Trust (Wellcome)/ ; BB/R012490/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/X011054/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/S017941/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
abstract = {Preterm infants (<37 weeks' gestation) are commonly given broad-spectrum antibiotics due to their risk of severe conditions like necrotising enterocolitis and sepsis. However, antibiotics can disrupt early-life gut microbiota development, potentially impairing gut immunity and colonisation resistance. Probiotics (e.g., certain Bifidobacterium strains) may help restore a healthy gut microbiota. In this study, we investigated the effects of probiotics and antibiotics on the gut microbiome and resistome in two unique cohorts of 34 very-low-birth-weight, human-milk-fed preterm infants - one of which received probiotics. Within each group, some infants received antibiotics (benzylpenicillin and/or gentamicin), while others did not. Using shotgun metagenomic sequencing on 92 longitudinal faecal samples, we reconstructed >300 metagenome-assembled genomes and obtained ~90 isolate genomes via targeted culturomics, allowing strain-level analysis. We also assessed ex vivo horizontal gene transfer (HGT) capacity of multidrug-resistant (MDR) Enterococcus using neonatal gut models. Here we show that probiotic supplementation significantly reduced antibiotic resistance gene prevalence, MDR pathogen load, and restored typical early-life microbiota profile. However, persistent MDR pathogens like Enterococcus, with high HGT potential, underscore the need for continued surveillance. Our findings underscore the complex interplay between antibiotics, probiotics, and HGT in shaping the neonatal microbiome and support further research into probiotics for antimicrobial stewardship in preterm populations.},
}

@article {pmid40813370,
year = {2025},
author = {Rakoff-Nahoum, S and Debelius, J and Valles-Colomer, M and Noordzij, HT and Esteban-Torres, M and Zhernakova, A and Brusselaers, N and Pettersen, VK},
title = {A reconceptualized framework for human microbiome transmission in early life.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7546},
pmid = {40813370},
issn = {2041-1723},
abstract = {Human development and physiology are fundamentally linked with the microbiome. This is particularly true during early life, a critical period for microbiome assembly and its impact on the host. Understanding microbial acquisition in early life is thus central to both our basic understanding of the human microbiome and strategies for disease prevention and treatment. Here, we review the historical approaches to categorize microbial transmission originating from the fields of infectious disease epidemiology and evolutionary biology and discuss how this lexicon has influenced our approach to studying the early-life microbiome, often leading to confusion and misinterpretation. We then present a conceptual framework to capture the multifaceted nature of human microbiome acquisition based on four key components: what, where, who, and when. We present ways these parameters may be assigned, with a particular focus on the 'transmitted strain' through metagenomics to capture these elements. We end with a discussion of approaches for implementing this framework toward defining each component of microbiome acquisition.},
}

@article {pmid40812606,
year = {2025},
author = {Loeven, AM and Brown, AN and Ebuara, FU and Jones, KM and Fadool, DA},
title = {Both obesogenic and isocalorically-controlled diets drive changes in microbiota composition in a sex-dependent manner in mice.},
journal = {Physiology & behavior},
volume = {},
number = {},
pages = {115062},
doi = {10.1016/j.physbeh.2025.115062},
pmid = {40812606},
issn = {1873-507X},
abstract = {We have observed the loss of structure and function of olfactory circuits following consumption of excess dietary fat as maintained by isocaloric feeding. Because changes in microbiome composition have not been examined during this type of diet that does not induce overt obesity, we performed isocaloric feeding of a moderately high-fat (MHF) diet, and assessed gut microbiome changes over 5 months by sequencing the 16s V4 region in fecal samples. MHF diet similarly reduced alpha diversity in both isocaloric and ad libitum fat-fed animals by 5 months. Bray-Curtis dissimilarity analysis revealed unique beta diversity in each dietary group in female mice at 3 and 5 months, while fat-fed groups of male mice were not different. Elevated abundance of Firmicutes was found in all MHF ad libitum fed male and female mice. Bacteroidetes was reduced in all MHF fed male mice, but only female mice fed the MHF diet ad libitum. Allobaculum abundance was positively associated with MHF ad libitum feeding, while Muribaculaceae abundance exhibited a negative association. Notable graded-abundance associations between ad libitum control-fat fed, isocalorically fat-fed, and ad libitum fat-fed mice were observed for bacteria such as Lactobacillus salivarius; providing insight into effects of dietary fat consumption vs. overconsumption. Transient abundance changes, observed with Ruminococcaceae for example, capture microbial dynamics reflective of diet-induced obesity onset that were not sustained in chronic obesity. We conclude that the gut microbiome is differentially modulated by consumption of excess dietary fat vs. overconsumption of excess dietary fat leading to obesity.},
}

@article {pmid40812589,
year = {2025},
author = {Liu, L and Liang, L and Liang, H and Wang, M and Zhou, W and Mai, G and Yang, C and Chen, Y},
title = {Microbiome-metabolome generated bile acids gatekeep infliximab efficacy in Crohn's disease by licensing M1 suppression and Treg dominance.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.08.017},
pmid = {40812589},
issn = {2090-1224},
abstract = {INTRODUCTION: Despite the effectiveness of infliximab in treating Crohn's disease (CD), up to 40 % of patients fail to respond adequately.

OBJECTIVES: This study aimed to identify predictive biomarkers of primary non-response to infliximab in treatment-naïve CD patients by characterizing baseline gut microbiome-metabolome interactions and to validate their mechanistic role in driving therapeutic resistance.

METHODS: In a prospective cohort of 100CD patients initiating infliximab therapy and 49 healthy controls, we performed longitudinal 16S rRNA sequencing and untargeted metabolomics on pre-/post-treatment fecal samples. Machine learning (twelve algorithms including K-Nearest Neighbors, Linear Discriminant Analysis, Naive Bayes, and LightGBM) identified predictive microbial and metabolic features, with findings experimentally validated through fecal microbiota transplantation (FMT) in a murine TNBS-induced colitis model.

RESULTS: Non-responders demonstrated significant microbial dysbiosis marked by reduced α-diversity, depletion of Bifidobacterium, Blautia, and Lachnospiraceae, and enrichment of Escherichia/Shigella. Metabolomic profiling identified 179 differentially abundant metabolites, including deficiencies in taurochenodeoxycholic acid (TCDCA) and perturbations in glycerophospholipid metabolism and primary bile acid biosynthesis pathways. Among single-omics models, the microbiome-based Linear Discriminant Analysis achieved optimal performance (test AUC = 0.805), surpassing metabolomics-only (best AUC = 0.634) and integrated multi-omics approaches (best AUC = 0.779). SHAP analysis revealed Bifidobacterium as the dominant protective predictor, with its depletion strongly associated with non-response. Mechanistically, MIMOSA2 analysis linked Bifidobacterium catenulatum to TCDCA production, while FMT from non-responders exacerbated murine colitis through Treg depletion and M1 macrophage polarization, confirming microbiome-driven immune dysregulation.

CONCLUSIONS: These findings establish gut microbiome composition, particularly Bifidobacterium abundance, as a critical determinant of anti-TNF response in CD, mediated through bile acid-dependent regulation of Treg/M1 macrophage homeostasis. While multi-omics integration did not enhance predictive performance, microbiome-based machine learning models offer clinically actionable biomarkers for treatment stratification, providing a roadmap for precision therapy to overcome biological resistance in inflammatory bowel disease.},
}

@article {pmid40812586,
year = {2025},
author = {Zhu, C and Zhang, D and Wang, Y and Zhang, C and Wang, S and Xue, J and Lan, Z and Xun, Z and Zhang, L and Chao, J and Liang, Y and Xue, W and Pu, Z and Zhu, T and Ning, C and Sang, X and Wang, H and Jiang, X and Yang, X and Zhao, H},
title = {Gut microbiota and metabolite signatures predict severe immune-related adverse events in advanced hepatobiliary cancers.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.08.016},
pmid = {40812586},
issn = {2090-1224},
abstract = {INTRODUCTION: Immune checkpoint inhibition (ICI) has proven to be a major breakthrough in hepatobiliary cancers treatment. However, immune-related adverse events (irAEs) remain a major concern. The gut microbiome has been implicated in ICI efficacy; however, specific alterations in the multi-kingdom gut microbiota associated with severe irAEs are not well understood.

OBJECTIVES: We aimed to identify the signatures of gut microbiota, fungi, and metabolites in patients with advanced hepatobiliary cancers with severe irAEs compared to those in patients experiencing mild or no irAEs.

METHODS: We enrolled 168 patients with advanced hepatobiliary cancers between June 2018 and June 2022 (72 in the train set, 31 in test set 1, and 65 in test set 2). Multi-kingdom microbiota profiles were investigated using metagenomic, ITS2, and metabolomic datasets.

RESULTS: The presence of severe irAEs was associated with significantly longer overall survival compared with the irAE-Mild and irAE-No groups. Patients with severe irAEs showed significant differences in the composition of bacteria and metabolites, but relatively few differences in fungi, and had more complex network associations of multi-kingdom gut microbiota compared with the irAE-Mild and irAE-No groups. A predictive model based on four bacteria and six metabolites simultaneously discriminated irAE-Severe from irAE-Mild and irAE-No with high accuracy.

CONCLUSION: Patients with severe irAEs exhibited unique changes in microbiota-fungi-metabolite interactions. Gut microbiota- and/or metabolite-based algorithms could be used as additional tools for predicting severe irAEs and as potential prognostic markers in advanced hepatobiliary cancers.},
}

@article {pmid40812480,
year = {2025},
author = {Amarasena, S and Hossain, KS and Rasouli, A and Bertolo, RF and Yuan, Q and Mayengbam, S},
title = {Vitamin VB6 Deficiency Induces Anxiety-like Behavior in Sprague-Dawley Rats by Disrupting Gut Homeostasis.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.08.012},
pmid = {40812480},
issn = {1541-6100},
abstract = {BACKGROUND: Vitamin B6 (VB6) is essential for numerous metabolic pathways, including neurotransmitter synthesis, and its deficiency has been linked to neurological disorders. Emerging evidence suggests that B-vitamin deficiencies can disturb the gut microbiome. Although the gut-brain axis is well recognized, the influence of VB6 deficiency on behavior via gut-mediated mechanisms remains poorly understood.

OBJECTIVE: To investigate the role of VB6 in modulating the gut-brain axis and its impact on neurobehavioral outcomes.

METHODS: Sixty-four Sprague-Dawley rats were fed an AIN-93G-based diet with either optimal (OB6) or deficient (DB6) levels of VB6 for 7 weeks. Half of the animals received antibiotics (Abx) in drinking water (Ampicillin 1 g/L, Metronidazole 1 g/L, and Neomycin 1 g/L) plus weekly gavage (Vancomycin 500 mg/L and Amphotericin-B 0.1 mg/mL). Plasma VB6, neurotransmitters, short-chain fatty acids (SCFAs), behavioral assessments, gut microbiome composition, and gut histology were assessed. Data were analyzed using two- or three-way ANOVA with Fisher's LSD post hoc test (p≤0.05).

RESULTS: DB6 rats showed up to 96% reduction in plasma VB6 (p<0.001), 22% decrease in brain γ-aminobutyric acid (p<0.01), and 32% increase in glutamic acid (p<0.01) compared to OB6 animals. In the open-field maze, DB6 animals reduced center-zone entries by 42% in males and 20% in females (p<0.05), indicating anxiety-like behavior. Gut microbiota profiling revealed significant increases in Lachnospiraceae sp.(+385%), Mucispirillum schaedleri (+174%), and Harryflintia sp. (+848%), and decreases in Muribaculaceae sp. (-36%), Bacteroides vulgatus (-69%), and Bilophila sp. (-81%) (p<0.50). Cecal SCFAs levels declined in DB6 animals (p=0.01), including propionate (-18%) in males, and isobutyrate (-37%) and isovalerate (-63%) in females. Significant correlations (p<0.05) were found between these taxa and neurochemicals and behavioral changes.

CONCLUSIONS: VB6 deficiency alters gut microbiota composition, SCFAs synthesis, and neurotransmitter balance, leading to anxiety-like behavior. These findings underscore the role of the gut microbiota in mediating VB6-dependent gut-brain interactions.},
}

@article {pmid40812476,
year = {2025},
author = {Bhuiyan, MNI and Saha, BK and Satter, MA},
title = {Harnessing Artificial Intelligence and Precision Diets for Brain Health and Cognitive Resilience.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.08.007},
pmid = {40812476},
issn = {1541-6100},
abstract = {Smart neuro-nutrition represents an emerging interdisciplinary field at the intersection of nutritional science, neuroscience, and artificial intelligence (AI), to enhance cognitive resilience, mental well-being, and healthy brain aging through precision dietary strategies. This review critically examined the current body of evidence on the impact of dietary patterns and nutrients on neurobiological processes involved in cognitive decline, such as oxidative stress, mitochondrial dysfunction, neuroinflammation, neurotransmitter imbalance, and gut-brain axis dysregulation. Neuroprotective dietary approaches, including the Mediterranean, MIND, DASH, and ketogenic diets, are highlighted for their anti-inflammatory effects, alongside specific nutrients-omega-3 fatty acids, B-complex vitamins, polyphenols, and microbiota-directed fibers-that have demonstrated benefits for memory, executive function, and emotional stability. Recent advancements in AI are driving the development of personalized nutrition tools that integrate multimodal data sources, including wearable biosensors, image-based dietary tracking, and machine learning models predicting cognitive trajectories. These technologies enable real-time nutrient monitoring, individualized dietary planning, and early identification of neurodegenerative risks. However, challenges remain in the validation, scalability, and generalizability of AI models, especially across diverse populations. Ethical concerns such as data privacy, algorithmic bias, and transparency further emphasize the need for careful regulation and interdisciplinary collaboration. This review offers a comprehensive synthesis of smart neuro-nutrition, aligning biological mechanisms with digital innovations, and proposes future research priorities. These include the development of explainable AI systems, integration of microbiome and omics data, and implementation of standardized frameworks for clinical applications. By bridging neuroscience, nutrition, and AI, smart neuro-nutrition has the potential to revolutionize cognitive healthcare, offering scalable, precise, and equitable strategies to combat the rising global burden of neurodegenerative disorders.},
}

@article {pmid40812303,
year = {2025},
author = {Huang, Y and Zhang, X and Yu, C and Liu, Y and Kang, H and Liu, Y and Ni, Y and Xia, Y and Jiang, Z and Chen, J and Zhao, K and Han, L and Zou, X and Wang, J and Lei, T and Gan, C and Zhang, H},
title = {Lactobacillus acidophilus promotes cognitive function recovery via regulating microglial peroxisomal function in cerebral ischemia.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.07.018},
pmid = {40812303},
issn = {1934-6069},
abstract = {Cerebral ischemia causes significant mortality and is accompanied by inflammatory reactions that exacerbate damage. While the gut microbiota is linked to clinical outcomes, specific treatments and mechanisms remain unclear. Our metagenomics linked low Lactobacillus abundance to cognitive decline in patients with cerebral ischemia. L. acidophilus supplementation alleviated post-ischemic deficits in murine middle cerebral artery occlusion and bilateral carotid artery stenosis models. The neuroprotective effects of L. acidophilus were driven by enhanced gut absorption of linoleic acid (LinA). L. acidophilus-induced LinA activates peroxisomes in microglia, triggering microglial reprogramming to an anti-inflammatory state via reactive oxygen species (ROS) scavenging and β-oxidation-mediated epigenetic changes. These L. acidophilus-driven effects are lost upon dietary deficits in LinA, microglia depletion, or peroxisome disruption. A randomized clinical trial showed that L. acidophilus improved cognition and cerebral blood flow in ischemic patients. This study was registered at ClinicalTrials.gov (NCT05845983). Collectively, these findings reveal a therapeutic axis whereby L. acidophilus drives microglial reprogramming, providing a basis for microbiome-targeted neurotherapies.},
}

@article {pmid40812187,
year = {2025},
author = {Tričković, M and Kieser, S and Zdobnov, EM and Trajkovski, M},
title = {Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research.},
journal = {Cell host & microbe},
volume = {33},
number = {8},
pages = {1446-1458.e4},
doi = {10.1016/j.chom.2025.07.015},
pmid = {40812187},
issn = {1934-6069},
abstract = {Microbial strains within a single species can exhibit distinct functional characteristics due to variations in gene content and often show individual specificity, which can obscure unbiased associations and hinder deductive research. Here, we comprehensively define the human gut microbiota at a consistently annotated operational subspecies unit (OSU) resolution in an unbiased, cohort-independent manner, demonstrating that this approach can generalize across diverse global populations while maintaining specificity and improving interstudy reproducibility. We develop panhashome-a sketching-based method for rapid subspecies and species quantification and identification of genes that drive intraspecies variations-and show that subspecies carry implicit information undetectable at the species level. We identify subspecies associated with colorectal cancer (CRC) whose sibling subspecies or species are not, while a machine-learning CRC diagnostic algorithm based on subspecies outperformed species-level methods. This subspecies catalog allows identification of genes that drive functional differences between subspecies as a fundamental step in mechanistically understanding microbiome-phenotype interactions.},
}

@article {pmid40812185,
year = {2025},
author = {Common, JE and Payne, RP},
title = {Microbial Makeover: Skin microbiome reset after stem cell transplantation.},
journal = {Cell host & microbe},
volume = {33},
number = {8},
pages = {1318-1320},
doi = {10.1016/j.chom.2025.07.014},
pmid = {40812185},
issn = {1934-6069},
abstract = {Inborn errors of immunity disrupt host-microbe interactions. In this issue of Cell Host & Microbe, Che et al.[1] examine DOCK8-deficient individuals undergoing stem cell transplantation and show that immune reconstitution rebalances the skin microbiome, underscoring the central role of immunity in shaping cutaneous microbial ecology.},
}

@article {pmid40812176,
year = {2025},
author = {Ramirez-Villacis, DX and Leon-Reyes, A and Pieterse, CMJ and Raaijmakers, JM},
title = {Born to rewild: Reconnecting beneficial plant-microbiome alliances for resilient future crops.},
journal = {Cell host & microbe},
volume = {33},
number = {8},
pages = {1241-1255},
doi = {10.1016/j.chom.2025.06.017},
pmid = {40812176},
issn = {1934-6069},
abstract = {Plant domestication is a coevolutionary process shaped by human selection, favoring traits supporting modern-day agriculture. This process has reduced genetic diversity and fixed alleles for desirable traits, coinciding with changes in agricultural practices, particularly soil tilling, crop monocultures, and the (over)use of fertilizers and pesticides. The combined effects-collectively termed "domestication syndrome"-have contributed to the homogenization of soil and plant-associated microbial communities, reducing diversity and disrupting beneficial plant-microbiome alliances. Microbiome rewilding has uncovered ecological, genetic, and molecular principles underlying these depleted plant-microbiome partnerships. Studies have revealed ancestral microbial taxa enriched in wild crop relatives, plant genes, and metabolites critical for microbial recruitment, as well as the potential of reintroducing microbes to enhance nutrient uptake, pathogen resistance, and stress tolerance. These findings offer models for restoring such interactions in modern crops. We review the current state of crop microbiome rewilding and highlight how these discoveries are instrumental for designing resilient crop systems.},
}

@article {pmid40812175,
year = {2025},
author = {Bhat, A and Haney, CH},
title = {The role of plant receptor-like kinases in sensing extrinsic and host-derived signals and shaping the microbiome.},
journal = {Cell host & microbe},
volume = {33},
number = {8},
pages = {1233-1240},
doi = {10.1016/j.chom.2025.07.012},
pmid = {40812175},
issn = {1934-6069},
abstract = {Microbiota provide diverse benefits to their hosts, including nutrient acquisition, stress tolerance, and disease resistance. However, the mechanisms by which plants coordinate intrinsic and extrinsic cues to shape microbial communities remain poorly understood. Receptor-like kinases (RLKs), one of the largest gene families in plants, are central to the perception of both exogenous and endogenous signals, including pathogens, mutualists, and plant physiology. Indeed, recent evidence has identified RLKs that regulate microbiome structure and function. This minireview focuses on how their quantity and ability to transduce diverse signals make RLKs strong candidates to coordinate plant physiology and immunity with the microbiome.},
}

@article {pmid40812107,
year = {2025},
author = {Guidoni, L and Tremblay, ÉD and Van der Heyden, H and Morales-Rodriguez, C and Vannini, A},
title = {Fungal communities in biowaste composting: a comparative study of multiple ratios of woodchips vs. a perlite-cardboard blend as bulking agents.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {126889},
doi = {10.1016/j.jenvman.2025.126889},
pmid = {40812107},
issn = {1095-8630},
abstract = {The large production of biowaste can cause environmental risks if not managed properly. Composting is considered a sustainable solution for the disposal of this material, but generating high-quality compost requires proper design of feedstock composition and operational procedures. Microorganisms mediate the degradation of organic matter into a nutrient-rich substrate yet their response to different compost recipes is still poorly understood. In this study, fruit and vegetable biowaste was co-composted with woodchips or a perlite + cardboard mix in four different recipes (two representing optimal composting conditions and the other two were unideal composting conditions). Then, using Illumina high throughput sequencing, was defined the core fungal community shared by all treatments, mapped fungal succession through all composting phases and treatments, and identified indicator taxa associated to compost's specific recipes or phases. Our results confirm the presence of a core microbiome common to all compost piles dominated by Aspergillus but also reveal that every recipe has a degree of uniqueness in its fungal community and that the type of bulking agent used can significantly affect the composition of the fungal community during the latest stages of composting. At least one biomarker was associated with every recipe, with some reflecting the environmental conditions occurring such as the yeast P. kudriavzevii when more biowaste was present or T. lanuginosus when higher temperatures were reached during the thermophilic phase. These findings will contribute to increasing the knowledge of microbial dynamics during composting and provide useful information for the future use of biological parameters to assess compost quality.},
}

@article {pmid40812094,
year = {2025},
author = {Lin, BC and Zhu, L and Xu, H and Xiao, YP and Xu, JQ and Huang, YF and Yang, CZ and Wang, MQ and Bai, ZJ and Zhu, W and Wei, YH and Li, HT and Chen, YR},
title = {Associations between per- and polyfluoroalkyl substances (PFAS) exposure via infant feeding and the gut microbiota of preterm infants: A study of mother-preterm infant dyads.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {118853},
doi = {10.1016/j.ecoenv.2025.118853},
pmid = {40812094},
issn = {1090-2414},
abstract = {Infants are exposed to per- and polyfluoroalkyl substances (PFAS) via feeding, yet the influence of PFAS on their gut microbiota remains poorly understood. In this study, 73 mother-preterm infant dyads were recruited in Shenzhen. We measured concentrations of 13 PFAS (PFBA, PFPeA, PFHxA, PFHpA, PFOA, PFNA, PFBS, PFHxS, PFOS, HFPO-DA, ADONA, 6:2 Cl-PFESA, and 8:2 Cl-PFESA) in the feeding substances (breast milk or formula) at the fourth week postpartum. Concurrently, fecal samples from preterm infants were collected for analysis of gut microbiota and metabolites. The highest mean concentrations were observed for two short-chain PFAS: PFBA and PFPeA. Eleven out of the 13 PFAS had detection rates exceeding 50 % and were included in subsequent analyses. Linear regression analysis indicated that daily intakes of PFBA, PFPeA, PFHxA, PFHpA, PFOA, PFNA, PFBS, and PFHxS were negatively associated with the ln-transformed PD_whole_tree index. Daily intakes of PFBA, PFBS, PFOA, and PFHxS were significantly linked with β diversity. The genus Veillonella was more abundant in the upper tertile groups of PFBA and PFBS. Moreover, daily intakes of PFHpA and PFOA were linked to predicted microbiome functions. Pathway analysis further revealed that PFAS daily intake was associated with synthesis or metabolism of multiple nutrients (including vitamins and amino acids). Notably, linear regression demonstrated that PFAS daily intake was negatively associated with levels of docosapentaenoic acid and docosahexaenoic acid. Our findings suggest that PFAS exposure through feeding may adversely affect the gut microbiota and normal development of preterm infants, potentially posing health risks.},
}

@article {pmid40811957,
year = {2025},
author = {Anuntakarun, S and Thaweesapphithak, S and Krasaesin, A and Prommanee, S and Arunyanak, S and Kungsadalpipob, K and Acharya, A and Porntaveetus, T and Mattheos, N},
title = {Microbiome Shifts in Peri-Implantitis: Longitudinal Characterization of Dysbiosis and Resolution.},
journal = {International dental journal},
volume = {75},
number = {5},
pages = {100951},
doi = {10.1016/j.identj.2025.100951},
pmid = {40811957},
issn = {1875-595X},
abstract = {OBJECTIVE: To characterize the longitudinal dynamics of the peri-implant microbiome in patients with peri-implantitis and healthy implants.

METHODS: The peri-implant microbiome was characterized longitudinally in patients with peri-implantitis and healthy implants via 16S rRNA gene sequencing. Samples were collected at baseline, 3-, and 6-months post-treatment. Bioinformatic analysis was performed to identify significant microbial shifts over time RESULTS: At baseline, peri-implantitis sites exhibited significantly higher relative abundances of Prevotella (8.44%) and Fusobacterium (16.91%), compared to healthy implant sites, which were dominated by Streptococcus (16.91%) and Neisseria (10.06%). Post-treatment, Haemophilus increased in both groups by 3 months, particularly in peri-implantitis sites (19.94%). At 6 months, Streptococcus increased in PI sites (13.10%), while Veillonella and Neisseria remained prevalent in healthy sites. Differential abundance analysis confirmed partial recovery of peri-implantitis sites, with baseline dysbiosis marked by increased Veillonella, Treponema denticola, and Porphyromonas gingivalis.

CONCLUSIONS: This study highlights dynamic shifts in the peri-implant microbiome during peri-implantitis progression and recovery, marked by specific changes in Prevotella, Fusobacterium, Haemophilus, Streptococcus, Veillonella, and key periodontal pathogens. These longitudinal changes offer insights into disease pathogenesis and underscore the potential of microbiome-targeted therapies.},
}

@article {pmid40811873,
year = {2025},
author = {Simpson, AM and Chase, AB and Rodríguez-Verdugo, A and Martiny, JB},
title = {Investigating bacterial evolution in nature with metagenomics.},
journal = {Current opinion in microbiology},
volume = {87},
number = {},
pages = {102654},
doi = {10.1016/j.mib.2025.102654},
pmid = {40811873},
issn = {1879-0364},
abstract = {Metagenomic sequencing has revolutionized our ability to capture the vast genetic diversity of microbiomes. The technique provides an especially detailed characterization of intraspecific diversity, and a growing number of studies are using that information to investigate bacterial evolution in nature. Here, we review how these studies operationally define evolution, the sampling approaches and metrics used, and the interpretation of the observed evolutionary signatures. Current studies address three main themes: (1) the mechanisms that generate genetic diversity, (2) the spatiotemporal structure of that diversity, and (3) the evolutionary processes that determine its fate. While metagenomics provides enormous potential to investigate in situ evolution, the approach also introduces new questions, including whether populations defined by read mapping are meaningful proxies for biological units of evolution. Addressing these questions will facilitate investigation of the role of evolution relative to ecological shifts in shaping a microbiome's response to environmental change.},
}

@article {pmid40811641,
year = {2025},
author = {Parsons, J and Decker, EL and Reski, R},
title = {Multiplication of peat moss (Sphagnum L.) species for climate action.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf367},
pmid = {40811641},
issn = {1460-2431},
abstract = {Mosses from the genus Sphagnum have experienced 350 million years of separate evolution, resulting in distinctive features, such as unlimited apical growth potential, unknown from other mosses. They are ecosystem engineers and the main components of peatlands. Although peatlands cover only a small part of Earth's landmass, they store more carbon than all living matter combined. Peat mining and agriculture result in degraded peatlands, and thus have a dramatic negative impact on our climate. Sphagnum farming is a promising approach to combat climate change. Here, we review the state of the art with a focus on the establishment of a peat moss collection and their growth in vitro, especially in photobioreactors. Axenic, monoclonal Sphagnum strains have been established from spore capsules that have been collected from different peatlands across Europe. Analyses with flow cytometry have revealed haploid as well as diploid accessions. Optimization of the media composition for several species have resulted in an up to 50-fold biomass increase in a photobioreactor process. Future work should employ transcriptomics for a further optimization of biomass gain. Moreover, the importance of the Sphagnum microbiome should be considered for transplantation of the axenic, clonal moss material to open fields.},
}

@article {pmid40811531,
year = {2025},
author = {Guo, D and Liu, Z and Raaijmakers, JM and Xu, Y and Yang, J and Erb, M and Zhang, J and Zhu, YG and Xu, J and Hu, L},
title = {Linalool-triggered plant-soil feedback drives defense adaptation in dense maize plantings.},
journal = {Science (New York, N.Y.)},
volume = {389},
number = {6761},
pages = {eadv6675},
doi = {10.1126/science.adv6675},
pmid = {40811531},
issn = {1095-9203},
abstract = {High planting density boosts crop yields but also heightens pest and pathogen risks. How plants adapt their defenses under these conditions remains unclear. In this study, we reveal that maize enhances its defense in high-density conditions through a plant-soil feedback mechanism triggered by the leaf volatile linalool. Linalool activates jasmonate signaling in neighboring plants and promotes root exudation of benzoxazinoids, especially 2-(2-hydroxy-4,7-dimethoxy-1,4-benzoxazin-3-one)-β-d-glucopyranose (HDMBOA-Glc). These exudates in turn reshape the rhizosphere microbiome composition to favor growth of specific bacterial taxa that trigger broad-spectrum resistance, albeit at the cost of maize growth. This microbiome-driven feedback loop is governed by salicylic acid signaling. Our findings uncover intricate chemical signaling in high-density cropping, which is instrumental for improving soil health and designing sustainable strategies that balance the trade-off between plant growth and defense.},
}

@article {pmid40811432,
year = {2025},
author = {Ting, TY and Lee, WJ and Goh, HH},
title = {Bioengineering of Probiotic Yeast Saccharomyces boulardii for Advanced Biotherapeutics.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00236},
pmid = {40811432},
issn = {2161-5063},
abstract = {Saccharomyces cerevisiae var. boulardii (Sb), a subspecies of S. cerevisiae (Sc), is widely recognized for its probiotic properties. Recently, Sb has attracted growing interest as a chassis organism for engineered live biotherapeutics and advanced microbiome therapies. Traditional genetic manipulation techniques developed for Sc are now being successfully adapted for Sb, facilitating diverse genome integration strategies to enable the in situ biomanufacturing of functional molecules for disease intervention. Concurrently, research efforts are advancing Sb's potential as a platform for biosensing applications and diagnostic tools through the development of disease-responsive biosensors. Biosafety concerns are also being addressed through the design of biocontainment strains that ensure controlled application. To the best of our knowledge, earlier reviews have largely emphasized its clinical applications, safety profile, and probiotic mechanisms. This review uniquely consolidates recent advances in genetic modification, metabolic engineering, and synthetic biology strategies applied to Sb for therapeutic use. Together, these synthetic biology advancements position Sb as a promising and versatile platform for next-generation microbiome-based therapeutics and expanding applications in human health and food biotechnology.},
}

@article {pmid40811381,
year = {2025},
author = {Tepekule, B and Lim, AI and Metcalf, CJE},
title = {A model of early-life interactions between the gut microbiome and adaptive immunity provides insights into the ontogeny of immune tolerance.},
journal = {PLoS biology},
volume = {23},
number = {8},
pages = {e3003263},
doi = {10.1371/journal.pbio.3003263},
pmid = {40811381},
issn = {1545-7885},
abstract = {To achieve immune and microbial homeostasis during adulthood, the developing immune system must learn to identify which microbes to tolerate and which to defend against. How such 'immune education' unfolds remains a major knowledge gap. We address this gap by synthesizing existing literature to develop a mechanistic mathematical model representing the interplay between gut ecology and adaptive immunity in humans during early life. Our results indicate that the inflammatory tone of the microenvironment is the mediator of information flow from pre- to post-weaning periods. We evaluate the power of postnatal fecal samples for predicting immunological trajectories and explore breastfeeding scenarios when maternal immunological conditions affect breastmilk composition. Our work establishes a quantitative basis for 'immune education', yielding insights into questions of applied relevance.},
}

@article {pmid40811355,
year = {2025},
author = {Liu, D and Zhou, H and Qu, Y and Zhang, H and Xu, Y},
title = {UMMAN: Unsupervised Multi-Graph Merge Adversarial Network for Disease Prediction Based on Intestinal Flora.},
journal = {IEEE transactions on computational biology and bioinformatics},
volume = {22},
number = {3},
pages = {1023-1033},
doi = {10.1109/TCBBIO.2025.3546729},
pmid = {40811355},
issn = {2998-4165},
abstract = {The abundance of intestinal flora is closely related to human diseases, but diseases are not caused by a single gut microbe. Instead, they result from the complex interplay of numerous microbial entities. This intricate and implicit connection among gut microbes poses a significant challenge for disease prediction using abundance information from OTU data. Recently, several methods have shown potential in predicting corresponding diseases. However, these methods fail to learn the inner association among gut microbes from different hosts, leading to unsatisfactory performance. In this paper, we propose a novel architecture, Unsupervised Multi-graph Merge Adversarial Network (UMMAN). UMMAN can obtain the embeddings of nodes in the Multi-Graph with an unsupervised scenario, which helps learn the multiplex and implicit association. Our method is the first to combine Graph Neural Networks with the task of intestinal flora disease prediction. We construct the Original-Graph using multiple relation types and generate the Shuffled-Graph by disrupting the nodes. We introduce the Node Feature Global Integration (NFGI) module to represent the global features of the graph. Furthermore, we design a joint loss comprising adversarial loss and hybrid attention loss to ensure that the real graph embedding aligns closely with the Original-Graph and diverges from the Shuffled-Graph. Comprehensive experiments on five benchmark OTU gut microbiome datasets demonstrate the effectiveness and stability of our method.},
}

@article {pmid40811344,
year = {2025},
author = {Rodriguez-Sanchez, A and Gonzalez-Lopez, J and Gonzalez-Martinez, A},
title = {Study on Robustness of Denoising and Clusterization Algorithms for the Computation of Microbiome Data.},
journal = {IEEE transactions on computational biology and bioinformatics},
volume = {22},
number = {4},
pages = {1752-1765},
doi = {10.1109/TCBBIO.2025.3570519},
pmid = {40811344},
issn = {2998-4165},
abstract = {One crucial factor for dissimilarity of microbiome studies is the choice between denoising or clusterization algorithms, respectively. Moreover, the robustness, or stability of these algorithms with respect to the number of sequences computed, and its effect on the calculated ecological metrics of the microbiome studied, are currently unknown. In this study, mock communities were used for the investigation of robustness of several denoising and clusterization algorithms. The effect that denoising error models and clusterization similarity thresholds, and the effect of rare biosphere removal from ecological analyses, were also assessed. The results showed robustness of α-diversity metrics, while β-diversity was clearly affected differentially for each of the algorithms tested. Taxonomic accuracy showed differences with respect to algorithms, number of sequences computed, and taxonomic closeness of the community studied. Removal of rare biosphere affected values of α-diversity and β-diversity metrics and taxonomic accuracy differently for algorithms and datasets tested. Clusterization and denoising algorithms showed different degrees of stability, which were influenced greatly by the dataset, and possibly the taxonomic similarity of microorganisms in the community studied. The results obtained are important for the future configuration of universal standards for microbiome exploration as well as for current methodological applications in this field.},
}

@article {pmid40811335,
year = {2025},
author = {Gadhia, N and Smyrnakis, M and Liu, PY and Blake, D and Hay, M and Nguyen, A and Richards, D and Xia, D and Krishna, R},
title = {A Novel Approach to Differential Expression Analysis of Co-Occurrence Networks for Small-Sampled Microbiome Data.},
journal = {IEEE transactions on computational biology and bioinformatics},
volume = {22},
number = {4},
pages = {1311-1322},
doi = {10.1109/TCBBIO.2025.3554740},
pmid = {40811335},
issn = {2998-4165},
abstract = {Graph-based machine learning methods are valuable tools for identifying and predicting variation in genetic data. In particular, understanding phenotypic effects at the cellular level is an accelerating area in pharmacogenomics. Insight into how drugs or disease affect bio-networks could aid drug development and precision medicine. This article proposes a novel graph-theoretic approach to infer a co-occurrence network from 16S microbiome data, designed specifically for smallsample datasets. Such datasets pose challenges due to sparsity, compositionality, and complex interactions. The methodology includes steps to enrich and statistically filter the inferred networks. The approach extracts informative, feature-rich, biologically meaningful, and statistically significant networks from limited data. While tailored for small datasets, it is broadly applicable and can be extended to multi-omics integration. The method is tested on data from chickens vaccinated and challenged with Eimeria tenella. Genetic reads are processed, and networks inferred to characterize intestinal ecosystems at three disease progression stages. Analysis of network features yields biologically intuitive conclusions using statistical methods. Notably, the distribution of node features evolves with disease progression, and distributions reveal mutualistic and parasitic species clusters. A sub-network consistently appears across all conditions, suggesting a 'persistent microbiome'. A clustering algorithm is also applied to demonstrate the methods utility for downstream analysis.},
}

@article {pmid40811268,
year = {2025},
author = {Chen, N and Schram, M and Bucur, D},
title = {gFlora: A Topology-aware Method to Discover Functional Co-response Groups in Soil Microbial Communities.},
journal = {IEEE transactions on computational biology and bioinformatics},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/TCBBIO.2025.3560853},
pmid = {40811268},
issn = {2998-4165},
abstract = {Microorganisms such as bacteria perform critical functions in the soil ecosystem: they mediate essential carbon, nitrogen, and nutrient cycling processes in soils. To manage the health and functions of soils, it is important to understand which soil functions are related the most to which microbial taxa-but this taxon-to-function link is difficult to discover because of the size and complexity of the soil ecosystem. A feasible solution is to discover functional links at the level of groups instead of individuals, using observational data of both taxa abundance and soil function indicators. We thus aim to learn the functional co-response group: a group of taxa whose co-response effect (the representative characteristic of the whole functional group) co-responds (associates well statistically) to a functional variable. Unlike the existing method, we model the soil microbial community as an ecological co-occurrence network with the taxa as nodes (weighted by their abundance) and their relationships (a combination from both spatial and functional ecological aspects) as edges (weighted by the strength of the relationships). Then, we design a method called gFlora which notably uses graph convolution over this co-occurrence network to compute the co-response effect of the group, such that the network topology is also considered in the discovery process. We evaluate gFlora on four real-world soil microbiome datasets (bacteria and nematodes combined with two soil functions: nitrogen mineralization and crop yield). gFlora outperforms the competing method on all evaluation metrics, and it discovers new functional evidence for taxa which were so far under-studied. We show that the graph convolution is crucial to taxa with relatively low abundance (thus removing the bias towards taxa with higher abundance), and the discovered bacteria of different genera are distributed in the co-occurrence network but remain tightly connected among themselves, demonstrating that topologically they fill different but collaborative functional roles in the ecological community.},
}

@article {pmid40811066,
year = {2025},
author = {Koperska, M and Kiraly, DD},
title = {Microbiome-derived metabolites in substance use disorders: Mechanisms and implications.},
journal = {Annals of the New York Academy of Sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/nyas.15416},
pmid = {40811066},
issn = {1749-6632},
support = {DA051551/DA/NIDA NIH HHS/United States ; DA056592/DA/NIDA NIH HHS/United States ; },
abstract = {Substance use disorders (SUDs) are a public health crisis with high mortality rates and significant societal costs. Current brain-targeted pharmacotherapies are often ineffective or poorly tolerated. Emerging evidence highlights the gut microbiome's role in influencing neurobiological and behavioral responses to drugs of abuse. This diverse microbial community communicates with the brain via neuroactive metabolites, immune modulation, and peripheral nervous system signaling. In SUDs, gut-derived metabolites such as short-chain fatty acids, tryptophan derivatives, neurotransmitters, bile acids, and immune molecules directly affect drug and alcohol use behaviors, as demonstrated in clinical and preclinical studies. Shared mechanisms across substances suggest these metabolites modulate addiction-like phenotypes. This review summarizes the role of gut microbiome-derived metabolites in addiction, their mechanisms of action, and neurobehavioral effects. It also discusses current methodologies for studying gut metabolites in SUDs and identifies critical research gaps. Advancing our understanding of the gut-brain axis may reveal novel therapeutic targets, paving the way for more effective SUDs treatments.},
}

@article {pmid40811065,
year = {2025},
author = {Torfs, JRR and Kreyer, M and Wittouck, S and Ahannach, S and Fruth, B and Lebeer, S and Eens, M and Staes, N},
title = {A comprehensive atlas of the bonobo gut bacteriome and its associated host and exposome factors.},
journal = {Cell reports},
volume = {44},
number = {8},
pages = {116128},
doi = {10.1016/j.celrep.2025.116128},
pmid = {40811065},
issn = {2211-1247},
abstract = {In great apes, the gut bacteriome shapes key physiological functions and is influenced by both the exposome and the host. Yet, isolating these independent contributions remains challenging. We sequenced 644 fecal samples from 212 wild and zoo-housed bonobos (Pan paniscus), matched with detailed data collection on host and exposome factors. This standardized dataset reveals clear differences in gut bacterial diversity and composition between wild and captive bonobos. Within the controlled zoo-housed cohort, factors such as age, transit time, diet, early life adversity, and medication use influence gut bacterial structure. Notably, social contact emerges as a stronger predictor of bacteriome similarity than genetics or other exposome factors, while maternal effects persist even in non-cohabiting mother-offspring dyads. By offering a unique, comprehensive, and standardized dataset, our work paves the way for future research into microbiome ecology, providing insights with far-reaching implications for both human and animal health in an increasingly industrialized world.},
}

@article {pmid40811063,
year = {2025},
author = {Qu, EB and Baker, JS and Markey, L and Khadka, V and Mancuso, C and Tripp, AD and Lieberman, TD},
title = {Intraspecies associations from strain-rich metagenome samples.},
journal = {Cell reports},
volume = {44},
number = {8},
pages = {116134},
doi = {10.1016/j.celrep.2025.116134},
pmid = {40811063},
issn = {2211-1247},
abstract = {Genetically distinct strains of a species can vary widely in phenotype, reducing the utility of species-resolved microbiome measurements for detecting associations with health or disease. While metagenomics theoretically provides information on all strains in a sample, current strain-resolved analysis methods face a tradeoff: de novo genotyping approaches can detect novel strains but struggle when applied to strain-rich or low-coverage samples, while reference database methods work robustly across sample types but are insensitive to novel diversity. We present PHLAME, a method that bridges this divide by combining the advantages of reference database approaches with novelty awareness. PHLAME explicitly defines clades at multiple phylogenetic levels and introduces a probabilistic, mutation-based framework to quantify novelty from the nearest reference. By applying PHLAME to publicly available human skin and vaginal metagenomes, we find clade associations with coexisting species, geography, and host age. The ability to characterize intraspecies associations and dynamics in previously inaccessible environments will enable strain-level insights from accumulating metagenomic data.},
}

@article {pmid40811058,
year = {2025},
author = {Geng, L and Fan, Z and Chen, R and Cho, KC and Liu, Y and Cheng, Y and Yang, J and Zhang, Y and Wei, X and Gong, L and Tang, Y and Xu, Z and Huang, W and Toufeeq, S and Zhai, Z and Pan, L and Zhang, J and Li, B and Beerntsen, BT and Lee, JH and Xiao, Y and Na, Y and Lee, WJ and Ling, E},
title = {The Nα-acetyl-L-lysine/Loxl2/H2O2 promotes intestinal tumor growth in Drosophila and cell proliferation in human colorectal cancer.},
journal = {Cell reports},
volume = {44},
number = {8},
pages = {116126},
doi = {10.1016/j.celrep.2025.116126},
pmid = {40811058},
issn = {2211-1247},
abstract = {A cancer-associated microbiome is considered a carcinogen capable of affecting tumor initiation and/or progression. However, little is known about the molecular mechanisms of tumor-microbiome interactions. Here, we show that Staphylococcus sciuri promotes Drosophila intestinal tumor growth by inducing intestinal stem cell (ISC) division. Metabolomic analysis revealed that Nα-acetyl-L-lysine derived from S. sciuri, but not other naturally Nα-acetylated L-type amino acids, promotes ISC division in germ-free and conventional animals. Biochemical analysis further shows that GCN5-related N-acetyl transferases of S. sciuri catalyze L-lysine and acetyl-CoA into Nα-acetyl-L-lysine. Drosophila lysyl oxidase-like 2 enzyme subsequently catalyzes Nα-acetyl-L-lysine to produce H2O2, forming the Nα-acetyl-L-lysine/Loxl2/H2O2 axis that activates ATR-Chk1 and JNK and subsequently triggers the JAK/STAT pathway required for ISC division and tumor growth. The Nα-acetyl-L-lysine/Loxl2/H2O2 axis also regulates human colorectal cancer cell division. The identification of Nα-acetyl-L-lysine/Loxl2/H2O2 axis provides distinct insights into the complex interplay among microbiome, tumor, and oxidative stress.},
}

@article {pmid40810979,
year = {2025},
author = {Lin, Y and Jia, Y and Zhou, C and Wang, H and Pan, C},
title = {Impact of Pesticide Abiotic Stresses on Plant Secondary Metabolism: From Plant Individuals to Ecological Interfaces.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c05713},
pmid = {40810979},
issn = {1520-5118},
abstract = {Pesticides, while essential for crop protection, act as chemical stressors that disrupt plant secondary metabolism─a critical mediator of environmental adaptation and crop quality. This review adopts a defense and detoxification mechanism-driven framework to analyze the mechanisms by which pesticides alter phytohormones, phenolics, volatile organic compounds, and specialized metabolites through direct phytochemical interactions, microbiome modulation, and soil environment shifts. We highlight pesticide-induced oxidative stress, transcriptional reprogramming, and enzymatic/nonenzymatic detoxification mechanisms, alongside effects via direct phytochemical interactions, microbiome modulation, and soil environment shifts. A comparative analysis of the differential impacts of distinct pesticide classes on plant secondary metabolism, with emphasis on molecular structural features and physicochemical properties. Integrating multiomics evidence, we elucidate the relationship between dynamic "pesticide-plant-microbe/soil" interactions and plant secondary metabolism. This review deepens the understanding of pesticide phytotoxicity from individual plants, plant-associated organisms, and soil environment, bridging molecular mechanisms with agricultural practices to balance crop protection and crop health.},
}

@article {pmid40810753,
year = {2025},
author = {Mahto, K and Kuwar, OK and Maloo, A and Kumar, A},
title = {Therapeutic potential of Boswellia serrata in arthritis management: mechanistic insights into COX-2, 5-LOX, and NFĸB modulation.},
journal = {Inflammopharmacology},
volume = {},
number = {},
pages = {},
pmid = {40810753},
issn = {1568-5608},
abstract = {Arthritis is a chronic inflammatory disorder characterized by joint pain, stiffness, and progressive cartilage degeneration, significantly impacting patient's quality of life. Current pharmacological treatments, including nonsteroidal anti-inflammatory drugs and corticosteroids, provide symptomatic relief but are associated with adverse effects and limited long-term efficacy. Boswellia serrata, a medicinal plant with a long history of use in traditional medicine, has gained attention for its potential in arthritis management due to its anti-inflammatory, chondroprotective, and immunomodulatory properties. The bioactive constituents, particularly boswellic acids, have been shown to inhibit primary inflammatory pathways including NFĸB, COX-2, and 5-LOX, thereby reducing inflammation and cartilage degradation. Preclinical and clinical studies suggest that Boswellia serrata alleviates pain, improves joint mobility, and slows disease progression with a favorable safety profile compared to conventional therapies. Despite these promising findings, challenges such as limited large-scale clinical trials, variability in extraction methods, and low bioavailability hinder its clinical application. Future research should focus on optimizing formulation strategies, exploring synergistic effects with existing therapies, and conducting high-quality randomized controlled trials to validate its efficacy and safety. In addition, mechanistic studies investigating its molecular targets and interactions with the gut microbiome could provide deeper insights into its therapeutic potential. This review critically evaluates the current evidence on Boswellia serrata in arthritis management, highlights existing research gaps, and discusses future directions for its clinical development. Addressing these challenges will facilitate its integration into mainstream medicine, offering a natural, safer, and potentially more effective alternative for arthritis treatment.},
}

@article {pmid40810667,
year = {2025},
author = {Shaw, D and Denoyelle, C and Tan, KSW and Clark, CG and Yoshikawa, H and Viscogliosi, E and Gentekaki, E and Jirků, K and Tsaousis, AD},
title = {Comprehensive Tools for Culturing Blastocystis: A Standardized Resource for Research and Diagnostics.},
journal = {Current protocols},
volume = {5},
number = {8},
pages = {e70175},
doi = {10.1002/cpz1.70175},
pmid = {40810667},
issn = {2691-1299},
abstract = {Blastocystis spp. is a widely prevalent anaerobic protozoan of uncertain pathogenicity found in the gastrointestinal tracts of over 1 billion people worldwide. Despite its potential significance in health and disease, Blastocystis spp. remains challenging to culture axenically due to its anaerobic nature and the diversity of its genetic subtypes. This manuscript presents a standardized toolkit for culturing Blastocystis spp. in xenic and axenic conditions, detailing protocols for the preparation of appropriate liquid and solid media, cryopreservation, and inoculation. By providing a comprehensive set of tools and methodologies, this work aims to streamline research on Blastocystis spp., enabling reproducibility, subtype characterization, and advancements in understanding its role in the gut microbiome and host health. © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Establishment of xenic Blastocystis culture from stool samples in liquid medium Basic Protocol 2: Subculturing from existing Blastocystis liquid culture Support Protocol 1: Preparation of modified Jones' medium for Blastocystis culturing Support Protocol 2: Preparation of trypticase-yeast extract-serum-gastric mucin-9 (TSGYM-9) medium for Blastocystis culturing Support Protocol 3: Preparation of liver extract-yeast extract-serum-gastric mucin (LYSGM) medium for Blastocystis culturing Basic Protocol 3: Subculturing xenic Blastocystis cultures in diphasic medium Support Protocol 4: Preparation of Robinson's medium for Blastocystis culturing Support Protocol 5: Preparation of Ringer's agar slants for Blastocystis culturing Basic Protocol 4: Axenization of Blastocystis cultures Basic Protocol 5: Subculturing axenic Blastocystis cultures in diphasic medium Support Protocol 6: Preparation of Boeck and Drbohlav's Locke-egg serum (LES) medium for Blastocystis culturing Support Protocol 7: Preparation of Boeck and Drbohlav's diphasic modified medium (BDMM) for Blastocystis culturing Basic Protocol 6: Establishment of axenic Blastocystis cultures in Iscove's modified Dulbecco's medium (IMDM) Basic Protocol 7: Establishment of axenic Blastocystis cultures in soft IMDM agar Basic Protocol 8: Establishment of axenic Blastocystis cultures on solid IMDM agar Basic Protocol 9: Optimized method for establishing axenic Blastocystis cultures on solid IMDM agar Basic Protocol 10: Establishment of axenic Blastocystis cultures in semi-solid Locke's agar Basic Protocol 11: Cryopreservation of xenic Blastocystis cultures Basic Protocol 12: Cryopreservation of axenic Blastocystis cultures Basic Protocol 13: Inoculation of liquid medium with xenic Blastocystis cultures from frozen stocks Basic Protocol 14: Inoculation of liquid medium with axenic Blastocystis cultures from frozen stocks.},
}

@article {pmid40810545,
year = {2025},
author = {Yu, R-g and Li, X-m and Zhang, L and Jiang, J and Zhang, B and Wu, X-b},
title = {RSV infection disrupts gut microbiota and metabolic homeostasis in mice, regulating pulmonary inflammation via the SPHK/S1P pathway.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0303524},
doi = {10.1128/spectrum.03035-24},
pmid = {40810545},
issn = {2165-0497},
abstract = {UNLABELLED: Respiratory syncytial virus (RSV) is a primary pathogen for lower respiratory tract infections in children, posing a significant health threat. However, the systemic effects of RSV, particularly on gut microbiota and immune regulation along the gut-lung axis, are not well understood. We utilized a mouse model of RSV infection and assessed dynamic changes in the gut microbiome via high-throughput sequencing. We also investigated the interplay between pulmonary inflammation and gut microbiota, as well as their metabolites, through metabolomics analysis. RSV infection did not substantially alter the gut microbiota's alpha diversity but modified the relative abundance of specific phyla and genera. Notably, there was an increase in taxa such as Bacteroidetes and Veillonella, which may be linked to inflammation. Concurrently, sphingolipid components, including sphingomyelin, sphingosine, and ceramide, were significantly reduced in RSV-infected mice, correlating with increased pulmonary sphingosine-1-phosphate (S1P) protein expression. Receiver operating characteristic analysis indicated the potential of sphingolipids as biomarkers for distinguishing healthy from RSV-infected states. Inhibition of the S1P metabolic pathway, using sphingosine kinase (SPHK) and S1P inhibitors, reduced S1P expression and pulmonary inflammation, as well as pro-inflammatory cytokines like interleukin-1 beta, interleukin-6, and tumor necrosis factor-alpha. Dietary changes, notably a low-fat diet, ameliorated lung inflammation and neutrophil accumulation in bronchoalveolar lavage fluid, highlighting the role of dietary intervention in managing RSV infection. Immunophenotyping revealed the effects of SPHK and S1P inhibitors on lymphocyte subpopulations, foreshadowing their roles in modulating immune responses. These findings offer novel insights into how RSV infection modulates pulmonary inflammation by altering gut microbiota and metabolic pathways, providing a basis for new therapeutic strategies.

IMPORTANCE: Our research provides new insights into how respiratory syncytial virus (RSV) infection affects the host's gut microbiota, lipid metabolism, and the immune-inflammatory network. The findings demonstrate that dietary modulation and pharmacological intervention of the sphingosine-1-phosphate pathway can mitigate inflammation caused by RSV infection, presenting potential avenues for the development of novel therapeutic strategies to treat RSV infections.},
}

@article {pmid40810543,
year = {2025},
author = {Gallo, M and Quagliariello, A and Dalla Rovere, G and Maietti, F and Cardazzo, B and Peruzza, L and Bargelloni, L and Martino, ME},
title = {Generating gnotobiotic bivalves: a new method on Manila clam (Ruditapes philippinarum).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0118924},
doi = {10.1128/spectrum.01189-24},
pmid = {40810543},
issn = {2165-0497},
abstract = {Understanding how microbiomes influence the physiology of animal hosts requires detailed mechanistic insights, often obtained through gnotobiological approaches. Model organisms are central to this research, offering key advantages such as experimental tractability, reproducibility, and ease of manipulation. However, there is a lack of established gnotobiotic models for the marine environment-especially for bivalves, which play a critical role in ecosystem functioning. This gap is particularly important in the context of climate change, where harnessing microbiome resilience could mitigate environmental challenges and enhance host responses. In this study, we present a protocol to generate microbiome-depleted and gnotobiotic clams (Ruditapes philippinarum), one of the most widely farmed molluscs in the world and a key sentinel species for environmental and climate change impacts. Our microbiome depletion protocol effectively eliminated all detectable bacterial genera in the clams, with the exception of Endozoicomonas elysicola, which was identified solely by 16S rRNA amplicon sequencing and not by cultivation methods. In addition, we developed a microbiome transplantation protocol using inoculation of a mock bacterial community that successfully colonized the recipient clams within 1 h of transplantation. By extending gnotobiotic methods to marine invertebrates, this work opens new avenues for investigating microbial influences on ecologically and economically important species, particularly under the pressure of a changing climate.IMPORTANCEThe extensive diversity of host-microbe symbioses across ecosystems requires the use of different models to identify conserved and specific processes underlying such relationships. The need for novel models is particularly relevant in the context of the rapid environmental modifications due to climate change. Bivalve molluscs play a crucial role in the functioning of marine ecosystems. In this study, we present the first experimental protocol for the generation of gnotobiotic clams of the species Ruditapes philippinarum, one of the most widely farmed molluscs in the world, and a sentinel organism for environmental pollution. Our work extends the current technical understanding of the establishment of gnotobiotic animals, providing an important method for testing research hypotheses on a key taxonomic group in animal ecology. This study will also open new avenues for investigating the influence of microorganisms on animal health and elucidate the transferability of mechanisms studied predominantly in vertebrates to marine invertebrates.},
}

@article {pmid40810521,
year = {2025},
author = {Kruasuwan, W and Arigul, T and Munnoch, JT and Nutaratat, P and Songvorawit, N},
title = {Gut-associated bacteria and their roles in wood digestion of saproxylic insects: The case study of flower chafer larvae.},
journal = {Insect molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imb.70010},
pmid = {40810521},
issn = {1365-2583},
support = {FF-2567A10512010//National Science, Research and Innovation Fund (NSRF), Thaksin University (Research Project Grant) Fiscal Year 2024/ ; CUFRB65_bcg(20)_088_23_18//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; R016841017//Mahidol University (Fundamental Fund: Fiscal Year 2025)/ ; B13F660073//Program Management Unit for Human Resources & Institutional Development, Research Innovation/ ; },
abstract = {Protaetia acuminata (Fabricius, 1775) (Coleoptera: Scarabaeidae) is widely distributed throughout Southeast Asia and plays a significant role in nutrient cycling by facilitating the decomposition of woody materials, a process that likely relies heavily on the contribution of symbiotic bacteria within their digestive system. However, their gut bacteria have not been thoroughly studied. By using V3-V4 amplicon sequencing, it was revealed that the midgut (MG) of Pr. acuminata larvae and fermented sawdust after rearing (FSD) share a similar microbial community, predominantly composed of Proteobacteria and Actinobacteriota, as well as functional genes associated with cellulolysis, nitrogen respiration, nitrate reduction and aerobic chemoheterotrophy. In contrast, the bacterial community in the hindgut (HG) was distinctly different, with anaerobic respiration being the dominant metabolic process. Agromyces, Altererythrobacter, Bacillus, Cellulomonas, Lysinibacillus, Pseudoxanthomonas and the family Promicromonosporaceae were the most common genera in MG, HG and FSD samples. The culture-based isolation method yielded 67 isolates from the larvae, with gram-positive bacteria predominating in HG and MG, whereas gram-negative bacteria were primarily found in the FSD. These microorganisms produce a range of lignocellulolytic enzymes including β-endoglucanase, laccase and xylanase that enable the beetles to digest their plant-based diet efficiently and also involve many biochemical pathways relating to biogeochemical cycling. Our results provide valuable insights into the gut-associated Pr. acuminata flower chafer larvae and could serve as a basis and reservoir for future studies on lignocellulolytic enzyme-producing bacteria.},
}

@article {pmid40810517,
year = {2025},
author = {Huffines, JT and Kiedrowski, MR},
title = {Staphylococcus aureus phenol-soluble modulins have dispersal and anti-aggregation activity towards corynebacteria.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0018325},
doi = {10.1128/jb.00183-25},
pmid = {40810517},
issn = {1098-5530},
abstract = {Staphylococcus aureus is a common upper respiratory tract (URT) pathobiont with high carriage rates in the upper airway disease chronic rhinosinusitis (CRS). CRS is associated with increased prevalence and abundance of S. aureus, and S. aureus-secreted toxins are implicated in CRS pathogenesis. Conversely, in CRS disease, the abundance of non-pathogenic commensal species has been observed to decline, leading to microbial dysbiosis that contributes to persistent inflammation. Here, we investigated possible mechanisms S. aureus could employ to outcompete commensal organisms and contribute to establishing the S. aureus-dominant microbiome found in individuals with CRS. We performed a targeted screen to identify S. aureus-secreted factors that affect the growth and aggregation of a URT commensal bacterium, Corynebacterium pseudodiphtheriticum, which is negatively correlated with S. aureus in CRS. S. aureus cell-free conditioned media prevented C. pseudodiphtheriticum aggregation; however, anti-aggregation activity was significantly reduced in S. aureus mutants lacking a functional accessory gene regulator (agr) quorum-sensing system, phenol-soluble modulin (PSM) transporters, and the PSM toxin δ-toxin. Addition of purified recombinant δ-toxin peptide or a related PSM, PSMα3, inhibited C. pseudodiphtheriticum aggregation and induced dispersal of aggregates. Recombinant δ-toxin also reduced C. pseudodiphtheriticum adherence and aggregation on human nasal epithelial cells. PSMs are known to play a role in biofilm structure and remodeling in staphylococci, and here, we demonstrate that PSMs have activity against other bacteria. These results identify a novel mechanism by which S. aureus can disrupt the commensal lifestyle of microbes that inhabit the same upper respiratory niche via secreted PSM toxins.IMPORTANCEIncreased Staphylococcus aureus abundance and microbial dysbiosis are associated with the pathogenesis of chronic rhinosinusitis disease. Here, we show that S. aureus δ-toxin, a secreted phenol-soluble modulin (PSM) toxin, can inhibit the ability of commensal Corynebacterium species to aggregate, adhere to, and grow in association with human nasal epithelial cells. PSMs are known to play a key role in the S. aureus biofilm life cycle, regulating S. aureus biofilm structure and detachment; however, a role for these toxins in modifying biofilm and aggregate structures of other bacteria has not been previously demonstrated. These results suggest a potential mechanism for S. aureus to establish dominance in the upper respiratory tract microbiome in disease through direct antagonism of commensal microbes with PSM toxins.},
}

@article {pmid40810454,
year = {2025},
author = {Mateos-Hernandez, L and Denis-Abuin, L and Wu-Chuang, A and Maitre, A and Roháčková, H and Rego, ROM and Piloto-Sardiñas, E and Valdes, J and Porcelli, S and Heckmann, A and Moutailler, S and Lucas-Torres, C and Moos, M and Opekar, S and Kratou, M and Obregon, D and Cabezas-Cruz, A},
title = {Anti-microbiota vaccine induces lysine-mediated modulation of tick immunity affecting Borrelia colonization.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf082},
pmid = {40810454},
issn = {1574-6941},
abstract = {Tick microbiota influences Borrelia colonization, but changes in the microbiota-derived metabolite and how this affects tick physiology and vector competence is unclear. We investigated whether microbiota-induced metabolite modifications influence tick physiology and pathogen transmission. Using an anti-microbiota vaccine (live Escherichia coli) to immunize mice, we generated host antibodies that modulated the tick microbiome, decreasing bacterial abundance and increasing lysine levels in ticks. Elevated lysine correlated with increased tick weight. Lysine supplementation experiments enhanced defensin expression with DefMT6 exhibiting anti-Borrelia activity, reducing pathogen load in ticks. Our findings demonstrate that anti-microbiota vaccines induce metabolite changes, affecting tick physiology, immunity, and vector competence. These insights open new avenues for developing microbiota-targeted strategies to control tick-borne diseases.},
}

@article {pmid40810386,
year = {2025},
author = {Chen, CC and Pilla, R and Toresson, L and Sung, CH and Blake, AB and Correa Lopes, B and Turck, J and Jergens, AE and Summers, SC and Unterer, S and Ishii, PE and Giaretta, PR and Tolbert, MK and Suchodolski, JS},
title = {Microbial Gene Profiling and Targeted Metabolomics in Fecal Samples of Dogs With Chronic Enteropathy With or Without Increased Dysbiosis Index.},
journal = {Journal of veterinary internal medicine},
volume = {39},
number = {5},
pages = {e70199},
doi = {10.1111/jvim.70199},
pmid = {40810386},
issn = {1939-1676},
support = {//Purina Petcare Research Excellence Fund/ ; },
abstract = {BACKGROUND: In previous studies, only a subset of dogs with chronic enteropathy (CE) had an increased dysbiosis index (DI) or altered fecal metabolites or both, suggesting differences in underlying intestinal pathophysiology between these subsets.

OBJECTIVES: To compare microbial functional genes and fecal metabolites between healthy dogs with DI < 0 (HC) and dogs with CE and DI > 0 (increased DI-CE) or DI < 0 (normal DI-CE).

ANIMALS: Retrospective cross-sectional study including 78 HC and 138 CE dogs.

METHODS: Fecal microbiome was assessed by DNA shotgun sequencing. Dysbiosis index was quantified by qPCR. Targeted fecal metabolites, long-chain fatty acids, sterols, bile acids (BAs), and carbohydrates were measured using gas chromatography-mass spectrometry (GC-MS).

RESULTS: In permutational analysis of variance (PERMANOVA), functional gene profiles showed larger shifts in increased DI-CE (median R[2] [95% confidence interval (CI)] = 0.12 [0.08-0.17]) than normal DI-CE (0.02 [0.01-0.04]) compared with HC (adjusted-p < 0.02), characterized by increased counts of carbohydrate and lipid degradation genes. Similarly, increased DI-CE (PERMANOVA, median R[2] [95% CI] = 0.23 [0.14-0.34]) had larger shifts in fecal metabolome than normal DI-CE (0.10 [0.04-0.20]; adjusted-p < 0.02). Increased DI-CE had lower fecal unconjugated secondary BAs percentage (95% CI; HC, 88.4%-96.4%; normal DI-CE, 79.8%-99.0%; increased DI-CE, 28.1%-64.1%) and transporter-independent carbohydrates (combined ribose, xylose, rhamnose, and arabinose) concentrations (1.6-2.6; 0.7-1.8; 0.3-1.3 ng/mg; adjusted-p < 0.01).

CONCLUSIONS: Results indicate differences in fecal microbial gene profiles and metabolome in increased DI-CE versus normal DI-CE and HC, suggesting dogs with an increased DI have more severe intestinal changes in metabolic functions.},
}

@article {pmid40810349,
year = {2025},
author = {Thompson, E and Shah, A and Zaransky, S and Dhanda, A and Bono, K and Bono, J and Lamichhane, S and Mudhar, A and Kaye, R and Johnson, WE and Cugini, C and Yan, K},
title = {Early Insights Into the Healthy Laryngeal Microbiome: A Pilot Study Evaluating Salivary and Oropharyngeal Sampling as Proxies.},
journal = {The Laryngoscope},
volume = {},
number = {},
pages = {},
doi = {10.1002/lary.70043},
pmid = {40810349},
issn = {1531-4995},
support = {PC 162-25//New Jersey Health Foundation/ ; },
abstract = {OBJECTIVES: The microbiome plays a critical role in health and disease. While the oral cavity microbiome is well-characterized, the healthy laryngeal microbiome remains underexplored despite its unique immunological role. Laryngeal sampling is more invasive, time-consuming, and costly than salivary and oropharyngeal sampling. Understanding microbial differences between sites can help optimize sampling strategies.

METHODS: Nineteen individuals undergoing otolaryngologic surgery for non-oral or laryngeal disease were included. Matched saliva, oropharyngeal swabs, and laryngeal swabs were collected. DNA was extracted, and the V3/V4 region of the 16S rRNA gene was amplified and sequenced using Illumina NextSeq 2000. Amplicon sequence variants were identified via DADA2, and taxa were classified using a hybrid alignment/naïve Bayes approach. Microbial diversity was assessed using alpha and beta diversity measures.

RESULTS: Among 19 participants (31.6% female, mean age 61), most identified as Spanish, Hispanic, or Latino (36.8%). No significant differences were found in taxa diversity between the saliva, oropharynx, and larynx. Core microbiomes shared 13 taxa, with unique taxa in saliva and larynx. While unadjusted comparisons showed that some taxa were differentially abundant between the saliva and the larynx, these differences did not remain significant after correction for multiple comparisons using false discovery rate. Microbiome composition did not predict sample site.

CONCLUSION: While both salivary and oropharyngeal samples showed similar taxonomic diversity to the larynx, the oropharynx is a superior surrogate, sharing more core taxa, and lacking unique core taxa of its own. The oropharynx could represent a cost-effective alternative for microbiome diagnostics, enhancing patient comfort and clinical feasibility without compromising insights.

LEVEL OF EVIDENCE: Level 3-small prospective cohort study.},
}

@article {pmid40810305,
year = {2025},
author = {In 't Zandt, D and Florianová, A and Šurinová, M and In 't Zandt, MH and Klanderud, K and Vandvik, V and Münzbergová, Z},
title = {Temperature and Precipitation Jointly Shape the Plant Microbiome by Regulating the Start of the Growing Season.},
journal = {Global change biology},
volume = {31},
number = {8},
pages = {e70431},
doi = {10.1111/gcb.70431},
pmid = {40810305},
issn = {1365-2486},
support = {RVO 67985939//Akademie Věd České Republiky/ ; 184912//Norges Forskningsråd/ ; 244525//Norges Forskningsråd/ ; 315249//Norges Forskningsråd/ ; 22-00761S//Grantová Agentura České Republiky/ ; },
abstract = {Climate change is altering associations between plants and soil microbiota, threatening ecosystem functioning and stability. Predicting these effects requires understanding how concomitant changes in temperature and precipitation influence plant-soil microbiota associations. We identify the pathways via which temperature and precipitation shape prokaryote and fungal rhizosphere and root-associated networks of the perennial grass Festuca rubra in cold-climate ecosystems. We found that joint effects of temperature and precipitation are key in shaping plant-soil microbiota associations, with the start of the growing season as a critical mediating factor. Specifically, the start of the growing season is advanced by increasing temperature but delayed by increasing precipitation. This joint pathway particularly shaped rhizosphere organic matter degrading microbiota and root-associated putative plant pathotroph-saprotrophs and beneficial microbiota. We conclude that understanding local temperature, precipitation, and seasonal changes is crucial to accurately predict how the unique plant-microbiota interactions shaping cold-climate ecosystems are evolving with the ongoing change in climate.},
}

@article {pmid40810243,
year = {2025},
author = {Nakayama, S and Yonekura, S and Murase, K and Nakagawa, I and Izawa, K and Nakajima, S and Kabashima, K},
title = {Dupilumab improves skin microbiome in a paediatric case of Netherton syndrome.},
journal = {Journal of the European Academy of Dermatology and Venereology : JEADV},
volume = {},
number = {},
pages = {},
doi = {10.1111/jdv.70006},
pmid = {40810243},
issn = {1468-3083},
support = {JP22H04925//Japan Society for the Promotion of Science (JSPS)/ ; 20gm6010014h0004//Japan Agency for Medical Research and Development [AMED]/ ; },
}

@article {pmid40810230,
year = {2025},
author = {Lina, Z and Xiu, L and Xin, Z and Wenjuan, LI and Ye, Z},
title = {Study on the mechanism of Fuzi Lizhong decoction in the treatment of colorectal cancer of spleen kidney deficiency from the perspective of intestinal flora and hypoxia inducible factor-1α signalling pathway.},
journal = {Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan},
volume = {45},
number = {4},
pages = {845-851},
pmid = {40810230},
issn = {2589-451X},
support = {2017GXNSFBA198216//Guangxi Natural Science Foundation "Controllable Synthesis of Ordered Mesoporous Seafoam-Loaded g-C3N4 Gomposites and Their Mechanism of Adsorption-Photocatalytic Degradation of Antidepressants in Water Bodies"/ ; 19-185-10-04//Open Fund for the Director of Guangxi Key Laboratory of Spatial Information and Geographic Information "Geographic Spatial Analysis of Regional Urinary Tract Stone Disease"/ ; },
abstract = {OBJECTIVE: To evaluate the effect of Fuzi Lizhong decoction on intestinal flora, serum inflammatory factors, and hypoxia inducible factor-1α (HIF-1α) in patients with colorectal cancer associated with spleen and kidney Yang deficiency.

METHODS: A total of 100 patients diagnosed with advanced colorectal cancer were randomly divided into two groups: a control group (CON, 50) and a Traditional Chinese Medicine (TCM) group (n = 50). The control group received treatment with the Capecitabine + Oxaliplatin (CAPEOX) regimen, while the TCM group received the same regimen along with Fuzi Lizhong decoction for six weeks. Changes in intestinal flora were assessed before and after six weeks in both groups. Serum markers, including HIF-1α, vascular endothelial growth factor (VEGF), interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-α), were measured using enzyme-linked immunosorbent assay. Adverse reactions, clinical efficacy, and TCM syndrome efficacy were also monitored.

RESULTS: After six weeks, the levels of Lactobacillus and Bifidobacterium were significantly higher, while the levels of Enterobacter and Enterococcus were significantly lower in the TCM group compared to the control group (P < 0.05). Serum levels of HIF-1α, VEGF, IL-6, and TNF-α were also significantly reduced in the TCM group compared to the control group (P < 0.05). Additionally, the incidence of adverse reactions was lower, and the clinical efficacy was higher in the TCM group compared to the control group (P < 0.05).

CONCLUSION: Fuzi Lizhong decoction effectively improves intestinal microbiota composition, reduces inflammatory factors and HIF-1α expression, alleviates chemotherapy-related adverse reactions, enhances clinical efficacy, and may inhibit tumor growth in patients with colorectal cancer.},
}

@article {pmid40810221,
year = {2025},
author = {Raoqiong, W and Linyao, H and Ye, LU and Lingxue, W and Jianrong, LI and Yan, P and Hongmei, T and Shuangyang, LI and Xue, B},
title = {Mechanism analysis of Tongqiao Yizhi decoction in treating vascular dementia rats by brain tissue untargeted metabonomics and fecal 16S rRNA gene sequencing.},
journal = {Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan},
volume = {45},
number = {4},
pages = {759-769},
pmid = {40810221},
issn = {2589-451X},
support = {southwest Medical University [2021] No. 1//Southwest Medical University Project: Exploring the Neuroprotective Mechanism of Tongqiao Yizhi Decoction on Vascular Dementia Rats Based on the Brain Gut Axis/ ; },
abstract = {OBJECTIVE: To analyze the mechanism of Tongqiao Yizhi decoction (TQYZD,) in treating vascular dementia (VaD) rats using brain tissue untargeted metabonomics and fecal 16S rRNA gene sequencing.

METHODS: The chemical composition of TQYZD was analyzed by ultra-high performance liquid chromatography-high resolution mass spectrometry. The effects of TQYZD on VaD rats were evaluated by water maze test, hematoxylin-eosin staining, enzyme-linked immunosorbent assay and Western blot. Untargeted metabolomics and 16S rRNA sequencing were utilized to explore the relationship between metabolic profiles and the structure and function of intestinal flora. Fecal microbiota transplantation (FMT) was used to validate the role of gut microbiota in VaD. Spearman correlation analysis of differential metabolites and gut microbiota was performed.

RESULTS: The results showed that TQYZD improved cognitive function and neuronal damage in VaD rats, and reduced inflammatory response and repaired the intestinal barrier. In addition, TQYZD had the effect of modulating gut microbes in VaD rats, and FMT further confirmed that gut flora plays an important role in TQYZD treatment of VaD. Untargeted metabolomics revealed that VaD could lead to metabolic disorders in brain tissues, and TQYZD significantly altered the metabolites of brain tissues in Middle Cerebral Artery Occlusion rats. The results of spearman correlation analysis showed that there was a significant correlation between intestinal flora and the metabolites of brain tissues.

CONCLUSION: In this study, we demonstrated that TQYZD can improve metabolic disorders in vascular dementia rats by acting on intestinal flora.},
}

@article {pmid40810199,
year = {2025},
author = {Lin, YT and Sayols-Baixeras, S and Graells, T and Dekkers, KF and Baldanzi, G and Nguyen, D and Larsson, A and Feldreich, TR and Nielsen, N and Eklund, AC and Holm, JB and Nielsen, HB and Bergström, G and Smith, JG and Malinovschi, A and Engström, G and Orho-Melander, M and Fall, T and Ärnlöv, J},
title = {Identification of gut microbiome signatures and metabolites associated with albuminuria in type 2 diabetes.},
journal = {The Journal of clinical endocrinology and metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1210/clinem/dgaf453},
pmid = {40810199},
issn = {1945-7197},
abstract = {CONTEXT: Type 2 diabetes is a growing global concern with serious complications, including kidney damage and cardiovascular morbidity and mortality. Monitoring albuminuria, which is associated with these complications, is crucial in optimal diabetes management. Gut microbiota composition has been suggested to impact albuminuria, but large studies with granular data are lacking.

METHODS: We investigated the relationship between 1002 gut microbial species, 1308 plasma metabolites and albuminuria in 752 participants with type 2 diabetes from the Swedish CArdioPulmonary BioImage Study. To determine the relative abundance of species, we employed deep shotgun metagenomic sequencing of fecal samples. Plasma metabolites were analyzed using mass spectrometry-based methods.

RESULTS: We identified three species that were associated with albuminuria, including Sellimonas intestinalis, Eggerthellales sp., Ellagibacter isourolithinifaciens. Two of these species were replicated in an independent pre-diabetic population (n=3,423) in SCAPIS. In total, 36 annotated metabolites were associated with the three albuminuria-signature species. Functional mapping of the signature species suggests a role in the regulation of the metabolites of imidazole propionate and trigonelline, which have previously been reported to play roles in the progression of albuminuria.

CONCLUSIONS: These findings provide additional evidence of the potential impact of microbial species and contribute to our understanding of the complex relationship between the gut microbiome, plasma metabolites, and albuminuria in individuals with diabetes.},
}

@article {pmid40810122,
year = {2025},
author = {Yassine, F and Najm, A and Bilen, M},
title = {The role of probiotics, prebiotics, and synbiotics in the treatment of inflammatory bowel diseases: an overview of recent clinical trials.},
journal = {Frontiers in systems biology},
volume = {5},
number = {},
pages = {1561047},
pmid = {40810122},
issn = {2674-0702},
abstract = {BACKGROUND: The increasing incidence of inflammatory bowel diseases (IBD) over the last two decades has prompted the need to create new types of therapeutic interventions. The gut microbiome has emerged as a key component in the prognosis and pathophysiology of IBDs. The alteration or dysbiosis of the gut microbiome has been shown to exacerbate IBDs. The bacterial composition of the gut microbiome can be modulated through the usage of probiotics, prebiotics, and synbiotics. These interventions induce the growth of beneficial bacteria. Additionally, these interventions could be used to maintain gut homeostasis, reduce the inflammation seen in these morbidities, and strengthen the gut epithelial barrier.

METHODS: The literature review was conducted in October 2024 using PubMed, Scopus, and Google Scholar screening for recent clinical trials in addition to reviews relevant to the topic.

AIMS: This review aims to summarize the recent clinical trials of probiotics, prebiotics, and synbiotics in IBD patients highlighting their potential benefits in alleviating symptoms and enhancing the quality of life.

CONCLUSION: Certain probiotic formulations such as single strain ones consisting of Lactobacillus, or mixed-strain combinations of Lactobacillus and Bifidobacterium, prebiotic compounds such as fructooligosaccharides, and synbiotic combinations of both have proven effective in improving the clinical, immunological, and symptomatic aspects of the disease course. While promising, these findings remain inconclusive due to inconsistent study designs, small sample sizes, and varying patient responses. This emphasizes the need for larger, well-controlled trials to determine their clinical efficacy.},
}

@article {pmid40810117,
year = {2025},
author = {van Donk, N and Raynal, A and Asin-Garcia, E},
title = {A Pseudomonas fluorescens AND-gate biosensor for protein expression at plant root proximity.},
journal = {Frontiers in systems biology},
volume = {5},
number = {},
pages = {1620608},
pmid = {40810117},
issn = {2674-0702},
abstract = {By 2050, global population growth will significantly increase food demand, placing additional pressure on agriculture, a sector already vulnerable to climate change. Traditional approaches like fertilizers and pesticides have helped boost yields but are increasingly seen as unsustainable. As bioengineering becomes more accessible, engineered soil microorganisms are emerging as promising alternatives. However, their application in the rhizosphere is often limited by poor survivability and the high metabolic cost of expressing heterologous genes without appropriate regulation. To address this, we developed a microbial whole-cell biosensor that activates gene expression only under favorable conditions: in close proximity to plant roots and at high bacterial population densities. We engineered the pSal/nahR system in our host Pseudomonas fluorescens SBW25 to respond to salicylic acid, a key root exudate. In parallel, we implemented a quorum sensing system based on LuxI and the luxpR/LuxR pair to monitor cell density. Both inputs were integrated using a toehold switch-based AND gate, triggering expression only when both conditions were met. This strategy minimizes metabolic burden and offers a tightly controlled system for expression at target locations. While further validation in rhizosphere-like conditions is required, our results provide a foundation for safer open-environment applications of microorganisms, making this biosensor a versatile tool for future agricultural biotechnology.},
}

@article {pmid40810014,
year = {2025},
author = {Fischer, MH and Rzepczynska, A and Kjøller, R},
title = {Taxonomic diversity in the global wheat phyllosphere mycobiome - a meta analysis.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1597807},
pmid = {40810014},
issn = {1664-462X},
abstract = {Wheat (Triticum aestivum L.) is a major crop grown on all continents. Due to environmental concerns, it is desirable to reduce the inputs of both chemical pesticides and inorganic fertilizers. However, yield reduction must be expected when switching to low-input systems. To mitigate such losses, the use of natural or introduced microbiomes may provide the key to maintaining sustainable yield. Phyllosphere fungi, both endophytic and phylloplane-associated, colonize aboveground plant structures, some of which have the potential to mitigate biotic and abiotic stressors. A first step toward realizing the potential of the wheat microbiome is to map the current knowledge on wheat phyllosphere fungi. This meta-analysis aims to map the diversity and abundance of fungal taxa associated with the wheat phyllosphere across global wheat-producing areas. To this end, we searched previous published literature and retrieved fungal community data from relevant studies. Retrieved studies included both culturing-based and metabarcoding amplicon sequence-based studies. We retrieved and analyzed 33 studies from five regions across the world, which differed greatly in their taxonomic composition. Across all regions, we found that while the majority of identified genera were unique to individual studies, some genera occurred across all five wheat growing regions, specifically Alternaria, Aspergillus, Bipolaris, Candida, Chaetomium, Cladosporium, Epicoccum, Fusarium, Nigrospora, Penicillium, Pyrenophora, Stemphylium and Trichoderma. Furthermore, we identified that while community composition differed between wheat growing regions, the identification method used was the most significant factor determining the depiction of community composition. We also highlight a lack of research in important wheat growing regions that are important for global wheat production. These considerations and other knowledge gaps are used to pinpoint future research.},
}

@article {pmid40809439,
year = {2025},
author = {Li, J and Chen, Y and Hu, B},
title = {The intricate interactions between the lungs and gut in patients: unraveling the crosstalk mechanism.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1624907},
pmid = {40809439},
issn = {2296-858X},
abstract = {There is a growing body of evidence indicating that the stimulation of one organ can significantly influence the functioning of another. For instance, intestinal complications are frequently observed during respiratory diseases, and conversely, pulmonary complications can arise during intestinal diseases-a phenomenon referred to as lung-gut crosstalk. Patients suffering from mechanical ventilator-induced lung injury, chronic obstructive pulmonary disease (COPD), acute respiratory distress syndrome (ARDS), and other pulmonary conditions have been shown to experience gastrointestinal dysfunction and related disorders. Similarly, individuals with inflammatory bowel disease (IBD) have also been found to develop pulmonary complications. However, these studies are not enough to fully explain the mechanism of lung-intestinal crosstalk, and more potential mechanisms need to be explored and further elucidated. In this paper, we summarize recent research advancements regarding lung-intestinal interactions in the context of pulmonary and intestinal diseases, analyzing the potential mechanisms of lung-intestinal crosstalk from the perspectives of respiratory mechanics, inflammation, and microbiota. Additionally, we review evidence suggesting that adipokines may play a role in lung-gut interactions, and we propose new avenues for investigating the mechanisms underlying these interactions.},
}

@article {pmid40809226,
year = {2025},
author = {Bae, J and Woo, W and Gardner, SE},
title = {The wound microbiome associated with deep sternal wound infection: a scoping review.},
journal = {Journal of thoracic disease},
volume = {17},
number = {7},
pages = {5330-5346},
pmid = {40809226},
issn = {2072-1439},
abstract = {BACKGROUND: Deep sternal wound infection (DSWI) is a serious complication following cardiovascular surgery, increasing patient mortality and healthcare burden. Understanding the wound microbiome, including microbial load, microbial diversity, presence/abundance of common wound microorganisms, and biofilm formation, is crucial for improving infection prevention, diagnosis, and management. This scoping review aims to: (I) summarize DSWI definitions, specimen acquisition methods, and microbial identification techniques; (II) synthesize current DSWI literature regarding microbial load, microbial diversity, presence/abundance of common wound microorganisms, and biofilm formation.

METHODS: A scoping review was conducted using PubMed and EMBASE to identify studies on the wound microbiome in DSWI. Studies were included if they were in English, focused on adults, and published in journals. Exclusion included secondary sources, case reports, transplant populations, and other nosocomial infections. Data extraction followed a standardized approach, and findings were synthesized narratively, with a table summarizing study details. Seventy-one studies were included in this scoping review.

RESULTS: The Centers for Disease Control and Prevention (CDC) criteria were most commonly used for DSWI. Specimen location was unspecified in 60.6% of studies, while 14.1% specified the mediastinum. Methods of specimen acquisition were reported in only 25.3% of studies. Culture techniques were predominant (91.5%), while molecular or imaging methods were used in only 8.5%. Among studies using culture, Staphylococcus aureus was the most common microorganism, and 22.5% investigated polymicrobial infections. Molecular studies identified resistance genes such as blaZ in Staphylococci and blaKPC in carbapenem-resistant Enterobacteriaceae (CRE). Biofilm formation was examined in only 2.8% of studies, with findings linking staphylococci to biofilm presence in DSWI.

CONCLUSIONS: This review revealed critical gaps in DSWI research, including poor reporting of specimen acquisition, a narrow focus on common wound microorganisms, and an overreliance on culture-based methods. The lack of standardized specimen collection reporting reduces data reliability and comparability. Limited use of molecular techniques restricts insights into microbial complexity. Advanced molecular techniques, including polymerase chain reaction, 16S ribosomal RNA (rRNA) sequencing, and metagenomic sequencing, are needed to improve microbiome characterization. Addressing these gaps will improve infection prevention and management for DSWI.},
}

@article {pmid40809124,
year = {2024},
author = {Trego, A and Palmeiro-Sánchez, T and Graham, A and Ijaz, UZ and O'Flaherty, V},
title = {First evidence for temperature's influence on the enrichment, assembly, and activity of polyhydroxyalkanoate-synthesizing mixed microbial communities.},
journal = {Frontiers in systems biology},
volume = {4},
number = {},
pages = {1375472},
pmid = {40809124},
issn = {2674-0702},
abstract = {Polyhydroxyalkanoates (PHA) are popular biopolymers due to their potential use as biodegradable thermoplastics. In this study, three aerobic sequencing batch reactors were operated identically except for their temperatures, which were set at 15 °C, 35 °C, and 48 °C. The reactors were subjected to a feast-famine feeding regime, where carbon sources are supplied intermittently, to enrich PHA-accumulating microbial consortia. The biomass was sampled for 16S rRNA gene amplicon sequencing of both DNA (during the enrichment phase) and cDNA (during the enrichment and accumulation phases). All temperatures yielded highly enriched PHA-accumulating consortia. Thermophilic communities were significantly less diverse than those at low or mesophilic temperatures. In particular, Thauera was highly adaptable, abundant, and active at all temperatures. Low temperatures resulted in reduced PHA production rates and yields. Analysis of the microbial community revealed a collapse of community diversity during low-temperature PHA accumulation, suggesting that the substrate dosing strategy was unsuccessful at low temperatures. This points to future possibilities for optimizing low-temperature PHA accumulation.},
}

@article {pmid40809055,
year = {2025},
author = {Shen, S and Liu, Y and Wang, N and Huang, Z and Deng, G},
title = {The role of microbiota in nonalcoholic fatty liver disease: mechanism of action and treatment strategy.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1621583},
pmid = {40809055},
issn = {1664-302X},
abstract = {Non-alcoholic fatty liver disease (NAFLD) is now the most prevalent chronic liver disease worldwide, ranging from simple hepatic steatosis to non-alcoholic steatohepatitis (NASH) and hepatocellular carcinoma. It poses a significant public health challenge. Growing evidence indicates that the gut microbiota plays a key role in the development and progression of NAFLD. Advances in sequencing technologies, microbiome and metabolomics have helped identify characteristic microbial patterns and microbial-derived metabolites associated with NAFLD. The gut-liver axis has emerged as a central pathway linking intestinal microbes to liver function. Microbiota-derived metabolites, such as short-chain fatty acids, bile acids (BAs), and trimethylamine N-oxide (TMAO), have dual roles in hepatic lipid accumulation, inflammation, and insulin resistance, providing new insight into NAFLD pathogenesis. This review summarizes the mechanisms by which disruptions in the gut-liver axis contribute to NAFLD progression. It also outlines the therapeutic effects and mechanisms of current probiotics, with particular emphasis on next-generation probiotics like Akkermansia muciniphila and the potential benefits of its inactivated forms. Furthermore, we explore the role of prebiotics, plant-derived compounds, and synthetic agents in modulating gut microbiota and liver health. The review highlights key associations between specific bacterial species, microbial metabolites, and NAFLD, offering a theoretical basis for microbiota-targeted precision interventions and new therapeutic directions.},
}

@article {pmid40809050,
year = {2025},
author = {Crane, YM and Crane, CF and Webb, C and Schemerhorn, BJ},
title = {Biotype and host relatedness influence the composition of bacterial microbiomes in Schizaphis graminum aphids.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1614492},
pmid = {40809050},
issn = {1664-302X},
abstract = {INTRODUCTION: The microbiome of greenbug aphid (Schizaphis graminum (Rondani)) was investigated in regard to greenbug biotype, collection date, host species, and host cultivar.

METHODS: DNA samples were collected from biotypes E and K feeding on 17 cultivars belonging to five host plant species, namely wheat, barley, rye, sorghum, and the goatgrass Aegilops triuncialis. Samples were taken immediately before infestation and two, four, and eight days thereafter. The V5-V7 hypervariable region of 16S rDNA was PCR amplified, Illumina sequenced, and aligned to a curated database of bacterial 16S rDNA sequences.

RESULTS AND DISCUSSION: The almost universal intracellular endosymbiont of aphids, Buchnera aphidicola, comprised 78.24 to 99.99% of the read counts among samples, largely because of its high copy number of genomes per bacteroid. Abundant non-Buchnera genera included Pseudomonas, Rhodanobacter, Massilia, and Enterobacter. Read counts of eight of 78 examined genera were more than 90% restricted to a single replicate of a single treatment. Shannon entropy was highest in biotype K and on the barley host, but it did not vary significantly among dates post infestation. Unweighted UniFrac distances most significantly varied with biotype, host plant species, infestation time, and almost all of their interactions. Weighted UniFrac and Jaccard distances varied less significantly. By counts of differentially populated genera, the factors biotype, host plant species, infestation time, and host plant resistance genes to greenbug, were consecutively less important. Functional analysis with PICRUSt2 illustrated a diminution of respiratory electron transport and long-chain fatty acids in the Buchnera endosymbiont, reflecting adaptation to an intracellular environment.},
}

@article {pmid40809045,
year = {2025},
author = {An, J and Wang, Q and Bai, Z and Ma, S and Yang, Z and Yu, D and Mo, X},
title = {Association between neurodevelopmental disorders in congenital heart disease and changes in circulatory metabolites and gut microbiota composition.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1639057},
pmid = {40809045},
issn = {1664-302X},
abstract = {BACKGROUND: Neurodevelopmental disorder (ND) has emerged as a critical factor affecting the long-term quality of life among patients with congenital heart disease (CHD). The aim of this study was to provide a multi-omics perspective on the mechanisms of ND.

METHODS: We analyzed the serum metabolome and gut microbiome of children with ND and non-ND (NND) in CHD populations.

RESULTS: In this prospective observational study, we identified associations between serum metabolites, gut microbial, and ND. Linolenic acid was most closely related to neurodevelopmental outcomes, showing positive correlations with multiple neurodevelopmental domains. Among the gut microbiota, the Escherichia genus was most strongly associated with neurodevelopmental outcomes, and negative correlations with neurodevelopmental domains.

CONCLUSION: This multi-omics study reveals significant association between altered serum metabolites, gut microbiota dysbiosis, and neurodevelopmental outcomes in children with CHD. The microbes and metabolites identified here may contribute to addressing the challenge of ND in the CHD population. Based on our findings, therapeutic strategies to reduce the risk of ND could be developed, including targeted manipulation of the gut microbiota and metabolites.},
}

@article {pmid40808833,
year = {2025},
author = {Wang, X and Feng, Y and Li, Y and Tian, Y and Zhang, S and Li, J and Zhang, J and Liu, F and Zhou, J and Li, T and Duan, S and Szeto, IM and Su, L and Luo, X},
title = {The influence of human milk composition and its microbiome on the gut microecology and early growth and development of preterm infants (the YI study): protocol design and cohort profile.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1566376},
pmid = {40808833},
issn = {2296-861X},
abstract = {INTRODUCTION: Breastfeeding can reduce the risk of serious illness in preterm infants. However, the influence of human milk on the gut microecology and early development of preterm infants remains unclear.

METHODS: The YI Study is a prospective cohort protocol conducted in China, designed to investigate the dynamic associations among breast milk composition, infant gut microecology, and health from a mother-breastmilk-preterm infant triad perspective. From January 2023 to May 2024, a total of 50 mother-term infant dyads and 35 mother-preterm infant dyads were enrolled and followed up at six timepoints: v1 (0-7 days), v2 (8-14 days), v3 (1 month), v4 (2 months), v5 (4 months), and v6 (6 months). Data collection included questionnaires, anthropometric measurements, and biospecimens. Questionnaires (including birth medical records, environment, feeding practices and illnesses status) and anthropometric measurements were collected at all visits. Biospecimens included paired samples of breast milk and feces were obtained at each visit, and comprehensively analyzed by multi-omics techniques. We also collected heel blood at birth to examine immune status and saliva at the v6 visit to explore the role of its constituents in dietary behaviors.

RESULTS: The average age of the mothers was 30.9 ± 3.5 years. The median gestational age was 36 (35, 36) weeks in the Preterm Group and 39 (38, 40) weeks in the Term group. The completion rate up to V6 was 82.9% in the Preterm Group and 94% in the Term Group. All samples were collected within the predefined visit windows, with a total of 452 breast milk, 465 infant feces, 227 maternal feces, 49 heel blood and 98 saliva.

DISCUSSION: Through ultra-early, multi-temporal, multi-sample collection, combined with multi-omics technologies, the YI study will provide an opportunity to explore the dynamic association of human milk as a complex biological system with gut microecology and health in preterm infants in depth.},
}

@article {pmid40808801,
year = {2025},
author = {Fehse, L and Tajabadi, M and Martin, R and Holzmann, H and Heider, D},
title = {gLinDA: A privacy-preserving, swarm learning toolbox for differential abundance analysis of microbiomes.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {3456-3463},
pmid = {40808801},
issn = {2001-0370},
abstract = {Count data, such as gene expression and microbiome composition, play a significant role in various diseases, including cancer, obesity, inflammatory bowel disease, and mental health disorders. For instance, understanding the differences in microbial abundance between patients is essential for uncovering the microbiome's impact on these conditions. Differential abundance analysis (DAA) can detect significant changes between groups of patients. However, since individuals have unique microbial fingerprints that could potentially be identifiable, microbiome data must be treated as sensitive patient data, which poses problems for collaborative studies in the medical field. In this work, we introduce gLinDA, a global differential abundance analysis tool that employs a privacy-preserving swarm learning approach for the analysis of distributed datasets. gLinDA maintains predictive performance while safeguarding patient sensitive data.},
}

@article {pmid40808715,
year = {2025},
author = {Pozdniakova, S and Uchida, A and Fontal, A and Cañas, L and Santamaria, S and Hui, LY and Luhung, I and Schuster, SC and Rodó, X and Borràs, S},
title = {Integrating air microbiome for comprehensive air quality analysis.},
journal = {iScience},
volume = {28},
number = {7},
pages = {113015},
pmid = {40808715},
issn = {2589-0042},
abstract = {Air quality monitoring typically overlooks the biological composition of airborne particles, despite its relevance to human health. This study evaluated the feasibility of using filters from high-volume air samplers, widely employed in air quality networks, to analyze bioaerosol content through shotgun metagenomic sequencing. We developed a DNA extraction method for ultra-low biomass samples and assessed the impact of sampling duration, particle size selection, and filter material on microbial diversity. Our findings show that prolonged continuous sampling reduces species detection, while larger particle size selectors capture a broader range of microbial content, particularly fungi. Comparisons with a dedicated bioaerosol sampler confirmed that these filters can yield comparable results. This work demonstrates that existing air quality infrastructure can be leveraged for airborne microbiome monitoring, offering a practical and cost-effective approach to integrate biological data into routine assessments and support a more comprehensive understanding of air quality and its implications for public health.},
}

@article {pmid40808678,
year = {2025},
author = {Agagündüz, D and Cocozza, E and Cemali, Ö and Bayazıt, AD and Nanì, MF and Cerqua, I and Morgillo, F and Saygılı, SK and Canani, RB and Amero, P and Capasso, R},
title = {Correction: Understanding the role of the gut microbiome in gastrointestinal cancer: A review.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1662597},
doi = {10.3389/fphar.2025.1662597},
pmid = {40808678},
issn = {1663-9812},
abstract = {[This corrects the article DOI: 10.3389/fphar.2023.1130562.].},
}

@article {pmid40808637,
year = {2025},
author = {Ferhaoui, N and Sebaihia, M and Sekizuka, T and Kuroda, M},
title = {Shotgun Metagenomic Investigation of the Microbiome in Diabetic Foot Infections Compared to Healthy Skin.},
journal = {Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society},
volume = {33},
number = {4},
pages = {e70074},
doi = {10.1111/wrr.70074},
pmid = {40808637},
issn = {1524-475X},
support = {//Algerian Ministry of Higher Education and Scientific Research (DGRSDT/MESRS)/ ; JP23fk0108666j0401//Research Program on Emerging and Reemerging Infectious Diseases of the Japan Agency for Medical Research and Development/ ; },
abstract = {Diabetic foot infection (DFI) is a major complication of diabetes, causing significant morbidity and mortality. Host factors and microorganisms in DFI can disrupt healing processes, leading to chronic, non-healing wounds. The aim of this study was to characterise the microbiome of DFIs and contralateral healthy foot skin (CHFS). Thirty-two diabetic patients were enrolled in this study. Samples were obtained from DFIs and CHFS from the same patient. The microbiome was profiled using metagenomic shotgun sequencing. All the samples were polymicrobial, with a predominance of the obligate anaerobes belonging to Bacteroidetes in PEDIS 4. While PEDIS 3 and 2 were dominated by Proteobacteria. CHFS showed similar bacterial composition across all grades of severity, and the most abundant genera detected were Corynebacterium, Staphylococcus, Pseudomonas, and Cutibacterium. The CHFS was more diverse than DFIs in PEDIS 3 and 4. However, DFIs and CHFS in PEDIS 2 present similar diversity. In addition, DFIs of this grade exhibited a high proportion of Corynebacterium as well as CHFS. PCoA analysis demonstrated that the community structure of DFIs was different from that of CHFS, with Prevotella, Bacteroides, and Porphyromonas the main contributors to the clustering. Neighbour-Net analyses revealed that DFIs exhibited lower diversity compared to CHFS and harboured a more homogeneous dominant bacterial community. Our study revealed a high abundance of obligate anaerobes, including Bacteroides, Prevotella, Morganella, and Porphyromonas, in more severe infections; along with a decrease in microbial diversity. Additionally, there was a decrease in the abundance of key bacteria from the normal skin microbiota.},
}

@article {pmid40808604,
year = {2025},
author = {Bornbusch, SL and Henry, BA and Gagliano, M and Muletz-Wolz, CR and Maslanka, MT},
title = {Gut Microbiomes of Ex Situ African Painted Dogs (Lycaon pictus) Reflect Social Group and Variation in Dietary Whole Prey.},
journal = {Zoo biology},
volume = {},
number = {},
pages = {},
doi = {10.1002/zoo.70020},
pmid = {40808604},
issn = {1098-2361},
support = {//Sally L. Bornbusch was supported by an NSF Postdoctoral Fellowship in Biology. Funding for this project came from Cincinnati Zoo and Botanical Garden discretionary funds./ ; },
abstract = {Understanding the factors that structure animal microbiomes across different species and environments is increasingly valuable to wildlife care and conservation efforts. Diet is a well-established driver of gut microbiome structure and function, and formulating nutritionally balanced diets is vital to ex situ animal care and management. Prebiotic dietary items can promote beneficial microbial communities in the guts of ex situ wildlife. Animal fibers (skin, hair, and connective tissue) can act as prebiotics for carnivores, influencing gut microbiome structure and function. Social interactions and differing environmental exposures can further shape animal microbiomes, with evidence of group and environmental signatures in the microbiomes of some social species. To test for respective patterns of diet and social group, we used 16S rRNA sequencing to track the gut microbiomes of two groups of African painted dogs (Lycaon pictus) housed at the Cincinnati Zoo & Botanical Garden. The diet of one group was shifted to include increased whole prey (e.g., rabbits), representing an uptick in animal fiber intake. We found that, despite both groups sharing a diverse set of core microbes, there were distinct group signatures in the dogs' microbiomes, a pattern that grew stronger over time. Furthermore, although the diversity of gut bacteria showed minimal variation between groups and over time, the overall microbial composition and the abundance of specific taxa varied significantly between groups and with increased dietary whole prey. The results of this study further demonstrate the value of zoo populations for understanding the factors that drive animal microbiome structure and highlight the influence of management decisions in shifting animal microbiomes.},
}

@article {pmid40808568,
year = {2025},
author = {Ma, W and Yang, L and Jing, Y and Ren, P and Liu, X and Zhang, M and Qi, X and Zhu, M and Zhang, Q},
title = {Multiomics reveals changes in lipid metabolism in the livers of landes geese before and after overfeeding.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.25.0405},
pmid = {40808568},
issn = {2765-0189},
abstract = {OBJECTIVE: : The aim of this experiment was to integrated production indices with omics sequencing to elucidate the systemic perturbations between hepatic metabolism and the gut microbiota during overfeeding.

METHODS: : A total of 120 seven-week-old male Landes geese were floor reared in a pen environment. Overfeeding commenced at week 8 using a corn-based diet containing 5% soybean oil. The feeding regimen consisted of three daily meals (150-180 g/meal) initially, gradually increasing to five meals (300-500 g/meal) after two weeks, and was maintained for a total overfeeding period of four weeks.

RESULTS: : The results demonstrated that overfeeding significantly increased liver weight and serum lipid levels, accompanied by intracellular lipid droplet accumulation. Concurrently, the downregulation of taurine-conjugated bile acids and the upregulation of free bile acids disrupted cholesterol homeostasis. Crucially, overfeeding triggered gut microbial dysbiosis characterized by Escherichia-Shigella enrichment and norank_o_Clostridia_UCG-014 depletion.

CONCLUSION: : Our work demonstrated that the identification of the "gut microbiota‒bile acid‒liver axis" could as a pivotal signaling pathway driving overfeeding-induced foie gras formation while providing a theoretical foundation for overfeeding strategies to mitigate metabolic pathologies in waterfowl production.},
}

@article {pmid40808417,
year = {2025},
author = {Chen, L and Zhang, M and Wei, W and Li, Q and Wang, L and Zhao, M and Li, H and Xu, H and Yang, P and Zhang, P},
title = {Lipid metabolism, microglia, and stroke.},
journal = {Neural regeneration research},
volume = {},
number = {},
pages = {},
doi = {10.4103/NRR.NRR-D-24-01523},
pmid = {40808417},
issn = {1673-5374},
abstract = {Microglia, lipids, and their interaction are found to play important roles in post-stroke immunity. Microglia are sensitive to detect environment change in injured brain. Activated microglia undergo phenotypical remodeling and trigger complex signal cascades to regulate immune responses after stroke. Lipids including peripheral lipid metabolism and lipid droplet biogenesis are involved in the control of microglia functions, such as activation, phagocytosis, proliferation, and pro-inflammation. In this review, we explore new scope of microglia and lipids in immune regulation of stroke. Implication of peripheral lipid metabolism after stroke is mentioned and advances in microglia-lipid interaction are discussed. We give a special focus on how diet and gut microbiome influence neuroinflammation system via gut-brain axis, and how these processes associate with the risk and outcome of stroke. Moreover, we reviewed the therapeutic targets related to lipid metabolism and microglial modulation after stroke. These can provide a prospective strategy for more efficient and safer treatment for ischemic and hemorrhagic stroke.},
}

@article {pmid40808288,
year = {2025},
author = {Rahimpour, H and Talebi, AA and Raz, A and Azarbad, H and Mehrabadi, M},
title = {Geographic variation and diversity of bacterial endosymbionts in Asian citrus psyllid, Diaphorina citri, from Iran.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70100},
pmid = {40808288},
issn = {1526-4998},
support = {//Iran National Science Foundation/ ; },
abstract = {BACKGROUND: The Asian citrus psylla (ACP, Diaphorina citri), a destructive insect, poses a significant threat to citrus industries worldwide. As the primary vector of huanglongbing (HLB), ACP infestations have caused devastating economic losses and declines in citrus production across many regions. Despite the role of endosymbionts in psyllid biology and HLB transmission, their geographic distribution in Iran remains uncharacterized. In this study, the composition of bacterial endosymbiont communities associated with ACP was examined across four geographic regions in Iran (Sarbaz, Roudan, Faryab, and Jahrom).

RESULTS: Using 16S rRNA gene sequencing and quantitative real-time polymerase chain reaction (qPCR), the presence and abundance of bacterial endosymbionts, including Carsonella, Profftella, and Wolbachia, were confirmed in both nymphal and adult stages of this insect across all populations. Other bacteria, such as Diplorickettsia, Hamiltonella, and Lactobacillus, were identified only in certain populations. Phylogenetic analysis, principal component analysis (PCA), and heatmap clustering highlighted geographical variation in the abundance and diversity of endosymbionts, with the Jahrom population exhibited considerable geographical variation than other regions.

CONCLUSION: Our results revealed significant geographic variation in the prevalence of key bacterial taxa, including Wolbachia and Carsonella. In addition, we report for the first time the presence of Hamiltonella defensa and Diplorickettsia in this insect vector, offering potential targets for microbiome-based pest control strategies tailored to local ACP populations. These findings underscore the importance of understanding how endosymbionts shape ACP biology and its ability to transmit pathogens, and they highlight the potential for innovative pest control approaches, such as manipulating symbiont populations to reduce ACP fitness or disease transmission. © 2025 Society of Chemical Industry.},
}

@article {pmid40808268,
year = {2025},
author = {Xu, G and Guo, J and Yu, X and Zhao, N and Li, X and Yuan, T and Xu, Z and Zhao, T and Zhao, S and Li, X and Liu, X},
title = {Multi-Omics Analysis Reveals Adaptive Strategies of Meconopsis horridula to UV-B Radiation in the Qinghai-Tibet Plateau.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70117},
pmid = {40808268},
issn = {1365-3040},
support = {//This study was supported by the Local Development Funds of the Science and Technology Department of Tibet (Grants XZ202001YD0028C and XZ202102YD0031C), and by the Graduate High-Level Talent Training Program of Tibet University (Grant 2025-GSP-B017)./ ; },
abstract = {Meconopsis horridula, an endemic medicinal and alpine horticultural species of the Qinghai-Tibet Plateau, exhibits remarkable adaptation to high-altitude UV-B radiation. Despite its ecological and medicinal significance, the mechanisms underlying its UV-B adaptation remain poorly understood. Here, we used a PacBio full-length transcriptome as a reference, integrating RNA-seq and metabolomic data from altitudinal populations, with field-based transcriptomic and microbiome profiling under shade-controlled UV-B gradients, to elucidate UV-B adaptive regulatory networks. KEGG enrichment and environmental correlation analyses highlighted flavonoid biosynthesis as a central pathway in UV-B adaptation at high altitudes. Controlled UV-B gradient experiments identified 10 conserved flavonoid biosynthesis genes, including chalcone synthase (CHS). Overexpression of CHS in Arabidopsis thaliana increased flavonoid content by approximately 1.2-fold. Co-expression analysis further revealed that CHS-associated regulatory factors mediate coordinated responses, including reduced light signalling, enhanced antioxidant capacity and suppression of defence genes and anthocyanin biosynthesis inhibitors. CHS, in coordination with immune regulation, modulates high-centrality microbes, contributing to differential network regulation and microbiome stability. Enriched key microbes may mitigate the growth-defence trade-off under UV-B stress through antimicrobial, growth-promoting and antioxidant activities. Collectively, our findings reveal a flavonoid-centred adaptation framework that deepens our understanding of UV-B resilience in alpine plants and offers potential resources for crop improvement.},
}

@article {pmid40808237,
year = {2025},
author = {Uttech, SK and Ordinola-Zapata, R and Noblett, WC and Martell, M and Lima, B and Staley, C},
title = {Multispecies Biofilms Treated With Endodontic Sealers or Calcium Hydroxide: Antimicrobial Activity and Changes in Community Composition.},
journal = {International endodontic journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/iej.70015},
pmid = {40808237},
issn = {1365-2591},
abstract = {INTRODUCTION: To evaluate the antimicrobial activity and changes in community composition in biofilms treated with two root canal sealers or calcium hydroxide.

MATERIAL AND METHODS: Forty-nine extracted bovine dentine cylinders were inoculated with subgingival dental plaque for 2 weeks in a CDC biofilm reactor. Three treatment groups were assigned: AH Plus, BC Sealer, and calcium hydroxide. Propylene glycol inert vehicle (PG) and untreated contaminated samples were used as controls. The infected root canal space was in direct contact with the materials for 7 days under anaerobic incubation. Anaerobic culture (colony forming units, CFU), quantification PCR (qPCR), and next generation sequencing were used to assess the effect of each material. Differences in the number of molecules (qPCR), CFU, and abundances of genera were evaluated using the Kruskal-Wallis test. The Shannon and Chao1 indices were used to measure alpha diversity. Differences in community composition were evaluated using non-parametric analysis of similarity (ANOSIM).

RESULTS: The CFU, Shannon, and Chao1 indices revealed significant differences between BC Sealer, AH Plus, and calcium hydroxide groups versus the untreated control group and PG (p < 0.003). Calcium hydroxide and BC Sealer significantly reduced the qPCR values compared to the control group and PG. The biofilm composition (98.5%) was primarily composed of Peptostreptococcus, Streptococcus, Parvimonas, Fusobacterium, Veillonela, Mogibacterium, Lancefieldella, Eubacterium, Slackia, and Prevotella. Significant differences in overall community composition and beta diversity between untreated controls and AH Plus were observed (ANOSIM R = 0.674, p < 0.001). Parvimonas, Streptococcus, Eubacterium, and Lancefieldella were not affected by any of the materials tested.

CONCLUSION: Calcium hydroxide and BC Sealer significantly reduced the viability and the total number of DNA copies. AH Plus sealer reduced the bacterial viability but did not affect the DNA concentration. AH Plus significantly alters overall biofilm community composition compared to other groups. None of the materials tested eliminated the multispecies biofilm completely.},
}

@article {pmid40808235,
year = {2025},
author = {Hansen, ML and Kordatos, KIT and Nørgaard, JK and Peter Bredal Jørgensen, J and Strube, ML and Schostag, MD and Yang, L and Jelsbak, L},
title = {Genetic Memory Devices to Detect Specialized Metabolites in Plant and Soil Microbiomes.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00073},
pmid = {40808235},
issn = {2161-5063},
abstract = {Root-associated microbiomes significantly influence plant growth and resilience through intricate chemical dialogues mediated by plant- and microbe-derived specialized metabolites. These metabolites play pivotal roles in shaping the assembly, dynamics, and ecological functions of soil microbiomes. Despite advances in in vitro and DNA sequencing studies, a comprehensive understanding of in situ chemical signaling within plant and soil microbiomes remains elusive due to experimental constraints. To address this gap, we developed and tuned a set of five whole-cell biosensors in Escherichia coli for spatiotemporal, nondisruptive detection of biologically relevant specialized metabolites, including 2,4-diacetylphloroglucinol, pyoluteorin, tetracycline, salicylic acid, and naringenin. Four of these biosensors were successfully adapted to the soil-compatible Pseudomonas putida KT2440 Δall-Φ strain. Additionally, the four sensors were shown to respond to their cognate ligand in a nonsterile soil extract medium containing a diverse microbiome extracted from soil. By employing genetic memory devices with DNA barcodes for readouts, our approach provides a scalable platform for sensing additional specialized metabolites in the future. This work demonstrates the potential of biosensor technologies to unravel the complex chemical interactions driving soil microbiome ecology, with implications for sustainable agricultural practices.},
}

@article {pmid40807689,
year = {2025},
author = {Theodoro, JMV and da Silva, LA and de São José, VPB and Willis, NB and Toledo, RCL and Grancieri, M and Carvalho, CWP and Pierre, JF and da Silva, BP and Martino, HSD},
title = {Processed Pearl Millet Improves the Morphology and Gut Microbiota in Wistar Rats.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {15},
pages = {},
doi = {10.3390/foods14152752},
pmid = {40807689},
issn = {2304-8158},
abstract = {This study evaluated the effect of pearl millet subjected to different processing on the intestinal health of rats. The animals were fed a standard iron-free diet (28 days) (hemoglobin depletion: 8.65 + 1.40 g/dL of hemoglobin). Subsequently, they were divided into four groups for hemoglobin repletion (21 days): standard diet + ferrous sulfate (SD + FS); standard diet + non-germinated open-pan cooked millet flour (SD + NGOPCMF); standard diet + germinated open-pan cooked millet flour (SD + GOPCMF); and standard diet + extrusion-cooked millet flour (SD + ECMF). Hemoglobin level did not differ among groups. The SD + NGOPCMF, SD + GOPCMF and SD + ECMF groups demonstrated a higher Chao index in the microbiome and a higher number and area of goblet cells and longitudinal muscle layer width. The SD + NGOPCMF and SD + GOPCMF groups demonstrated increased cecum weight, crypt depth, crypt thickness, and circular muscle layer width; lower fecal pH; and a higher relative abundance of Bacteroidota, while the SD + FS group showed the highest abundance of Actinobacteriota. The SD + GOPCMF group stood out for showing the lowest fecal pH, better α-diversity (Chao and Shannon index), and the highest width of the longitudinal muscle layer. In conclusion, pearl millet subjected to different processing, mainly germination, has the potential to improve the composition of the intestinal microbiota and the intestinal morphology in rats induced to iron deficiency.},
}

@article {pmid40807590,
year = {2025},
author = {Zhang, P and Dong, J and Lu, J and Cai, Z and Zhou, B and Zhang, Q and Zhu, C and Laghi, L},
title = {Dietary Interventions with Bletilla striata Polysaccharides and/or Composite Polysaccharides Remodel Liver Lipid Profiles and Ameliorate Gut Metabolic Disturbances in High-Fat Diet-Induced Obese Mice.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {15},
pages = {},
doi = {10.3390/foods14152653},
pmid = {40807590},
issn = {2304-8158},
support = {2024NSFSC0364//Natural Science Foundation of Sichuan Province/ ; ZYN2025244//Fundamental Research Funds for the Central Universities/ ; },
abstract = {The global obesity epidemic and associated metabolic disorders present urgent public health challenges. This study employed a multi-omics approach (lipidomics, metabolomics, and gut microbiome analysis) to investigate how Bletilla striata polysaccharides (BSPs) and composite polysaccharides modulate liver lipid metabolism and gut microbiota in high-fat diet (HFD)-induced obese mice. HFD elevated hepatic phosphatidylcholines, cholesteryl esters (CEs), and acylcarnitines (CARs), alongside increased cecal choline and trimethylamine. BSP interventions reduced hepatic CEs, free fatty acids (FAs), CARs, and cecal sarcosine while restoring gut microbial diversity. Notably, BSP enriched beneficial genera, including Jeotgalicoccus and Atopostipes, and the network analysis revealed negative correlations between these genera and hepatic triglycerides (TGs), implicating the gut-liver axis in lipid metabolism regulation. These findings elucidate the anti-obesity mechanisms of polysaccharides through gut microbiota remodeling and cross-tissue metabolic interactions, providing a foundation for leveraging plant polysaccharides in developing safer, effective obesity therapies.},
}

@article {pmid40807561,
year = {2025},
author = {Coronas, R and Bianco, A and Sanna, AML and Zara, G and Budroni, M},
title = {Type I Sourdough Preservation Strategies and the Contribution of Microbial Biological Resource Centers to Biodiversity Protection: A Narrative Review.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {15},
pages = {},
doi = {10.3390/foods14152624},
pmid = {40807561},
issn = {2304-8158},
support = {code n. IR0000005//European Commission-NextGenerationEU, Project SUS-MIRRI.IT "Strengthening the MIRRI Italian Research Infrastructure for Sustainable Bioscience and Bioeconomy",/ ; Hermaion 2.0//Sardinia Region PSR 2014-2022/ ; MicroBiodiverSar project//Sardinia Regional Government/ ; },
abstract = {Traditional type I sourdoughs are being rediscovered and increasingly used in artisanal and industrial bakeries due to the unique taste and texture, potential health benefits, and longer shelf life they confer on to baked products. These unique properties are attributed to the diverse microbial communities of sourdough, comprising both yeasts and bacteria. The traditional preservation method for type I sourdough (i.e., continuous backslopping) may lead, over time, to taxonomic and functional rearrangements of its microbial communities. Consequently, significant deviations in the characteristics of baked products can occur. In this context, this review aims to summarize the recent literature on the long-term preservation and maintenance strategies for type I sourdough and highlight the essential role that microbial biological resource centers (mBRCs) could play in the preservation and sharing of sourdough microbiomes. Specifically, the identification of appropriate preservation methods, implementation of well-defined access and benefit-sharing protocols, and development of microbiome-specific datasets, should be encouraged within the context of mBRCs. These infrastructures are expected to play a pivotal role in preserving the microbiota of fermented foods, serving as a crucial element for innovation and the safeguarding of traditional foods and culinary heritage.},
}

@article {pmid40807505,
year = {2025},
author = {Georgalaki, M and Ferrocino, I and Buzzanca, D and Anastasiou, R and Zoumpopoulou, G and Giabasakou, D and Ziova, D and Kokkali, A and Paraskevakos, G and Tsakalidou, E},
title = {The Natural Fermentation of Greek Tsounati Olives: Microbiome Analysis.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {15},
pages = {},
doi = {10.3390/foods14152568},
pmid = {40807505},
issn = {2304-8158},
support = {60148//Zoëfarma Inc., Headquarters in #320-3484 Boul. Des Sources, Dollard-des-Ormeaux, Québec, H9B 1Z9 Canada/ ; },
abstract = {The comprehensive analysis of microbial communities reveals the unique microbial identity of different olive varieties, paving the way for new strategies in their development and commercial exploitation. In this context, the present study aimed to explore the microbial diversity and functional characteristics of Tsounati variety olives from the Monemvasia region of Peloponnese, Greece, that were naturally fermented for three months. The bacterial and fungal microbiota of both olives and brines were fingerprinted throughout the fermentation through classical microbiological analysis combined with molecular techniques. Among the 148 isolated bacteria, 85 were lactic acid bacteria (LAB), and 63 belonged to the Enterobacteriaceae family, while the 178 fungal isolates comprised 136 yeasts and 42 non-yeast or yeast-like fungi. Metataxonomic analysis confirmed the dominance of the bacterial genera Lactiplantibacillus, Leuconostoc, along with the Enterobacteriaceae family, and it revealed the presence of Coleofasciculaceae cyanobacteria mostly in olives. The dominant fungal genera were yeasts, namely Saccharomyces, Nakazawaea, and Cyberlindnera. Using the Folin-Ciocalteu assay, the average total polyphenol content of Tsounati fermented olive samples was 761.80 ± 128.87 mg gallic acid equivalents kg[-1] after 90 days of fermentation. The concentrations of the triterpenic, maslinic, and oleanolic acids, as determined by HPLC, remained stable throughout fermentation, with average values of 4764 and 1807 mg kg[-1], respectively. Finally, sensory analysis revealed the rich aromatic character of Tsounati variety, highlighting its potential to be used for Greek-style table olive production.},
}

@article {pmid40807286,
year = {2025},
author = {Wróblewska, J and Długosz, A and Czarnecki, D and Tomaszewicz, W and Błaszak, B and Szulc, J and Wróblewska, W},
title = {The Role of Oxidative Stress in Skin Disorders Associated with Alcohol Dependency and Antioxidant Therapies.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {15},
pages = {},
doi = {10.3390/molecules30153111},
pmid = {40807286},
issn = {1420-3049},
abstract = {Alcohol dependency is a complex and chronic condition that negatively impacts multiple organ systems, including the skin. A key pathological factor in this process is oxidative stress, leading to progressive cellular damage, chronic inflammation, and accelerated cutaneous aging. Alcohol metabolism generates reactive oxygen species (ROS), which overwhelm endogenous antioxidant defenses and contribute to a range of skin alterations, including nonspecific changes such as xerosis, erythema, and wrinkle formation, as well as inflammatory and neoplastic skin disorders. Additionally, alcohol-induced alterations of the skin microbiome may further exacerbate skin barrier dysfunction and inflammatory responses. This review explores the biochemical mechanisms and skin microbiome alterations linking alcohol-induced oxidative stress to skin damage and disease. Furthermore, it evaluates the therapeutic potential of antioxidant-based interventions, both natural and synthetic. Antioxidants may offer protective and regenerative effects by scavenging free radicals, modulating inflammatory responses, and enhancing skin barrier function. The paper aims to provide a comprehensive overview of the molecular and microbial interplay between alcohol, oxidative stress, and skin health, while identifying future directions for targeted antioxidant therapy in individuals with alcohol dependency.},
}

@article {pmid40807099,
year = {2025},
author = {Torrecillas-Quiles, L and Gómez-Ríos, I and Jiménez-García, I and Serrano-Belmonte, I and Ortiz-Ruiz, AJ and Serna-Muñoz, C},
title = {Oral and Dental Sequelae After Oncological Treatment in Children: A Systematic Review.},
journal = {Journal of clinical medicine},
volume = {14},
number = {15},
pages = {},
doi = {10.3390/jcm14155479},
pmid = {40807099},
issn = {2077-0383},
abstract = {Background: Childhood cancer is considered one of the main causes of mortality and morbidity worldwide. There is strong evidence of the oral toxic effects of oncologic treatments, but their incidence is difficult to determine. The novel therapeutic strategies in Pediatric Oncology have led to increased survival in this population, resulting in an increased incidence of long-term effects, which diminish the patient's quality of life. Methods: The search for articles started on 5 November 2024 and ended on 5 December 2024. Following the PRISMA Statement, a total of 1266 articles were obtained, from which 13 were selected for review. All articles were considered to be of high quality. The antineoplastic treatments used in them were chemotherapy, radiotherapy, surgery and immune therapy. Results: Most articles were cohorts and case controls. Only one case report was obtained. The results revealed that the most prevalent sequelae in the pediatric population after antineoplastic treatment were enamel alterations, microdontia, dental caries, periodontal disease, gingivitis, hyposalivation, alteration of the oral microbiome, alteration of mandibular bone density and malocclusion. The lesions are different depending on the therapy used. Conclusions: Oncologic treatments in children with cancer cause multiple oral sequelae such as microdontia, dental caries, enamel alterations, salivary gland alterations, mucositis and root resorption. It cannot be concluded which therapy has the most detrimental effect as each has a different mechanism of action in the oral cavity.},
}

@article {pmid40806882,
year = {2025},
author = {Lahoud, C and Habib, T and Kalta, D and Dimachkie, R and El Sayegh, S and Deeb, L},
title = {Intestinal Microbiota and Fecal Transplantation in Patients with Inflammatory Bowel Disease and Clostridioides difficile: An Updated Literature Review.},
journal = {Journal of clinical medicine},
volume = {14},
number = {15},
pages = {},
doi = {10.3390/jcm14155260},
pmid = {40806882},
issn = {2077-0383},
abstract = {Background/Objectives: Inflammatory bowel disease (IBD) is characterized by chronic relapsing and remitting inflammation of the gastrointestinal tract. Fecal microbiota transplantation (FMT) has emerged as an FDA-approved treatment for recurrent Clostridioides difficile infections (CDIs), with promising potential in patients with IBD. This manuscript aimed to provide a comprehensive and updated review of the available literature on fecal microbiota transplantation, its clinical use in IBD in general, as well as in patients with IBD and CDI. Methods: An extensive literature search was performed from October 2024 to March 2025. All publications available within PubMed, Medline, Embase, Google Scholar, and Cochrane databases were reviewed. All original articles, case reports, review articles, systematic reviews, and meta-analyses were included. Qualitative and quantitative data were both extracted. Discussion: Intestinal microbiota is an integral part of the human body, and dysbiosis (an imbalance in the gut's microbial community) has been linked with several pathologies. Dysbiosis in IBD is marked by reduced beneficial bacteria and increased pro-inflammatory pathogens, contributing to mucosal damage and immune dysregulation. FMT has emerged as a solution to dysbiosis, with the first case recorded in 1917. FMT has been successful in treating patients with CDI. The diagnostic value of the gut microbiome is currently being explored as a possible therapeutic approach to IBD. Several studies have assessed FMT in patients with IBD and CDI with promising results in both ulcerative colitis (UC) and Crohn's disease (CD) but varying efficacy based on administration routes, donor selection, and processing methods. In the context of recurrent CDI in patients with IBD, FMT demonstrates a high cure rate and potential benefit in concurrently improving IBD activity. However, risks such as IBD flare-ups post-FMT remain a concern. Conclusions: FMT holds promising potential in the management of CDI in patients with IBD. By restoring microbial diversity and correcting dysbiosis, FMT offers a novel, microbiota-targeted alternative to conventional therapies. While data support its efficacy in improving disease remission, variability in outcomes underscores the need for standardized protocols and additional large-scale, controlled studies. Continued research efforts into donor selection, treatment regimens, and long-term safety will be critical to optimizing FMT's role in IBD and CDI care as well as improving patient outcomes.},
}

@article {pmid40806673,
year = {2025},
author = {Zakaria, A and Diawara, I and Bouziyane, A and Louanjli, N},
title = {Exploring Human Sperm Metabolism and Male Infertility: A Systematic Review of Genomics, Proteomics, Metabolomics, and Imaging Techniques.},
journal = {International journal of molecular sciences},
volume = {26},
number = {15},
pages = {},
doi = {10.3390/ijms26157544},
pmid = {40806673},
issn = {1422-0067},
abstract = {Male infertility is a multifactorial condition often associated with disruptions in sperm metabolism and mitochondrial function, yet traditional semen analysis provides limited insight into these molecular mechanisms. Understanding sperm bioenergetics and metabolic dysfunctions is crucial for improving the diagnosis and treatment of conditions such as asthenozoospermia and azoospermia. This systematic review synthesizes recent literature, focusing on advanced tools and techniques-including omics technologies, advanced imaging, spectroscopy, and functional assays-that enable comprehensive molecular assessment of sperm metabolism and development. The reviewed studies highlight the effectiveness of metabolomics, proteomics, and transcriptomics in identifying metabolic biomarkers linked to male infertility. Non-invasive imaging modalities such as Raman and magnetic resonance spectroscopy offer real-time metabolic profiling, while the seminal microbiome is increasingly recognized for its role in modulating sperm metabolic health. Despite these advances, challenges remain in clinical validation and implementation of these techniques in routine infertility diagnostics. Integrating molecular metabolic assessments with conventional semen analysis promises enhanced diagnostic precision and personalized therapeutic approaches, ultimately improving reproductive outcomes. Continued research is needed to standardize biomarkers and validate clinical utility. Furthermore, these metabolic tools hold significant potential to elucidate the underlying causes of previously misunderstood and unexplained infertility cases, offering new avenues for diagnosis and treatment.},
}

@article {pmid40806618,
year = {2025},
author = {Bryliński, Ł and Brylińska, K and Woliński, F and Sado, J and Smyk, M and Komar, O and Karpiński, R and Prządka, M and Baj, J},
title = {Trace Elements-Role in Joint Function and Impact on Joint Diseases.},
journal = {International journal of molecular sciences},
volume = {26},
number = {15},
pages = {},
doi = {10.3390/ijms26157493},
pmid = {40806618},
issn = {1422-0067},
abstract = {Proper joint function has a significant impact on people's quality of life. Joints are the point of connection between two or more bones and consist of at least three elements: joint surfaces, the joint capsule, and the joint cavity. Joint diseases are a serious social problem. Risk factors for the development of these diseases include overweight and obesity, gender, and intestinal microbiome disorders. Another factor that is considered to influence joint diseases is trace elements. Under normal conditions, elements such as iron (Fe), copper (Cu), cobalt (Co), iodine (I), manganese (Mn), zinc (Zn), silver (Ag), cadmium (Cd), mercury (Hg), lead (Pb), nickel (Ni) selenium (Se), boron (B), and silicon (Si) are part of enzymes involved in reactions that determine the proper functioning of cells, regulate redox metabolism, and determine the maturation of cells that build joint components. However, when the normal concentration of the above-mentioned elements is disturbed and toxic elements are present, dangerous joint diseases can develop. In this article, we focus on the role of trace elements in joint function. We describe the molecular mechanisms that explain their interaction with chondrocytes, osteocytes, osteoblasts, osteoclasts, and synoviocytes, as well as their proliferation, apoptosis, and extracellular matrix synthesis. We also focus on the role of these trace elements in the pathogenesis of joint diseases: rheumatoid arthritis (RA), osteoarthritis (OA), psoriatic arthritis (PsA), ankylosing spondylitis (AS), and systemic lupus erythematosus (SLE). We describe the roles of increased or decreased concentrations of individual elements in the pathogenesis and development of joint diseases and their impact on inflammation and disease progression, referring to molecular mechanisms. We also discuss their potential application in the treatment of joint diseases.},
}

@article {pmid40806562,
year = {2025},
author = {Polio, A and Wagner, V and Bender, DP and Goodheart, MJ and Gonzalez Bosquet, J},
title = {A Natural Language Processing Method Identifies an Association Between Bacterial Communities in the Upper Genital Tract and Ovarian Cancer.},
journal = {International journal of molecular sciences},
volume = {26},
number = {15},
pages = {},
doi = {10.3390/ijms26157432},
pmid = {40806562},
issn = {1422-0067},
support = {NIH 5R01CA99908-18/GF/NIH HHS/United States ; },
abstract = {Bacterial communities within the female upper genital tract may influence the risk of ovarian cancer. In this retrospective cohort pilot study, we aim to detect different communities of bacteria between ovarian cancer and normal controls using topic modeling, a natural language processing tool. RNA was extracted and analyzed using the VITCOMIC2 pipeline. Topic modeling assessed differences in bacterial communities. Idatuning identified an optimal latent topic number and Latent Dirichlet Allocation (LDA) assessed topic differences between high-grade serous ovarian cancer (HGSOC) and controls. Results were validated using The Cancer Genome Atlas (TCGA) HGSOC dataset. A total of 801 unique taxa were identified, with 13 bacteria significantly differing between HGSOC and normal controls. LDA modeling revealed a latent topic associated with HGSOC samples, containing bacteria Escherichia/Shigella and Corynebacterineae. Pathway analysis using KEGG databases suggest differences in several biologic pathways including oocyte meiosis, aldosterone-regulated sodium reabsorption, gastric acid secretion, and long-term potentiation. These findings support the hypothesis that bacterial communities in the upper female genital tract may influence the development of HGSOC by altering the local environment, with potential functional implications between HGSOC and normal controls. However, further validation is required to confirms these associations and determine mechanistic relevance.},
}