@article {pmid40803456,
year = {2025},
author = {Ekwudo, MN and Masson, B and Di Natale, MR and Kiridena, P and van de Garde, N and Lei, E and Sarkar, SK and Narayana, VK and Renoir, T and Furness, JB and Gubert, C and Hannan, AJ},
title = {Prebiotics improve motor function, cognition and gut health in a preclinical model of Huntington's disease.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106074},
doi = {10.1016/j.bbi.2025.106074},
pmid = {40803456},
issn = {1090-2139},
abstract = {Huntington's disease (HD) is a currently incurable neurodegenerative disorder characterised by psychiatric, cognitive and motor deficits, as well as peripheral manifestations, including gastrointestinal (GI) and immunological impairments. The R6/1 mouse model of HD, expressing a mutant human huntingtin transgene, exhibits excellent construct and face validity. Evidence of gut dysbiosis has been reported in clinical and preclinical HD and is strongly associated with disease symptoms, including cognitive and behavioural outcomes. Recently, high dietary fibre was shown to rescue cognitive and affective deficits and improve gut function in HD mice, by unknown mechanisms. Hence, we aimed to evaluate the therapeutic potential of gut microbial modulation by prebiotics in the treatment of HD. Given the well-documented role of prebiotics such as fructooligosaccharide (FOS) and galactooligosaccharide (GOS) as substrates of beneficial microbes, we hypothesised that chronic supplementation of FOS + GOS (PREB intervention) would ameliorate the gut dysbiosis associated with HD and consequently attenuate other deficits in this preclinical model. Here, R6/1 HD mice and wild-type (WT) littermate controls were randomised to receive PREB or vehicle (drinking water) from 6-20 weeks of age. We assessed the onset and progression of motor, cognitive and affective deficits, as well as GI parameters and gut macroscopy Additionally, we profiled the gut microbiota in faecal samples collected at week 14 (using 16S rRNA gene sequencing) and assessed their derivatised short-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs). Compared to vehicle controls, PREB improved the motor performance of female HD mice and enhanced the cognitive performance of female HD and WT mice. Furthermore, PREB increased caecal weight (both sexes), stool softness (females) and faecal levels of SCFAs, including butyrate (males), acetate(both sexes) and propionate in both HD and WT males but female HD mice only. The prebiotics intervention also decreased gut transit time in females at late onset and faecal output in both HD and WT males at early onset, as well as juxtauterine fat (in females). Furthermore, PREB decreased α-diversity and increased β-diversity in both sexes, including a remarkable increase in SCFA-producing microbes such as Bifidobacterium animalis in PREB-treated animals. Taken together, PREB effectively modulated the HD core phenotype, particularly motor coordination, cognition and GI parameters as described above, and remodelled the gut microbiota of HD mice. This prebiotic intervention has a strong safety profile and is directly translatable to future clinical trials of HD. Our findings suggest that targeting the gut microbiota in HD is a plausible clinical strategy and may inform novel therapeutic approaches to delay the onset and/or progression of this debilitating condition and other neurological disorders with similar manifestations.},
}

@article {pmid40803427,
year = {2025},
author = {Li, XG and Zhao, X and Zheng, J and Xian, C and Liu, Z and Chen, H},
title = {The potential and underlying mechanisms of punicalagin in mitigating enterotoxigenic Escherichia coli-induced diarrhea.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.08.002},
pmid = {40803427},
issn = {1541-6100},
abstract = {Punicalagin is a well-studied polyphenolic compound with a wide array of pharmacological effects. This review summarizes its potential mechanisms of action along with the pathogenic implications and molecular pathways associated with Enterotoxigenic Escherichia coli (ETEC). One primary mechanism by which punicalagin exerts its effects is through antibacterial activity that suppresses ETEC proliferation and mitigates intestinal infections. It further promotes the growth of beneficial microbiota, including bifidobacteria and lactic acid-producing bacteria, thereby improving the symbiotic balance of the gut microbiome and bolstering resistance to ETEC colonization. In addition, punicalagin has been shown to inhibit the activity of ETEC, thereby enhancing intestinal mucosal integrity and fortifying the intestinal barrier. This action reduces the permeability of harmful substances, ultimately protecting gut health. Moreover, punicalagin has the potential to chelate metals, leading to various biological activities and applications. This positions it as a candidate for further exploration as a novel therapeutic agent or a raw material in health products. In conclusion, this study offers preliminary insights into the potential application of punicalagin in managing ETEC-induced diarrhea, highlighting its pharmacological efficacy. However, it should be emphasized that current clinical evidence supporting its effectiveness for this specific use remains limited and preliminary, requiring validation through rigorous clinical trials.},
}

@article {pmid40803378,
year = {2025},
author = {Kim, JH and Seong, JE and Lee, YS and Lee, JA and Ahn, JY and Jeong, SJ and Ku, NS and Yeom, JS and Yong, D and Choi, JY},
title = {Origin and transmission of carbapenemase-producing Enterobacterales and vancomycin-resistant Enterococci in hospitalized patients: a genomic and epidemiological analysis.},
journal = {The Journal of hospital infection},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhin.2025.07.017},
pmid = {40803378},
issn = {1532-2939},
abstract = {BACKGROUND: Antimicrobial resistance is an emergent threat, with Carbapenemase-Producing Enterobacterales (CPE) and Vancomycin-Resistant Enterococcus (VRE) posing substantial challenges. We investigated CPE/VRE acquisition and spread in hospitalized patients by analysing resistance genes and microbiomes using whole genome sequencing (WGS) and exploring epidemiological and clinical risk factors.

METHODS: This retrospective study included patients from the infectious disease department of a tertiary hospital. Stool samples were collected weekly, together with clinical and epidemiological information. Those in which CPE/VRE was isolated underwent WGS to evaluate the presence of resistance genes. Microbiome analysis was performed at admission and discharge. WGS was also performed for all positive samples collected within the hospital during the study period.

RESULTS: Of the 102 participants, 16 (15.7%) had CPE/VRE at admission. Key risk factors for harbouring CPE/VRE at admission included recent hospitalization, surgery, and antibiotic use. The first week of hospitalization was critical for acquiring CPE/VRE, with dementia, central or urinary catheters, and carbapenem use being significant risk factors. CPE/VRE acquired post-admission shared resistance genes with circulating hospital strains, whereas those present at admission featured novel genes such as blaOXY-4-1 and optrA. Microbiome analysis revealed significant differences in species abundance and reduced diversity at discharge.

CONCLUSIONS: The probability of having CPE/VRE at admission to the infectious diseases department was high. Stringent infection control measures are essential for preventing CPE/VRE spread and the introduction of novel resistance genes.},
}

@article {pmid40803339,
year = {2025},
author = {Brazee, P and Allen, N and Knipe, R and Redente, EF and Le Saux, CJ},
title = {Peeling Back the Layers of the Bleomycin Model of Lung Fibrosis: Lessons Learned, Factors to Consider, and Future Directions.},
journal = {Seminars in respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-2649-9402},
pmid = {40803339},
issn = {1098-9048},
support = {DISC0-13788//California Institute for Regenerative Medicine/ ; K01HL174822 [P.B.]//U.S. Department of Health and Human Services, National Institutes of Health, National Heart, Lung, and Blood Institute/ ; K08HL169723 [N.A.]//U.S. Department of Health and Human Services, National Institutes of Health, National Heart, Lung, and Blood Institute/ ; R01 HL168138 [R.K.]//U.S. Department of Health and Human Services, National Institutes of Health, National Heart, Lung, and Blood Institute/ ; R35HL150767 [C.J.L.S.]//U.S. Department of Health and Human Services, National Institutes of Health, National Heart, Lung, and Blood Institute/ ; RO1 HL147860 [E.R.]//U.S. Department of Health and Human Services, National Institutes of Health, National Heart, Lung, and Blood Institute/ ; RO1 HL149741[E.R.]//U.S. Department of Health and Human Services, National Institutes of Health, National Heart, Lung, and Blood Institute/ ; RO1 HL166250 [E.R.]//U.S. Department of Health and Human Services, National Institutes of Health, National Heart, Lung, and Blood Institute/ ; U01HL134766 [C.J.L.S.]//U.S. Department of Health and Human Services, National Institutes of Health, National Heart, Lung, and Blood Institute/ ; },
abstract = {Bleomycin-induced lung injury remains the most widely used and well-characterized experimental model for studying pulmonary fibrosis, particularly idiopathic pulmonary fibrosis (IPF). This review provides a comprehensive analysis of the bleomycin model's utility, phases, variability, and translational relevance. Bleomycin administration in rodents induces acute epithelial injury followed by inflammation, fibroblast activation, extracellular matrix deposition, and eventual fibrosis. The model progresses through defined stages, acute inflammation (days 1-7), fibrogenesis (days 7-28), and in most cases, spontaneous resolution (days 42-63), making it suitable for understanding temporal aspects of fibrosis and repair, the cell populations involved, and the signaling mechanisms involved. Despite its advantages, the single-dose model lacks key features of human IPF, including persistent fibrosis, honeycomb cysts, and fibroblastic foci. Repetitive dosing and the use of aged mice have improved chronicity and recapitulation of progressive disease and observation of the expansion of aberrant epithelial cell populations in simple cyst structures. This review discusses route-specific effects, strain and sex susceptibilities, and the growing role of microbiome and genetic background in influencing fibrosis outcomes. It also highlights cellular responses across epithelial cell populations, fibroblasts, endothelial cells, and immune cell populations. Although limitations exist in this model-such as reversibility and incomplete modeling of human pathology-bleomycin remains invaluable for mechanistic studies and preclinical drug screening. Importantly, all FDA-approved antifibrotic drugs demonstrated efficacy in bleomycin models prior to clinical success. The review advocates for careful model selection, incorporation of persistent fibrosis models, and parallel use of human-relevant systems to enhance translational relevance in pulmonary fibrosis research.},
}

@article {pmid40803228,
year = {2025},
author = {Ağagündüz, D and Çelik, E and Cemali, Ö and Yesildemir, O and Demirci, KŞ and Akkus, G and Esatbeyoglu, T and Ozogul, F},
title = {Mechanism of actions of probiotics on type 2 diabetes: Development and complications.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {191},
number = {},
pages = {118421},
doi = {10.1016/j.biopha.2025.118421},
pmid = {40803228},
issn = {1950-6007},
abstract = {Type 2 diabetes mellitus (T2DM) is a multifactorial metabolic disorder described by chronic hyperglycemia, insulin resistance, as well as low-grade inflammation. Recent research highlights the vital role of the gut microbiota in the pathogenesis and progression of T2DM. Dysbiosis can impair intestinal barrier integrity, promote systemic inflammation, and contribute to insulin resistance and glucose metabolism dysfunction. This review article investigates the mechanisms by which probiotics interact with gut microbiota and host signaling pathways to impact the onset and complications of T2DM. Databases were searched, and related articles were added, to get a thorough overview of the relationship between probiotics and T2DM and its complications. Probiotics have appeared as potential modulators of the gut microbiome, capable of restoring microbial balance and strengthening intestinal barrier function. Probiotics can influence glucose homeostasis through their multifaceted effects on the gut microbiota and host metabolism. Through the production of beneficial metabolites, suppress α-glucosidase activity, enhance short-chain fatty acid (SCFA) levels, competitive inhibition of pathogenic bacteria, regulation of gut-derived neurotransmitters such as serotonin, improve intestinal, and immune functions, probiotics may alleviate key mechanisms involved in T2DM development and its complications.},
}

@article {pmid40803134,
year = {2025},
author = {Wu, F and Campbell, BC and Greenfield, P and Hose, GC and Midgley, DJ and George, SC},
title = {There and back again: Genomic insights into microbial life in a recirculating petroleum refinery wastewater biotreatment system.},
journal = {Microbiological research},
volume = {301},
number = {},
pages = {128299},
doi = {10.1016/j.micres.2025.128299},
pmid = {40803134},
issn = {1618-0623},
abstract = {Petroleum refinery wastewater biotreatment relies on microbes to remediate carbon, nitrogen, and sulfur compounds, yet their life strategies and ecological roles remain unclear. This study characterises the ecological functions of 20 metagenome-assembled genomes (MAGs) from a full-scale petroleum refinery wastewater treatment plant in southern China. The taxonomic identity, nutrient metabolism genes (including C/N/S cycling), carbohydrate-active enzymes, and CRISPR-Cas systems of these MAGs were analysed. The recovered MAGs represented bacteria primarily from the Pseudomonadota and Bacteroidota phyla. The major carbon sources for the represented organisms are likely aromatic and aliphatic compounds, as well as carbohydrates including peptidoglycan, chitin, and starch. Almost all MAGs contained genes for nitrate or nitrite reduction, while metabolic pathways for sulfur metabolism were generally less prevalent. Meiothermus sp. bin.89 was the most metabolically versatile MAG. This organism possessed genes that allowed it to recycle biomass, break down aliphatic and monoaromatic compounds, and perform anaerobic respiration using nitrate. However, it was likely the most susceptible to viral predation, as indicated by the high abundance of CRISPR spacers. Overall, the results revealed that stress-tolerant ecological traits were common among organisms in this microbiome, showcasing the ability of the microbes to obtain carbon from aromatic and aliphatic compounds. This study provides a substantial contribution towards future efforts in optimising microbiome stability for pollutant removal in petroleum refinery wastewater biotreatment systems.},
}

@article {pmid40803054,
year = {2025},
author = {Moutsoglou, D and Blake, M and Belhasan, DC and Peichel, G and Vang, BM and Weir, EK and Lopez, S and Prins, KW and Kabage, AJ and Prisco, SZ and Kremer, BP and Khoruts, A and Thenappan, T},
title = {Microbiota Transplant Therapy Is Safe and Feasible in Pulmonary Arterial Hypertension.},
journal = {JACC. Basic to translational science},
volume = {10},
number = {9},
pages = {101347},
doi = {10.1016/j.jacbts.2025.101347},
pmid = {40803054},
issn = {2452-302X},
abstract = {Pulmonary arterial hypertension (PAH) is a complex inflammatory disease that the gut microbiome likely contributes to and may be a potential therapeutic avenue for nontoxically improving outcomes. Here, we show that microbiota transplant therapy (MTT) is safe and feasible. The MTT regimen achieves only modest levels of donor microbiota engraftment but is accompanied by a transient reduction in circulating pro-inflammatory cytokines. These findings of decreased systemic inflammation with only modest donor engraftment support the potential of MTT as a novel treatment for PAH. (Microbiota Transplant Therapy for Pulmonary Arterial Hypertension: Early Safety and Feasibility Study; NCT04884971).},
}

@article {pmid40802913,
year = {2025},
author = {Narang, P and D'Souza, S},
title = {Chronic Ocular Sequelae of Stevens-Johnson Syndrome: Recent Advances in Understanding of Patho-Physiology and Management.},
journal = {Seminars in ophthalmology},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/08820538.2025.2545264},
pmid = {40802913},
issn = {1744-5205},
abstract = {BACKGROUND: Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) are severe mucocutaneous reactions primarily triggered by drugs or infections. Although acute management focuses on systemic stabilization, chronic ocular sequelae remain a significant concern with vision-threatening complications arising in up to 75% of the affected patients. Ocular manifestations range from dry eye disease, lid margin keratinization (LMK), and conjunctival cicatrization to more severe complications like limbal stem cell deficiency (LSCD), cicatricial entropion, symblepharon, corneal perforation and scarring.

PURPOSE: This review aims to summarize the recent advances in understanding the pathophysiology and management strategies for chronic ocular sequelae of SJS.

METHODS: A comprehensive literature search was conducted using PubMed database, identifying published studies addressing the roles of persistent immune dysregulation, autoantibodies, and microbiome alterations in perpetuating chronic ocular inflammation and scarring. The recent treatment modalities for such sequelae of SJS were also evaluated.

CONCLUSION: Elevated levels of pro-inflammatory cytokines, neutrophil predominance, and aberrant keratinization pathways have been identified as key contributors. Management strategies have evolved to include timely surgical interventions like mucous membrane grafting (MMG) for LMK, scleral lenses for ocular surface protection, and limbal stem cell transplantation for LSCD. The introduction of advanced therapies, such as topical autologous serum, platelet-rich plasma, and recombinant growth factors, has enhanced ocular surface rehabilitation. Emerging treatments, including simple oral mucosal epithelial transplantation (SOMET), cultivated oral mucosal epithelial transplantation (COMET), and keratoprostheses, offer hope for severe cases. Additionally, the integration of artificial intelligence (AI) in prognosis prediction and the development of targeted biologics highlight the potential for personalized care. Despite these advancements, challenges persist in early diagnosis, access to specialized care, and the high cost of novel therapies. Multidisciplinary collaboration and awareness are imperative for optimizing outcomes. Future directions emphasize the need for precision medicine approaches, AI integration, and nationwide registries to facilitate research and enhance patient support. Such comprehensive understanding and management approach aims to mitigate the long-term visual disability associated with chronic ocular sequelae of SJS/TEN, thereby improving quality of life.},
}

@article {pmid40802648,
year = {2025},
author = {Stamper, CE and Hoisington, AJ and Ellis, JC and Lowry, CA and Brenner, LA},
title = {Stabilized and unstabilized sampling methods result in differential fecal 16S rRNA microbial sequencing results.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0324351},
doi = {10.1371/journal.pone.0324351},
pmid = {40802648},
issn = {1932-6203},
abstract = {Over the past decade, studies have been conducted to increase the understanding of associations between the fecal microbiome and human health. In conjunction, researchers have investigated the effects of study design, methods, molecular processing, and sequencing techniques. However, a lack of standardization of fecal sample collection methodology has introduced heterogeneity in sequencing results. Sources of variability include sample collection methods, storage temperatures, and transport times. Here we present 16S rRNA gene amplicon sequencing results from two sample collection methods (unstabilized sterile swab and stabilized OmniGene Gut Kits) collected from the same fecal specimens. The paired samples were collected either at the research facility or the participants' home and ground shipped to the research facility at ambient temperature. Therefore, samples were exposed to variable temperatures and transport times. We found that fecal sample collection methods resulted in taxonomic and diversity differences that showed distinct patterns between swab and OmniGene samples. Swab samples were disproportionally affected by increased transport time, but differences in taxa and diversity were driven more by sample collection method, as compared to transport time. Based on previous studies, many of the taxa that were associated with sample collection methods and transport times have clinical relevance. Collectively, this research highlights: 1) the need for further standardization of methods for fecal microbiome studies; 2) limitations of direct comparisons between different fecal sample collection methods; and 3) the importance of careful consideration of sample collection methods for future studies and meta-analyses.},
}

@article {pmid40802513,
year = {2025},
author = {Song, Q and Li, X and Li, Q and Shang, S and Ma, S and Zhai, Z and Sun, F and Mo, Y and Wei, L and Wu, M and Ma, Y and Yu, J and Chen, D},
title = {Bifidobacterium animalis suppresses non-small cell lung cancer progression and modulates tumor immunity through indole-3-acetic acid.},
journal = {Cell reports},
volume = {44},
number = {8},
pages = {116132},
doi = {10.1016/j.celrep.2025.116132},
pmid = {40802513},
issn = {2211-1247},
abstract = {Emerging evidence implicates the significant influence of gut microbiome and its metabolic byproducts in the non-small cell lung cancer (NSCLC). Here, we identify distinct disparity in the gut microbiota composition between patients with NSCLC and healthy controls, with Bifidobacterium animalis being markedly decreased in NSCLC. B. animalis suppresses tumor progression in two NSCLC mouse models and NSCLC cell lines. Integrative metabolomic analysis identifies indole-3 acetic acid (IAA) as the pivotal metabolite of B. animalis, with significant anti-NSCLC properties. Mechanistically, B. animalis and its derived IAA activate aryl hydrocarbon receptor (AHR) in lung to suppress METTL3 and the m6A methylation of STAT3. Moreover, B. animalis and IAA diminish polarization of M2 macrophage and enhance CD8[+] T cell functions by suppressing interleukin-6 (IL-6). B. animalis and its derived IAA protect against NSCLC by modulating AHR/METTL3/STAT3 and bolstering antitumor immunity through gut-lung axis. B. animalis and IAA supplementation represent a promising prophylactic for NSCLC prevention.},
}

@article {pmid40802482,
year = {2025},
author = {Griffin, C and Schreiber, J and Bierwert, A and Kajihara, K and Weber, D and Medeiros, MCI},
title = {Integrating network analysis with in vivo-in situ manipulation to elucidate microbiome dynamics in Aedes albopictus.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf084},
pmid = {40802482},
issn = {1574-6968},
abstract = {Host-associated microbiomes have significant impacts on host biology and physiology, but the underlying processes governing their structure and assembly are not well understood. One approach to better understanding those process is the use of computationally-driven modeling tools such as network analysis to identify patterns of cooccurring taxa across microbiomes. Those patterns can then be tested to identify taxa that are potentially more important in the overall structuring and assembly processes. Here we used network analysis to explore cooccurrence patterns within the microbiome of Aedes albopictus. We identified important nodes in the network using the centrality metrics of node degree and betweenness. Among the nodes with the highest centrality values, more ITS ASVs were present than 16S ASVs. We then tested the network analysis predictions in vivo/in situ in A. albopictus. A series of exclusion experiments were used to manipulate environmental microbiome source pools by filtering the source pool by cell size. Our results show that including microbial eukaryotes, such as fungi, in the source pool affects microbiome assembly and structure in A. albopictus, which aligns with the network analyses predictions of this system. To our knowledge, this is the first study to integrate microbial network centrality analysis with in vivo/in situ validation using filtration-based microbial community exclusion.},
}

@article {pmid40802476,
year = {2025},
author = {Wunderlich, G and Bull, M and McGilchrist, N and Zhao, C and Ross, T and Rose, M and Chapman, B},
title = {The horse gut bacteriome and anaerobic mycobiome are influenced by seasonal forages and small intestinal starch digestibility.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf203},
pmid = {40802476},
issn = {1365-2672},
abstract = {AIMS: The equine gut microbiome is a complex and dynamic ecosystem, housing a diverse consortium of bacteria and anaerobic fungi (AF) capable of breaking down complex plant matter and converting it into vital energy sources for their host. The aim of this study was to broaden our current understanding of bacterial and AF diversity in the equine hindgut and how it differs between cohorts and responds to dietary shifts.

METHODS AND RESULTS: Faecal samples were collected from 48 horses and the bacteriome and anaerobic mycobiome analysed using long-read amplicon sequencing. Samples were collected from racehorses (RH) on high-concentrate diets and wild-foraging (WF) horses grazing on seasonally variable pastures. Distinct microbial profiles were observed, with bacterial diversity and composition strongly influenced by season. Reduced hindgut starch availability in RH promoted fibrolytic taxa such as Roseburia and reduced amylolytic Lactobacillus. AF communities, though relatively stable across dietary and seasonal changes, differed between the horse cohorts. Piromyces and Khoyollomyces were found to be more strongly associated with WF horses and Caecomyces with RH.

CONCLUSION: These findings emphasize the dynamic interplay between diet and microbial composition. Future multi-omics research will enhance our understanding of microbial functionality and inform strategies to optimise equine gut health.},
}

@article {pmid40802401,
year = {2025},
author = {Sira, HRS and Hacioglu, O},
title = {The development and evaluation of a microbiota education programme intended for women.},
journal = {Revista da Associacao Medica Brasileira (1992)},
volume = {71},
number = {7},
pages = {e20242017},
pmid = {40802401},
issn = {1806-9282},
abstract = {OBJECTIVE: Findings in the literature indicate that women often have incorrect or incomplete knowledge about the concepts of microbiota, microbiome, probiotics, prebiotics, and their relationship with women's health, pregnancy, childbirth methods, and breast milk. In this regard, designing educational programs that contribute to preventing reproductive system infections, achieving positive fertility outcomes, and supporting the health processes of women and newborns through the microbiota of the female body can contribute to the current situation. In line with this aim, in this study, the development and evaluation of a microbiota education program for women were conducted.

METHODS: The research was conducted with 151 female participants in a pre-test and post-test, single-group, quasi-experimental design. The trainings were conducted for 2 days, with a total of 4 h for each group, 2 h each day. The microbiota knowledge test applied before the training was repeated as a post-test after 4 weeks. SPSS 25.0 was used for data analysis.

RESULTS: It was determined that there was a statistically significant difference between the pre-training and post-training knowledge scores of the participants, with the post-training knowledge scores being higher than the pre-training scores (p<0.05). It was found that there was an increase in intra-group means for age, education level, occupation, number of pregnancies, number of births, and method of delivery after the training.

CONCLUSION: As a result of the evaluations, it was concluded that the microbiota education program developed and implemented for women addressed all female participants.},
}

@article {pmid40802226,
year = {2025},
author = {Jangra, N and Chahar, N and Parmar, A and Gulati, P},
title = {Synbiotics: An Emerging Frontier in Infectious Diseases Control.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40802226},
issn = {1867-1314},
support = {(Grant No. 3/52-2O21 Adv./HSHEC)//Haryana State Higher Education Council (CM Research Fellowships)/ ; },
abstract = {The human gut microbiome is critical in promoting human health in many aspects, like facilitating nutrient absorption, digestion, immune system regulation, and protecting against pathogens. Gut microbiota dysbiosis is associated with the pathogenesis of several infectious diseases. In this context, a combination of prebiotics and probiotics as synbiotics is emerging as a popular approach for managing immune and gastrointestinal health. Synbiotics have exhibited considerable potency in restoring eubiosis via modulating the gut microbiome. The dietary supplementation of synbiotics has shown promising results in treating infectious diseases like hepatitis, gastroenteritis, dental caries, and sepsis. Synbiotics antagonise pathogens by maintaining gut microbiota homeostasis, competing with pathogenic microorganisms for adhesion and nutrition, producing antimicrobial compounds, and stimulating immunomodulatory cells in vivo. The present article has been conceptualised to understand the potential of synbiotics as an alternative or adjunct to antibiotics in managing infectious diseases. Furthermore, it elaborates on the different formulations of synbiotics available for clinical use and their mode of action. Challenges associated and recent approaches to improve the efficacy of these therapeutics have also been addressed.},
}

@article {pmid40802223,
year = {2025},
author = {Sarkar, S and Maparu, K and Aran, KR},
title = {Postbiotics as a Therapeutic Tool in Depression: Exploring into Molecular Pathways and Neuroprotective Effects.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40802223},
issn = {1867-1314},
abstract = {Depression, a debilitating mood disorder characterized by persistent sadness and anhedonia, affects millions worldwide, yet available therapies remain suboptimal and often cause undesirable side effects. Emerging evidence highlights the crucial role of gut microbiota in regulating mental health through the gut-brain axis, paving the way for novel therapeutic strategies. As per preclinical and clinical studies, there is a causal relationship between gut dysbiosis and depression via modulation of brain activity through the gut-brain axis (GBA), and the key to targeting microbes is key to treating depression. Postbiotics-bioactive compounds derived after fermentation have been shown to provide several health benefits, particularly in terms of neuroinflammation, neurotransmitter imbalance, mitochondrial dysfunction, and restoration of neuroplasticity associated with depression. This review explores the neuroprotective mechanisms by which postbiotics alleviate depression, including the modulation of neurotransmitter synthesis, suppression of neuroinflammation, mitigation of oxidative stress and mitochondrial dysfunction, and restoration of neuroplasticity. Furthermore, postbiotics hold potential as adjuvant therapy alongside conventional antidepressants, enhancing treatment efficacy and minimizing side effects. Despite promising initial findings, challenges such as standardized formulation, clinical dose optimization, and regulatory framework development must be addressed. Large-scale clinical trials are imperative to validate their therapeutic potential and facilitate integration into mainstream depression management. As research advances, postbiotics may redefine mental health treatment, emerging as a revolutionary microbiome-based approach for long-term patient care.},
}

@article {pmid40801952,
year = {2025},
author = {Eckl-Dorna, J and Pjevac, P},
title = {[Principles of microbiome research].},
journal = {HNO},
volume = {},
number = {},
pages = {},
pmid = {40801952},
issn = {1433-0458},
abstract = {Microbiome research in the ear nose and throat (ENT) field has substantially gained in importance in recent decades. Modern sequencing methods have largely replaced traditional cultivation. Standardized protocols are essential to ensure reliable and comparable data. The article explains key terms, such as microbiome (the entire microbial community and its environment) and microbiota (only living microorganisms), along with the microbial taxonomy. Important measures for microbiome assessment include the alpha-diversity (species richness and distribution within a sample) and beta-diversity (differences between samples). A differentiation is made between two main approaches to microbiome sequencing: 1) 16S rRNA gene amplicon sequencing (identifies microbial community composition by sequencing the PCR product of a specific gene), 2) metagenomic sequencing (sequences the entire genomic material of a sample, allowing deeper insights). As nasal microbiome biomass is low, careful study design and controls are crucial. Microbiome research is a rapidly growing field with great potential but it requires meticulous planning and bioinformatics expertise for meaningful results.},
}

@article {pmid40801813,
year = {2025},
author = {Wang, Y-H and Xu, H-T and Liu, M-W and Yuan, B-J and Gao, X-Y and Zhang, X-H and Tian, H-D and Yu, H and Lai, J-R and Liu, L and Johnston, RN and Liu, G-R and Liu, S-L},
title = {Streptomyces sp. BI87 from human gut: potent anticancer activities and divergence from known Streptomyces lineages.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0085825},
doi = {10.1128/spectrum.00858-25},
pmid = {40801813},
issn = {2165-0497},
abstract = {Cancer is among the deadliest diseases with few truly curative therapies. Recent studies have shown that the human intestinal microbiota contains bacteria that exhibit potent suppressive effects on cancer or coordinate anticancer functions with the immune system. However, whether the peculiar anticancer trait was acquired stochastically by a strain of a non-anticancer bacterial species or an intrinsic property of a phylogenetic lineage of bacteria remained unclear. In this study, we compared a human gut isolate Streptomyces sp. BI87, which had highly effective anticancer activities, with the type strain of Streptomyces albidoflavus, DSM 40455[T], which was most closely related to BI87 among 30 type strains of the genus Streptomyces but did not show any detectable anticancer activities. We found that, although BI87 and DSM 40455[T] had >99% 16S rDNA sequence similarity, they are phylogenetically separated by a genetic boundary into distinct natural species as evaluated by the 3Cs definition of bacterial species based on the ratio of common genes with zero sequence degeneracy. In addition to the anticancer activities, BI87 encodes several biological characteristics different from DSM 40455[T], including those of antibacterial and antiviral spectra, secondary metabolites, structural composition in the cell wall, and major cellular fatty acids. Based on the genomic and phenotypic distinctions of BI87 from closely related Streptomyces strains, we propose that the anticancer bacterial strain BI87 represents a new lineage at the natural species level within the genus Streptomyces.IMPORTANCEThe characterization of the anticancer bacterial strain, Streptomyces sp. BI87, isolated from a healthy human, suggests the prevalent existence of anticancer microbes in the gut microbiome of humans, which may be nurtured and harnessed for cancer prevention or treatment without the need for the introduction of engineered and non-indigenous microbes to a person or the use of radio- or chemo-therapies. Also important is the finding that a close relative of BI87, Streptomyces albidoflavus DSM40455[T], does not express appreciable anticancer properties in the same in vitro and in vivo experiments, demonstrating that Streptomyces sp. BI87 represents a novel bacterial lineage with selective suppressive activities on cancer, at the phylogenetic level of natural species. Genomic comparisons between BI87 and DSM40455[T] demonstrate that phylogenetic delineation of closely related bacteria needs to be conducted at the level of natural species rather than OTUs, as an OTU may contain phenotypically or even phylogenetically radically distinct bacteria.},
}

@article {pmid40801731,
year = {2025},
author = {Jackowetz, JN and Hanson, CS and Michael, M and Tsoukalas, K and Villanueva, C and Kozak, PA},
title = {Effects of Ultrafine Bubble Water on Gut Microbiota Composition and Health Markers in Rats.},
journal = {Nanomaterials (Basel, Switzerland)},
volume = {15},
number = {15},
pages = {},
doi = {10.3390/nano15151193},
pmid = {40801731},
issn = {2079-4991},
abstract = {Ultrafine bubbles (UFBs) represent an emerging technology with unique physicochemical properties. This study investigated the effects of air-filled UFBs infused in drinking water on gut microbiota composition and the associated health markers in Sprague Dawley rats over a 12-week period. Using a two-phase design, UFB concentration was increased from 1.7 × 10[6] to 6.5 × 10[9] UFBs/mL at week 7 to assess dose-dependent effects. Administration of UFBs in drinking water induced significant shifts in gut microbiome populations, characterized by increased Bacteroidetes (+122% weeks 8-12) and decreased Firmicutes (-43% weeks 8-12) compared to controls. These microbial shifts coincided with enhanced short-chain fatty acid production (butyrate +56.0%, p ≤ 0.001; valerate +63.1%, p ≤ 0.01) and reduced inflammatory markers (TNF-α -84.0%, p ≤ 0.05; IL-1β -41.0%, p ≤ 0.05; IL-10 -69.8%, p ≤ 0.05). UFB effects demonstrated systematic concentration-dependent threshold responses, with 85.7% of parameters exhibiting directional reversals between low (1.7 × 10[6] UFBs/mL) and high (6.5 × 10[9] UFBs/mL) concentration phases rather than linear dose-response relationships. The systematic nature of these threshold effects, with 71.4% of parameters achieving statistical significance (p ≤ 0.05), indicates concentration-dependent biological mechanisms rather than random effects on gut biology. Despite current metagenomic techniques identifying only 25% of the total gut microbiome, the observed changes in characterized species and metabolites demonstrate UFB technology's therapeutic potential for conditions requiring microbiome modulation, providing new insights into UFB influence on complex biological systems.},
}

@article {pmid40801650,
year = {2025},
author = {Giri, AK and Subramanian, P and Periyasamy, L and Aravindan, S and Aravindan, N},
title = {Microbiome in Neuroblastoma: A Virgin Island in the World of Onco-Microbiome.},
journal = {Cells},
volume = {14},
number = {15},
pages = {},
doi = {10.3390/cells14151218},
pmid = {40801650},
issn = {2073-4409},
support = {DoD CA-210339//Department of Defense/ ; OCAST-HR19-045//Oklahoma Center for the Advancement of Science and Technology/ ; P20GM103639//The National Institutes of Health/ ; },
abstract = {The composition of the gut and/or tumor microbiome has been intricately involved in the onset of carcinogenesis, tumor progression, therapy response, and patient outcomes in diverse solid cancers. The microbiome type, composition, and their metabolome have been functionally implicated in the multifarious cellular processes, transformation, proliferation, tumor immune evasion, cellular migration, etc. Despite such compelling evidence on the role of microbiome interactions in cancer, the realization of their role in neuroblastoma (NB), the deadly extracranial tumor in infants is few and fragmentary. This review comprehends the composition, diversity, and significance of microbiota in human health. Further, this review discusses the microbiota composition, their mode of action, and their signaling flow through and cellular processes in diverse cancers including NB. Precisely, this study for the first time has realized the functional relevance and clinical significance of the gut and tumor microbiome for NB. Interestingly, large cohort clinical and preclinical in vivo models of NB realized the following: gut microbiota predicts the risk for NB; postnatal (and or not maternal transmission) microbiome rearrangements; gut microbial effect on NB pathogenesis; tumor-altering gut microbial composition; microbial composition predicts treatment outcomes in NB; prebiotic remedies for stabilizing NB-associated microbial rearrangements; microbial composition in tumor-infiltrating microbiota predicts NB outcomes.},
}

@article {pmid40801536,
year = {2025},
author = {Yang, JL and Zhu, H and Sadh, P and Aumiller, K and Guvener, ZT and Ludington, WB},
title = {Commensal acidification of specific gut regions produces a protective priority effect against enteropathogenic bacterial infection.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0070725},
doi = {10.1128/aem.00707-25},
pmid = {40801536},
issn = {1098-5336},
abstract = {The commensal microbiome has been shown to protect against newly introduced enteric pathogens in multiple host species, a phenomenon known as a priority effect. Multiple mechanisms can contribute to this protective priority effect, including antimicrobial compounds, nutrient competition, and pH changes. In Drosophila melanogaster, Lactiplantibacillus plantarum has been shown to protect against enteric pathogens. However, the strains of L. plantarum studied were derived from laboratory flies or non-fly environments and have been found to be unstable colonizers of the fly gut that mainly reside on the food. To study the priority effect using a naturally occurring microbial relationship, we isolated a wild fly-derived strain of L. plantarum that stably colonizes the fly gut in conjunction with a common enteric pathogen, Serratia marcescens. Flies stably associated with the L. plantarum strain were more resilient to oral Serratia marcescens infection as seen by longer life span and lower S. marcescens load in the gut. Through in vitro experiments, we found that L. plantarum inhibits S. marcescens growth due to acidification. We used gut imaging with pH indicator dyes to show that L. plantarum reduces the gut pH to levels that restrict S. marcescens growth in vivo. In flies colonized with L. plantarum prior to S. marcescens infection, L. plantarum and S. marcescens are spatially segregated in the gut, and S. marcescens is less abundant where L. plantarum heavily colonizes, indicating that acidification of specific gut regions is a mechanism of a protective priority effect.IMPORTANCEThe gut microbiomes of animals harbor an incredible diversity of bacteria, some of which can protect their hosts from invasion by enteric pathogens. Understanding the mechanisms behind this protection is essential for developing precision probiotics to support human and animal health. This study used Drosophila melanogaster as a model system due to its low cost, experimentally tractable gut microbiome, and overlap with bacterial species found in mammals. While resident microbes can protect hosts through various means, including toxin production and immune stimulation, we found that acidification was sufficient to limit a pathogen that normally reduces life span. Remarkably, specific gut regions are acidified either by host mechanisms or by the resident bacterium, Lactiplantibacillus plantarum, highlighting joint microbial and host control of gut chemistry. These findings are broadly relevant to microbiology and gut health, providing insight into how hosts may manage pathogens through their symbiotic microbiota.},
}

@article {pmid40801484,
year = {2025},
author = {Song, S and McDonald, KJ and Bhat, A and Chen, MY and Morales Moreira, Z and Haney, CH},
title = {FERONIA Kinase Interacting Cell Wall Sensors LRX1/2 Regulate the Plant Rhizosphere Microbiome.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {},
number = {},
pages = {},
doi = {10.1094/MPMI-05-25-0064-R},
pmid = {40801484},
issn = {0894-0282},
abstract = {Plants establish beneficial associations with microbiota, enhancing their resilience to environmental challenges. FERONIA (FER) kinase shapes the microbiome; despite extensive knowledge on FER interactors that regulate development and immunity against pathogens, the specific partners involved in microbiome modulation remain underexplored. Through a reverse genetic screen of Arabidopsis leucine-rich repeat extensin (LRX) genes, which encode FER-interacting cell wall sensors, we found that loss-of-function of lrx1/2 leads to enriched rhizosphere Pseudomonas, similar to fer mutants. When grown in natural soil, 16S rRNA sequencing revealed that lrx1/2 and fer-4 have similarly altered rhizosphere microbiomes with decreased bacterial diversity. Notably, lrx1/2 and fer-4 mutants both exhibit growth defects in high pH natural soil that could be rescued by lowering soil pH and increasing phosphate. Microbiome sequencing under conditions that rescued fer-4 and lrx1/2 stunting showed that the altered microbiome of lrx1/2 and fer-4 persists independently of changes in plant growth. This indicates that FER and LRX1/2 play an integral role in shaping the rhizosphere microbiome.},
}

@article {pmid40801440,
year = {2025},
author = {Bai, L and Zhu, A},
title = {Microbiome-Mediated Modulation of the Tumour Immune Microenvironment in Oesophageal Squamous Cell Carcinoma.},
journal = {Advanced biology},
volume = {},
number = {},
pages = {e00823},
doi = {10.1002/adbi.202400823},
pmid = {40801440},
issn = {2701-0198},
abstract = {Oesophageal squamous cell carcinoma (ESCC) is the most prevalent type of oesophageal cancer. It is an aggressive malignancy with a poor prognosis, and recent studies have revealed the critical role of the microbiota in its occurrence and development. In this review, the current understanding of the impact of microbiota is summarized on the tumour immune microenvironment (TIME) in ESCC, focusing on intratumoural microbes and the oral-gut microbiota axis as potential therapeutic targets. The mechanisms are discussed by which specific bacterial species, such as Fusobacterium nucleatum (F. nucleatum), Porphyromonas gingivalis (P. gingivalis), Streptococcus spp., and Lactobacillus spp., influence immune responses and contribute to the progression of ESCC. Additionally, the potential of the microbiota is highlighted as a biomarker for early detection, prognosis, and prediction of treatment responses, and explore emerging strategies in microbiota-based immunotherapy that exploit the tumour-targeting properties of bacteria to improve cancer treatment outcomes. Despite these promising developments, the complex interactions between the microbiota and the immune system remain unclarified, and translating research findings into clinical practice is a significant challenge. In this review, the current advancements and emphasise the need for further investigation is summarized into the mechanisms of microbiota-mediated immunotherapy, while outlining future directions for developing personalised treatments for ESCC.},
}

@article {pmid40801410,
year = {2025},
author = {Dhabuwala, A and Senapati, SG and Lapsiwala, B and Wala, L and Madhavaram, NJ and Kolli, D and Desai, R},
title = {Causal Factors of Nonischemic Cardiomyopathy: A Contemporary Review of Mendelian Randomization Studies.},
journal = {Cardiology in review},
volume = {},
number = {},
pages = {},
doi = {10.1097/CRD.0000000000001006},
pmid = {40801410},
issn = {1538-4683},
abstract = {Nonischemic cardiomyopathies (NICMs), encompassing hypertrophic (HCM), dilated (DCM), restrictive, arrhythmogenic right ventricular cardiomyopathy/dysplasia, and nondilated left ventricular cardiomyopathies, contribute significantly to cardiovascular morbidity, representing nearly 50% of cardiac transplants. Despite improved genetic and imaging techniques, underdiagnosis persists, particularly for HCM. Mendelian randomization (MR) studies provide a powerful method to identify causal risk factors, overcoming limitations of observational studies and randomized controlled trials. This manuscript reviews MR studies to identify causal factors for NICM, including endocrine, neurological, psychological, musculoskeletal, and microbial influences, and evaluates their implications for diagnostics and therapeutics. We reviewed MR studies using genetic variants as instrumental variables to establish causality. Studies employed one-sample and 2-sample MR, univariable and multivariable analyses, and large-scale genome-wide association study data. Causal relationships between exposures (eg, thyroid dysfunction, type-1 diabetes, iron overload, gut microbiome) and NICM subtypes were assessed, focusing on mediators such as inflammatory biomarkers. MR studies confirmed causal links between NICM and autoimmune endocrinopathies (eg, Hashimoto's thyroiditis and type-1 diabetes), iron overload, obesity, smoking, stress/irritability, and gut microbial taxa. Inflammatory biomarkers, such as monokine induced by interferon-gamma, mediated endocrine pathways. Alzheimer's disease showed a protective effect, while bone mineral density and homocysteine lacked causality. Genetic loci (eg, SVIL and RBM20) were implicated in HCM and DCM. Population stratification biased results, limiting generalizability. MR studies reveal diverse NICM causal factors, supporting precision medicine via enhanced screening and therapies targeting inflammatory mediators and microbial influences. Future research should improve population diversity, validate causal pathways, and explore the cardiac-gut-microbiome axis.},
}

@article {pmid40801368,
year = {2025},
author = {West, SR and Adekoya, AE and Arriaga, SK and Rajagopol, S and Varriale, SL and Planet, PJ and Ibberson, CB},
title = {Genomic analysis of eight clinical Rothia isolates.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0015325},
doi = {10.1128/mra.00153-25},
pmid = {40801368},
issn = {2576-098X},
abstract = {Here, we report the genome sequences of eight clinical isolates of Rothia, seven of which were isolated from the upper respiratory tract of people with cystic fibrosis (pwCF). Analyzing the genomes of members of the respiratory microbiome in pwCF can elucidate possible interactions among microbial community members.},
}

@article {pmid40801346,
year = {2025},
author = {Bai, W and Qiao, X and Li, G and Dong, J and Chen, Y and Li, T},
title = {Analysis of Gut Microbiota in Individuals With Distinct Types of Chronic Rhinosinusitis.},
journal = {The Laryngoscope},
volume = {},
number = {},
pages = {},
doi = {10.1002/lary.70051},
pmid = {40801346},
issn = {1531-4995},
support = {202203021222358//Fundamental Research Program of Shanxi Province, China/ ; },
abstract = {OBJECTIVES: We aimed to characterize the gut microbiota compositions in individuals with distinct types of chronic rhinosinusitis (CRS) and investigate their association with clinical, hematological, and histopathological changes.

METHODS: Fecal samples were collected from 68 patients with CRS and 33 healthy controls (HCs). The patients with CRS were classified into distinct subtypes based on the presence or absence of nasal polyps and the occurrence of eosinophilic tissue inflammation. The microbiome structures of all samples were analyzed using high-throughput 16S rRNA gene sequencing. Clinical, hematological, and histopathological analyses were conducted.

RESULTS: Gut microbiota dysbiosis was found in individuals with distinct types of CRS. The abundances of members from the phylum Proteobacteria and its major genera (Escherichia-Shigella and Klebsiella) decreased significantly in the patients with CRS phenotypes and decreased correspondingly in the patients with CRS endotypes, compared with those in the HCs. The abundances of members from the phylum Bacteroidetes and its major genus (Bacteroides) increased significantly in the patients with CRS with nasal polyps (CRSwNP) and increased correspondingly in the patients with CRSwNP endotypes, compared with those in the HCs and patients with CRS without nasal polyps (CRSsNP) and its endotypes. Most of the bacteria were correlated with the clinical indicators of CRS.

CONCLUSIONS: Gut microbiota dysbiosis is characterized by the presence of unique bacterial flora in distinct types of CRS. The dysbiosis of gut microbiota was correlated with different subtypes and the severity of CRS. Our findings will provide novel insights into the pathogenesis of CRS.

LEVEL OF EVIDENCE: Level 3.},
}

@article {pmid40801314,
year = {2025},
author = {Yildirim, H and Demir, B and Bakal, U and Ucer, O and Sevinc, NS and Yildirim, EA},
title = {From Gut Dysbiosis to Skin Inflammation: Exploring the Hirschsprung's Disease-Psoriasis Link.},
journal = {Pediatric dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/pde.16036},
pmid = {40801314},
issn = {1525-1470},
abstract = {Psoriasis is a skin disease characterized by erythematous and scaly lesions, influenced by genetic and environmental factors. Hirschsprung disease (HD) is a congenital disorder associated with gut microbiome dysbiosis, which can trigger inflammatory skin conditions. We report a case of psoriasis vulgaris in a male infant with HD whose skin lesions completely resolved after HD treatment. This case highlights a potential link between HD-related gut dysbiosis and psoriasis.},
}

@article {pmid40801249,
year = {2025},
author = {Li, Z and Cai, M and Chen, Z},
title = {Cold Atmospheric Plasma in the Treatment of Autoimmune Diseases: Mechanisms, Applications, and Prospects.},
journal = {Immunity, inflammation and disease},
volume = {13},
number = {8},
pages = {e70245},
doi = {10.1002/iid3.70245},
pmid = {40801249},
issn = {2050-4527},
support = {//This study was supported by the USTC Research Funds of the Double First-Class Initiative (No. YD9110002012), Anhui Provincial Natural Science Foundation (No. 2408085J046) and Anhui Provincial Key Research and Development Plan (No. 2022h11020009)./ ; },
abstract = {BACKGROUND: Autoimmune diseases, including rheumatoid arthritis (RA), are characterized by an aberrant immune responses that leads to chronic inflammation and tissue damage. Traditional treatments, such as immunosuppressive drugs, only provide symptomatic relief and often cause significant side effects. Cold atmospheric plasma (CAP), a form of nonthermal plasma, has emerged as a potential therapeutic tool, offering antimicrobial, anti-inflammatory, and immune-modulatory effects.

OBJECTIVE: This review aims to explore the mechanisms of CAP, its application in autoimmune diseases, and its potential to improve existing treatments.

METHODS: The review synthesizes recent studies investigating the biological effects of CAP, particularly its interaction with immune cells. Key mechanisms discussed include the generation of reactive oxygen and nitrogen species (ROS/RNS), which modulate immune responses, promote wound healing, and target pathogenic cells. The therapeutic potential of CAP in treating autoimmune diseases, such as RA, atopic dermatitis, allergic contact dermatitis, psoriasis, and vitiligo is examined through current research findings.

RESULTS: Studies have demonstrated that CAP can modulate fibroblast-like synoviocytes in RA, reducing their viability and inducing apoptosis. In skin diseases like atopic dermatitis, CAP has been shown to alleviate symptoms and reduce microbial load by altering the skin microbiome. In psoriasis, CAP suppresses Th17 cell differentiation and reduces keratinocyte hyperproliferation. Additionally, CAP enhances wound healing by promoting macrophage M2 polarization and collagen remodeling. Despite promising results, concerns remain about the long-term safety of CAP, particularly regarding the accumulation of ROS/RNS.

CONCLUSION: CAP offers a novel approach for treating autoimmune diseases by modulating immune responses, enhancing drug efficacy, and promoting tissue repair. Its ability to selectively target pathogenic cells and its antimicrobial properties make it a promising therapeutic tool in autoimmune diseases.},
}

@article {pmid40801095,
year = {2025},
author = {Bose, A and Visweswariah, SS},
title = {Gut reactions and gut instincts: regulation of intestinal homeostasis by receptor guanylyl cyclase C (GC-C).},
journal = {The Biochemical journal},
volume = {48},
number = {16},
pages = {},
doi = {10.1042/BCJ20253055},
pmid = {40801095},
issn = {1470-8728},
abstract = {The important role that the gut plays in directing and modulating the well-being of the entire organism cannot be underestimated. We are beginning to dissect molecular players that are intrinsic to the functioning of the epithelial cells of the gut, which, in turn, control the responses of various tissues. In this review, we provide an overview of the role of a receptor guanylyl cyclase in regulating fluid-ion homeostasis, cell proliferation and the microbiome in the gut. Further elucidation of molecular details, aided by the development of novel mouse models and organoid cultures, should increase our understanding of the role of this receptor and cyclic guanosine 3',5'-monophosphate in congenital secretory diarrhoea and inflammatory bowel disease.},
}

@article {pmid40800619,
year = {2025},
author = {van Eijnatten, AL and van Zon, L and Manousou, E and Bikineeva, M and Wubs, ERJ and van der Putten, WH and Morriën, E and Dutilh, BE and Snoek, LB},
title = {SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf036},
pmid = {40800619},
issn = {2730-6151},
abstract = {Correlation networks are commonly used to explore microbiome data. In these networks, nodes are microbial taxa and edges represent correlations between their abundances. As clusters of correlating taxa (co-abundance clusters) often indicate a shared response to environmental drivers, network visualization contributes to the system understanding. Currently, most tools for creating and visualizing co-abundance networks from microbiome data either require the researcher to have coding skills or are not user-friendly, with high time expenditure and limited customizability. Furthermore, existing tools lack a focus on the association between environmental drivers and the structure of the microbiome, even though many edges in correlation networks can be understood through a shared association of two taxa with the environment. For these reasons, we developed SpeSpeNet (Species-Species Network, https://tbb.bio.uu.nl/SpeSpeNet), a practical and user-friendly R-shiny tool to construct and visualize correlation networks from taxonomic abundance tables. The details of data preprocessing, network construction, and visualization are automated, require no programming ability for the web version, and are highly customizable, including associations with user-provided environmental data. Here, we present the details of SpeSpeNet and demonstrate its utility using three case studies.},
}

@article {pmid40800617,
year = {2025},
author = {Fuschi, A and Merlotti, A and Remondini, D},
title = {Microbiome data: tell me which metrics and I will tell you which communities.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf125},
pmid = {40800617},
issn = {2730-6151},
abstract = {In microbial community studies, analyzing diversity is crucial for uncovering ecological complexity. However, the intrinsic characteristics of Next-gen sequencing data challenge the use of Euclidean metrics for estimating proximity and correlation. Consequently, a variety of distance measures have been developed within ecological frameworks. In this study, we compare several of these metrics-including Bray-Curtis, Canberra, Jensen-Shannon, Hellinger, Euclidean, and Aitchison distances-demonstrating how the choice of metric can significantly influence the interpretation of microbial community structures. Among these, Aitchison distance specifically defined for compositional data shows markedly different behavior from the others, highlighting different features related to the data. We consider two real-world examples: the human gut microbiome sampled using 16S rRNA sequencing with multiple measurements for different patients (G-HMP2) and urban sewage environmental metagenomes collected over time at different sites through shotgun sequencing (E-WADES). We show that, for the same dataset-independently on the sequencing technique or on the sampling context-the community structure depends strongly on the choice of specific metrics. This can be explained by the mathematical properties of the chosen metrics and the specific characteristics of microbiome data, namely their high heterogeneity in species abundance. This provides clear insights into how distance metrics influence interpretation and assists in choosing the most appropriate one for the study objectives.},
}

@article {pmid40800616,
year = {2025},
author = {Fronton, F and Gandin, A and Deslauriers, D and Small, D and Robert, D and St-Pierre, Y},
title = {Expanding the use of circulating microbiome in fish: contrast between the gut and blood microbiome of Sebastes fasciatus.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf116},
pmid = {40800616},
issn = {2730-6151},
abstract = {The study of microbiomes in fish populations offers vital insights for ecological and fisheries management, particularly in responses to environmental changes. Although traditional studies have concentrated on the gut microbiome, the emerging concept of a circulating blood microbiome suggests it may act as an early indicator of dysbiosis and various health conditions by reflecting transient bacterial DNA presence. In this study, we examined the gut and blood microbiomes of Sebastes fasciatus (Storer, 1854), a species of redfish of significant economic and ecological importance in the Gulf of St. Lawrence, to obtain critical information for health monitoring, pathogen detection, and ecological management in fisheries. Our results revealed that the gut and blood microbiomes of S. fasciatus have distinct bacterial DNA signatures, with significant differences in microbial diversity. Notably, although both microbiomes exhibited similar dominant genera, specific amplicon sequence variants varied significantly. Through a controlled experimental design, we found that the dietary impacts on microbiome composition were statistically significant yet minimal, suggesting that environmental factors play a more substantial role in shaping microbial communities. Finally, we report the presence of potential pathogens and opportunistic bacteria found exclusively in the blood microbiome. Our results highlight the blood microbiome's value as a sensitive health and environmental stress indicator, essential for sustainable fish population management. Integrating microbiome indicators can improve fisheries management and ecosystem sustainability, offering a model applicable to various marine species and environments.},
}

@article {pmid40800601,
year = {2025},
author = {Wei, H and Han, C and Song, Y},
title = {Exploring the Causal Relationship Between Saliva Microbiota Abundance and Chronic Obstructive Pulmonary Disease/Idiopathic Pulmonary Fibrosis: A Two-Sample Mendelian Randomization Study.},
journal = {International journal of chronic obstructive pulmonary disease},
volume = {20},
number = {},
pages = {2801-2813},
pmid = {40800601},
issn = {1178-2005},
abstract = {BACKGROUND: Idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD) are progressive lung diseases with overlapping risk factors but distinct pathologies. This study employed bidirectional two-sample Mendelian randomization (MR) to explore potential causal relationships between saliva microbiota abundance and the risk of both diseases.

METHODS: Saliva microbiota abundance datasets were analyzed for forward and reverse causal associations with both diseases. Of 44 datasets, 43 met the inclusion criteria for instrumental variable selection. MR analyses were performed using inverse variance weighted (IVW), MR-Egger, weighted median, and weighted mode methods. Steiger filtering confirmed directionality. Sensitivity analyses included Cochran's Q, MR-Egger intercept, MR-PRESSO, and leave-one-out to assess heterogeneity, pleiotropy, and the influence of individual variants.

RESULTS: In forward MR, higher abundance of species parvula was significantly associated with reduced COPD risk (IVW OR = 0.9546, 95% CI = 0.9224-0.9879, P = 0.0020; adjusted P = 0.019). Nominal inverse associations were observed for Bacilli, Porphyromonas, and Fusobacterium with IPF, though these did not remain significant after multiple testing correction. All key associations passed Steiger directionality tests, with no evidence of horizontal pleiotropy or heterogeneity. In reverse MR, COPD showed a nominal positive association with Periodonticum abundance.

CONCLUSION: This exploratory study suggests potential directional associations between specific salivary microbiota and chronic respiratory diseases. Parvula abundance may be protective against COPD, while Bacilli, Porphyromonas, and Fusobacterium may influence IPF risk. These findings support the salivary microbiome as a potential contributor to respiratory disease pathogenesis and warrant further validation in mechanistic and longitudinal studies.},
}

@article {pmid40800233,
year = {2025},
author = {Rojahn, A and Leps, AS and Goericke-Pesch, S},
title = {German veterinarians asked: a cross-sectional study on microbiological examination and antimicrobial use in canine reproductive medicine.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1645496},
pmid = {40800233},
issn = {2297-1769},
abstract = {Despite the growing global threat of antimicrobial resistance, many dog breeders still request antimicrobial treatment prior to mating, often based on vaginal bacterial culture examinations. However, several previous studies failed to identify differences in the vaginal microbiota between healthy dogs and those with reproductive tract disorders; thus, treating healthy bitches with antimicrobials regardless of the bacterial findings is contraindicated. To investigate current practices of German small animal veterinarians regarding microbiological sampling and antimicrobial treatment in canine reproductive medicine, we conducted an online survey using LimeSurvey®. The questionnaire included questions (single/multiple choice) about procedures of microbiological swab sampling and handling in general and in canine reproductive medicine specifically, as well as on antimicrobial use in the respective field. The objective was to identify educational and research needs regarding vaginal bacterial culture interpretation and antimicrobial treatment in canine breeding. We found that treating clinically healthy breeding bitches remains common practice among both breeders and veterinarians. Our findings highlight the importance of continuous education and improved communication to reduce inappropriate antimicrobial use in canine reproduction. Furthermore, research on the reproductive microbiome in relation to fertility is essential for evidence-based treatment decisions.},
}

@article {pmid40800112,
year = {2025},
author = {Yang, R and Jia, M and Xu, Y and Wu, Z and Wu, D and Fan, G and Gui, Y},
title = {Microbiome and metabolome integrated analysis: exploring potential diagnostic approaches for Parkinson's disease using tongue coating samples.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1621468},
pmid = {40800112},
issn = {1664-302X},
abstract = {Parkinson's disease (PD) is a prevalent neurodegenerative disorder with complex pathogenesis and limited treatment options. The current reliance on clinical evaluation for diagnosis, due to the absence of reliable non-invasive methods, presents significant challenges. Traditional diagnostic approaches, including cerebrospinal fluid or blood sampling, are invasive, pose risks of infection, are costly, and often require complex procedures. Tongue coating sampling presents a non-invasive, cost-effective, and repeatable alternative, indicating that it could be a valuable tool for early detection and monitoring of PD, warranting further investigation. This study explores the feasibility of using tongue coating samples as a diagnostic tool for PD through microbiome analysis, with metabolomics data providing additional context and validation via machine learning models. A cohort of 36 PD patients and 31 controls was recruited. 16S rRNA sequencing was used for microbiome analysis, revealing significant alterations in the relative abundances of various microbial taxa, including Firmicutes, Bacteroidetes, and Actinobacteria. Concurrent metabolomics analysis using UPLC-Q/TOF-MS revealed a decrease in palmitoylethanolamide (PEA) levels in Parkinson's disease (PD) patients, and also showed reduced carnitine levels specifically in the severe Hoehn-Yahr (H-Y) stage and mild cognitive impairment (MCI) subgroups. These findings provide preliminary evidence suggesting a potential link between specific microbial alterations and PD progression, which may warrant further investigation. Additionally, the analysis indicates a correlation between certain microbial and metabolomic changes and the advancement of PD. Our results also suggest that tongue coating may serve as a potential non-invasive tool for PD diagnosis, with a particular emphasis on the combined role of the microbiome and metabolome in the pathogenesis of the disease.},
}

@article {pmid40800105,
year = {2025},
author = {Degani, O and Levy, M and Horwitz, BA},
title = {Editorial: Plant-friendly microorganisms as a bio-barrier against pathogens.},
journal = {Frontiers in fungal biology},
volume = {6},
number = {},
pages = {1659453},
pmid = {40800105},
issn = {2673-6128},
}

@article {pmid40799936,
year = {2025},
author = {Luo, F and Sun, L and Wan, R and Tian, Z and He, Z},
title = {Global research trends on the interaction between gut microbiome and bile acids: a bibliometric and visualized analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1616995},
pmid = {40799936},
issn = {2235-2988},
abstract = {BACKGROUND: An increasing number of studies have shown that gut microbiome-bile acids interactions play a crucial role in host health and disease. This bibliometric analysis aims to identify the global scientific output, research hotspots, and frontiers of gut microbiome-bile acids in the past two decades.

METHODS: We searched the relevant studies of gut microbiome-bile acids published between 2004 and 2024 in the Web of Science Core Collection database. Microsoft Excel 2019, VOSviewer 1.6.18, Tableau Desktop 2024.2.2, Scimago Graphica 1.0.45, and CiteSpace 6.2.R3 were used to analyze the publications, countries/regions, institutions, journals, authors, references, and keywords.

RESULTS: A total of 4795 original articles and reviews were collected. A visual analysis of the results showed that the number of publications increased rapidly over time. China published the most papers, the United States had the most citations, and the most productive institution was Shanghai Jiaotong University. The most prolific author was Jia Wei, and Jason M. Ridlon was the most frequently co-cited author. Nutrients was the most productive journal. In the keyword co-occurrence network, except for gut microbiome and bile acids, inflammation becomes the keyword with the highest frequency. Keywords and reference analysis show that metabolic diseases (such as obesity and type 2 diabetes mellitus), cancer (such as colorectal cancer), and disease-related mechanisms (such as tgr5 and pathway) are the hot topics and future research trends in this field.

CONCLUSION: In this study, bibliometric analysis was utilized to explore the relationship between gut microbiome and bile acids. The findings can reflect the current hotspots and new directions of gut microbiome-bile acids, and provide an objective description and comprehensive guidance for future related studies.},
}

@article {pmid40799824,
year = {2025},
author = {Zhang, W and Zhang, X and Xu, S and Waheed, YA and Xu, Y and Li, S and Sun, D},
title = {The effects of Shenkang suppository on kidney function and gut microbiota in nondialysis patients with chronic kidney disease stages 3-4: A randomized controlled trial.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1621208},
pmid = {40799824},
issn = {1663-9812},
abstract = {BACKGROUND: Chronic kidney disease (CKD) patients have high prevalence and mortality rates; however, current treatment options remain limited. The Shenkang suppository (SKS) is a traditional Chinese medicine used in the clinical management of CKD. Increasing evidence suggests a close relationship between the gut microbiome and CKD. We aimed to investigate the impact of SKS on kidney function and the gut microbiota in CKD stage 3-4 patients.

METHODS: It's a single-center randomized controlled trial (n = 80). CKD stage 3-4 patients were randomly assigned at a 1:1 ratio to either the control group (n = 40) or the SKS group (n = 40) and followed for 8 weeks. Baseline data, clinical indicators, kidney markers, and stool samples were obtained from participants before and after treatment. The bacterial DNA was isolated from fecal samples and analyzed via high-throughput 16S rRNA sequencing.

RESULTS: A total of 34 patients in the SKS group and 36 in the control group completed the study. Kidney function in the control group significantly worsened after 8 weeks (P < 0.05), whereas SKS had a positive effect on slowing the progression of kidney function decline. After 8 weeks of SKS intervention, the beneficial bacteria Coriobacteriaceae and Ruminococcaceae-Ruminococcus proliferated dramatically, whereas the abundance of the harmful bacteria Veillonellaceae decreased. Linear discriminant analysis (LDA) revealed that SKS treatment increased the proportion of Streptococcus and decreased the proportions of Planctomycetes, Spirochaetes, Rhodocyclales, Actinomycetaceae, Veillonellaceae, and Dechloromonas. These changes were not observed in the control group. Correlation analysis revealed a negative association between Bifidobacterium, Blautia, Enterococcaceae_Enterococcus, and clinical kidney function indicators, whereas Parabacteroides, Acinetobacter, Sutterella, Oscillospira, and Alistipes were positively correlated with kidney function.

CONCLUSION: SKS could delay the progression of kidney function in CKD stage 3-4 patients, possibly by modulating the dysbiosis of the gut microbiota. The close associations between certain gut microbiota and clinical kidney function indicators suggest that the gut microbiota could serve as a new therapeutic target for CKD.

CLINICAL TRIAL REGISTRATION: https://www.chictr.org.cn/, Chinese Clinical Trial Registry Identifier: ChiCTR2200058493.},
}

@article {pmid40799652,
year = {2025},
author = {Liu, M and Geng, J and Liu, T and Liu, X},
title = {Gut microbiome dysregulation in noninfectious uveitis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1614304},
pmid = {40799652},
issn = {1664-3224},
abstract = {Noninfectious uveitis (NIU) is a vision-threatening autoimmune disease of the eye, but its pathogenesis is still not fully understood. Recently, accumulating evidence suggests that gut microbiome dysbiosis may affect the development and progression of NIU through potential mechanisms, including translocation, molecular mimicry, and bystander activation. Understanding the mechanisms of gut microbiome-host interactions, especially the gut-eye axis regulation, can offer a theoretical foundation for developing novel therapeutic strategies. We summarized current evidence on the dysregulation of gut microbiome and metabolites in NIU, and explored potential mechanisms involved. Furthermore, possible therapeutic measures are discussed, including probiotics, prebiotics, dietary modifications, antibiotic interventions, as well as fecal microbial transplantation, aiming to exert beneficial effects on NIU progression by reshaping the gut microbial composition.},
}

@article {pmid40799180,
year = {2025},
author = {Lechien, JR and Al Barajraji, M and Maniaci, A and Laurent, S and Benali, S and Ris, L and Massager, N and Raquez, JM and Baudouin, R and Hans, S and Dubois, P and Manto, M},
title = {Micro- and Nanoplastic Toxicity in Upper Respiratory Tract: A Scoping Review.},
journal = {The Laryngoscope},
volume = {},
number = {},
pages = {},
doi = {10.1002/lary.70033},
pmid = {40799180},
issn = {1531-4995},
abstract = {OBJECTIVES: To review the current literature findings dedicated to the toxicity of nano- and microplastics (NMPs) in the upper respiratory tract.

DATA SOURCES: PubMED, Cochrane Library and Embase databases.

REVIEW METHODS: Three independent investigators conducted the literature search for the documentation and toxicity of NMP in the upper respiratory tract according to the PRISMA statements. Primary outcomes included NMP types, shape, density, sizes, the environment (air, mask wearing, plasticdevice), and the histological and physiological modifications associated with the deposit of NMP.

RESULTS: The scoping review included 12 studies (10 clinical, 2 experimental) with 356 human subjects. NMPs were detected in all samples, predominantly as fragments (10-500 μm), except in mask-wearers where fibers predominated. Polypropylene, polycarbonate, and polyurethane were the most common. Clinical studies showed higher NMP density in patients with nasal disorders with an increased permeability of mucosa (rhinosinusitis and allergic rhinitis) than in healthy controls. Mask wearing and nasal lavage devices contributed to NMP deposition. Experimental studies demonstrated NMP cellular internalization with potential physiological disruption, including oxidative stress, autophagy dysfunction, and respiratory microbiome alterations. There was substantial heterogeneity across studies for NMP detection methods.

CONCLUSIONS: The current clinical and experimental studies demonstrate that both exposed and unexposed humans have nasal NMP detected in their nasal tissues and fluids. Mask wearing and the use of old plastic nasal lavage devices can contribute to this deposition. While experimental studies suggest changes in tissue and cell physiology, the toxicity of NMP in nasal tissue remains poorly investigated and has not been conclusively demonstrated.},
}

@article {pmid40798967,
year = {2025},
author = {Shi, S and Gong, X and Cheng, S and Tao, D and Chen, X and van der Heijden, MGA and Trivedi, P and Baquerizo, MD and Liu, M},
title = {Maize growth as a function of cover crop-mediated soil microbiome.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70460},
pmid = {40798967},
issn = {1469-8137},
support = {2022YFD1500203//National Key Research and Development Program of China/ ; 24RCKB002//Science and Technology Program of Gansu Province/ ; },
abstract = {Soil microbes are critical drivers of maize growth and soil health by regulating soil fertility and suppressing diseases. Yet, the relative contribution to maize growth across diverse soil types, particularly following cover crop management, remains virtually unknown. Such knowledge is pivotal for soil ecological engineering, as microbiome management is emerging as a highly promising tool for more sustainable agriculture. Here, we collected 27 soils from different regions of China and subjected them to controlled conditions with two cover crop types (legume and gramineae) to investigate the contribution of soil microbes to maize growth. Our study demonstrates the functional importance of soil microbial taxa in explaining the capacity of soils to support maize growth. Soil microbes explained up to 29% of the variation in maize biomass, with key taxa such as Geodermatophilus, Lapillicoccus, and Acidipila bacteria strongly positively correlated with maize biomass. These important linkages remained robust even after accounting for the contribution of geographic, climatic, and soil factors in our analyses. Furthermore, we observed that gramineae cover crops significantly reduced both soil nitrogen availability and maize growth, whereas legume cover crops reduced soil nitrogen availability without impairing maize growth, highlighting the role of agricultural practices in steering microbiome-mediated soil functions. Together, our work highlights the fundamental contribution of soil microbes to explaining maize growth across contrasting soil environments, which is critical to predicting the future of food security in a changing world.},
}

@article {pmid40798872,
year = {2025},
author = {Wang, Y and Zhou, J and Zhang, X and Li, R and Li, Y and Yi, X},
title = {Foliar-Feeding Weevils Recruit Phyllosphere-Derived Tannin-Degrading Bacteria to Increase Their Fitness.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70119},
pmid = {40798872},
issn = {1365-3040},
support = {//This study was supported by the Natural Science Foundation of Shandong Province (ZR2024MC092) and the National Science Foundation of China (32070447)./ ; },
abstract = {The gut microbiota plays a crucial role in shaping animal life history, particularly by mediating interactions between herbivorous insects and their host plants. Phytophagous insects that feed on oak leaves must overcome the challenge of detoxifying tannins. While gut microbes contribute significantly to this detoxification process, the mechanisms by which insects acquire tannin-degrading bacteria remain poorly understood. In this study, we investigated tannin-degrading bacterial communities in Nothomyllocerus illitus, a phytophagous weevil that primarily consumes oak leaves. Through 16S rRNA sequencing, bacterial isolation, enzymatic activity assays, and fluorescence tracing experiments, we identified Bacillus, Acinetobacter, and Enterobacter as key tannin-degrading genera associated with N. illitus. These bacteria are predominantly acquired from the oak phyllosphere rather than from soil sources. Fluorescently labelled Bacillus and Acinetobacter strains were shown to successfully colonise the weevil gut, underscoring their functional relevance in tannin degradation. Furthermore, supplementation of oak leaves with these bacterial strains enhanced feeding behaviour, larval growth, and reproductive performance, whereas antibiotic treatment diminished these effects, thereby confirming the critical contribution of phyllosphere-derived bacteria to the overall fitness of foliar-feeding weevils N. illitus.},
}

@article {pmid40797510,
year = {2025},
author = {Zhao, R and Li, Y and Han, M and Zhang, Y and Lin, S and Yu, M and Li, D and Zhang, B and Peng, L and Che, Y},
title = {Genetic causality linking skin microbiota to skin cancer: Mendelian randomization study and meta-analysis.},
journal = {Medicine},
volume = {104},
number = {32},
pages = {e43571},
pmid = {40797510},
issn = {1536-5964},
abstract = {The skin microbiome has been linked to the etiology and progression of skin cancer, but the causal relationship remains unclear. This study employs two-sample Mendelian randomization (TSMR) and meta-analysis techniques to elucidate the putative genetic causal relationships between skin microbiota and skin cancer. Genetic variant data for the skin microbiome and skin cancer, drawn from large-scale genome-wide association studies, were extracted from European populations. TSMR analysis, heterogeneity tests, horizontal pleiotropy assessments, sensitivity analysis, and directional tests were conducted, followed by a meta-analysis to enhance the reliability of the findings. The TSMR and meta-analysis results indicate a significant association between the Proteobacteria phylum, including Gammaproteobacteria, and an increased risk of melanoma. Conversely, the Staphylococcus genus is significantly associated with a reduced risk of melanoma. Additionally, the Bacteroidetes phylum exhibits a statistically significant association with an elevated risk of basal cell carcinoma. This study furnishes genetic evidence substantiating the causal nexus between the skin microbiome and skin cancer. Further research is warranted to elucidate the underlying mechanisms and explore skin microbiome-centric prophylactic and therapeutic strategies for skin cancer.},
}

@article {pmid40797468,
year = {2025},
author = {Guo, T and Chang, L and Huang, PW and Yao, JP and Zhang, YC and Ren, CY and Bao, CQ},
title = {Investigating the mediating effect of plasma metabolites on the gut microbiome in influencing Behçet disease: A multi-omics validated Mendelian randomization study.},
journal = {Medicine},
volume = {104},
number = {32},
pages = {e42698},
pmid = {40797468},
issn = {1536-5964},
support = {Z202213//Wuxi Municipal Health Commission's research project/ ; },
abstract = {Although an established correlation between gut microbiota (GM) and Behçet syndrome exists, the potential mediating involvement of plasma metabolites remains unclear. Using the most recent statistical data from genome-wide association studies conducted in 2024, we investigated the causal relationships between 473 GM taxa, 233 circulating metabolites, and Behçet syndrome (Behçet disease [BD]) through a 2-sample Mendelian randomization approach. This analysis was further supported by incorporating transcriptome and metagenomic data related to BD. A 2-step methodology was employed to evaluate the extent to which the effect of GM on BD is mediated through plasma metabolites. These results were subsequently validated in a separate validation set. Our Mendelian randomization results demonstrated correlations between various GM and the risk of Behçet syndrome. The potential link between GM and BD risk may be mediated through plasma circulating metabolite levels. Specifically, for every standard deviation, an increase in the abundance of Turicibacter sp001543345 was correlated with a 403% increase in BD risk (odds ratio : 5.03 [95% confidence interval, 1.77-14.25]). Meanwhile, the cholesteryl esters to total lipids ratio in large very low-density lipoprotein and the total cholesterol to total lipids ratio in very large very low-density lipoprotein increased by 4%. The proportion of indirect effects is 3.026% and 3.338%, respectively. Our study established a causal link between distinct GM and BD and quantified the proportion of effects mediated through plasma metabolites. These findings provide further insights for the treatment of BD.},
}

@article {pmid40797364,
year = {2025},
author = {Wall, CB and Perreault, MG and Demmel, MY and Diaz, EM and Dominguez, JH and Shurin, JB},
title = {Geography and Host Identity Shape Intraseasonal Variation of Free-Living and Zooplankton Associated Microbial Communities in Alpine Lakes.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70069},
doi = {10.1111/mec.70069},
pmid = {40797364},
issn = {1365-294X},
support = {2018058//USA-National Science Foundation/ ; },
abstract = {Microbes contribute to aquatic ecosystem function and the fitness of macroscopic organisms, including zooplankton. Many factors affect the taxonomic compositions of free-living (bacterioplankton) and zooplankton-associated microbial communities in lakes; yet how these communities vary seasonally and among lakes remains poorly understood. Here, we investigate how free-living bacterial communities and those associated with different crustacean zooplankton hosts change in response to fluctuations in their natural environment across time and space. We repeatedly sampled bacterioplankton, zooplankton communities, zooplankton microbiomes, and water chemistry parameters of six lakes in the eastern Sierra Nevada mountains of California across a summer season. 16S rRNA gene sequencing revealed clear differences in the community composition and relative abundance of bacterial taxa between bacterioplankton and zooplankton microbiomes, which was best explained by lake and host identity rather than intraseasonal sampling times. Bacterioplankton communities were highly conserved across the summer season and showed higher alpha diversity, but lower species turnover, than zooplankton microbiomes, which were more variable and largely partitioned by host taxa and phylogenetics (Copepoda vs. Cladocera). Spatial and local environmental context (drainage basin, home-lake habitat) interacted secondarily with community types (free-living, host-associated) and zooplankton host identity to shape bacterial community composition. These results show that deterministic processes related to host filtering, host taxonomy, and spatial/environmental variation among lakes drive changes in microbial communities more than temporal changes within lakes. Higher beta diversity among zooplankton-associated microbes suggests dispersal limitation and/or local selection play stronger roles for zooplankton microbiomes than for free-living bacterioplankton.},
}

@article {pmid40797356,
year = {2025},
author = {Rashwan, HH and Ali, MH and Mostafa, MM and Ramadan, R and Mysara, M},
title = {Insights into the tripartite relationship between cervical cancer, human papillomavirus, and the vaginal microbiome: a mega-analysis.},
journal = {Human genomics},
volume = {19},
number = {1},
pages = {89},
pmid = {40797356},
issn = {1479-7364},
abstract = {BACKGROUND: Cervical cancer (CC) is the fourth most prevalent malignancy among women worldwide, where 99.7% of the cases are linked to persistent human papillomavirus (HPV) infections. While emerging evidence suggests a role for vaginal microbiome dysbiosis in HPV-driven CC, the specific microbial alterations and their functional implications remain unclear. However, inconsistencies in identifying specific microbial signatures-largely due to heterogeneous study designs, targeted 16S rRNA regions, and data processing methods-have limited the generalizability of existing findings. To address these challenges, we conducted a standardized mega-analysis using a compositionality-aware approach to ensure consistency and minimize technical bias across studies.

RESULTS: Our mega-analysis consolidates findings from five case-control 16S rRNA ampilicon sequencing studies, encompassing 215 samples. Compared to healthy controls, CC patients exhibited significantly higher alpha diversity (Shannon index, p <0.005) and a shift from a Lactobacillus-dominant to a polymicrobial vaginal microbiome. This microbial dysbiosis was characterized by an increased abundance of Porphyromonadaceae, particularly Porphyromonas asaccharolytica, and other anaerobic bacterial species such as Campylobacter ureolyticus, Peptococcus niger, and Anaerococcus obesiensis (FDR <0.05). Functional profiling of the altered microbiome revealed enrichment in pathways associated with chronic inflammation, fatty acid biosynthesis, amino acid metabolism, cellular proliferation, invasion, and metastasis.

CONCLUSIONS: This mega-analysis presents the most methodologically homogeneous study to date of CC-associated vaginal microbiome using publicly available 16S datasets. Our findings not only deepen our understanding of microbial influences on CC but also pave the way for novel diagnostic and therapeutic approaches potentially enhancing patient outcomes in CC care. These insights open new avenues for clinical interventions that extend beyond conventional HPV-centric strategies.},
}

@article {pmid40797302,
year = {2025},
author = {Baborski, A and Barth, SA and Jung, EM and Bloos, F and Rödel, J and Löffler, B and Bauer, M and Busch, A},
title = {Surviving antibiotic treatment as a gut bacterium: genomic characterization of an Enterobacter cloacae.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {56},
pmid = {40797302},
issn = {2730-6844},
abstract = {Enterobacter cloacae complex is a group of common opportunistic pathogens on intensive care units. On intensive care units sepsis is treated with high doses of antibiotics. This treatment does not only eliminate pathogenic bacteria but parts of the microbiome community as well. This leads to an imbalance of the gut microbiome. However, some bacteria can survive such treatment due to certain survival and resistance mechanisms. Not only antibiotic resistance mechanisms but also forming strong communities via biofilm formation promotes cell survival. Here, we investigated the properties of the isolate AT70PIP076 from a sepsis patient treated with piperacillin and tazobactam. After biochemical analysis and MALDI-TOF analysis, the strain was found to be Enterobacter cloacae. In addition to in vitro, antimicrobial susceptibility testing the genome was further investigated in situ regarding antibiotic resistance. Further live/dead staining was performed, and the biofilm formation was investigated using confocal laser microscopy (cLSM). The genome shows the presence of biofilm-associated genes EU554560, bcsABZC_AP010953, ehaB, KF662843, and crl. The understanding of the underlying mechanism of survival of potential pathogens might contribute to elucidate potential treatment options.ObjectivesGenomic analysis of a bacterium that can survive antibiotic treatment within the gut of an antibiotictreated patient to elucidate survival and resistance mechanisms.Data descriptionThe isolate AT70PIP076 was isolated in 2021 from feces collected from a patient treated with Piperacillin and tazobactam. Whole genome DNA was isolated using the Nextera DNA Flex microbial colony extraction protocol and the Nextera Flex DNA preparation kit according to the manufacturer's instructions. Following paired-end sequencing was performed on the MiSeq platform (Illumina, Inc., San Diego, CA, USA) using a 300-cycle MiSeq reagent kit and a read length of 151 bp. Contamination check and identification of 16 S RNA sequences was done by using ContESt16S. The genomic sequence contained 4,988,237 bp and the G + C content is represented at 54.80%. This genome and its associated data set will serve as a useful resource for further analyses.},
}

@article {pmid40797178,
year = {2025},
author = {Liu, Q and Han, Y and Sun, Q and Gu, Q and Jiang, L and Su, X and Zhong, R},
title = {Novel silage from pea sprout roots and corn straw: a step towards agricultural waste utilization.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {503},
pmid = {40797178},
issn = {1471-2180},
support = {2024YFD1301105-03//the National Key Research and Development Program/ ; 24GXYSZZ11//Changchun Science and Technology Development Plan Project/ ; 2025SYHZ0017//Technology Cooperation High-Tech Industrialization Project of Jilin Province and the Chinese Academy of Sciences/ ; TL2023YF026//Science and Technology Development Project of Tongliao City/ ; 2023QN20//Jilin Province Innovation and Entrepreneurship Talent Project/ ; SNYCQN138-2022//Shennong Talent Plan of the Ministry of Agriculture and Rural Affairs/ ; },
abstract = {This study was conducted to evaluate the effects of microbial compound agent (Cellulose degrading bacteria + lactic acid bacteria) on the microbiome, fermentation, and aerobic stability of co-ensiled corn stover and pea sprout roots under various times. Corn stover and pea sprout roots in five different ratios (100:0, 75:25, 50:50, and 25:75) were ensiled without (100C, 75G, 50G and 25G) or with microbial additives (100CF, 75GF, 50GF and 25GF) for 35 and 60 days. The results revealed that whether ensiling 35 days or 60 days, the CP content increased significantly in 75G (P < 0.05); The ADL content in 75GF was significantly decreased (P < 0.05); the molds, yeast and EB counts were lowest in silage by adjusting the ratio of the two mixtures with additional microbial additives compared without. Only ensiling 35 days, the WSC content was significantly increased in 75G (P < 0.05); the HL content was significantly decreased in 50G (P < 0.05); the CP content increased significantly in 75GF (P < 0.05); the LA content was significantly higher in 75G and 75GF (P < 0.05); the EB counts in 75GF decreased during aerobic exposure from 1 to 7 days; the molds counts in 75GF and 50GF decreased to the lowest values after 3 days of aerobic exposure. In conclusion, mixing dry corn stover and pea sprout roots as silage in a proper proportion with microbial additives supplementation and proper ensiling time can improve silage quality and aerobic stability. And 75% dry corn stover + 25% pea sprout roots and 50% dry corn stover + 50% pea sprout roots combined with microbial additives and after 35 days ensiling can obtain better quality silage.},
}

@article {pmid40797015,
year = {2025},
author = {Najarpoor, A and Mohamadzade Namin, S and Ghosh, S and Jung, C},
title = {Impact of carbohydrate sources on the longevity and physiological traits of the European honey bee workers.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {29532},
pmid = {40797015},
issn = {2045-2322},
support = {NRF-2018R1A6A1A03024862//National Research Foundation of Korea/ ; NRF-2018R1A6A1A03024862//National Research Foundation of Korea/ ; NRF-2018R1A6A1A03024862//National Research Foundation of Korea/ ; RS-2023-00232847//Rural Development Administration/ ; RS-2023-00232847//Rural Development Administration/ ; },
abstract = {Carbohydrates are vital for honey bee energy, fitness, and survival, influencing colony dynamics and resilience. This study examined the effects of various carbohydrate sources on honeybee longevity, hypopharyngeal gland size, gene expression, and gut microbiome composition. Newly emerged bees were fed white sugar, brown sugar, corn syrup (CS), maltose, acacia honey, chestnut honey, and oligosaccharide ad libitum. Bees fed CS showed the highest longevity, followed by acacia honey and white sugar, while oligosaccharide-fed bees had the lowest longevity. CS-fed bees also exhibited larger hypopharyngeal glands, correlating with improved survival. Gene expression analysis revealed upregulation of Ilp2 and Vg and downregulation of Ilp1 in 14-day-old bees fed with CS which may be linked to enhanced longevity. Gut microbiome analysis showed the higher composition of Frischella in honey fed treatment groups and Bartonella in processed carbohydrates treated groups, potentially compensating for dietary amino acid deficiencies. However, the absence of core symbionts like Snodgrassella in CS-fed bees may weaken immunity and heighten disease susceptibility. These findings suggest starch-derived corn syrup as a promising carbohydrate source under laboratory conditions, however, long-term colony-level studies are essential to fully understand its benefits and potential risks. This research provides valuable insights for honey bee management and conservation strategies.},
}

@article {pmid40796904,
year = {2025},
author = {Nowak, KH and Hartop, E and Prus-Frankowska, M and Buczek, M and Kolasa, MR and Roslin, T and Ovaskainen, O and Łukasik, P},
title = {What lurks in the dark? An innovative framework for studying diverse wild insect microbiota.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {186},
pmid = {40796904},
issn = {2049-2618},
support = {2016-203 4.3//Swedish Taxonomy Initiative/ ; 856506//Horizon 2020/ ; 856506//Horizon 2020/ ; 336212//Research Council of Finland/ ; PPN/PPO/2018/1/00015//Narodowa Agencja Wymiany Akademickiej/ ; 2018/31/B/NZ8/01158//Narodowe Centrum Nauki/ ; },
abstract = {BACKGROUND: Symbiotic microorganisms can profoundly impact insect biology, including their life history traits, population dynamics, and evolutionary trajectories. However, microbiota remain poorly understood in natural insect communities, especially in 'dark taxa'-hyperdiverse yet understudied clades.

RESULTS: Here, we implemented a novel multi-target amplicon sequencing approach to study microbiota in complex, species-rich communities. It combines four methodological innovations: (1) To establish a host taxonomic framework, we sequenced amplicons of the host marker gene (COI) and reconstructed barcodes alongside microbiota characterisation using 16S-V4 rRNA bacterial gene amplicons. (2) To assess microbiota abundance, we incorporated spike-in-based quantification. (3) To improve the phylogenetic resolution for the dominant endosymbiont, Wolbachia, we analysed bycatch data from the COI amplicon sequencing. (4) To investigate the primary drivers of host-microbe associations in massive multi-dimensional datasets, we performed Hierarchical Modelling of Species Communities (HMSC). Applying this approach to 1842 wild-caught scuttle flies (Diptera: Phoridae) from northern Sweden, we organised them into 480 genotypes and 186 species and gained unprecedented insights into their microbiota. We found orders-of-magnitude differences in bacterial abundance and massive within-population variation in microbiota composition. Patterns and drivers differed among microbial functional categories: the distribution and abundance of facultative endosymbionts (Wolbachia, Rickettsia, Spiroplasma) were shaped by host species, genotype, and sex. In contrast, many other bacterial taxa were broadly distributed across species and sites.

CONCLUSIONS: This study highlights facultative endosymbionts as key players in insect microbiota and reveals striking variations in distributional patterns of microbial clades. It also demonstrates the power of integrative sequencing approaches in uncovering the ecological complexity and significance of symbiotic microorganisms in multi-species natural communities. Video Abstract.},
}

@article {pmid40796882,
year = {2025},
author = {He, Y and Li, Q and Sun, Q and Li, H and Yu, T and Chen, M and Zhang, G and Zhang, B and Wang, W and Ju, S},
title = {Gut microbiota contributes to polystyrene nanoplastics-induced fetal growth restriction by disturbing placental nicotinamide metabolism.},
journal = {Journal of nanobiotechnology},
volume = {23},
number = {1},
pages = {561},
pmid = {40796882},
issn = {1477-3155},
support = {PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; KYCX24_0999//Graduate Research and Innovation Projects of Jiangsu Province/ ; },
abstract = {Polystyrene nanoplastics (PS-NPs) are ubiquitous in the environment, eliciting significant concerns about their possible risks to human health, especially reproductive health. Various reproductive toxicities of PS-NPs have been reported, however, information regarding the effects of PS-NPs exposure during pregnancy on offspring development and the underlying mechanisms remains limited. In this study, pregnant mice were orally administered PS-NPs (approximately 100 nm in diameter) at different concentrations (1, 10, and 100 mg/kg/day) for 17.5 consecutive days, from gestational day (GD) 0.5 to GD 17.5. The relevant samples were collected on GD 18.5 to investigate the intergenerational effects. The results indicated that PS-NPs induced placental injury and metabolic abnormalities, leading to adverse pregnancy outcomes. Specifically, PS-NPs exposure observably reduced the levels of nicotinamide (NAM) and nicotinamide adenine dinucleotide (NAD[+]) in the placenta, resulting in decreased ATP production, increased oxidative stress and ferroptosis. Meanwhile, PS-NPs disrupted the maternal gut microbiome, specifically manifested as a reduction in Lactobacillus levels and abundances of norank_f_Muribaculaceae, Turicibacter, Alloprevotella, Parabacteroides and Ruminococcus. Fecal microbial transplant (FMT) experiments demonstrated that the microbiota from PS-NPs-administered pregnant mice could similarly induce intestinal barrier damages and placental injury. Treatment with NAM effectively mitigated disruptions in placental metabolism and reversed the adverse pregnancy outcomes caused by PS-NPs. These findings highlight the novel role of the gut microbiota in PS-NPs-induced placental injury and adverse pregnancy outcomes, and suggest that NAM could serve as a promising preventative strategy against this intergenerational damage caused by PS-NPs.},
}

@article {pmid40796784,
year = {2025},
author = {Zhao, D and Shiga, RT and Song, Z and Shu, R and Loo, L and Wong, ACN},
title = {Microbiome drives age-dependent shifts in brain transcriptomic programs at the single-cell level in Drosophila.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {162},
pmid = {40796784},
issn = {2055-5008},
support = {R35GM147651/NH/NIH HHS/United States ; R35GM147651/NH/NIH HHS/United States ; R35GM147651/NH/NIH HHS/United States ; },
abstract = {The gut microbiome plays a critical role in brain function and the brain-gut axis, yet its cellular and molecular mechanisms remain unclear. Here, we present the first comprehensive single-cell transcriptomic atlas of brain cells from adult Drosophila melanogaster raised under axenic and microbiome-associated conditions, spanning young and old ages. Profiling 34,427 cells across 101 clusters, we annotated 56 cell types and identified cell type-specific gene signatures influenced by the microbiome. Transcriptional shifts were most pronounced in old flies, with glial cells and dopaminergic neurons among the most microbiome-responsive cell types. Differentially expressed genes (DEGs) were enriched in pathways related to mitochondrial activity, energy metabolism, and Notch signaling. We also quantified age-associated changes in the gut microbiome, observing reduced Acetobacter dominance and increased microbial diversity that corresponded with heightened brain transcriptional responses. These findings illuminate the cell type-specific impacts of the microbiome on brain gene expression and lay the groundwork for understanding the molecular underpinnings of the microbiome-gut-brain axis.},
}

@article {pmid40796779,
year = {2025},
author = {Wu, H and Liu, B and Liu, WV and Wen, Z and Yang, W and Yang, H and Li, J and Zha, Y},
title = {Glymphatic system dysfunction correlated with gut dysbiosis and cognitive impairment in schizophrenia.},
journal = {Schizophrenia (Heidelberg, Germany)},
volume = {11},
number = {1},
pages = {113},
pmid = {40796779},
issn = {2754-6993},
abstract = {Structural and functional brain abnormalities in schizophrenia (SZ) are well-documented, yet the role of the glymphatic system remains largely unexplored. Given emerging evidence linking the microbiome-gut-brain axis to SZ, this study aims to investigate the glymphatic system function in SZ patients using diffusion tensor image analysis along the perivascular space (DTI-ALPS) and to explore its associations with gut microbiota and cognitive performance. Multi-omics data were obtained from a cohort of 87 SZ patients and 70 healthy controls (HCs), including fecal 16S rRNA sequencing, DTI-ALPS index analysis, and cognitive assessments. Correlation and mediation analyses were conducted to explore the relationships among the gut microbiome, DTI-ALPS index, and cognitive performance. Compared to HCs, patients with SZ exhibited significantly lower DTI-ALPS indices in the left, right, and bilateral hemispheres. These indices were positively associated with multiple cognitive domains. In addition, gut microbial dysbiosis was observed in SZ, characterized by a decrease in butyrate-producing bacteria and an increase in pathogenic bacteria. Exploratory analyses further revealed a tripartite link among the key microbial genera, DTI-ALPS indices, and cognitive performance. Notably, the higher abundance of Proteus as well as the lower abundance of Blautia and Faecalibacterium may contribute to poorer cognitive performance, potentially through disruptions in the right DTI-ALPS index. These findings provide novel insights into glymphatic dysfunction in SZ and highlight a potential microbiota-glymphatic-cognition pathway contributing to cognitive impairments.},
}

@article {pmid40796700,
year = {2025},
author = {Jabbari Shiadeh, SM and Chan, WK and Rasmusson, S and Hassan, N and Joca, S and Westberg, L and Elfvin, A and Mallard, C and Ardalan, M},
title = {Bidirectional crosstalk between the gut microbiota and cellular compartments of brain: Implications for neurodevelopmental and neuropsychiatric disorders.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {278},
pmid = {40796700},
issn = {2158-3188},
support = {2023-02602//Vetenskapsrådet (Swedish Research Council)/ ; },
abstract = {The gut-brain axis serves as a crucial communication pathway, with microbial metabolites such as short-chain fatty acids (SCFAs) playing a central role in regulating neuroinflammation and maintaining neuronal health. The gut microbiota's impact on neurodevelopment is highlighted, particularly its relevance to autism, anxiety, and other psychiatric conditions. In this review, we explored the intricate relationship between the gut microbiota (GM) and the central nervous system (CNS), emphasizing the bidirectional communication that forms the gut-brain axis. Associations between specific gut microbiota and neurodegenerative diseases are explored, focusing on the role of certain bacteria in processes such as amyloid aggregation and neuroinflammation in Alzheimer's disease (AD) and Parkinson's disease (PD). The potential for therapeutic modulation of the gut microbiota is discussed, with a focus on dietary interventions and probiotics as strategies to improve outcomes in neurodegenerative diseases by restoring gut health. We concluded by emphasizing the significance of understanding the gut-brain connection and calls for further research to investigate therapeutic approaches targeting the gut microbiome for brain health.},
}

@article {pmid40796472,
year = {2025},
author = {Lucky, CW and Kelly, BJ and Kwon, JH and Woodworth, MH and Medernach, RL},
title = {Microbiome Therapeutics for Clostridioides difficile Infection.},
journal = {Infectious disease clinics of North America},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.idc.2025.07.007},
pmid = {40796472},
issn = {1557-9824},
abstract = {Microbiota-based therapies are used increasingly for the treatment and prevention of Clostridioides difficile infection (CDI), particularly in cases of recurrent CDI (rCDI). This review discusses the different types of microbiota-based therapies, including fecal microbiota transplant, fecal microbiota products, and live biotherapeutic products. The authors present efficacy data regarding clinical use in rCDI and highlight the unique aspects of each product.},
}

@article {pmid40796374,
year = {2025},
author = {Pan, S and Du, H and Zheng, R and Zhang, C and Pan, J and Yang, X and Wang, C and Lin, X and Li, J and Liu, W and Zhou, H and Yu, X and Mo, S and Zhang, G and Zhao, G and He, Z and Tian, Y and Jiang, C and Qu, W and Liu, Y and Li, M},
title = {A holistic genome dataset of bacteria and archaea of mangrove sediments.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf081},
pmid = {40796374},
issn = {2047-217X},
support = {2023B0303000017//Guangdong Major Project of Basic and Applied Basic Research/ ; 92251306//National Natural Science Foundation of China/ ; 92051102//National Natural Science Foundation of China/ ; 92251307//National Natural Science Foundation of China/ ; 92351303//National Natural Science Foundation of China/ ; 32370055//National Natural Science Foundation of China/ ; 32200099//National Natural Science Foundation of China/ ; 32070108//National Natural Science Foundation of China/ ; 32225003//National Natural Science Foundation of China/ ; 31970105//National Natural Science Foundation of China/ ; 42303064//National Natural Science Foundation of China/ ; 42430707//National Natural Science Foundation of China/ ; JCYJ20200109105010363//Shenzhen Science and Technology Program/ ; KCXFZ20201221173404012//Shenzhen Science and Technology Program/ ; JCYJ20230808105711023//Shenzhen Science and Technology Program/ ; 20220809161641002//Shenzhen Science and Technology Program/ ; SML2023SP218/SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory/ ; 2022B002//Shenzhen University/ ; },
abstract = {BACKGROUND: Mangroves are one of the most productive marine ecosystems with high ecosystem service value. The sediment microbial communities contribute to pivotal ecological functions in mangrove ecosystems. However, the study of mangrove sediment microbiomes is limited.

FINDINGS: Here, we applied metagenome sequencing analysis of microbial communities in mangrove sediments across Southeast China from 2014 to 2020. This genome dataset includes 966 metagenome-assembled genomes with ≥50% completeness and ≤10% contamination generated from 6 groups of samples. Phylogenomic analysis and taxonomy classification show that mangrove sediments are inhabited by microbial communities with high species diversity. Thermoplasmatota, Thermoproteota, and Asgardarchaeota in archaea, as well as Proteobacteria, Desulfobacterota, Chloroflexota, Acidobacteriota, and Gemmatimonadota in bacteria, dominate the mangrove sediments across Southeast China. Functional analyses suggest that the microbial communities may contribute to carbon, nitrogen, and sulfur cycling in mangrove sediments.

CONCLUSIONS: These combined microbial genomes provide an important complement of global mangrove genome datasets and may serve as a foundational resource for enhancing our understanding of the composition and functions of mangrove sediment microbiomes.},
}

@article {pmid40796367,
year = {2025},
author = {Akhi, R and Lavrinienko, A and Hakula, M and Hindström, R and Wang, C and Nissinen, A and Kullaa, AM and Salo, T and Kaikkonen, K and Tervonen, T and Ylöstalo, P and Koskimäki, JJ and Hörkkö, S},
title = {Oral Microbiota Linking Humoral Response, Periodontitis and Atherosclerosis.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.70001},
pmid = {40796367},
issn = {1600-051X},
support = {//Selma and Maja-Lisa Selander's Fund/ ; //Suomen Hammaslääkäriseura Apollonia/ ; //The Finnish Cultural Foundation/ ; },
abstract = {AIM: The humoral immune system is implicated in the link between periodontitis and atherosclerosis. This study aims to explore how interactions between the oral microbiota and humoral immune responses may contribute to this association.

MATERIALS AND METHODS: We analysed data from the Northern Finland Birth Cohort 1966, which included 1560 participants who underwent comprehensive health and oral examinations. Serum antibodies against phosphorylcholine (PCho) and malondialdehyde acetaldehyde (MAA) adducts were measured using chemiluminescence immunoassays. In a sub-cohort (n = 868), the oral microbiome from saliva samples was characterised using 16S rRNA gene sequencing.

RESULTS: Higher serum levels of IgA and IgG to PCho, as well as IgA to MAA, were associated with an increased number of teeth with probing pocket depths (PPD) ≥ 4 mm. Several oral bacterial species, including Prevotella dentalis, Filifactor alocis and Treponema denticola, correlated with both PPD ≥ 4 mm and IgA/IgG responses to PCho. Mediation analysis, adjusted for periodontitis risk factors, identified F. alocis as a mediator linking elevated plasma IgG to PCho with the number of teeth with PPD ≥ 4 mm. Additionally, individuals harbouring F. alocis exhibited increased carotid intima-media thickness.

CONCLUSIONS: Our findings suggest that F. alocis may serve as a microbial link between periodontitis and atherosclerosis. Future mechanistic studies should investigate how F. alocis induces systemic IgG responses and contributes to atherosclerosis.},
}

@article {pmid40796326,
year = {2025},
author = {Patel, SM and Farirai, J and Patel, MZ and Boiditswe, S and Tawe, L and Lekalake, S and Matshaba, M and Steenhoff, AP and Arscott-Mills, T and Feemster, KA and Shah, SS and Thielman, N and Cunningham, CK and David, LA and Murdoch, DM and Kelly, MS},
title = {Alterations of the upper respiratory microbiome among children living with HIV infection in Botswana.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf429},
pmid = {40796326},
issn = {1537-6613},
abstract = {Children living with HIV (CLWH) are at high risk of colonization and infection by respiratory pathogens, though this risk can be reduced by other microbes in the upper respiratory microbiome. The impact of HIV infection on the pediatric upper respiratory microbiome is poorly understood, and we sought to address this knowledge gap by identifying associations between HIV infection and the nasopharyngeal microbiomes of Batswana children. We enrolled Batswana CLWH (<5 years) and age- and sex-matched HIV-exposed, uninfected (HEU) and HIV-unexposed, uninfected (HUU) children in a cross-sectional study. We used shotgun metagenomic sequencing to compare nasopharyngeal microbiomes by HIV status. Among the 143 children in this study, HIV and HIV-associated immunosuppression were associated with alterations in nasopharyngeal microbiome composition, including lower abundances of Corynebacterium species associated with resistance to bacterial pathogen colonization. These findings suggest that the upper respiratory microbiome may contribute to the high risk of respiratory infections among CLWH.},
}

@article {pmid40790469,
year = {2025},
author = {Qin, M and Ding, W and Qin, L and Liang, R and Guo, Y and Zhao, Y and Xu, H and Wen, Y and Pang, Y and Li, L},
title = {Dysbiosis associated with enhanced microbial mobility across the respiratory tract in pulmonary tuberculosis patients.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {499},
pmid = {40790469},
issn = {1471-2180},
support = {2022TFC2304803//National Key Research and Development Program of China,China/ ; },
abstract = {BACKGROUND: The microbiota is actively engaged in interaction networks both with the host and among its own constituent members. However, comprehensive studies examining the microbiome profiles across various respiratory sites in pulmonary tuberculosis (PTB) are lacking. Here, we explored the diversity of the microbiome in PTB patients across multiple respiratory sites and investigated potential interactions between the microbiomes of these sites.

METHODS: A total of 130 respiratory tract samples were collected from multiple sites of 22 patients with PTB and 14 healthy individuals, including the oral cavity, trachea, and both the healthy and affected sides of the lungs. These samples were subjected to metagenomic sequencing to analyze the characteristics and diversity of the respiratory microbiome.

RESULTS: We found that the respiratory tract of PTB patients had higher microbial diversity than seen in the healthy individuals (8,182 vs 6,465). Among them, Rothia, Prevotella and Actinomyces exhibited higher proportions in PTB. The characteristics of high diversity features in the oral site were more prominent with PTB, especially the notable difference of Rothia mucilaginosa. Additionally, Streptococcus, Neisseria, Prevotella and Fusobacterium have strong interactions with other species at present at various sites of PTB patients, as well as frequent communication between these species during migration in the upper and lower respiratory tract.

CONCLUSIONS: The diversity and translocation of microbiota across the respiratory tract in PTB patients are associated with increased susceptibility of microbiome. The predominance of Rothia, Prevotella, and Actinomyces may represent progression-associated microbial signatures, warranting mechanistic studies on their pathogenic potential through host-microbe interactions to guide therapeutic targeting.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04206-x.},
}

@article {pmid40790209,
year = {2025},
author = {Youssef, RA and Sakr, MM and Shebl, RI and Aboshanab, KM},
title = {Recent insights on challenges encountered with phage therapy against gastrointestinal-associated infections.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {60},
pmid = {40790209},
issn = {1757-4749},
abstract = {Gastrointestinal (GI) infections, caused by pathogens such as Escherichia coli, Salmonella sp., Shigella sp., and Clostridium difficile, pose significant global health challenges due to their prevalence, severity, and increasing resistance to conventional treatments. While phage therapy offers a targeted, adaptable, and potentially safer approach for treating these infections, several challenges hinder its widespread clinical application. This review explores the current state of phage therapy for GI-associated infections, highlighting key obstacles such as phage stability in the harsh GI environment, host immune responses that can impede phage efficacy, phage-bacteria interactions, and bacterial adaptation mechanisms, such as mutations in phage receptors, which can lead to phage-insensitive mutants. Additionally, the specificity of phages to bacterial strains necessitates the development of diverse phage cocktails tailored to individual infections. The complex interactions between phages and the gut microbiome present challenges in ensuring that phage therapy does not disrupt beneficial gut bacteria. Despite these challenges, advances in phage isolation, genetic engineering, and delivery systems offer promising avenues to optimize phage therapy for GI infection. This review underscores the pharmacokinetics and pharmacodynamics of phage therapy while emphasizing the need for multidisciplinary approaches to overcome existing barriers and translate this innovative treatment into clinical practice. Accordingly, ongoing research is necessary to optimize phage delivery methods, develop effective phage combinations, and understand the interactions between phages and the gut microbiome to ensure safe and effective treatments.},
}

@article {pmid40796291,
year = {2025},
author = {Mohr, AE and Mach, N and Pugh, J and Grosicki, GJ and Allen, JM and Karl, JP and Whisner, CM},
title = {Mechanisms underlying alterations of the gut microbiota by exercise and their role in shaping ecological resilience.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf037},
pmid = {40796291},
issn = {1574-6976},
abstract = {The gut microbiota (GM) is a dynamic ecosystem intricately linked to human health, including metabolic, immune, endocrine, and gastrointestinal functions. Exercise is recognized as a significant modifier of this microbial ecosystem, yet the complexities of this relationship are underexplored. Here, we delve into the multifaceted interactions between structured physical activity and the GM, emphasizing the role of exercise-induced stressors in shaping microbial composition and function. Unique to our review, we discuss the acute effects of different forms of exercise-induced stress on the GM and explore how these responses may influence long-term adaptability, stability, and resilience. Furthermore, we address critical junctures in microbial dynamics leading to shifts between different stable states. Finally, we explore the implications of host-controlled factors such as diet, exercise training, and nutritional supplementation in modulating the microbial community in the gut to optimize athletic performance. We conclude that while the potential to harness the synergistic effects of exercise-induced stressors, dietary interventions, and microbial adaptations appears promising, current evidence remains preliminary, highlighting the need for additional targeted research to guide future strategies that manipulate the GM for optimal health and athletic performance.},
}

@article {pmid40796247,
year = {2025},
author = {Che, PN and Jiang, J and Breslin, M and Thompson, M and Vinding, RK and Stokholm, J and Scheepers, LEJM},
title = {Gut Microbiome in early life and Bone Health Outcomes at Age 6: a Danish Mother-Child Cohort Study.},
journal = {Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research},
volume = {},
number = {},
pages = {},
doi = {10.1093/jbmr/zjaf108},
pmid = {40796247},
issn = {1523-4681},
abstract = {The gut microbiome is associated with bone mass acquisition, yet evidence in childhood remains limited. Given that lower peak bone mass predicts osteoporosis in later life, understanding early influences is important. This analysis explores the association between the early life gut microbiome and bone health in later childhood. Data was obtained from 700 children recruited in pregnancy and followed prospectively within the Copenhagen Prospective Studies on Asthma in Childhood2010 cohort, a population-based mother-child cohort. The infant gut microbiome was measured at 1 wk (n = 445), 1 mo (n = 492), 1 yr (n = 508), 4 yr (n = 350), and 6 yr (n = 327) of age by 16S ribosomal ribonucleic acid amplicon sequencing targeting the fourth variable region. Total body less head bone mineral density and area-adjusted bone mineral content were measured by dual-energy X-ray absorptiometry at 6 yr of age. Associations were investigated by multiple linear regression, permutational analysis of variance, differential abundance analysis, and Random Forest machine learning. There were few associations between the early-life gut microbiome and bone health outcomes at age six. We found negative associations between alpha (within-sample) diversity and area-adjusted bone mineral content at 4 yr. Beta (between-sample) diversity of the gut microbiome at 6 yr was associated with concurrent bone mineral density. Escherichia-Shigella abundance at 1 mo of age associated with lower bone mineral density. Sutterella abundance at 1 yr was associated with lower bone mineral density and area-adjusted bone mineral content at 6 yr. There were no other associations between the gut microbiome and bone outcome measures at any time point. In a well-powered unselected cohort study with longitudinal sampling of the gut microbiome, there were some suggestive but no consistent associations between the early gut microbiome and bone health outcomes at 6 yr of age.},
}

@article {pmid40796226,
year = {2025},
author = {Skawratananond, S and McCrea, G and Lie, P and Buxton, MB and Daly, SP and Vojtkofsky, NA and Smith, SC and Zhang, C and Hernandez, M and Hindle, A and Logsdon, AF and Lawrence, JJ},
title = {The Synergistic Interplay between Vitamin A, Dietary Fiber, and the Microbiota-Gut-Brain Axis: A Potential Mechanism for Preventing Alzheimer's Disease.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00097.2025},
pmid = {40796226},
issn = {1522-1547},
support = {AG071859//HHS | NIH | National Institute on Aging (NIA)/ ; MSSRP//Texas Tech University Health Sciences Center (TTUHSC)/ ; MSSRP//Texas Tech University Health Sciences Center (TTUHSC)/ ; AG073826//HHS | NIH | National Institute on Aging (NIA)/ ; },
abstract = {The human gastrointestinal tract harbors a vast and diverse microbial community, with the gut microbiome playing a fundamental role in numerous biological processes that influence overall health and disease progression. Emerging evidence has identified bacterial lipopolysaccharides in the hippocampus of Alzheimer's disease (AD) patients, highlighting the intricate relationship between the gastrointestinal tract, gut microbiome, and the central and enteric nervous systems-commonly referred to as the "microbiota-gut-brain axis." In this review, we explore the mechanisms by which the microbiota-gut-brain axis contributes to AD pathogenesis. We propose that sufficient levels of all-trans retinoic acid (ATRA), the bioactive form of vitamin A, enhance intestinal barrier integrity by upregulating tight junction proteins and modulating immune function through the induction of regulatory T-cell differentiation, thereby mitigating inflammation. Furthermore, dietary fiber complements this process by promoting the production of short-chain fatty acids, such as butyrate, via bacterial fermentation. Butyrate, in turn, acts as a histone deacetylase inhibitor, upregulating ATRA bioavailability by elevating aldehyde dehydrogenase gene expression. Our mechanistic framework is supported by the endotoxin hypothesis of AD, which purports that the movement of infectious pathogens across the blood-brain barrier causes a vicious cycle of neuroinflammation, a key factor of AD pathogenesis, leading to amyloid-beta deposition, microglial activation, and CYP26A1-mediated ATRA degradation. Finally, we discuss microbiome-based therapeutic strategies and dietary interventions, including prebiotic compounds, probiotic bacteria, fecal microbiota transplantation, the MIND diet, and a combined approach consisting of vitamins A/D, and dietary fiber, as potential approaches to mitigate AD progression via the microbiota-gut-brain axis.},
}

@article {pmid40796204,
year = {2025},
author = {Jo, J and Carlson, TJ and Hu, C and Williamson, JC and Belin, YT and Horvath, TD and Haidacher, SJ and Bassères, E and Begum, K and Alam, MJ and Garey, KW},
title = {Faecal pharmacokinetics, microbiome, and bile acid changes in healthy subjects given intravenous followed by oral omadacycline; a Phase 1 clinical trial.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {},
number = {},
pages = {},
doi = {10.1093/jac/dkaf278},
pmid = {40796204},
issn = {1460-2091},
support = {G0505124//Paratek Pharmaceuticals, Inc/ ; //University of Houston New Investigator Award/ ; //NIH NIAID/ ; //National Institute Allergy and Infectious diseases/ ; 2R01AI139261/NH/NIH HHS/United States ; T32 AI141349/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: There is an urgent need to develop new antimicrobials effective intravenously for Clostridioides difficile infection (CDI). Omadacycline is an aminomethylcycline tetracycline available orally and intravenously with potent in vitro activity against C. difficile and a low propensity to cause CDI. The purpose of this study was to assess the safety, faecal pharmacokinetics, microbiome and bile acid changes in healthy subjects given a course of intravenous omadacycline with oral omadacycline step down after 5 days.

METHODS: This Phase 1, open-label study was conducted in healthy volunteers 18-40 years. Subjects received a 5-day course of omadacycline given intravenously followed by 5 days of oral omadacycline. Stool samples were analysed for omadacycline concentrations, gut microbiome changes and bile acid changes from baseline.

RESULTS: Eight healthy volunteers aged 30 ± 4 years (50% Female) were recruited and all completed therapy. All subjects had detectable omadacycline stool concentrations after 48 hours of intravenous dosing and averaged 195 ± 97 µg/g (mean ± SD) by day 5. Omadacycline concentrations increased rapidly after the start of oral therapy on day 6 with average concentrations of 854 ± 404 µg/g of stool by day 10. Microbiome and bile acid evaluations showed preservation of key microbiome taxa that confer health benefit and preservation of bile acid homeostasis.

CONCLUSION: Intravenous omadacycline followed by oral step-down administration in healthy adults achieved high faecal concentrations while preserving key bacterial species and bile acid homeostasis in the gut. These findings support Phase 2 studies directed towards the development of omadacycline as a CDI-targeted antibiotic.},
}

@article {pmid40796154,
year = {2025},
author = {Galindo-Castañeda, T and Kost, E and Giuliano, E and Conz, RF and Six, J and Hartmann, M},
title = {Locating the microbes along the maize root system under nitrogen limitation: a root phenotypic approach.},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcaf185},
pmid = {40796154},
issn = {1095-8290},
abstract = {BACKGROUND: A major challenge in agriculture is the low nitrogen (LN) uptake efficiency of crops, which poses environmental and economic costs. Root adaptive architectural and anatomical phenotypes in synergy with root microbes could be a promising approach to improve plant N uptake. However, little is known about such synergies. Here, we aimed to characterize the spatial distribution of the root prokaryotes of maize (Zea mays) under LN in 30 L mesocosms, where root architecture and anatomy are freely expressed, searching for correlations between prokaryotic genus abundance and 10 phenotypes.

METHODS: We studied the root prokaryotic community of 4-week-old plants growing in 30 L mesocosms under LN using two sandy soil mixtures. We collected root, rhizosphere, and bulk soil samples at various locations, including depths (0-20, 20-70, 70-150 cm), root classes (lateral and axial), and root types (seminal and crown). We measured plant growth response to low N availability and performed 16S rRNA gene metabarcoding on extracted DNA.

KEY RESULTS: Sampling location was the third most important factor after soil mixture and compartment, explaining ∼5% of the variance in root prokaryotic diversity. Seminal roots (0-20 cm depth), shallow crown roots (0-20 cm), and deep crown roots (20-150 cm) showed well-separated root microbial communities. Lateral root branching density (LRBD) explained 10% of this variance in the rhizosphere and the root tissue. We identified prokaryotic genera specific to depth, soil-root compartment, root class, and type under LN. Moreover, architectural phenotypes LRBD and lateral root length significantly correlated with the abundance of 37 genera.

CONCLUSIONS: We highlight the importance of sampling location and architectural traits that may be associated with the microbial cycling of soil N. The exploration of synergies between root traits and microbes that participate in the N cycle has the potential to increase sustainability in agriculture.},
}

@article {pmid40795952,
year = {2025},
author = {Pluer, BD and Travis, J},
title = {The Digestive Microbiome Diversity of the Least Killifish, Heterandria formosa, and Its Implications for Host Adaptability to Varying Trophic Levels.},
journal = {Environmental microbiology reports},
volume = {17},
number = {4},
pages = {e70164},
doi = {10.1111/1758-2229.70164},
pmid = {40795952},
issn = {1758-2229},
support = {G2020031598770049//Sigma Xia/ ; //Florida State University/ ; },
abstract = {Symbiotic microbes, in associations with aquatic hosts, aid in the acquisition of nutrients, breakdown xenobiotics, and contribute to immune system function. If associations with microbial communities facilitate host adaptation to different ecosystems, understanding the important ecological factors that act as drivers of differences among conspecific populations' microbiomes can help conservation efforts to promote beneficial interactions between fish and their microbiome for freshwater fish species facing rapid environmental changes. Here we describe the microbial communities in the gut of a freshwater fish, Heterandria formosa, in spring habitats using 16S rRNA sequencing. We quantified microbiota composition and diversity among springs ranging from oligotrophic to near eutrophic to determine the extent to which the microbiota are associated with different environmental conditions. We found higher microbial richness at sites with lower nutrient load stress. At more eutrophic sites, we detected the potential for increased metabolic capacity for pollutant degradation in the associated microbiota. We noted greater phylogenetic similarity between more environmentally similar sites, supporting previous evidence that the microbiota of freshwater fish is influenced by site water chemistry. Our findings bring to light microbial taxa and pathways that might play critical roles in the bioremediation of stressful environmental conditions.},
}

@article {pmid40795888,
year = {2025},
author = {Man, JJ and Yang, M and Hu, QY and Wang, W and Wang, P and Lv, XF and Luo, J},
title = {Effects of increased rapeseed meal addition on production performance, health, rumen fermentation, and microbial community in dairy goats.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf261},
pmid = {40795888},
issn = {1525-3163},
abstract = {This experiment was designed to assess the influences of adding varying proportions of rapeseed meal (RSM) to the dietary concentrate on the production performance, milk quality, health status, rumen fermentation, and the characteristics of rumen and fecal flora of mid-lactation Xinong Saanen dairy goats. Thirty-six mid-lactation dairy goats, matched for age, parity, lactation stage, and body weight were randomly divided into three groups of 12 goats each, namely RSM5(with 5% of RSM in the concentrate feed), RSM10(with 10% of RSM in the concentrate feed), and RSM15 (with 15% of RSM in the concentrate feed). The experiment lasted for 49 days, including a 7-day pre-feeding period and a 42-day trial period. During the trial period, milk yield and feed intake were recorded daily to assess production performance. Milk samples were collected biweekly to analyze milk composition. On day 42 of the experiment, blood, rumen fluid, and fecal samples were collected to evaluate health status and the structure of rumen and fecal microbiota. Results：With increasing addition of RSM, no significant changes were observed in milk production and milk components (P > 0.05). However, total antioxidant capacity and glutathione concentration in the blood significantly increased (P < 0.01), while malondialdehyde decreased (P < 0.01), and rumen NH3-N content declined (P < 0.05). Compared with the RSM5 group, the RSM10 group elevated the relative abundance of Bacteroidota and Rikenellaceae_RC9_gut_group in the rumen (P < 0.05) and reduced the relative abundance of Prevotellaceae_UCG-003 in the feces (P < 0.05). To sum up, this research indicates that substituting 10% of the soybean meal with RSM in the concentrate during the mid-lactation period has no adverse influence on the productive performance of dairy goats, but enhances the antioxidant capacity and improves the gastrointestinal microbiota.},
}

@article {pmid40795845,
year = {2025},
author = {Morsy, Y and Hubeli, B and Turko, P and Barysch, M and Martínez-Gómez, JM and Zamboni, N and Rogler, G and Dummer, R and Levesque, MP and Scharl, M},
title = {The serum metabolome serves as a diagnostic biomarker and discriminates patients with melanoma from healthy individuals.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102283},
doi = {10.1016/j.xcrm.2025.102283},
pmid = {40795845},
issn = {2666-3791},
abstract = {Melanoma is a deadly cancer with increasing incidence and mortality rates, and biomarkers for diagnosis are urgently needed. The impact of the microbiome, genetic factors, and immunologic markers on disease outcomes is described, but a comprehensive serum metabolome profiling is missing. The serum metabolome of patients with melanoma might be valuable to identify potential biomarkers. We present an untargeted metabolomics analysis in an exploratory cohort (87 patients with melanoma), an independent validation cohort (37 additional patients with melanoma featuring late-stage tumors), and 18 healthy control individuals, revealing striking differences. We identify and validate six serum metabolites that can predict the diagnosis of melanoma with an area under the curve (AUC) >0.9544 in advanced-stage melanoma. The AUC of our lead biomarker, muramic acid, is 0.964, 0.908, and 0.9936 in patients with stage I (n = 22), stage II (n = 67), and advanced melanoma (n = 86), respectively. In summary, we identify potentially very powerful diagnostic biomarkers for clinical practice.},
}

@article {pmid40795730,
year = {2025},
author = {D'Ugo, E and Mukherjee, A and Resitano, M and Giuseppetti, R and Fortini, D and Bruna Matturro, and Chirico, M and Pisanu, ME and Tucci, M and Pozzi, R and Lovecchio, N and Slawomir, O and Iosi, F and Villa, L and Iorio, E and Aulenta, F and Viggi, CC and Bertuccini, L and Magurano, F},
title = {Fishing out microorganisms for bioremediation using metagenomics: Isolation and whole-genome sequencing of the metabolically versatile Rhodococcus erythropolis LP27217 strain from oil spill lake.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139463},
doi = {10.1016/j.jhazmat.2025.139463},
pmid = {40795730},
issn = {1873-3336},
abstract = {Isolating microorganisms from oil spill-contaminated environments is essential for advancing bioremediation strategies and discovering novel bioprocesses for hydrocarbon degradation. In this study, we report the isolation of a novel strain, Rhodococcus erythropolis LP27217, from Pertusillo Lake (Italy) on february 2017. Water samples were collected during an oil spill event and microbial community was previously characterized using 16S rRNA gene-targeted metagenomic analysis and functional prediction. The Rhodococcus genus was identified as the dominant member of this microbiome, and functional predictive analyses guided the isolation of the R. erythropolis LP27217 strain under various growth conditions, including the presence of hydrocarbons and in Liquid Microbial Fuel Cell (L-MFC) systems. This strain exhibits a versatile hydrocarbon-degrading and transforming metabolism, effectively addressing pollutants such as crude oil, polycyclic aromatic hydrocarbons (PAHs), and dibenzothiophene (DBT), even under psychrophilic conditions. Additionally, R. erythropolis LP27217 demonstrated the ability to produce lipopeptide biosurfactants and lipophilic polymers, with the latter being associated with the formation of an electrogenic hydrocarbonoclastic biofilm at the anoxic oil-water interface. Overall, this study demonstrated that R. erythropolis LP27217 is a promising candidate for sustainable applications, including in situ bioremediation of oil spills in lake ecosystems and the biosynthesis of innovative polymers and biosurfactants for biotechnological and environmental purposes. Furthermore, its ability to operate across oxic and hypoxic conditions, at the oil-water interface and within the water column, highlights a novel microbial mechanism with significant ecological and industrial potential.},
}

@article {pmid40795553,
year = {2025},
author = {Bechtner, JD and Lopez-Rodulfo, IM and Gallego-Lobillo, P and Hosek, J and Schwab, C and Martinez, MM},
title = {Polyphenols non-covalently bound to artificial plant cell walls are readily accessible to fecal microbiota and transiently alter fermentation activity.},
journal = {Food chemistry},
volume = {493},
number = {Pt 2},
pages = {145817},
doi = {10.1016/j.foodchem.2025.145817},
pmid = {40795553},
issn = {1873-7072},
abstract = {This study aimed to elucidate three-way interactions among dietary fiber, polyphenols (PPs), and the gut microbiota at physiologically relevant concentrations. A three-component bacterial cellulose analogue of the apple cell wall (aACW) soaked in a PP extract from apples (aACW + PP) was produced and gut microbial responses were tested using in vitro fecal microbiota batch fermentations of five donors. Soaking left ∼17 % of PPs bound to aACWs, with flavonols being the most retained. Several flavonoids were detected early during aACW + PPs in vitro fecal fermentation and were rapidly metabolized with differences between individual fecal microbiota. aACW-bound PP increased fermentation activity, as indicated by higher acetic acid and lower formic acid levels after 5 h of fermentation. Beta-diversity analysis identified donor individuality as a stronger determinant of microbiota composition than treatment. Baseline interindividual microbiota composition emerged as the dominant factor shaping both PP metabolism and microbial community trajectories under the tested, physiologically relevant concentrations.},
}

@article {pmid40795534,
year = {2025},
author = {Fetarayani, D and Vidyani, A and Sutanto, H},
title = {Gut microbiome-centric nutritional strategies in inflammatory bowel disease: Modulating dysbiosis for therapeutic benefit.},
journal = {Semergen},
volume = {51},
number = {8},
pages = {102575},
doi = {10.1016/j.semerg.2025.102575},
pmid = {40795534},
issn = {1578-8865},
abstract = {Inflammatory bowel disease (IBD), encompassing Crohn's disease and ulcerative colitis, arises from complex interactions among genetics, immunity, environmental triggers, and, critically, the gut microbiome. Dysbiosis - marked by a loss of beneficial microbes and expansion of pro-inflammatory taxa - plays a pivotal role in disease pathogenesis. This review highlights the central role of gut microbiota in IBD and explores evidence-based nutritional interventions aimed at restoring microbial balance and immune regulation. Dietary fiber, prebiotics, and fermented foods promote short-chain fatty acid production and barrier integrity, while omega-3 fatty acids and polyphenols modulate inflammatory pathways. Exclusive enteral nutrition (EEN), especially in Crohn's disease, alters microbial profiles and reduces mucosal inflammation. Targeted micronutrient supplementation addresses common deficiencies impacting immune function. Through the lens of microbiota modulation, dietary therapy emerges not merely as supportive care, but as a primary therapeutic tool in IBD management. Microbiome-directed nutrition offers promising adjunctive strategies to induce and maintain remission.},
}

@article {pmid40795390,
year = {2025},
author = {Vázquez, AEG and Chou, MY and Hockemeyer, KR and Vang, M and Koch, PL},
title = {Seasonal Environmental Variation Impacts 2,4-D Fate and Metabolism in Urban Landscapes.},
journal = {Environmental toxicology and chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/etojnl/vgaf205},
pmid = {40795390},
issn = {1552-8618},
abstract = {The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) is commonly applied to urban landscapes such as turfgrass lawns. Though 2,4-D's degradative pathway has been extensively researched, the interaction of soil microbiota with 2,4-D under varying seasonal conditions remains unclear. This study aimed to assess the role of seasonal environmental conditions on the soil bacterial community and the resulting impact on the degradation of 2,4-D and the formation of its major transformation product, 2,4-dichlorophenol (2,4-DCP). Field and controlled environment studies were conducted near Madison, WI, USA in 2018 and 2019 and demonstrated that 2,4-D concentrations steadily declined in both the soil and leaves in the 10 days following application. The metabolite 2,4-DCP was only detected in the controlled environment study and was always below the limit of quantification. The impact of seasonal environmental variations on bacterial community structure, function, and composition were also assessed. Distinct bacterial communities were observed between season-simulated temperatures, soil depths, field sites, and 2,4-D treatment application timings. These findings emphasize that environmental variations shift the soil bacterial community over the course of a growing season with potentially important implications for the degradation of 2,4-D in urban landscapes.},
}

@article {pmid40795332,
year = {2025},
author = {Aguilera-Campos, KI and Boisard, J and Törnblom, V and Jerlström-Hultqvist, J and Behncké-Serra, A and Cotillas, EA and Stairs, CW},
title = {Anaerobic breviate protist survival in microcosms depends on microbiome metabolic function.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf171},
pmid = {40795332},
issn = {1751-7370},
abstract = {Anoxic and hypoxic environments serve as habitats for diverse microorganisms, including unicellular eukaryotes (protists) and prokaryotes. To thrive in low-oxygen environments, protists and prokaryotes often establish specialized metabolic cross-feeding associations, such as syntrophy, with other microorganisms. Previous studies show that the breviate protist Lenisia limosa engages in a mutualistic association with a denitrifying Arcobacter bacterium based on hydrogen exchange. Here, we investigate if the ability to form metabolic interactions is conserved in other breviates by studying five diverse breviate microcosms and their associated bacteria. We show that five laboratory microcosms of marine breviates live with multiple hydrogen-consuming prokaryotes that are predicted to have different preferences for terminal electron acceptors using genome-resolved metagenomics. Protist growth rates vary in response to electron acceptors depending on the make-up of the prokaryotic community. We find that the metabolic capabilities of the bacteria and not their taxonomic affiliations determine protist growth and survival and present new potential protist-interacting bacteria from the Arcobacteraceae, Desulfovibrionaceae, and Terasakiella lineages. This investigation uncovers potential nitrogen and sulfur cycling pathways within these bacterial populations, hinting at their roles in syntrophic interactions with the protists via hydrogen exchange.},
}

@article {pmid40795274,
year = {2025},
author = {Madsen, CS and Kimbrel, JA and Diep, P and Ricci, DP},
title = {Synthetic communities as a model for determining interactions between a biofertilizer chassis organism and native microbial consortia.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf170},
pmid = {40795274},
issn = {1751-7370},
abstract = {Biofertilizers are critical for sustainable agriculture since they can replace ecologically disruptive chemical fertilizers while improving the trajectory of soil and plant health. Yet, for improving deployment, the persistence of biofertilizers within native soil consortia must be elucidated and enhanced. We describe a high-throughput, modular, and automation-friendly in vitro approach to screen for biofertilizer persistence within soil-derived consortia after co-cultivation with stable synthetic soil microbial communities (SynComs) obtained through a top-down cultivation process. We profiled ~1200 SynComs isolated from various soil sources and cultivated in divergent media types, and detected significant phylogenetic diversity (e.g., Shannon index >4) and richness (observed richness >400) across these communities. We observed high reproducibility in SynCom community structure from common soil and media types, which provided a testbed for assessing biofertilizer persistence within representative native consortia. Furthermore, we demonstrated the screening method described herein can be coupled with microbial engineering to efficiently identify soil-derived SynComs where an engineered biofertilizer organism (i.e. Bacillus subtilis) persists. Accordingly, we discovered that B. subtilis persisted in approximately 10% of SynComs that generally followed the diversity-invasion principle. Additionally, our approach enables analysis of the ecological impact of B. subtilis inoculation on SynCom structure and profile alterations in community diversity and richness associated with the presence of a genetically modified model bacterium. Ultimately, this work establishes a modular pipeline that could be integrated into a variety of microbiology/microbiome-relevant workflows or related applications that would benefit from assessing persistence and interaction of a specific organism of interest with native consortia.},
}

@article {pmid40795028,
year = {2025},
author = {Park, HS and Chavarria, X and Shatta, A and Kang, D and Oh, S and Choi, DY and Choi, JH and Kim, M and Cho, YH and Yi, MH and Kim, JY},
title = {Distinct microbial communities of drain flies (Clogmia albipunctata) across sites with differing human influence.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf078},
pmid = {40795028},
issn = {1574-6968},
abstract = {Drain flies (Clogmia albipunctata) are insects that thrive in humid urban environments such as bathrooms drains and sewage systems. While their role in pathogen transmission has been suggested, little is known about their microbiome or ecology in non-clinical contexts. Using 16S rRNA gene metabarcoding, we characterized the bacterial communities of drain flies from three locations in South Korea, public bathrooms from a college in Seoul, a rural port in Ulleungdo island, and a highly frequented public park in Yeouido. In total, we obtained 221 families and 1 474 features. We found significant differences in microbiome composition and diversity as well as a small core microbiome shared among locations, with environmental bacteria such as Pseudomonas and Ralstonia being the dominant taxa across samples. The majority of the detected amplicon sequence variants (ASV) were not shared among locations. These findings suggest drain fly transport a location-specific environmental bacteria. Notably, we also identified ASVs of potential clinical relevance, including Mycobacterium, Acinetobacter baumanii, Providencia, and Nocardia. This is the first metagenomic insight into the microbiome of this species and adds to a renewed interest in the role that non-hematophagous insects play in urban microbial ecology and the spread of microbes.},
}

@article {pmid40794955,
year = {2025},
author = {Dai, Y and Qian, Y and Qu, Y and Guan, W and Xie, J and Wang, D and Butler, C and Dashper, S and Carroll, I and Divaris, K and Liu, Y and Wu, D},
title = {Decoding longitudinal microbiome trajectories: an interpretable machine learning approach for biomarker discovery and prediction.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
doi = {10.1093/bib/bbaf374},
pmid = {40794955},
issn = {1477-4054},
support = {1R03DE034507-01/NH/NIH HHS/United States ; U01DE025046/NH/NIH HHS/United States ; },
mesh = {Humans ; *Machine Learning ; *Biomarkers ; *Microbiota ; Longitudinal Studies ; Gastrointestinal Microbiome ; },
abstract = {Information generated from longitudinally sampled microbial data has the potential to illuminate important aspects of development and progression for many human conditions and diseases. Identifying microbial biomarkers and their time-varying effects can not only advance our understanding of pathogenetic mechanisms, but also facilitate early diagnosis and guide optimal timing of interventions. However, longitudinal predictive modeling of highly noisy and dynamic microbial data (e.g. metagenomics) poses analytical challenges.To overcome these challenges, we introduce a robust and interpretable machine-learning-based longitudinal microbiome analysis framework, LP-Micro, that encompasses (i) longitudinal microbial feature screening via a polynomial group lasso, (ii) disease outcome prediction implemented via machine learning methods (e.g. XGBoost, deep neural networks), and (iii) interpretable association testing between time points, microbial features, and disease outcomes via permutation feature importance. We demonstrate in simulations that LP-Micro can not only identify incident disease-related microbiome taxa, but also offers improved prediction accuracy compared with existing approaches. Applications of LP-Micro in two longitudinal microbiome studies with clinical outcomes of childhood dental disease and weight loss following bariatric surgery yield consistently high prediction accuracy. Moreover, LP-Micro highlights critical time points and associated microbial changes: oral microbial changes, including Streptococcus mutans, are most informative for predicting childhood dental disease at around 39 months of age, while gut microbial changes shortly after bariatric surgery strongly predict future weight loss. These findings are both informative and aligned with clinical expectations. The tool LP-Micro can be seen at https://github.com/IV012/LPMicro.},
}

Humans
*Machine Learning
*Biomarkers
*Microbiota
Longitudinal Studies
Gastrointestinal Microbiome

@article {pmid40794807,
year = {2025},
author = {Méndez, SG and Mertens, S and Temmerman, A and Van den Eynde, H and Vermeersch, M and Vlaminck, L and Berteloot, O and Van Dingenen, J and Clarysse, A and De Keyser, A and Beullens, S and de Baenst, I and Roy, N and De Paepe, Q and Michiels, J and Roldan-Ruiz, I and Pannecoucque, J and Willems, A and Maere, S and Goormachtig, S},
title = {Fast track to environmentally adapted rhizobia for growing soybean at northern latitudes using citizen science.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf152},
pmid = {40794807},
issn = {1751-7370},
abstract = {Soybean serves as a crucial source of plant-based protein for human diets. Recently, there is a growing incentive to extend the range of this crop to more northern latitudes, in order to enable profitable soybean production in Europe. To reach economic yields, soybean requires inoculation with symbiotic, diazotrophic rhizobial bacteria. However, the performance of commercial inocula is often variable under local conditions. Here, we present the citizen science project "Soy in 1,000 Gardens", a large-scale trapping experiment for isolating local soybean-nodulating rhizobia in Flanders, Belgium. We identified two locally isolated Bradyrhizobium strains performing at least as well as commercial strain B. diazoefficiens G49 in local field trials. Additionally, we found that nutrient content, microbial alpha diversity, and the presence of arbuscular mycorrhizal fungi in the soil were correlated with nodulation. Finally, we report a correlation between low bacterial alpha diversity and red nodule interior, and identified Tardiphaga as a dominant colonizer of red nodules.},
}

@article {pmid40794770,
year = {2025},
author = {Chia, M and Pop, M and Salzberg, SL and Nagarajan, N},
title = {Challenges and Opportunities in Analyzing Cancer-Associated Microbiomes.},
journal = {Cancer research},
volume = {},
number = {},
pages = {},
doi = {10.1158/0008-5472.CAN-24-3629},
pmid = {40794770},
issn = {1538-7445},
abstract = {The study of cancer-associated microbiomes has gained significant attention in recent years, spurred by advances in high-throughput sequencing and metagenomic analysis. Microbiome research holds promise for identifying non-invasive biomarkers and possibly new paradigms for cancer treatment. In this review, we explore the key computational challenges and opportunities in analyzing cancer-associated microbiomes (in tumor/normal tissues and other body sites, e.g. gut, oral, skin), focusing on sequencing-driven strategies and associated considerations for taxonomic and functional characterization. The discussion covers the strengths and limitations of current analysis tools for identifying contamination, determining compositional bias, and resolving species and strains, as well as the statistical, metabolic, and network inferences that are essential to uncover host-microbiome interactions. Several key considerations are required to guide the choice of databases used for metagenomic analysis in such studies. Recent advances in spatial and single-cell technologies have provided insights into cancer-associated microbiomes, and AI-driven protein function prediction might enable rapid advances in this field. Finally, we provide a perspective on how the field can evolve to manage the ever-growing size of datasets and to generate robust and testable hypotheses.},
}

@article {pmid40794318,
year = {2025},
author = {Khoshbayan, A and Narimisa, N and Razavi, S and Shariati, A and Tavakoli-Yaraki, M and Darban-Sarokhalil, D and Emami Razavi, A},
title = {The interactions of Fusobacterium nucleatum and Porphyromonas gingivalis with microRNAs: contributions to oral squamous cell carcinoma.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {821},
pmid = {40794318},
issn = {1573-4978},
support = {1402-3-104-26926//Iran University of Medical Sciences/ ; },
mesh = {Humans ; *Fusobacterium nucleatum/genetics/pathogenicity/isolation & purification ; *MicroRNAs/genetics/metabolism ; *Porphyromonas gingivalis/genetics/pathogenicity/isolation & purification ; Male ; Female ; Middle Aged ; *Mouth Neoplasms/genetics/microbiology ; *Carcinoma, Squamous Cell/genetics/microbiology ; Aged ; Gene Expression Regulation, Neoplastic ; Iran ; Adult ; Microbiota/genetics ; Squamous Cell Carcinoma of Head and Neck/microbiology/genetics ; },
abstract = {BACKGROUND: Oral squamous cell carcinoma (OSCC) is the most prevalent form of oral cancer, with about one-third of patients facing life-threatening and recurrent cases. Certain pathobionts in the oral microbiome contribute to the rise of inflammation and are directly involved in carcinogenesis. Analysis of the microbial profiles in OSCC patients reveals significant differences compared to healthy individuals. This study investigates the microbial composition, microRNA (miRNA) expression, and their related genes for the first time in Iranian patients diagnosed with OSCC.

METHODS: The relative presence of Fusobacterium nucleatum, Porphyromonas gingivalis, Fusobacterium periodonticum, and Prevotella intermedia was assessed in both tumor and adjacent normal tissues using Real-time PCR on 20 pairs of fresh-frozen OSCC samples. The expression levels of four miRNAs (miR-21, miR-31, miR-26a, and miR-29a) and five target genes were investigated. Eventually, any potential association between these bacteria's presence and miRNAs' expression was analyzed.

RESULTS: P. gingivalis and F. nucleatum were significantly more abundant in tumor samples than in the control samples. However, the other two bacteria did not show significant differences between the tumor and control samples. The relative expression levels of both oncomiRs were significantly higher in tumors compared to control samples. The analysis indicates a significant association between the presence of F. nucleatum and miR-21 expression. Additionally, a significant association was identified between P. gingivalis and the expression of miR-31. In addition, LOXL2 was the only miRNA-related gene that showed a substantial increase in tumor tissue compared to the control.

CONCLUSION: There is a significant association between the presence of F. nucleatum and miR-21; a relationship has been reported in colorectal cancer and is now observed in OSCC, and the expression of miR-31 was significantly correlated with P. gingivalis. Further research is needed to explore the prevalence and potential mechanisms of pathobionts and miRNA expression in OSCC.},
}

Humans
*Fusobacterium nucleatum/genetics/pathogenicity/isolation & purification
*MicroRNAs/genetics/metabolism
*Porphyromonas gingivalis/genetics/pathogenicity/isolation & purification
Male
Female
Middle Aged
*Mouth Neoplasms/genetics/microbiology
*Carcinoma, Squamous Cell/genetics/microbiology
Aged
Gene Expression Regulation, Neoplastic
Iran
Adult
Microbiota/genetics
Squamous Cell Carcinoma of Head and Neck/microbiology/genetics

@article {pmid40794299,
year = {2025},
author = {El-Halim, HMA and El-Hadidi, M and Fouad, N and Hamed, RR and Megid, IA and Taha, MH and Radwan, KH},
title = {Metagenomic insight into drought-induced changes in the Egyptian wheat rhizosphere microbiome.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {8},
pages = {310},
pmid = {40794299},
issn = {1573-0972},
mesh = {*Triticum/microbiology ; *Rhizosphere ; *Droughts ; Egypt ; *Microbiota/genetics ; Soil Microbiology ; Phylogeny ; *Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; Stress, Physiological ; RNA, Ribosomal, 16S/genetics ; Metagenome ; },
abstract = {Wheat is one of the most important cereal crops and an important source of food for billions of people worldwide. However, drought stress can pose a real threat to its productivity and lead to significant yield losses, especially in Egypt. The rhizospheric microbiome of wheat can play an important role in drought stress and help wheat to respond to this abiotic stress. Understanding this microbiome is therefore also important to improve drought stress resilience and productivity. In this study, a metagenomic analysis was performed to investigate how the composition and diversity of microbial communities associated with the wheat rhizosphere change under drought. Taxonomic and phylogenetic analyses revealed a shift in microbial abundance, with Actinobacteria, Bacteroidetes, Proteobacteria and Verrucomicrobia being the four most abundant phyla of the ethnic microbiota. Remarkably, other classes, including Alphaproteobacteria and Cytophagia, were significantly enriched under drought, which could be a promising enhancement of plant stress altruism. Differential abundance analysis showed that the control samples had higher abundance of microbial taxa such as OD1, WS2, Chlorobi, ABY1 and SHA-109 compared to the drought-treated genotypes. Functional prediction analysis using PICRUSt showed that an uncharacterized ATP-binding protein within the AAA + superfamily is overrepresented under drought conditions. This suggests that these genes may play a role in stress adaptation, possibly via energy-dependent regulation of cellular processes involved in plant survival. Our results expand our understanding of the complexity of responses of the wheat rhizosphere microbiome to drought and have practical implications for the development of microbial target combinations to improve wheat tolerance and productivity in the context of climate change challenges.},
}

*Triticum/microbiology
*Rhizosphere
*Droughts
Egypt
*Microbiota/genetics
Soil Microbiology
Phylogeny
*Metagenomics
*Bacteria/classification/genetics/isolation & purification
Stress, Physiological
RNA, Ribosomal, 16S/genetics
Metagenome

@article {pmid40794276,
year = {2025},
author = {Pudavar, AE and Baksi, KD and Pokhrel, V and Kuntal, BK},
title = {Microbiome knowledge graph as a tool to understand bacteria-host associations.},
journal = {Archives of microbiology},
volume = {207},
number = {9},
pages = {222},
pmid = {40794276},
issn = {1432-072X},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification ; *Host Microbial Interactions ; *Microbiota ; *Computational Biology/methods ; },
abstract = {Gut bacteria are well known to significantly influence human health and physiology. Knowledge Graph (KG) can effectively integrate the heterogenous factors modulating gut bacteria-host associations. Limited studies describe the construction and application of KGs capturing these associations for domain experts. This work outlines a methodology for constructing microbiome-centric KG and demonstrates how it enhances conventional microbiome data analysis workflows. Towards construction and deployment of this domain centric KG, methodologies involved in collection of data, selecting relevant entities and relationships, and preprocessing them are discussed. Key relevant entities include bacteria, host genetic and immune factors, chemicals and diseases. The KG construction in both RDF (Resource Description Framework) and LPG (Labeled Property Graph) models are demonstrated. Comparison of the querying techniques in both these models and applications of the KG using biologically relevant case studies are also presented. Overall, the work is intended to provide domain experts with a complete protocol for construction of a microbiome-centric KG starting from entity selection and schema design to utilizing the KG for microbiome data analysis and hypothesis generation.},
}

Humans
*Gastrointestinal Microbiome
*Bacteria/genetics/classification
*Host Microbial Interactions
*Microbiota
*Computational Biology/methods

@article {pmid40794147,
year = {2025},
author = {Addissouky, TA and Wang, Y and Sayed, IETE and Naser, NA and Jalal AlAhmed, M},
title = {Probiotics and Diet Modifications: A Holistic Approach to Tackling Helicobacter pylori with the Help of the Gut Microbiota.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40794147},
issn = {1867-1314},
abstract = {BACKGROUND: Helicobacter pylori (H. pylori) is a common gastrointestinal pathogen that can persist for decades and lead to diseases like gastritis, peptic ulcers, and gastric cancer. Conventional antibiotic treatments have limitations like resistance and side effects, requiring alternative therapies. The gut microbiota may influence H. pylori colonization and eradication success. Strategies like probiotics, prebiotics, diet, and lifestyle changes may modulate the gut microbiota composition and function to inhibit H. pylori growth. Specific probiotic strains produce antimicrobial compounds, modulate immune responses, and alter gut microbiota in ways that can promote H. pylori eradication. Diets high in fiber, polyphenols, omega-3s, and fermented foods appear to inhibit H. pylori by supporting growth of beneficial bacteria. Lifestyle factors like stress, smoking, and alcohol negatively impact the gut microbiota. Personalized therapies based on the gut microbiome could optimize eradication rates.

CONCLUSION: The gut microbiota represents a promising target for enhancing H. pylori eradication. Further research on microbiota-modulating therapies like probiotics, diet, and lifestyle changes may help develop more effective, personalized treatment approaches.},
}

@article {pmid40794137,
year = {2025},
author = {Fischler, TS and Reshef, L and Godny, L and Goren, I and Ollech, JE and Avni-Biron, I and Eran, HB and Snir, Y and Broitman, Y and Pfeffer-Gik, T and Freidenberg, A and Pauker, MH and Rabinowitz, KM and Gophna, U and Dotan, I and Yanai, H and , },
title = {Microbial Shift over One Year among Patients with Newly Diagnosed Crohn's Disease Reflects Clinical Trajectory and Exposure to Biologic Treatment: A Prospective Real-World Inception Cohort.},
journal = {Clinical and translational gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ctg.0000000000000902},
pmid = {40794137},
issn = {2155-384X},
abstract = {BACKGROUND: The gut microbiome in Crohn's disease (CD) shows variability and conflicting associations with disease activity. We aimed to assess microbial and clinical trajectories in newly diagnosed CD (ndCD) over one year.

METHODS: This prospective longitudinal inception cohort study followed treatment-naïve ndCD patients for one year. The primary outcome was sustained corticosteroid-free clinical remission (CSFR) after one year. Paired fecal samples were collected at diagnosis and one year later, analyzed using bacterial 16S rRNA gene high-throughput sequencing. Microbial composition changes were compared between baseline and one-year follow-up and between biologics-treated and conservatively managed patients. Fecal samples from healthy volunteers served as controls.

RESULTS: Seventy-three patients participated; 64.4% achieved sustained CSFR after one year. During follow-up, 60.3% had moderate to severe disease activity and received biologics (95.5% anti-TNF), while 39.7% were managed conservatively. Significant microbial improvements, including increased Shannon diversity and decreased microbial dysbiosis index (MDI), were observed only in patients achieving sustained CSFR (both p<0.001). Biologic-treated patients had more disrupted baseline microbiome composition than conservatively managed ones (Shannon, p=0.04; MDI, p=0.03); they showed significant microbial improvement regardless of clinical success, shifting toward a healthier microbiome profile. Changes in clinical outcomes over one year correlated with microbial alterations.

CONCLUSION: Over one year, treatment-naïve ndCD patients showed microbial improvements paralleling clinical outcomes, with shifts toward a healthier state. Biologic therapy enhanced microbial profiles, likely due to greater baseline disruption in these patients. These findings suggest that the microbiome is a marker of inflammation and a modifiable factor in CD management.},
}

@article {pmid40793961,
year = {2025},
author = {Yu, L and Bi, M and Xie, L},
title = {Correlation Between Polypharmacy and Gut Microbiota Compositional Changes in Older People Who Were Treated with Multidrug Therapy.},
journal = {Rejuvenation research},
volume = {},
number = {},
pages = {},
doi = {10.1177/15491684251365971},
pmid = {40793961},
issn = {1557-8577},
abstract = {This study investigates the correlation between polypharmacy and gut microbiota compositional changes in older people who were treated with multidrug therapy, aiming to provide insights into the complex interplay between medication use, gut microbiota, and aging. High-throughput sequencing of the 16S rRNA gene was employed to analyze microbial diversity in older patients with multiple chronic diseases and polypharmacy, and the results were compared with a control group of older people without multiple chronic diseases and not undergoing polypharmacy. The study revealed distinct differences in gut microbiota composition between the two groups, with lower alpha-diversity observed in multidrug therapy group. Furthermore, the analysis identified several significant differences in microbiome composition at the genus and family levels between the multidrug therapy and the control group. The findings underscore the importance of understanding the impact of polypharmacy on the gut microbiota and its relationship to overall health in older people. Additionally, the study provides insights into the potential effects of specific medications, such as antihypertensive drugs, proton pump inhibitors, and antibiotics, on the gut microbiota, highlighting the need for continued research in this critical area to optimize therapeutic strategies for the older population.},
}

@article {pmid40793931,
year = {2025},
author = {Peng, M-W and Wu, Y-H and Ren, Z-R and Narigen, and Hou, R-S and Xin, G-Y and Liao, Y-Q and Wang, J and Le, S-J and Shi, P-B and Zhao, H-L and Deng, Z-Q and Wang, D-X and Chaolemen, and Shi, M},
title = {Meta-transcriptomics characterization of individual Marmota sibirica reveals a wide spectrum of viral and bacterial pathogens in Inner Mongolia of China.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0018025},
doi = {10.1128/spectrum.00180-25},
pmid = {40793931},
issn = {2165-0497},
abstract = {Mongolian marmot is a reservoir for various zoonotic pathogens, including Yersinia pestis, Bartonella, and hantaviruses. However, our understanding of the marmot's pathogen profile remains incomplete. Here, we used an unbiased metatranscriptomic approach to comprehensively characterize the virome and bacterial microbiome of 106 Mongolian marmot sampled from Chen Barag Banner, Inner Mongolian, China. A total of 12 mammalian-associated viruses from five families were identified, including novel species such as Chenqi marmot mastadenovirus 1 and Chenqi marmot enterovirus 1. Additionally, 62 species of picobirnaviruses were detected though they were not classified as mammalian viruses in this context. Co-infection was common, with an average of 1.35 mammalian viruses per marmot fecal sample, excluding picobirnaviruses. Phylogenetic analysis showed high homology between these viruses and those found in Himalayan marmots although some showing close relationship with rodent and pig viruses. Ribosomal binding site analysis suggested that 32 picobirnaviruses contained Shine-Dalgarno sequences, indicating potential bacterial association. Based on meta-transcriptomics sequencing data, our study also revealed five potential bacterial pathogens though Yersinia pestis was not found. In summary, this study provides a more comprehensive view of pathogen diversity in Mongolian marmots and contributes important insights to support disease monitoring and prevention efforts in border areas of China.IMPORTANCEThe Mongolian marmot (Marmota sibirica) is a critical mammalian species in Hulunbuir, playing a key role in harboring and transmitting Yersinia pestis, the causative agent of plague. However, research on the diversity, abundance, co-infection dynamics, and spillover potential of viruses and bacteria in these animals remains limited. This study characterizes pathogen diversity and ecology by examining the viral and bacterial microbiomes of Mongolian marmots in China's northeastern border regions. The findings offer unique insights into potential threats to both animal and human health and contribute valuable data to inform disease prevention and control efforts in these regions.},
}

@article {pmid40793873,
year = {2025},
author = {Manning, S and Hackney, E and Dunneram, Y and Hull, MA and Mitra, S and Stewart, CJ and Louca, P and Meader, N and Sharp, L and Rees, C},
title = {Systematic Review: The Relationship Between the Faecal Microbiome and Colorectal Neoplasia in Shotgun Metagenomic Studies.},
journal = {Alimentary pharmacology & therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1111/apt.70252},
pmid = {40793873},
issn = {1365-2036},
support = {//Guts UK/ ; },
abstract = {BACKGROUND: The human gut microbiome is of academic and clinical interest. Associations between certain organisms and colorectal neoplasia have been reported, but findings have limited reproducibility in different populations.

METHODS: We performed a systematic review of whole metagenome shotgun sequencing studies using faecal samples from patients with colorectal neoplasia and control populations. Searches were performed on 30th June 2023. We identified 26 studies, reporting on 22 study populations (13 from Asia, five from Europe and four from North America). Study size ranged from 14 to 971 individuals (mean 170).

RESULTS: Some reproducible data were identified, such as the significant enrichment of Fusobacterium nucleatum and Parvimonas micra in colorectal cancer patients compared to controls (in 10 and nine studies, respectively). However, 21 out of 26 studies scored poorly on quality appraisal, specifically surrounding selection of cases and controls. Definitions of controls varied; some studies used individuals with normal endoscopic investigations, some used 'healthy' individuals where no colonoscopy was performed, and one used those with non-neoplastic findings (haemorrhoids). There was even less reproducibility of data in studies where individuals with colorectal polyps were compared to controls, possibly because of heterogeneity in these patient groupings as a variety of definitions for 'polyp cases' were used.

CONCLUSIONS: Heterogeneity and potential for bias indicates that findings should be interpreted with caution. Standardised protocols to ensure robust methodology and allow pooling of large-scale data are required before these findings can be used in clinical practice (PROSPERO: CRD42023431977).},
}

@article {pmid40793786,
year = {2025},
author = {Kramer, DJ and Wang, W and Loque, I and Walters-Laird, CJ and Morisseau, C and Xiao, X and Nearing, M and Santos Rocha, C and Dandekar, A and Hammock, B and Dandekar, S},
title = {Microbial biotherapeutic metabolite alleviates liver injury by restoring hepatic lipid metabolism through PPARα across the gut-liver axis.},
journal = {mBio},
volume = {},
number = {},
pages = {e0171825},
doi = {10.1128/mbio.01718-25},
pmid = {40793786},
issn = {2150-7511},
abstract = {Infectious and non-infectious liver diseases are marked by disrupted liver metabolism and are frequently accompanied by gut epithelial barrier dysfunction and microbial dysbiosis, reflecting the compromised gut-liver axis. Despite the pivotal role of the gut-liver axis in health, transformative therapeutic interventions that simultaneously target both the liver and gut remain underexplored. Peroxisome proliferator-activated receptor alpha (PPARα) suppression drives both gut and liver metabolic diseases. In this study, we report on the therapeutic impact of microbial metabolite, 10-hydroxystearic acid (10-HSA), on restoring lipid metabolism and liver regeneration through PPARα activation, leading to a functional gut-liver axis in an in vivo liver injury model. We previously identified 10-HSA, a known PPARα agonist, in Lactiplantibacillus plantarum-treated intestine. Here, we report that oral administration of 10-HSA prevented AFB1-induced gut epithelial barrier disruption and preserved mucosal T cell populations. Prominent downstream effects of 10-HSA-activated PPARα signaling included significant upregulation of known PPARα-regulated gene expression in the gut and liver; prevention of fibrotic changes and reduction of TGF-β signaling-related gene expression in the gut and liver; and activation of toxicant clearance metabolic pathways in the liver through the PPARα-NRF2 pathway. Restoration of the functional gut microenvironment during 10-HSA treatment was evident by increased gut microbial diversity and circulating citrulline levels. Our findings unveil a novel therapeutic trajectory that harnesses a single microbial metabolite to activate PPARα-mediated tissue repair/renewal pathways across the gut-liver axis, offering a promising biologic therapeutic for treatment of metabolic and inflammatory liver diseases.IMPORTANCEChronic liver diseases, including liver steatosis and fibrosis, are driven in part by dysregulation of PPARα and lipid metabolism. These diseases also generate gut barrier disruption and microbiome dysbiosis, leading to dysfunction of the gut-liver axis. Therapeutic strategies that concurrently support liver regeneration and gut mucosal repair can be highly effective in resolving liver metabolic diseases but remain underexplored. Microbial biotherapeutic metabolite 10-HSA induced repair and regeneration of both liver and gut through the activation of PPARα and restored lipid metabolism. Our findings reveal the therapeutic potential of a single microbial bioactive lipid molecule to repair both hepatic and gut mucosal sites simultaneously with important ramifications for treatment of diseases that disrupt the gut-liver axis.},
}

@article {pmid40793782,
year = {2025},
author = {Jeong, S and Tollison, T and Brochu, H and Chou, H and Huntress, I and Yount, KS and Zheng, X and Darville, T and O'Connell, CM and Peng, X},
title = {Cervicovaginal microbial features predict Chlamydia trachomatis spread to the upper genital tract of infected women.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0005725},
doi = {10.1128/iai.00057-25},
pmid = {40793782},
issn = {1098-5522},
abstract = {Chlamydia trachomatis (CT) infection can lead to pelvic inflammatory disease, infertility, and other reproductive sequelae when it ascends to the upper genital tract. Factors including chlamydial burden, coinfection with other sexually transmitted bacterial pathogens, and oral contraceptive use influence risk for upper genital tract spread. Cervicovaginal microbiome composition influences CT susceptibility, and we investigated if it contributes to spread by analyzing amplicon sequence variants (ASVs) derived from the V4 region of 16S rRNA genes in vaginal samples collected from women at high risk for CT infection and for whom endometrial infection had been determined. Participants were classified as CT negative (CT-, n = 70), CT positive at the cervix (Endo-, n = 79), or CT positive at both cervix and endometrium (Endo+, n = 68). Although we were unable to identify many significant differences between CT-infected and -uninfected women, differences in abundance of ASVs representing Lactobacillus iners and Lactobacillus crispatus subspecies but not dominant lactobacilli were detected. Thirteen informative ASVs predicted endometrial chlamydial infection (area under the curve = 0.72), with CT ASV abundance emerging as a key predictor. We also observed a positive correlation between levels of cervically secreted cytokines previously associated with CT ascension and abundance of the informative ASVs. Our findings suggest that vaginal microbial community members may influence chlamydial spread directly by nutrient limitation and/or disrupting endocervical epithelial integrity and indirectly by modulating proinflammatory signaling and/or homeostasis of adaptive immunity. Further investigation of these predictive microbial factors may lead to cervicovaginal microbiome biomarkers useful for identifying women at increased risk for disease.},
}

@article {pmid40793771,
year = {2025},
author = {Bhandari, R and Wong, AC-N and Lee, JC and Boyd, A and Shelby, K and Ringbauer, J and Kang, DS},
title = {Microbiome composition and co-occurrence dynamics in wild Drosophila suzukii are influenced by host crop, fly sex, and sampling location.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0260824},
doi = {10.1128/spectrum.02608-24},
pmid = {40793771},
issn = {2165-0497},
abstract = {Microbial control of insect pests offers promising alternatives to traditional pesticides. However, the microbial communities and factors influencing these communities within insect hosts remain poorly understood. This study examined the whole-body bacterial communities in wild Drosophila suzukii, commonly known as spotted wing Drosophila (SWD). Fly samples were collected from two farms growing wild Himalayan blackberries near blueberry crops, one blackberry farm, and one elderberry farm across four locations in the United States. Our analyses showed significant differences in microbial communities in flies across various host crops and sampling locations. We identified co-occurring bacterial genera, dominated by Gluconobacter and Morganella, and the overall microbiome was distinct from those found in laboratory-grown flies. Our findings suggest that the host crop, sex of the fly, sampling location, and their interactions play a crucial role in shaping microbial communities in SWD, indicating the influence of various ecological interactions. While no significant differences in microbiome composition were observed between male and female flies, network analysis revealed distinct sex-specific microbial co-occurrence patterns. Female flies displayed a more stable and interconnected microbial network than male flies, suggesting that sex-specific factors might influence bacterial interactions. Interestingly, the most abundant microbial taxa were not necessarily the most connected in the networks, showing that less abundant taxa may also play a significant role in shaping the fly microbiome. This study underscores the complexity of microbial ecology in SWD and highlights the necessity of considering these dynamics when developing pest management strategies in agriculture.IMPORTANCEStudies on the microbiome of spotted wing Drosophila (SWD) have primarily focused on laboratory-reared flies in controlled environments and fed artificial diets. In contrast, we examined microbial communities in wild flies from various host crops across four locations in the United States. Our findings show that these communities are distinct from those of laboratory-grown flies and are influenced by the fly's sex, host crop, geographical location, and their interactions. Our study identifies several dominant bacterial genera across samples, suggesting that these may represent the core microbial communities in wild SWD. Given that microbial communities influence physiological activities in SWD, manipulating the microbiome may have either a positive or negative impact on insect fitness. This study enhances our understanding of microbial dynamics in understudied wild SWD populations, emphasizing the importance of these dynamics in effective integrated pest management strategies.},
}

@article {pmid40792629,
year = {2025},
author = {Kardish, MR and Mugge, RL and Lee, JS},
title = {Comparison of microbial community profiles from hydro-processed renewable diesel and F-76 diesel.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0005925},
doi = {10.1128/mra.00059-25},
pmid = {40792629},
issn = {2576-098X},
abstract = {To better understand the microbial communities that drive microbiologically influenced corrosion (MIC), we characterized the bacterial communities present on various surfaces in tanks containing either petroleum-based Navy F76 diesel (F76) or hydro-processed renewable diesel (HRD) collected at the U.S. Naval Research Laboratory, Stennis Space Center, MS, USA.},
}

@article {pmid40792513,
year = {2025},
author = {Wu, N and Jiang, X and Wang, Y and Zhang, M and Yue, M and Chen, F and Wu, W and Liu, Y and Wang, Q and Zhang, L},
title = {Gut microbiota alterations modulate high-fat diet-induced precocious puberty.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0326424},
doi = {10.1128/spectrum.03264-24},
pmid = {40792513},
issn = {2165-0497},
abstract = {The link between gut microbiota and precocious puberty has garnered increasing attention; however, the underlying mechanisms remain poorly understood, and most existing studies are cross-sectional, making it difficult to capture the longitudinal changes in gut microbiota throughout precocious puberty. Here, female rats were fed high-fat diets supplemented with antibiotics to establish a model of precocious puberty with gut microbiota perturbation. Gut microbiota dynamics were characterized based on stool samples collected at postnatal day (PND) 21, 25, 29, and 33. Serum metabolomic profiles on PND 33 were analyzed to investigate the potential mechanisms by which gut microbiota may influence precocious puberty. We found that alterations in gut microbiota alleviated high-fat diet-induced precocious puberty. Temporal changes in gut microbiota that potentially regulate precocious puberty were identified, with specific contributions from Lactobacillus intestinalis, Romboutsia, Lactobacillus, and others. Additionally, the modified gut microbiota ameliorated the dysregulation of steroid hormones, bile acids, and lipid molecules at PND 33. Notably, lysoPE 16:0, 23-nordeoxycholic acid, and psoralidin were not only influenced by the gut microbiota but also closely associated with indicators of pubertal development. This study highlights key gut microbiota and metabolites that may inform future mechanistic studies and intervention strategies for managing precocious puberty.IMPORTANCEPrevious studies have highlighted the link between gut microbiota and precocious puberty. Our research further explored this connection, demonstrating that microbial shifts modulated the onset and progression of precocious puberty, characterized by increased hypothalamic sirtuin-1 gene expression and decreased kisspeptin-1 and gonadotropin-releasing hormone gene expressions. At the same time, we explored the longitudinal trajectories of the gut microbiota and identified the key microbes involved in regulating precocious puberty, including Romboutsia, Lactobacillus, and others. In addition, an integrated analysis of the microbiome and metabolome revealed specific bacteria and metabolites that contribute to the onset of puberty. These findings offer valuable insights into the mechanisms driving precocious puberty and may inform future research and potential therapeutic interventions.},
}

@article {pmid40792508,
year = {2025},
author = {Khan, ZA and Sobkowiak, MJ and Ghorbani, M and Poojabahen, T and Al-Manei, K and Halimi, A and Ateeb, Z and Özenci, V and Heuchel, R and Löhr, M and Sällberg Chen, M},
title = {Survival mechanism of pancreatic tumor bacteria and their ability to metabolize chemotherapy drugs.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0182025},
doi = {10.1128/spectrum.01820-25},
pmid = {40792508},
issn = {2165-0497},
abstract = {UNLABELLED: Pancreatic cancer (PC) remains one of the most lethal malignancies, with limited treatment efficacy. While surgical resection is the most effective option, chemotherapy with agents such as 5-fluorouracil (5-FU) and gemcitabine may improve survival. Intraductal papillary mucinous neoplasms (IPMNs) are pancreatic cystic tumors and important precursor lesions frequently detected during PC screening. Emerging evidence suggests that IPMNs can harbor a distinct tumor microbiome, but the microbial persistence and potential influence on cancer treatment remain poorly understood. In this study, we analyzed bacterial isolates from clinical IPMN samples and investigated their interactions with chemotherapeutic agents using functional assays and whole-genome sequencing (WGS). We found that most isolates reduced the cytotoxic effect of 5-FU and gemcitabine on pancreatic cancer cell lines (PANC-1, AsPC-1, and Capan-2). WGS revealed that the Gammaproteobacteria strains were enriched in genes associated with antibiotic resistance, drug transport, and virulence compared to the Bacilli strains. Further pathway analysis showed that Gammaproteobacteriawere enriched in pyrimidine metabolism pathways, while Bacilli were enriched in purine metabolism. These findings indicate that IPMN-associated bacteria are metabolically active and capable of modulating chemotherapy drug efficacy. Together, our findings suggest that the microbial adaptation mechanisms supporting bacterial survival within tumor lesions also enable them to interact with pyrimidine analogs. This underscores the importance of elucidating the functional roles of tumor-associated microbiota in modulating the tumor microenvironment and treatment efficacy.

IMPORTANCE: Chemotherapy is a primary treatment for pancreatic cancer, and emerging evidence indicates that the gut microbiota can modulate its efficacy. While most studies have focused on gut-residing microbes, characterization of intra-tumoral microbes within the pancreas remains limited. Here, we report new insights into metabolic interactions between chemotherapeutic agents and patient-derived pancreatic tumor bacteria. These bacteria were isolated from intraductal papillary mucinous neoplasms (IPMNs), the main precursors to pancreatic cancer. Our findings demonstrate that patient-derived pancreatic tumor bacteria tolerate two commonly used chemotherapeutic drugs, 5-fluorouracil (5-FU) and gemcitabine, and can attenuate their cytotoxic effects on pancreatic cancer cells. Through whole-genome and transcriptomic analyses, we further reveal potential adaptation mechanisms that could enable these bacteria to persist in the tumor microenvironment and metabolize chemotherapeutics.},
}

@article {pmid40792269,
year = {2025},
author = {Nakoa, JWP and Burns, JHR and Pascoe, M and Cortes, M and Ferreira, SB and Pascoe, KH and Kane, HH and Kapono, CA},
title = {Sediment exposure decreases diversity in the surface mucus layer microbiome of Porites lobata at Honoli'i, Hawai'i.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1626064},
pmid = {40792269},
issn = {1664-302X},
abstract = {INTRODUCTION: Coral reefs are diverse marine ecosystems that provide essential ecological services, yet they are becoming increasingly degraded by anthropogenic stressors. Sediment deposition from land-based runoff can smother corals, reduce light availability, and alter the chemical and microbial composition of the water column. Prolonged sediment exposure disrupts coral-associated microbial communities, particularly within the surface mucus layer (SML), a physical barrier that mediates host-microbe interactions.

METHODS: We investigated shifts in the SML microbiome of Porites lobata corals in response to an acute sedimentation event at Honoli'i, Hawai'i. Microbial community structure was characterized using 16S rRNA gene sequencing, at three time points, before, during, and after the sedimentation event, to identify changes in microbial composition and diversity.

RESULTS: Sedimentation caused a significant decline in microbial diversity and shifted community composition, with the most pronounced changes observed post-sedimentation. Indicator species analyses identified 206 bacterial taxa associated with specific sedimentation periods, including enrichment of Flavobacteriaceae during sedimentation and dominance of Endozoicimonaceae after sedimentation.

DISCUSSION: These findings demonstrate that sedimentation induces both immediate and delayed shifts in the SML microbiome, with potential implications for coral resilience. This study advances our understanding of how sedimentation affects coral-associated microbiomes and emphasizes the need to investigate the functional roles of microbial taxa involved in community transitions and recovery to inform conservation strategies.},
}

@article {pmid40792268,
year = {2025},
author = {Zhong, J and Li, J and Liao, J and Ma, Y and Li, Z and Yang, L and Chang, W and Miao, M},
title = {Alpine radish rhizosphere microbiome assembly and metabolic adaptation under PBAT/PLA humic acid biodegradable mulch films.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1623052},
pmid = {40792268},
issn = {1664-302X},
abstract = {INTRODUCTION: Alpine agroecosystems present unique crop production challenges due to extreme environmental conditions, where rhizosphere microbiomes significantly influence plant adaptation.

METHODS: To investigate mulch-induced microbial changes in high-altitude agriculture, this study analyzed a radish field in China using SMRT sequencing (16S rRNA/ITS) and metagenomics, comparing PBAT/PLA biodegradable films with/without humic acid (HA) at varying thicknesses.

RESULTS: Results demonstrated that radish cultivation selectively enriched Proteobacteria and Acidobacteriota while depleting Chloroflexi and Actinobacteria, with fungal communities shifting from Basidiomycota-to Ascomycota-dominance. Notably, HA-amended mulches enhanced bacterial diversity and specifically promoted polymer-degrading microbes (Chitinophagaceae, Candidatus_Udaeobacter, Chaetomiaceae). Metagenomic profiling revealed thickness-dependent increases in functional genes related to carbohydrate and amino acid metabolism in HA-treated soils.

CONCLUSION: These findings advance our understanding of how biodegradable mulch formulations can be optimized to enhance microbial ecosystem services in alpine farming systems.},
}

@article {pmid40792266,
year = {2025},
author = {Li, J and Li, Z and Sun, Y and Lu, J and Zhang, Q and He, X and Xu, M},
title = {Succession characteristics and assembly process of soil microbiome at reclaimed farmlands in coal mining area.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1633687},
pmid = {40792266},
issn = {1664-302X},
abstract = {Clarifying the succession patterns and assembly mechanisms of soil bacterial and fungal communities across reclamation chronosequences is essential for restoring soil health and ensuring ecological stability in mining areas. We analyzed soil microbial diversity, composition, co-occurrence network structure, and assembly processes using 16S rDNA/ITS sequencing and null models at 0 (R0), 1 (R1), 6 (R6), and 10 (R10) years of post-reclamation. Results showed that (1) Compared to R0, the R10 treatment resulted in significant increases in soil organic matter (SOM), total nitrogen (TN), available phosphorus (AP), and available potassium (AK) by 2.1-fold, 1.3-fold, 1.5-fold, and 0.4-fold, and also in activities of β-glucosidase (BG), N-acetyl-β-glucosaminidase (NAG), and leucine aminopeptidase (LAP), by 17-fold, 8.7-fold, and 1.8-fold, respectively (p < 0.05). (2) Rising bacterial diversity (Shannon, Chao1) over time, contrasting with fungal diversity that declined initially before recovering. (3) As the reclamation progressed, the network complexity was increased for both bacteria and fungi, improving stability. The number of bacterial keystone taxa was first increased and then decreased, with Bacillota (formerly Firmicutes) being the dominant keystone phylum. Bacteroidetes, Proteobacteria, and Acidobacteria exhibited rapid temporal responses. The fungal keystone taxa increased progressively, with Ascomycota as the dominant keystone phylum, while Basidiomycota and Mortierellomycota responded rapidly. (4) Enhanced bacterial functional potential (chemoheterotrophy, aerobic chemoheterotrophy, nitrification) and fungal saprotrophic capacity (undefined, wood saprotrophs) (5) Community assembly involved both deterministic (bacteria: dominated by heterogeneous selection) and stochastic processes (fungi: dispersal limitation/undominated). The partial least squares path modeling (PLS-PM) analysis showed that both the reclaimed coal mining and undisturbed normal farmland (NL) soils directly influenced microbial diversity and indirectly shaped microbial communities by influencing their assembly processes. These results underscore the critical role of reclamation in rebuilding soil microbial communities and restoring ecological functions in coal-mining areas.},
}

@article {pmid40792181,
year = {2025},
author = {You, YH and Bae, HJ and Park, JM and Ku, YB and Nam, GH and Kwak, TW and Bang, YJ and Jeong, TY and Hong, JW},
title = {Fungal and Bacterial Community Dynamics in the Rhizosphere and Rhizoplane of Diabelia spathulata in Relation to Soil Properties.},
journal = {Mycobiology},
volume = {53},
number = {5},
pages = {605-619},
pmid = {40792181},
issn = {1229-8093},
abstract = {Diabelia spathulata, a rare deciduous shrub native to East Asia, is critically endangered in Korea, yet little is known about its interactions with soil fungal communities. This study presents the first comprehensive analysis of fungal and bacterial communities in the rhizoplane (RP), rhizosphere (RS), and surrounding soil (SS) of D. spathulata in its natural habitat on Mt. Cheonseong, South Korea. High-throughput sequencing of the ITS and 16S rRNA gene regions revealed distinct microbial assemblages across soil compartments. Fungal taxa such as Russula, Trechispora, and Capronia were enriched in RP and RS, highlighting their potential roles in nutrient cycling, organic matter (OM) decomposition, and symbiosis. In contrast, the SS exhibited greater fungal richness but lower specialization. Among bacteria, root-associated compartments were enriched with plant-beneficial genera such as Bacillus and Bradyrhizobium, while bulk soil hosted more generalist taxa. Soil physicochemical analyses showed higher OM and total nitrogen in RS compared to SS, indicating root-driven enrichment. Correlation and network analyses identified strong links between specific fungal and bacterial taxa and key soil properties including pH, OM, and cation exchange capacity. These results suggest that D. spathulata modulates its RS microbiome to enhance nutrient availability and stress tolerance. This study highlights the ecological significance of fungal communities in root-associated microhabitats and provides foundational knowledge for incorporating soil microbiota into conservation and habitat restoration efforts for endangered plant species.},
}

@article {pmid40792108,
year = {2025},
author = {Khan, I and Irfan, M and Khan, I and Noor, U and Xie, X and Li, Z},
title = {Blood microbiome signatures in systemic diseases: current insights, methodological pitfalls, and future horizons.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1616029},
pmid = {40792108},
issn = {2235-2988},
mesh = {Humans ; *Microbiota ; *Dysbiosis/microbiology/blood ; Biomarkers/blood ; *Blood/microbiology ; Bacteria/classification/genetics/isolation & purification ; Neurodegenerative Diseases/microbiology/blood ; Immune System Diseases/microbiology/blood ; },
abstract = {The human-associated microbiome, encompassing diverse microbial communities across body sites, plays a pivotal role in maintaining host homeostasis. Disruption of this balance, termed dysbiosis, has been implicated in a spectrum of pathophysiological conditions. Traditionally, blood was considered a sterile microenvironment. However, emerging insights into the blood microbiome challenge the paradigm of blood sterility, revealing microbial signatures, including cell-free DNA and viable taxa, with putative implications for host physiology and disease. The blood taxonomic profile at the phylum level is dominated by Proteobacteria, with Bacteroidetes, Actinobacteria, and Firmicutes following in abundance. Dysbiosis in blood microbiome composition may indicate or contribute to systemic dysregulation, pointing to its potential role in disease etiology. These findings highlight the blood microbiome as a possible driver in the pathogenesis of infectious and non-infectious diseases, neurodegenerative disorders, and immune-mediated conditions. The detection of specific microbial profiles in circulation holds promise for biomarker discovery, enhancing disease stratification, and informing precision therapeutic strategies. However, advancing this field requires overcoming methodological challenges, including contamination control, standardization, and reproducibility. This review aims to present blood microbiome biomarkers across infectious, non-infectious, neurodegenerative, and immune-mediated diseases, while critically examining methodological variations, controversies, limitations, and future research directions. Elucidating these factors is critical to advancing blood microbiome biomarker validation and therapeutic targeting, thereby refining mechanistic insights into systemic disease pathogenesis.},
}

Humans
*Microbiota
*Dysbiosis/microbiology/blood
Biomarkers/blood
*Blood/microbiology
Bacteria/classification/genetics/isolation & purification
Neurodegenerative Diseases/microbiology/blood
Immune System Diseases/microbiology/blood

@article {pmid40792105,
year = {2025},
author = {Han, W and Zhou, Y and Wang, Y and Liu, X and Sun, T and Xu, J},
title = {Exploring fecal microbiota signatures associated with immune response and antibiotic impact in NSCLC: insights from metagenomic and machine learning approaches.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1591076},
pmid = {40792105},
issn = {2235-2988},
mesh = {Humans ; *Machine Learning ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Metagenomics/methods ; *Feces/microbiology ; *Carcinoma, Non-Small-Cell Lung/immunology/microbiology/drug therapy/therapy ; *Lung Neoplasms/immunology/microbiology/therapy/drug therapy ; Immunotherapy ; Male ; Female ; Middle Aged ; Aged ; Bacteria/classification/genetics/drug effects ; },
abstract = {BACKGROUND: Substantial interstudy heterogeneity in cancer immunotherapy-associated biomarkers has hindered their clinical applicability. To address this challenge, we performed a comprehensive integration of publicly available global metagenomic datasets. By leveraging metagenomic profiling and machine learning approaches, this study aimed to elucidate gut microbial signatures associated with immune response in lung cancer (LC) and to evaluate the modulatory effects of antibiotic exposure.

METHODS: A systematic literature search was conducted to identify relevant datasets, resulting in the inclusion of 209 fecal metagenomic samples: 154 baseline samples (45 responders, 37 non-responders, and 72 healthy controls) and 55 longitudinal samples collected during immunotherapy. We performed taxonomic and functional characterization of gut microbiota (GM) differentiating responders from non-responders, delineated microbiome dynamics during treatment, and assessed the impact of antibiotics on key microbial taxa. Among eight machine learning algorithms evaluated, the optimal model was selected to construct a predictive framework for immunotherapy response.

RESULTS: Microbial α-diversity was significantly elevated in responders compared to non-responders, with antibiotic administration further amplifying this difference-most notably at the species level. Integrative multi-omics analysis identified two pivotal microbial biomarkers, s_Bacteroides caccae and s_Prevotella copri, which were strongly associated with immunotherapy efficacy. A random forest-based classifier achieved robust predictive performance, with area under the curve (AUC) values of 0.82 and 0.79 at the species and genus levels, respectively. Notably, P. copri was further enriched in responders with poor progression-free survival (PFS <3 months), indicating a potential deleterious role. Antibiotic exposure significantly influenced the abundance and functional potential of these key taxa. KEGG-based functional analysis revealed the enrichment of amino acid metabolism pathways in responders. Additionally, CARD database annotation demonstrated that the majority of antibiotic resistance genes were associated with Bacteroidetes and Proteobacteria, implicating these taxa in shaping microbial-mediated therapeutic responses.

CONCLUSIONS: This study represents the first large-scale, cross-cohort integration of metagenomic data to identify reproducible GM signatures predictive of immune checkpoint inhibitor efficacy in LC. The findings not only underscore the prognostic relevance of specific taxa but also establish a foundation for developing microbiome-informed, personalized immunotherapeutic strategies.},
}

Humans
*Machine Learning
*Anti-Bacterial Agents/therapeutic use/pharmacology
*Gastrointestinal Microbiome/drug effects
Metagenomics/methods
*Feces/microbiology
*Carcinoma, Non-Small-Cell Lung/immunology/microbiology/drug therapy/therapy
*Lung Neoplasms/immunology/microbiology/therapy/drug therapy
Immunotherapy
Male
Female
Middle Aged
Aged
Bacteria/classification/genetics/drug effects

@article {pmid40792100,
year = {2025},
author = {Liao, WC and Li, SW and Hsing, EW and Hsiao, SH and Chang, IY and Chen, YC and Chen, YY and Pan, YJ and Hsieh, YC},
title = {Respiratory microbiome and metabolome features associate disease severity and the need for doxycycline treatment in children with macrolide-resistant Mycoplasma pneumoniae-mediated pneumonia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1537182},
pmid = {40792100},
issn = {2235-2988},
mesh = {Humans ; *Pneumonia, Mycoplasma/drug therapy/microbiology ; *Doxycycline/therapeutic use ; Female ; Male ; *Mycoplasma pneumoniae/drug effects/genetics ; *Macrolides/pharmacology ; *Metabolome ; Child, Preschool ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Child ; *Microbiota/drug effects ; Severity of Illness Index ; *Drug Resistance, Bacterial ; RNA, Ribosomal, 16S/genetics ; Community-Acquired Infections/microbiology/drug therapy ; Infant ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {INTRODUCTION: Commensal bacterial community along the upper respiratory tract functions against pathogens. The host determinants of Mycoplasma pneumoniae severity should be identified against the increasing threat of macrolide-resistant M. pneumoniae (MRMP) infection. We hypothesized that respiratory microbiome is involved in the clinical manifestations of M. pneumoniae infection.

METHODS: From 2017 to 2020, 92 children with MRMP-mediated pneumonia were enrolled among 845 children with community-associated pneumonia. Oropharyngeal samplings were collected within 48 h after admission. We compared respiratory microbiome and metabolites based on patients' later development of prolonged fever and the need for doxycycline treatment (DT, n = 57) and the cured control without fever or doxycycline treatment (WDT, n = 35) by using 16S rRNA-based sequencing and untargeted metabolome analysis.

RESULTS: Significantly higher diversity and different respiratory microbiomes were evaluated in WDT patients in contrast to DT patients. Fusobacterium, Haemophilus, Gemella, Oribacterium, Actinomyces lingnae, Fusobacterium periodonticum, Gemella sanguinis, and Solobacterium moorei were inversely correlated with disease severity. We assumed that metabolites of divergent microbiomes were related to MRMP development. We identified 15 discriminative amino-acid- and fatty-acid-related metabolites in two groups. F. periodonticum abundance was negatively associated with an inflammatory metabolite: a platelet-activating factor. Fusobacterium and Oribacterium were related to the decrease in LysoPE(18:1(9Z)/0:0) and LysoPC(18:1(9Z)).

CONCLUSIONS: Microbiota dysbiosis with dysregulated inflammatory glycerolphospholipid-related metabolites was related to disease severity and the need for doxycycline treatment in children with MRMP-mediated pneumonia. Anaerobic bacteria metabolites and metabolic pathway could be beneficial therapeutic targets against M. pneumoniae infection.},
}

Humans
*Pneumonia, Mycoplasma/drug therapy/microbiology
*Doxycycline/therapeutic use
Female
Male
*Mycoplasma pneumoniae/drug effects/genetics
*Macrolides/pharmacology
*Metabolome
Child, Preschool
*Anti-Bacterial Agents/therapeutic use/pharmacology
Child
*Microbiota/drug effects
Severity of Illness Index
*Drug Resistance, Bacterial
RNA, Ribosomal, 16S/genetics
Community-Acquired Infections/microbiology/drug therapy
Infant
Bacteria/classification/genetics/isolation & purification

@article {pmid40792057,
year = {2025},
author = {Atuahene, D and Wolfe, L and Vanhatalo, OE and Veenstra, BT and Skarlupka, JH and Anderson, KL and Suen, G and Meineri, G and Pritchard, JC},
title = {Limited day-to-day variation in the canine gut microbiota: implications for microbiome studies.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1632686},
pmid = {40792057},
issn = {2297-1769},
abstract = {The gut microbiome is vital for health and affects gastrointestinal, systemic, and neurological functions. In dogs, fecal samples provide an effective mechanism to assess the gut microbiota as they are non-invasive, easily obtained, and representative of the gut microbiome. However, traditional methods usually require sampling across three consecutive days per time point to minimize the presumed variation in the gut microbiome. Here, we sought to investigate whether the gut microbiome obtained from a single-day fecal sampling is reflective of the microbiome obtained from three-day collections. To accomplish this, we collected fecal samples from 12 dogs over 3 days and compared each single-day microbiome against the combined microbiotas of the three-day samples. We found no significant daily variation in the gut microbiota, as determined by two one-sided tests of equivalence (TOST) analysis, indicating that there are little to no day-to-day changes in the microbiota. Further microbial comparisons using PERMANOVA (p = 0.98) and non-metric multidimensional scaling also showed no significant differences in the microbial composition across the sampled days. Taken together, our findings suggest that a single sample can represent the gut microbiome as accurately as samples obtained across three consecutive days. As such, a single-day sampling approach can be used in dog microbiome studies, which would reduce both labor and costs while preserving overall data quality.},
}

@article {pmid40792034,
year = {2025},
author = {Li, J and Wu, C and Liu, Q and Liu, M and Liu, T and Li, A and Fu, G and Zou, Z and Guo, D and Chen, K and Xia, Y and Yao, D},
title = {Mozart's rhythm influence on Alzheimer's disease progression via modulation of pathological damage and cognition.},
journal = {iScience},
volume = {28},
number = {8},
pages = {113168},
pmid = {40792034},
issn = {2589-0042},
abstract = {Rhythm perception is considered a conserved trait across species, and musical rhythm exposure (MRE) has been demonstrated to enhance cognitive functions in healthy individuals. Alzheimer's disease (AD), characterized by cognitive decline and pathological degeneration, may potentially be delayed by MRE. In this study, the APP/PS1 AD mouse model was exposed to Mozart's K.448 rhythm for six months, with APP/PS1 and wild-type C57BL/6J mice serving as controls. The Morris water maze test was employed to assess the impact of MRE on spatial learning and memory. Pathological damage was evaluated through amyloid-beta and phosphorylated tau levels. Additionally, hippocampal microglia activation, inflammatory markers, and gut microbiota composition were analyzed. The study revealed that MRE improves cognitive function, reduces amyloid plaque accumulation, suppresses microglial activation and neuroinflammation, and modulates gut microbiota composition. This suggests that MRE offers a promising non-pharmacological approach to slowing cognitive decline and pathological damage in AD.},
}