@article {pmid40473125,
year = {2025},
author = {Darwiche, S and Gacesa, R and Ferraro, RB and Alwan, W and Oben, JA and Rashidghamat, E and Long, PF},
title = {Prevalence of skin fungi markedly declines in the lesions of two patients with moderate Hidradenitis Suppurativa.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107778},
doi = {10.1016/j.micpath.2025.107778},
pmid = {40473125},
issn = {1096-1208},
abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory disorder affecting hair follicles in intertriginous regions, leading to painful nodules, sinus tracts, and scarring. The pathogenesis of HS is far from clear, but alterations in the bacterial community of the skin microbiome has been debated, yet the potential involvement of fungi - the mycobiome - has received almost no attention. Large areas of skin were sampled for amplicon metagenomics sequencing to negate the inference of low-sequence counts with the objective of examining the provenance of fungi between lesion and lesion-free skin from the same individuals. The DNA from skin swabs was isolated and the V4 region of the 18S rRNA gene was amplified and sequenced. Total fungal counts were inferred from taxonomic assignment of unique operational taxonomic units and absolute numbers then compared between skin sites. There were dramatically lower numbers of fungi in HS lesions with Malassezia dominance, as expected, across samples. This finding suggested, for the first time, that fungal depletion in lesions might be linked to HS pathology through disruption of normal skin barrier function and immunity, potentially due to reduced sebum production essential for fungal growth.},
}

@article {pmid40473107,
year = {2025},
author = {Mascaux, C and Sen, T and Sanchez-Cespedes, M and Ortiz-Cuaran, S and Bossé, Y and Dammeijer, F and Cavic, M and Barr, MP and Arulananda, S and Armisen, R and Berger, AH and Bianchi, F and Carbone, DP and Cerciello, F and Lockwood, WW and Mitsudomi, T and Ohara, S and Politi, K and Qin, S and Roisman, LC and Samstein, R and Skoulidis, F and Tan, AC and Thomas, A and Zhang, J and Wynes, MW and John, T and Tsao, MS and , },
title = {Advances in lung cancer basic and translational research in 2025 - Overview and perspectives focusing on non-small cell lung cancer.},
journal = {Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtho.2025.05.024},
pmid = {40473107},
issn = {1556-1380},
abstract = {Basic and translational research in lung cancer is a rapidly evolving field with transformational impact in early detection, diagnosis, therapeutic development and personalization of care. Recent advances have greatly increased our understanding in the molecular genomics, proteomics, pathogenesis and cellular biology of this deadly malignancy. The International Association for the Study of Lung Cancer (IASLC) recently formed a Basic and Translational Science (BaTS) Committee to further enhance the scientific leadership of IASLC in thoracic cancer research. This review by members of the committee highlights the breadth of current research in NSCLC, with a focus on molecular risk factors and processes in tumorigenesis, heterogeneity, phenotypic plasticity, metabolic reprograming, immunobiology, the immune microenvironment and microbiome. This review also identifies future research areas that may lead to further improvement in survival outcomes and curative therapies especially for patients with advanced NSCLC.},
}

@article {pmid40473000,
year = {2025},
author = {Carbone, E and Fabrizi, E and Rivabene, R and Cappella, M and Fortini, P and Conti, L and Locuratolo, N and Lorenzini, P and Lacorte, E and Piscopo, P},
title = {Human oral microbiome in aging: a systematic review.},
journal = {Mechanisms of ageing and development},
volume = {},
number = {},
pages = {112080},
doi = {10.1016/j.mad.2025.112080},
pmid = {40473000},
issn = {1872-6216},
abstract = {Studying aging and risk factors associated with chronic non-communicable diseases is increasingly relevant due to the progressive aging of the global population. Risk factors have focused on diet, physical exercise, cognitive activity, and lifestyle habits; however, recent research has begun to explore how the oral microbiome may influence health and contribute to chronic diseases. The aim of our systematic review is to evaluate the link between human oral microbiome and aging. This SR was carried out using PubMed, Cochrane Library, and Embase, identifying 3,490 records, of which 6 met our inclusion/exclusion criteria. These studies were qualitatively assessed using the Revised Risk of Bias Assessment Tool for Nonrandomized Studies of Interventions. Overall, the evidence suggests that while the bacterial and fungal communities remain similar across age groups, there is an increased presence of periodontal pathogens in older subjects. Moreover, bacterial species richness and alpha-diversity decrease with advancing age, though no clear age clustering was observed. Although the reviewed studies offer insights into the association between aging and changes in the oral microbiome, further research is required to address confounding factors, limitations in sample size, and gender differences, in order to better elucidate the role of microbiome alterations in general health.},
}

@article {pmid40472755,
year = {2025},
author = {Chen, M and Xing, L and Gao, S and Guo, Y and Qiu, T and Wang, X and Gao, M},
title = {Metagenomic analysis deciphers airborne pathogens with enhanced antimicrobial resistance and virulence factors in composting facilities.},
journal = {Environment international},
volume = {201},
number = {},
pages = {109569},
doi = {10.1016/j.envint.2025.109569},
pmid = {40472755},
issn = {1873-6750},
abstract = {The composting process has been shown to effectively reduce antimicrobial resistance (AMR) in animal manure, but its influence on surrounding airborne AMR remains unknown, particularly with regard to human-pathogenic antibiotic-resistant bacteria (HPARB). In this study, air and paired compost samples were collected from a full-scale composting facility, and the antibiotic resistome, microbiome, and HPARB were systematically analyzed in both two habitats using metagenomic analysis. Current result uncovered the profiles of HPARB in air, showing that significantly more airborne HPARB were assembled than that in compost samples. Airborne pathogens harboredan increased abundance and diversity of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in comparison with compost-borne HPARB. The core antibiotic resistome represents 18.58% of overall ARG subtypes, contributing to 86.31% of ARG abundance. A higher number of enriched core ARGs (2.16- to 13.36-times higher), including mexF, tetW, and vanS, were observed in air samples compared to compost samples. As an important human pathogen, Mycobacterium tuberculosis was prevalent in the air and carried more ARG (6) and VFG (130) subtypes than those in compost. A significantly higher risk score was detected for airborne AMR in the composting facility compared to that in hospital and urban environments. This study revealed the enhanced airborne HPARB through comparative experiments between air and composting habitats. It highlighted the unrecognized AMR risks associated with air in composting site and provided a scientific basis for accurately assessing health outcomes caused by occupational exposure.},
}

@article {pmid40472699,
year = {2025},
author = {Yang, Q and Cao, X and Li, S and Yang, X and Bai, P and Yan, Y and Qi, C and Deng, Z and Wu, B and Song, B},
title = {Chronic ozone exposure induces hippocampal microglia activation by microbial dysbiosis in rat lungs.},
journal = {Ecotoxicology and environmental safety},
volume = {300},
number = {},
pages = {118393},
doi = {10.1016/j.ecoenv.2025.118393},
pmid = {40472699},
issn = {1090-2414},
abstract = {Ozone (O3) pollution has become a significant international public health issue with adverse effects on human health. Recent studies have confirmed that O3 exposure induces neuroinflammation and cognitive dysfunction. It is hypothesized that O3 exposure affects the pulmonary microbiome, triggering inflammatory responses that subsequently contribute to neuroinflammation. After 40 days of O3 exposure in rats, distinct changes in the microbial community were identified using 16S rRNA gene sequencing. This was followed by an assessment of the impact of pulmonary microbiota on serum NETs (neutrophil extracellular traps). Additionally, changes in the hippocampal P2X4R/NLRP3 signaling pathway were investigated following O3 exposure. In vitro experiments were conducted to evaluate the effects of O3 on BV-2 cells. In vivo results indicated that O3 exposure led to an increased abundance of Pseudomonas aeruginosa within the pulmonary microbiota and significantly increased NET levels in rat serum. O3 exposure caused a loose arrangement of hippocampal neurons in rats, resulting in cell atrophy and even death. Compared to controls, O3 exposure significantly upregulated the expression of P2X4R/NLRP3 and pro-inflammatory factors. Similarly, BV-2 cells treated with serum from 1.0 ppm O3-exposed rats exhibited comparable changes. Treatment with a P2X4R inhibitor significantly reduced pathway protein and pro-inflammatory factors expression compared to O3 serum intervention alone. In conclusion, O3 exposure significantly alters the pulmonary microbiome, induces hippocampal damage, and NETs may act as a mediator between the lung and brain axes.},
}

@article {pmid40472561,
year = {2025},
author = {Lin, Z and Qiao, Y and Xu, K and Lu, L and Shu, QY and Tian, S},
title = {The endophytic fungus Serendipita indica reshapes rhizosphere soil microbiota to improve Salix suchowensis growth and phytoremediation.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138620},
doi = {10.1016/j.jhazmat.2025.138620},
pmid = {40472561},
issn = {1873-3336},
abstract = {Soil cadmium (Cd) contamination, a global issue threatening human health, can be mitigated through phytoremediation using plant growth-promoting microorganisms (PGPMs), which enhance heavy metal extraction. Endophyte Serendipita indica promotes plant growth and alleviates abiotic/biotic stress, but its role in reshaping rhizosphere microecology remains unclear. We combined in situ zymography, diffusive equilibration in thin films (DET), and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) to explore Cd rhizosphere processes. S. indica inoculation significantly increased stems and leaves biomass by 36.52 % and 31.63 %, respectively, and Cd accumulation by 44.30 % in stems and 33.17 % in leaves. DET and zymography mapping showed that S. indica inoculation reduced pH and enhanced enzyme activity in the rhizosphere. LA-ICP-MS mappings revealed that S. indica increased Cd concentration in the root-soil interface and enhanced Cd and phosphorus (P) bioavailability, promoting root uptake and transport to shoots. S. indica inoculation recruited a more complex and stable network, supporting willow growth and Cd absorption. Key strains like Gemmatimonas, Subgroup_10, and Sandaracinus facilitated organic matter degradation, releasing bioavailable P and Cd, thus enhancing the phytoremediation efficiency. In summary, a mutualistic system between S. indica and willow was established, enhancing Cd phytoremediation efficiency by altering rhizosphere microenvironment and microbiome.},
}

@article {pmid40472289,
year = {2025},
author = {Lim, LWZ and Toh, KY and Cook, AR and Lee, JWJ and Lim, JFY},
title = {Public knowledge, awareness and perception of gut microbiome and faecal microbiota transplantation in Singapore: a survey study.},
journal = {Singapore medical journal},
volume = {},
number = {},
pages = {},
pmid = {40472289},
issn = {2737-5935},
abstract = {INTRODUCTION: Despite the exponential increase in microbiome research, knowledge and beliefs about the gut microbiome and faecal microbiota transplantation (FMT) remain unclear. The aim of this study was to identify the extent of knowledge, awareness and perception among the general public regarding the gut microbiome and FMT.

METHODS: An online questionnaire on knowledge and beliefs about the gut microbiome and FMT was administered to 1831 participants. Data analysis software was used to generate descriptive statistics and explore associations between knowledge and sociodemographic variables.

RESULTS: Even though only 33% of participants had heard of the gut microbiome, more than 92% had consumed probiotic drinks or supplements. While 85% had not heard of the FMT procedure, 72% of respondents would consider having FMT to treat Clostridioides difficile infection (CDI). Willingness to receive FMT depended mainly on recommendation from healthcare providers (77%). Knowledge and awareness regarding the gut microbiome and FMT were relatively low, despite most participants having prior gut health-related behaviours.

CONCLUSION: This study identified the public's perceptions of FMT and the potential barriers to its uptake. Insights from the study highlight the need for health education to enhance acceptance of FMT and the importance of using information supported by medical professionals to immunise the public against poorly validated science.},
}

@article {pmid40472245,
year = {2025},
author = {Baeringsdottir, B and Haraldsson, A and Hrafnkelsson, B and Thors, V},
title = {Infant Antibiotic Exposure Is Associated With Increased Risk of Later Childhood Infections, Antibiotic Use and Asthma.},
journal = {The Pediatric infectious disease journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/INF.0000000000004867},
pmid = {40472245},
issn = {1532-0987},
abstract = {BACKGROUND: Antimicrobials have saved millions of lives. Antibiotics are essential in treating infant infections, but may disrupt the gut microbiome and have adverse effects on later health.

METHODS: This population-based birth cohort study included full-term children born in Iceland from 2010 to 2019 with follow-up for 2-12 years. The cohort was divided into 4 groups according to antibiotic exposure; I: elective cesarean section, II: vaginal birth and maternal intrapartum antibiotics, III: vaginal birth and infants received antibiotics during the first week of life for >48 hours and IV: vaginal birth without antibiotic exposure. Rates of infections, antibiotic use and the risk of asthma later in childhood were calculated.

RESULTS: Of 43,600 children born in Iceland from 2010 to 2019, 22,393 were included. Group I had 1496 children, group II 3413, group III 356 and group IV 17,128 children. For all antibiotic exposure groups, the risk of infections and antibiotic use was significantly higher (20%-100%), with the largest effect observed for infants treated with antibiotics. This group also had a 2-fold risk of asthma diagnosis when compared with controls (odds ratio: 1.91, P < 0.05).

CONCLUSIONS: In this cohort study, children with early antibiotic exposure had higher rates of infections and antibiotic use later in childhood compared with controls. Diagnoses of asthma were significantly more common in children with early antibiotic exposure and this effect was most evident after the age of 8 years. The observed late side-effects of antibiotic use, possibly mediated through a disrupted microbiome, should promote a conservative approach to antibiotic treatment in young infants.},
}

@article {pmid40472200,
year = {2025},
author = {Hatch-McChesney, A and Suther, C and Thompson, LA and Radcliffe, PN and Cherian, RV and Liechty, ZS and Stamps, BW and Krieger, S and Nelman-Gonzalez, M and Crucian, B and Diak, D and Mehta, S and Goodson, MS and Barringer, N and Smith, TJ and Karl, JP},
title = {Sex Differences in Immune and Gut Microbiota Responses to Military Training.},
journal = {Medicine and science in sports and exercise},
volume = {},
number = {},
pages = {},
doi = {10.1249/MSS.0000000000003772},
pmid = {40472200},
issn = {1530-0315},
abstract = {PURPOSE: Military training includes multiple stressors that together may increase risk for illness by degrading immune function and altering gut microbiota. However, whether sex differences exist in those responses is undetermined. This study aimed to determine immune and gut microbiota responses during military training and identify sex differences in those responses.

METHODS: Seventy-two military cadets (33% female) participated in an arduous 17-day training event. Blood, saliva and stool were collected upon beginning (PRE) and completing (POST) training. Immune function was assessed by salivary secretory IgA (SIgA), latent virus reactivation, peripheral leukocyte distribution, circulating cytokines and mitogen-stimulated cytokine profiles. Gut microbiota composition was assessed by 16S rRNA amplicon sequencing.

RESULTS: Participants experienced a ~ 4% body weight loss and sex-independent increases in concentrations of cortisol, myoglobin, catecholamines and multiple cytokines. The granulocyte-to-lymphocyte ratio increased and SIgA decreased PRE to POST in males but not females (Pinteraction ≤ 0.02). Mitogen-stimulated cytokine profiles were generally reduced at POST versus PRE independent of sex. No differences in virus reactivation were observed. Sex differences in gut microbiota responses were limited to Bifidobacterium and Ruminococcus, which increased in males relative to females (log2 fold change (FC) = 2.0-2.4; qinteraction = 0.19). Independent of sex, 24 genera differed at POST versus PRE with Lactobacillus demonstrating the largest decrease (log2FC = -0.90; qtime = 0.02) and Veillonella the largest increase (log2FC = 1.09; qtime = 0.03). Multiple correlations between markers of stress, immune function and gut microbiota composition were observed (q ≤ 0.15).

CONCLUSIONS: Immune redistribution, leukocyte compromise and interrelated changes in gut microbiota composition were evident within this training environment. Those responses demonstrated associations with markers of stress severity but also sex differences suggesting a more pronounced depression of immune function in males.},
}

@article {pmid40472034,
year = {2025},
author = {Noack, C and Jenderny, S and Giez, C and Merza, O and Hofacker, LM and Wittlieb, J and Repnik, U and Bramkamp, M and Ochs, K and Bosch, TCG},
title = {Assembly of a functional neuronal circuit in embryos of an ancestral metazoan is influenced by temperature and the microbiome.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {23},
pages = {e2501225122},
doi = {10.1073/pnas.2501225122},
pmid = {40472034},
issn = {1091-6490},
support = {CRC 1182 C1; CRC 1461 A1//Deutsche Forschungsgemeinschaft (DFG)/ ; HMB//Canadian Institute for Advanced Research (ICRA)/ ; CRC 1461 A1//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {Animals ; *Microbiota/physiology ; *Hydra/embryology/microbiology/physiology ; *Neurons/physiology ; Temperature ; *Nerve Net/physiology/embryology ; Biological Evolution ; Embryo, Nonmammalian/physiology ; Gap Junctions/physiology ; },
abstract = {Understanding how neural populations emerge to give rise to behavior is a major goal in neuroscience. Here, we explore the self-assembly of neural circuits in Hydra, an organism with a simple nervous system but no centralized information processing, to enhance the understanding of nervous system evolution. We define self-assembly as spontaneous organization of neurons into functional circuits without requiring a prespecified structural template. In this context, the N4 neuronal circuit, which we have previously found to be particularly important in the feeding of the animal, develops in embryos through activity-driven self-assembly, a process in which intrinsic calcium activity drives connectivity and synchronization among spatially distributed neurons over time. Gap junctions and vesicle-mediated communication between neuronal and non-neuronal cells drive rapid assembly, with the embryo's prospective oral region exhibiting the highest neuronal density. An artificial electrical circuit-based model as a biophysically inspired simulation demonstrates dynamic increases in synchronization over time, along with predictions for selective dynamic adaptions of connections. Environmental factors, like temperature and an absent microbiome, modify neural architecture, suggesting the existence of a certain adaptability during neural development. We propose that these fundamental features originated in the last common bilaterian ancestor, supporting the hypothesis that the basic architecture of the nervous system is universal. Since in the natural habitat of Hydra both temperature fluctuations and changes in the microbiome can occur, our work not only illuminates a fundamental developmental process but also may guide environmental and evolutionary studies by explaining how organisms adapt to environmental variations.},
}

Animals
*Microbiota/physiology
*Hydra/embryology/microbiology/physiology
*Neurons/physiology
Temperature
*Nerve Net/physiology/embryology
Biological Evolution
Embryo, Nonmammalian/physiology
Gap Junctions/physiology

@article {pmid40472016,
year = {2025},
author = {MacIntosh, GH and Nuyens, AC and Vickery, JL and Berthold, A and Lloyd, VK},
title = {Epigenetic responses in Borrelia-infected Ixodes scapularis ticks: Over-expression of euchromatic histone lysine methyltransferase 2 and no change in DNA methylation.},
journal = {PloS one},
volume = {20},
number = {6},
pages = {e0324546},
doi = {10.1371/journal.pone.0324546},
pmid = {40472016},
issn = {1932-6203},
mesh = {Animals ; *Ixodes/microbiology/genetics ; *DNA Methylation ; *Epigenesis, Genetic ; *Borrelia burgdorferi/physiology ; *Histone-Lysine N-Methyltransferase/genetics/metabolism ; Lyme Disease/microbiology ; },
abstract = {Borrelia burgdorferi, a tick-vectored spirochete bacteria best known for causing Lyme disease, has been found to induce physiological and behavioural changes in its tick vector that can increase tick fitness and its ability to transmit the bacteria. The mechanism by which this bacterium modulates these changes remains unknown. Epigenetics plays a central role in transducing external and internal microbiome environmental influences to the organism, so we investigated DNA methylation and the expression of a key histone modification enzyme in Borrelia-infected and uninfected Ixodes scapularis ticks. DNA methylation of the pericentromeric tandem repeats family, Ixodes scapularis Repeats (ISR), were assessed by methylated-DNA immunoprecipitation (MeDIP) followed by qPCR of the ISR regions. DNA methylation of the ISR sequences was found. The different repeats had different levels of DNA methylation, however, these levels were not significantly affected by the presence or absence of B. burgdorferi. The epigenetic regulator euchromatic histone lysine methyltransferase 2 (EHMT2) is recognized as having a key role in modulating the organismal stress response to infections. To assess EHMT2 transcription in Borrelia-infected and uninfected ticks, real-time reverse transcriptase PCR was performed. Uninfected ticks had over 800X lower EHMT2 expression than infected ticks. This study is among the first to identify a gene that may be involved in producing epigenetic differences in ticks depending on infection status and lays the groundwork for future epigenetic studies of I. scapularis in response to B. burgdorferi as well as other pathogens that these ticks transmit.},
}

Animals
*Ixodes/microbiology/genetics
*DNA Methylation
*Epigenesis, Genetic
*Borrelia burgdorferi/physiology
*Histone-Lysine N-Methyltransferase/genetics/metabolism
Lyme Disease/microbiology

@article {pmid40471941,
year = {2025},
author = {Ritz, T and Rosenkranz, MA and Celedón, JC and Davenport, PW and Djukanovic, R and Feldman, JM and Forsythe, P and Jajour, NN and Vercelli, D and von Leupoldt, A and Wright, RJ},
title = {Asthma: Biomedical and Psychobiological Perspectives for the Disease of the Year 2023.},
journal = {Biopsychosocial science and medicine},
volume = {},
number = {},
pages = {},
doi = {10.1097/PSY.0000000000001410},
pmid = {40471941},
issn = {2998-8756},
abstract = {Substantial knowledge about asthma has accumulated in past decades from biomedical and psychobiological research. This white paper reports on synergistic perspectives for these fields discussed at the first Annual Disease-A-Year Symposium of the American Psychosomatic Society. Progress has been made in identifying mechanical, cellular and molecular mechanisms of asthma and influences of psychosocial factors on development, pathophysiology, and management have been demonstrated. However, much remains to be learned about mechanisms of asthma development, in particular the role of genes and the microbiome, and their interaction with psychosocial factors. Additional psychobiological analysis of immunobiological pathways and pathophysiological features is also needed, as well as integration with asthma phenotypes. Although traditionally viewed as a peripheral disease of the airways, its effect on the central nervous system and cognition have begun to garner attention due to neuroscientific and technological advances. Brain-body interaction are also the focus of airway interoception research, with practical consequences for management of over- and underperception of airway obstruction. An integrative perspective on asthma recognizes societal factors that worsen and consolidate disparities in asthma outcomes and explores mechanisms of building resilience in patients from disadvantages communities. Biomedical treatment with novel monoclonal antibodies promises a personalized medicine approach, while improvements to asthma management trainings have increased disease control and quality of life. Psychobiological and mind-body interventions, such as exercise, breathing training, cognitive behavioral therapy, or meditation techniques, require further exploration in large-scale multicenter trials. Close interdisciplinary collaboration will bring the field closer to the ideal of a holistic biopsychosocial treatment of asthma.},
}

@article {pmid40471835,
year = {2025},
author = {Robinson, LA and Pascual, V},
title = {Recent insights into the role of innate immunity in lupus.},
journal = {Human molecular genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/hmg/ddaf066},
pmid = {40471835},
issn = {1460-2083},
support = {CORT P50AR070594/AR/NIAMS NIH HHS/United States ; //Center for Lupus Research (VP)/ ; U19 AI082715/AI/NIAID NIH HHS/United States ; },
abstract = {Systemic Lupus Erythematosus (SLE) is a complex autoimmune disorder characterized by loss of self-tolerance to nucleic acids, resulting in multisystem inflammation and organ damage. The genetic underpinning of SLE spans from common risk variants with modest effect sizes to rare monogenic mutations with high penetrance. Recent advances in next-generation sequencing and transcriptomic profiling have illuminated the central role of innate immune pathways in disease pathogenesis. This review synthesizes emerging evidence regarding innate immunity in SLE, with emphasis on toll-like receptor (TLR) signaling and regulatory mechanisms, NLRP3 inflammasome activation, myeloid cell dysregulation, and microbiome-immune interactions. Understanding these pathways provides a foundation for developing targeted therapeutics that may offer precision medicine approaches for this heterogeneous disease.},
}

@article {pmid40471540,
year = {2025},
author = {Zhang, Y and Zhang, K and Song, D and Yan, T and Ma, S and Liu, R and Jin, Y and Gong, H and Yang, L and Wang, X and Liu, S and Wang, C and Zhao, M},
title = {Combination of Rare Sugars L-arabinose, D-mannose, D-xylose, D-allulose, and D-tagatose Alleviates Cognitive Impairment in Mice with Type 2 Diabetes Mellitus.},
journal = {Molecular neurobiology},
volume = {},
number = {},
pages = {},
pmid = {40471540},
issn = {1559-1182},
support = {82071515//National Natural Science Foundation of China/ ; },
abstract = {Herein, the study was conducted to elucidate the impact of a rare sugar complex (RSC) containing L-arabinose, D-mannose, D-xylose, D-allulose, and D-tagatose on cognitive impairment in a Type 2 diabetes mellitus (T2DM) mouse model. Specifically, a diabetes model was established by administering a high-fat diet (HFD) followed by streptozotocin injection. Behavioral performance in T2DM mice was assessed using multiple behavioral tests, including the Morris water maze, Y maze, novel object recognition test, and novel location recognition test. Neuronal damage in the hippocampal region was detected through hematoxylin and eosin staining. Superoxide dismutase (SOD) and malondialdehyde (MDA) constituted key biomarkers for assessing oxidative stress, with SOD indicating antioxidant capacity and MDA reflecting lipid peroxidation. Both were quantified via enzyme-linked immunosorbent assay. Additionally, the types and richness of microorganisms in the feces of each group of mice were analyzed through 16S sequencing of gut microbiota. Behavioral assays demonstrated that T2DM mice exhibited learning and memory impairments, which were notably mitigated by the administration of RSC. SOD activity decreased significantly, whereas MDA levels increased substantially. HE staining revealed that RSC effectively suppressed hippocampal cell apoptosis in T2DM mice. Furthermore, RSC treatment restored the diversity and abundance of gut microbiota in T2DM mice. Collectively, these findings suggest that RSC alleviates cognitive impairment in T2DM mice by reducing cerebral oxidative stress and modulating the intestinal microbiome composition.},
}

@article {pmid40471453,
year = {2025},
author = {Birkeland, E and Bamigbetan, WA and Molven, KD and Thorsby, PM and Gulseth, HL and Aas, AM and Dahl, C},
title = {Can supplements with prebiotic fibres positively influence bone health in type 2 diabetes? Insights from a randomised controlled crossover trial.},
journal = {Archives of osteoporosis},
volume = {20},
number = {1},
pages = {71},
pmid = {40471453},
issn = {1862-3514},
support = {2013-2-267//The DAM Foundation/ ; 36660//Diabetesforbundet/ ; 36660//Mills DA/ ; },
mesh = {Humans ; *Prebiotics/administration & dosage ; *Diabetes Mellitus, Type 2/blood/physiopathology ; Cross-Over Studies ; Male ; Female ; Middle Aged ; Aged ; Double-Blind Method ; *Dietary Supplements ; Calcium/blood ; Vitamin D/blood/analogs & derivatives ; Magnesium/blood ; Bone Remodeling/drug effects ; Biomarkers/blood ; Inulin/administration & dosage ; Gastrointestinal Microbiome ; Fructans ; Collagen Type I/blood ; Procollagen/blood ; Peptides/blood ; Peptide Fragments/blood ; },
abstract = {UNLABELLED: Inulin-type fructans did not significantly improve serum levels of calcium, magnesium, vitamin D, or bone turnover markers in people with type 2 diabetes (T2D). However, interactions between gut microbiota and bone health were suggested, indicating the need for further research in this population.

BACKGROUND: Evidence suggests that a healthy gut microbiome benefits bone health, especially in immunocompromised populations like the elderly and people with T2D.

OBJECTIVE: We investigated the effect of prebiotics (inulin-type fructans) on serum concentrations of calcium, magnesium, 25(OH) vitamin D, and the bone turnover markers N-terminal propeptide of type 1 collagen (P1NP), and C-terminal telopeptide of type 1 collagen (CTX-1) in people with T2D.

DESIGN: Participants (29) were treated for 6 weeks with 16 g inulin-type fructans and 16 g control supplement (maltodextrin) in randomised and double-blind crossover design, with a 4-week washout between treatments.

RESULTS: Compared to the control, inulin-type fructans did not significantly affect serum concentrations (mean ± SEM) of calcium (0.05 ± 0.02 mmol/L vs. 0.02 ± 0.03 mmol/L, p = 0.324), magnesium (0.02 ± 0.01 mmol/L vs. 0.00 ± 0.01 mmol/L, p = 0.352), 25(OH) vitamin D (-3.60 ± 1.94 nmol/L vs. -2.00 ± 1.97 nmol/L, P = 0.564), P1NP (0.81 ± 0.95 ug/L vs. -0.89 ± 0.97 ug/L, p = 0.210), or CTX-1 (-0.01 ± 0.01 ug/L vs. 0.00 ± 0.01 ug/L, p = 0.438). However, post hoc analyses of correlations between changes support that cross-talk between the human host and gut microbiota may influence bone health in this population.

CONCLUSION: This study does not support that inulin-type fructans may improve serum levels of calcium, magnesium, or 25(OH) vitamin D, nor that they affect bone turnover markers in people with T2D over 6 weeks. Interactions between microbiota and bone health in this population warrants further investigations. The trial is registered at clinicaltrials.gov (NCT02569684).},
}

Humans
*Prebiotics/administration & dosage
*Diabetes Mellitus, Type 2/blood/physiopathology
Cross-Over Studies
Male
Female
Middle Aged
Aged
Double-Blind Method
*Dietary Supplements
Calcium/blood
Vitamin D/blood/analogs & derivatives
Magnesium/blood
Bone Remodeling/drug effects
Biomarkers/blood
Inulin/administration & dosage
Gastrointestinal Microbiome
Fructans
Collagen Type I/blood
Procollagen/blood
Peptides/blood
Peptide Fragments/blood

@article {pmid40471139,
year = {2025},
author = {Gawish, R and Varada, R and Deckert, F and Hladik, A and Steinbichl, L and Cimatti, L and Milanovic, K and Jain, M and Torgasheva, N and Tanzer, A and De Paepe, K and Van de Wiele, T and Hausmann, B and Lang, M and Pechhacker, M and Ibrahim, N and De Vries, I and Brostjan, C and Sixt, M and Gasche, C and Boon, L and Berry, D and Jantsch, MF and Pereira, FC and Vesely, C},
title = {Filamin A editing in myeloid cells reduces intestinal inflammation and protects from colitis.},
journal = {The Journal of experimental medicine},
volume = {222},
number = {9},
pages = {},
doi = {10.1084/jem.20240109},
pmid = {40471139},
issn = {1540-9538},
support = {57-B28//Austrian Science Fund/ ; V 1025-B//Austrian Science Fund/ ; DOC32-B28//Austrian Science Fund/ ; F8007//Austrian Science Fund/ ; P32678//Austrian Science Fund/ ; //Medical University of Vienna/ ; },
mesh = {*Filamins/genetics/metabolism ; Animals ; *Myeloid Cells/metabolism/pathology ; Humans ; *Colitis/genetics/pathology/prevention & control ; *Inflammation/pathology/genetics ; Mice ; Mice, Inbred C57BL ; Neutrophils/metabolism ; *RNA Editing ; Macrophages/metabolism ; Male ; },
abstract = {Patho-mechanistic origins of ulcerative colitis are still poorly understood. The actin cross-linker filamin A (FLNA) impacts cellular responses through interaction with cytosolic proteins. Posttranscriptional A-to-I editing generates two forms of FLNA: genome-encoded FLNAQ and FLNAR. FLNA is edited in colon fibroblasts, smooth muscle cells, and endothelial cells. We found that the FLNA editing status determines colitis severity. Editing was highest in healthy colons and reduced during murine and human colitis. Mice that exclusively express FLNAR were highly resistant to DSS-induced colitis, whereas fully FLNAQ animals developed severe inflammation. While the genetic induction of FLNA editing influenced transcriptional states of structural cells and microbiome composition, we found that FLNAR exerts protection specifically via myeloid cells, which are physiologically unedited. Introducing fixed FLNAR did not hamper cell migration but reduced macrophage inflammation and rendered neutrophils less prone to NETosis. Thus, loss of FLNA editing correlates with colitis severity, and targeted editing of myeloid cells serves as a novel therapeutic approach in intestinal inflammation.},
}

*Filamins/genetics/metabolism
Animals
*Myeloid Cells/metabolism/pathology
Humans
*Colitis/genetics/pathology/prevention & control
*Inflammation/pathology/genetics
Mice
Mice, Inbred C57BL
Neutrophils/metabolism
*RNA Editing
Macrophages/metabolism
Male

@article {pmid40470946,
year = {2025},
author = {Wei, Y and Jia, W and Sun, Y and Zhang, T and Miao, H and Wu, Z and Dong, R and Ning, F and Kim, WJ},
title = {Investigating the immunomodulatory effects of honeybee venom peptide apamin in Drosophila platforms.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0013125},
doi = {10.1128/iai.00131-25},
pmid = {40470946},
issn = {1098-5522},
abstract = {Apamin, an 18-amino-acid honeybee venom peptide, although traditionally recognized for its neurotoxic effects, demonstrates potent antimicrobial properties in our research when genetically expressed in Drosophila. This antimicrobial efficacy is independent of its disulfide bonds and is enhanced when the peptide is membrane-tethered. Apamin selectively inhibits pathogenic bacteria, such as Pseudomonas aeruginosa, Enterococcus faecalis, and Escherichia coli, while promoting beneficial bacteria like Lactobacillus plantarum, thereby improving the gut microbiome. This gut-localized antimicrobial activity is associated with increased intestinal stem cell proliferation, midgut acidification, and enteroendocrine cell calcium signaling. Furthermore, apamin's antimicrobial function relies on specific peptidoglycan recognition proteins, particularly PGRP-LA and PGRP-SCs. Apamin expression alone is sufficient to restore the integrity of the gut barrier compromised by stressful conditions. Ultimately, apamin supplementation enhances honeybee gut health in the presence of ingested bacteria. The expression of other honeybee antimicrobial peptides also significantly reduces bacterial infection in flies. Overall, our study provides a comprehensive understanding of honeybee venom peptides and antimicrobial peptides functions, utilizing the Drosophila model system to unravel their mechanisms of action and therapeutic potential.},
}

@article {pmid40470930,
year = {2025},
author = {Ekregbesi, P and Seibert, B and Parish, MA and Flores-Garcia, Y and Creisher, PS and Hoffmann, JP and Liu, JA and Brayton, C and Zavala, F and Klein, SL},
title = {Multi-system dysregulation in placental malaria contributes to adverse perinatal outcomes in mice.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0002125},
doi = {10.1128/iai.00021-25},
pmid = {40470930},
issn = {1098-5522},
abstract = {Sequestration of Plasmodium parasites in the placental vasculature contributes to increased morbidity and mortality in pregnant compared to non-pregnant patients in malaria-endemic regions. In this study, outbred pregnant CD1 mice with semi-allogeneic fetuses were infected with transgenic Plasmodium berghei or mock inoculated by mosquito bite at either embryonic day (E)6 (first trimester-equivalent) or 10 (second trimester-equivalent) and were compared to non-pregnant females. P. berghei-infected mosquitoes had greater biting avidity for E10 dams than uninfected mosquitoes, which was not apparent for E6 dams nor non-pregnant females. Infected E10 dams had greater numbers of parasites than E6 dams in the uterus and spleen, but not in the blood or liver. While parasites were found in placentas, no parasites were present in fetuses. Maternal infection at E6 caused greater maternal morbidity, with greater rates of fetal reabsorption and stillbirths than at E10. Infection at E10 caused adverse offspring outcomes, including growth restriction. To identify possible mechanisms of adverse offspring outcomes, E10 dams were euthanized during peak parasitemia (8 days postinfection [dpi]), and outcomes were compared to mock-infected dams. P. berghei caused significant systemic maternal immune activation with elevated circulating lymphocytes, eosinophils, and neutrophils and splenic cytokine concentrations. P. berghei infection at E10 increased corticosterone and decreased progesterone concentrations, which could contribute to adverse perinatal outcomes through immunomodulation. There were limited changes in the maternal fecal microbiome after P. berghei infection. Mosquito bite infection of outbred dams with P. berghei causes placental malaria and provides a novel, tractable model to investigate therapeutic treatments.},
}

@article {pmid40470429,
year = {2025},
author = {Ahmad, OM and Rukh, S and Dos Santos Pereira, S and Saran, A and Chandran, VI and Muneeb, A and Banderas Echeverry, WM and Shoyoye, M and Akintunde, DM and Hassan, D and Morani, Z and Masood, L},
title = {A Comprehensive Review of the Role of Virulence Factors in Enteropathogenic Escherichia coli-Induced Intestinal Injury.},
journal = {Cureus},
volume = {17},
number = {5},
pages = {e83475},
pmid = {40470429},
issn = {2168-8184},
abstract = {Escherichia coli (E. coli) is a rod-shaped gram-negative bacterium that includes the diarrheagenic strains, an identical group of intestinal pathogens.E. coli diarrhea is transmitted through the feco-oral route, through contaminated food and water. Enteropathogenic E. coli (EPEC) is one of the leading causes of diarrhea in the pediatric age group in developing and developed countries. Depending on the absence or presence of E. coli adherence factor plasmids, they are classified as typical or atypical isolates. The distinguishing feature of EPEC's pathology is the attaching and effacing lesions, which facilitate localized damage by tightly adhering to intestinal epithelial cells, disarranging their surfaces, and effacing microvilli. Typical EPEC possess the locus of enterocyte effacement (LEE), a pathogenicity island, encoding adherence factors, including the Type III Secretion System (T3SS), a needle-like structure injecting effector proteins into host cells. EPEC also have other effector genes like cif or nleC encoded by non-LEE pathogenicity islands, which enable destruction of tight junctions in the host cell. Another key virulence factor is bundle-forming pili (BFP), which aids in the first attachment to enterocytes. Methods like quantitative PCR exist to diagnose EPEC accurately. As of today, no licensed vaccine exists to prevent EPEC infections. Virulence factors for attachment, such as bfpA and intimin, and immunogenic carriers can be potential candidates for vaccine development. Moreover, studies are required to better understand the interaction of EPECwith the intestinal microbiome and immune evasion strategies. This article is aimed at providing a comprehensive review of the epidemiology, transmission, virulence factors, challenges in studying EPEC virulence factors, pathogenesis, host-pathogen interaction, mechanism of intestinal injury, diagnosis, treatment, antibiotic resistance, and vaccination strategy for EPEC, and future research implications. We conducted a comprehensive literature search using credible sources such as PubMed, Google Scholar, and Scopus. We refined our keywords, applied database filters, and assessed citations in the included studies. No meta-analysis, statistical aggregation, or formal evaluation of risk bias was carried out as this review consolidates the literature narratively. High-quality English articles published in reputable peer-reviewed journals from 2010 to 2025 were analyzed, and their findings have been summarized in this comprehensive review.},
}

@article {pmid40470262,
year = {2025},
author = {Fu, F and Yu, Y and Wang, B and Zhao, X and Wang, N and Yin, J and Wu, K and Zhou, Q},
title = {Prostate and urinary microbiomes in prostate cancer development: focus on Cutibacterium acnes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1562729},
pmid = {40470262},
issn = {2235-2988},
mesh = {Humans ; Male ; *Prostatic Neoplasms/microbiology/pathology ; *Microbiota ; *Prostate/microbiology/pathology ; *Propionibacteriaceae/isolation & purification ; *Urine/microbiology ; },
abstract = {Prostate cancer (PCa) is one of the most prevalent malignancies among men, with its incidence steadily increasing worldwide. Recent advances in microbiome research have opened new avenues for understanding and treating PCa; however, studies focusing specifically on the prostate tissue microbiome remain limited. Evidence suggests that the microbial communities within PCa tissues exhibit significant diversity and regional variability, with certain bacteria potentially contributing to PCa initiation and progression through chronic inflammation. The prostate microbiome comprises not only bacteria but also viruses, fungi, and parasites, and its diversity is influenced by a complex interplay of genetic, environmental, and lifestyle factors. Methodological limitations and sample contamination further complicate the interpretation of microbiome data. The urinary microbiome is similarly diverse and shaped by multiple overlapping influences. Although urine, prostatic fluid, and prostate tissue are anatomically and functionally connected, whether urine and prostatic fluid can accurately reflect the prostate tissue microbiome remains to be conclusively determined. Among the microorganisms detected, Cutibacterium acnes is frequently identified in prostate tissue, urine, and prostatic fluid from PCa patients. This bacterium is known to elicit inflammatory responses through various pathways, potentially impacting tumorigenesis and cancer progression. Nevertheless, findings across studies remain inconsistent. Further research is necessary to elucidate the underlying mechanisms by which the microbiome influences PCa. Such efforts may offer novel insights and strategies for the diagnosis, treatment, and prevention of this disease.},
}

Humans
Male
*Prostatic Neoplasms/microbiology/pathology
*Microbiota
*Prostate/microbiology/pathology
*Propionibacteriaceae/isolation & purification
*Urine/microbiology

@article {pmid40470258,
year = {2025},
author = {Demirci, M and Gadhave, K},
title = {Editorial: Human microbiome and COVID-19.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1613825},
pmid = {40470258},
issn = {2235-2988},
}

@article {pmid40470050,
year = {2025},
author = {Issilbayeva, A and Sergazy, S and Zhashkeyev, A and Gulyayev, A and Kozhakhmetov, S and Shulgau, Z and Nurgaziyev, M and Nurgaziyeva, A and Zhetkenev, S and Mukhanbetzhanov, N and Jarmukhanov, Z and Mukhanbetzhanova, Z and Vinogradova, E and Zhumadilov, Z and Kushugulova, A and Aljofan, M},
title = {Polyphenol-mediated microbiome modulation in STEMI patients: a pilot study.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1522373},
pmid = {40470050},
issn = {2296-858X},
abstract = {INTRODUCTION: This study investigates the effects of polyphenol supplementation on gut microbiome composition and cardiovascular health in patients with ST-segment elevation myocardial infarction (STEMI).

METHODS: Double-blind randomized control trial where participants received either polyphenol supplementation or placebo for 3 months, after which composition of the gut microbiome; clinical and laboratory parameters, including TMAO levels and oxidative stress levels, were assessed.

RESULTS: The stable TMAO levels (from 0.5 [0.2-0.9] to 0.4 [0.3-0.9] μmol, p > 0.05) were observed in the polyphenol group, compared to the increase observed in the placebo group (from 0.5 [0.3-0.6] to 0.7 [0.5-1.4] μmol, p < 0.001). Polyphenol supplementation significantly decreased the Firmicutes/Bacteroidetes ratio (p = 0.04) and increased beneficial bacteria such as Roseburia (p = 0.01), Agathobaculum sp. (p = 0.004), Alistipes finegoldii (p = 0.04) and Sellimonas (p = 0.002). Predicted metabolic pathways analysis supports potential mechanisms linking polyphenol intake to microbiome modulation and TMAO regulation.

CONCLUSION: Our findings demonstrate that polyphenol supplementation maintains stable TMAO levels by restructuring gut microbiome composition in STEMI patients, evidenced by a more focused microbiome with a significant increase in beneficial butyrate-producing bacteria (Roseburia, Agathobaculum sp., Alistipes finegoldii, and Sellimonas) and a decreased Firmicutes/Bacteroidetes ratio, suggesting microbiome-mediated cardioprotective effects. While promising,l our preliminary findings require further studies with larger cohorts and more advanced sequencing methods to establish their significance for cardiovascular health.

CLINICAL TRIAL REGISTRATION: ClinicalTrial.gov, identfier: NCT06573892.},
}

@article {pmid40469771,
year = {2025},
author = {Muthumula, CMR and Yanamadala, Y and Gokulan, K and Karn, K and Cunny, H and Sutherland, V and Santos, JH and Khare, S},
title = {Effect of in utero and lactational exposure to antiretroviral therapy on the gut microbial composition and metabolic function in aged rat offspring.},
journal = {Experimental biology and medicine (Maywood, N.J.)},
volume = {250},
number = {},
pages = {10468},
pmid = {40469771},
issn = {1535-3699},
mesh = {Animals ; Female ; *Gastrointestinal Microbiome/drug effects ; Pregnancy ; Male ; *Prenatal Exposure Delayed Effects/microbiology ; *Lactation/drug effects ; Rats ; Fatty Acids, Volatile/metabolism ; *Anti-Retroviral Agents/adverse effects/pharmacology ; Feces/microbiology ; },
abstract = {Despite the highly effective impact of antiretroviral therapy (ART) in reducing mother-to-child transmission of human immunodeficiency virus (HIV), there are concerns of long-term impacts of ART on the health of the offspring. The implications of perinatal exposure to antiviral drugs on the gut bacterial population and metabolic function in the offspring is unclear but may influence health outcomes given the various reported effects of the microbiome in human health. This study aims to gain insight into the potential effect of in utero and lactational exposure to ART on gut microbiota populations and short-chain fatty acids (SCFAs) production in aged rat offspring. Pregnant rats were administered a combination of antiretroviral drugs (abacavir/dolutegravir/lamivudine) at two different dose levels during gestation and throughout lactation, and the fecal bacterial abundance and SCFA levels of the offspring were analyzed when they reached 12 months of age. Our results showed dose-dependent and sex-based differences in fecal microbial abundance at various taxonomic levels. Specifically, we found a decline in Firmicutes in males, and an increase in Actinobacteria among males and females. Furthermore, a sex-specific distribution reorganization of Lactobacillus, Bifidobacterium, and Akkermansia was identified. No significant difference in the concentration of prominent SCFAs and IgA levels were identified. These findings provide preliminary information indicating the need to evaluate perinatal effects of ART more comprehensively on the gut bacterial and metabolic function in future studies, and their potential role in offspring health outcomes.},
}

Animals
Female
*Gastrointestinal Microbiome/drug effects
Pregnancy
Male
*Prenatal Exposure Delayed Effects/microbiology
*Lactation/drug effects
Rats
Fatty Acids, Volatile/metabolism
*Anti-Retroviral Agents/adverse effects/pharmacology
Feces/microbiology

@article {pmid40469741,
year = {2025},
author = {Qi, JQ and Yuan, HY and Sun, SC and Zama, EF and Tao, BX and Liu, J and Zhang, BH},
title = {Biochar amendment alters rare microbial taxa and enhances wheat growth in alkaline farmland: insights into soil microbiome dynamics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1563712},
pmid = {40469741},
issn = {1664-302X},
abstract = {INTRODUCTION: Biochar is recognized as a promising soil amendment for maintaining soil fertility and improving soil conditions. Alkaline farmland is widely distributed globally. Soil microbial taxa, including rare, intermediate, and abundant bacteria, fungi, protists, and phoD-harboring microbes, play essential roles in carbon, nitrogen, and phosphorus cycling. However, the impacts of biochar on the community composition of these taxa in alkaline farmland are not well understood. Gaining insights into how the soil microbiome responds to biochar application and its association with crop biomass is crucial for sustainable agriculture. In particular, the responses of rare microbial communities, such as rare protists and phoD-harboring microbial taxa, to biochar and their relationship with crop biomass remain largely unexplored.

METHODS: In this study, topsoil (0-10 cm) samples were collected from a three-year field experiment in a wheat (Triticum aestivum cv. Jimai 22)-maize (Zea mays cv. Jiyuan 169) rotational cropping system. The experiment included treatments with and without biochar application (CK). Gene abundance of bacterial 16S rRNA and phoD, a gene encoding an alkaline phosphatase involved in phosphorus cycling, was quantified using quantitative polymerase chain reaction (qPCR). The compositions and diversities of bacterial, fungal, protistan, and phoD-harboring microbial communities were analyzed by Illumina MiSeq sequencing.

RESULTS: Biochar application significantly reduced soil total phosphorus (TP) and ammonium nitrogen (NH4 [+]-N) contents. It increased soil N:P ratios by 19.63%, 2.80%, 23.36%, and 27.10% in B0.5, B1.0, B1.5, and B2.0 treatments, respectively. Soil dissolved organic carbon (DOC) positively correlated with bacterial 16S rRNA gene abundance, while total nitrogen (TN) linked to the ratio of phoD to bacterial 16S rRNA gene abundance and rare protistan taxa. In terms of crop yield, the B1.5 treatment (3.42 t ha[-1]) increased wheat yield by 35% compared to the CK treatment. Mantel test and random forest analyses indicated that rare phoD-harboring, protistan, and fungal communities significantly contributed to wheat growth.

DISCUSSION: This study offers valuable insights into the effects of biochar on soil microbiomes, especially the responses of abundant, intermediate, and rare taxa. The changes in soil nutrient contents and the correlations between soil properties and microbial communities suggest that biochar can modify the soil environment and microbial structure. The significant contribution of rare microbial communities to wheat growth emphasizes their importance in maintaining agricultural ecosystem health and ensuring sustainable ecosystem services. These findings can guide the rational application of biochar in alkaline farmland to promote sustainable agriculture.},
}

@article {pmid40469735,
year = {2025},
author = {Heisel, T and Gonia, S and Dillon, A and Hoops, SL and Al-Ghalith, GA and Gohl, D and Mukhopadhyay, S and Puopolo, K and Kennedy, P and Sadowsky, MJ and Knights, D and Johnson, AJ and Gerber, JS and Gale, CA},
title = {Gut mycobiome maturation and its determinants during early childhood: a comparison of ITS2 amplicon and shotgun metagenomic sequencing approaches.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1539750},
pmid = {40469735},
issn = {1664-302X},
abstract = {INTRODUCTION: Microbial colonization of the gut in early life is important for the development of metabolism, immunity, and the brain. Fungi and bacteria both colonize the human infant gut. The relatively smaller contribution of fungi to the gut microbiome, as compared to bacteria, has posed technical challenges for the precise characterization of fungal communities (mycobiomes) and limited the ability to longitudinally examine mycobiome development.

BACKGROUND: The aims of this study were to (1) characterize mycobiome maturation and identify clinical determinants of mycobiome compositional variation during the first 2 years of life and (2) compare two sequencing approaches (ITS2 amplicon and whole genome metagenomics) for characterizing mycobiome maturational features. Longitudinal fecal samples and associated clinical metadata were obtained from subjects enrolled as part of the MAGIC (Microbiome, Antibiotics and Growth Infant Cohort) study.

RESULTS: Overall, fungal richness increased and mycobiome composition changed in a similar ordered pattern during the first 2 years of life utilizing either amplicon or metagenomic sequencing approaches. Less resolution of taxa to species and genera levels was observed for the metagenomic dataset. The predominant taxa identified by both sequencing approaches, Candida albicans, Saccharomyces/S. cerevisiae, and Malassezia restricta, each exhibited similar dynamics in abundances and prevalences over the first 2 years of life, irrespective of sequencing approach. Antibiotic exposure and breastfeeding status contributed to time-specific mycobiome compositional variation, results that were consistent for both types of sequence datasets. Candida albicans exhibited altered abundance dynamics in association with perinatal antibiotic exposure and birth mode for both sequencing approaches. Post hoc analyses suggested that the birth mode association could be driven by exposure to perinatal antibiotics in children delivered by cesarean section rather than by birth mode itself.

DISCUSSION: In summary, amplicon and metagenomic sequencing approaches provide generally similar results with respect to mycobiome maturational dynamics and the contribution of clinical variables to variation. Differences in taxa identification by the two approaches likely due to sequence database differences, primer/genome sequence variation, and/or sequencing depth should be taken into consideration.},
}

@article {pmid40469729,
year = {2025},
author = {Sakha, M and Gweyi-Onyango, JP and Masso, C and Baijukya, FP},
title = {Diversity, characteristics, and abundance of native arbuscular mycorrhizal fungi in the semi-arid lands of Eastern Kenya.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1582476},
pmid = {40469729},
issn = {1664-302X},
abstract = {Elucidating the diversity of native arbuscular mycorrhizal (AM) fungi is essential for the sustainable management of semi-arid land ecosystems. This is because they significantly improve plant nutrient uptake and decrease the stress caused by biotic and abiotic factors. In this study, we examined the AM fungal communities and the key drivers influencing their diversity and occurrence in the smallholder farming systems of Eastern Kenya. Soils samples were collected from 34 diverse agricultural fields and AM fungal spores were extracted using wet-sieving and decantation techniques. The spores were quantified, and AM fungal communities were identified based on their morphological characteristics. Statistical data analyses, including relative abundance, the Shannon-Wiener index, analysis of variance (ANOVA), and principal component analysis (PCA), were performed using R software 4.4.0. The results revealed that two AM fungal families dominated the agricultural fields, namely Gigasporaceae (61.0%) and Acaulosporaceae (39.0%). These fungal families comprised a total of five genera, with the following relative abundances: Acaulospora (39.0%), Gigaspora (35.05%), Scutellospora (23.92%), Dentiscutata (1.32%), and Rococetra (0.72%). The AM fungal morpho-species were ranked from 1 to 26 across the five genera. Acaulospora denticulata ranked the highest, with a proportion of 25.19%. The Shannon-Wiener diversity index revealed a higher diversity of AM fungi in agricultural fields with greater spore richness. The PCA showed that the composition of AM fungal communities was strongly related to soil physiochemical characteristics. Dryland farming systems also played a role in AM fungal composition. Overall, the distribution of AM fungal communities across the agricultural fields was lower, implying the need to adopt sustainable dryland farming systems to enhance native AM fungal communities and support the development of context-specific biofertilizers.},
}

@article {pmid40469726,
year = {2025},
author = {Wang, N and Li, X and Weng, H and Zhang, Y and Li, Q and Luo, X and Chen, Y and Dong, Y},
title = {A bibliometric study of global trends in diabetic nephropathy and intestinal flora research.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1577703},
pmid = {40469726},
issn = {1664-302X},
abstract = {BACKGROUND: Diabetic nephropathy is chronic kidney damage caused by diabetes and is one of the most common microvascular complications of diabetes. In diabetic patients, prolonged hyperglycemia leads to progressive damage to kidney structure and function. With the increasing incidence of diabetes, the number of patients with Diabetic Nephropathy is also increasing year by year. At present, there is no drug to cure Diabetic Nephropathy. More and more evidence shows that the development of Diabetic Nephropathy is inseparable from the intestinal axis, and the disorder of intestinal flora is related to the progress of diabetes. Maybe we can explore the pathogenesis of Diabetic Nephropathy from the intestinal flora and find new methods to treat Diabetic Nephropathy.

METHODS: This article uses CiteSpace VOSviewer and Bibliometrix statistical software explore research hotspots and trends of intestinal flora and Diabetic Nephropathy. The Web of Science Core Collection (WoSCC) was searched for literature from database establishment to December 4, 2024, and ultimately 238 articles were included for quantitative analysis.

RESULTS: The number of publications has been increasing year by year, reaching its peak in 2024. The high-yield institution is Beijing University of Chinese Medicine, and the most productive country is China. Zhang Yi ranks first in the number of publications by the author. After removing the theme word, inflammation appears the most frequently, followed by oxidative stress. The outbreak hotspots are mainly concentrated in uremic toxin, short chain fatty acid, soy milk, aryl hydrocarbon receptor.

CONCLUSION: The exploration of the mechanism of action and therapeutic or adjuvant therapeutic targets of the gut microbiome and its metabolites in DN patients may become a research hotspot in the future direction of DN and gut microbiome. Inflammation, oxidative stress, and the production of urinary toxins in DN patients are the directions for researchers to explore the mechanisms related to DN patients and gut microbiome. Aryl hydrocarbon receptor (AhR), Short-chain fatty acids (SCFAs), Traditional Chinese medicine and soy milk provide researchers with treatment ideas for diabetic nephropathy. Exploring the specific mechanisms and therapeutic effects of DN and gut microbiome requires cohort studies and clinical trials for validation.},
}

@article {pmid40469724,
year = {2025},
author = {Zhu, G and Song, H and Duan, M and Wang, J and Luo, J and Yang, S and Wu, F and Jiang, J and Chen, J and Tang, W},
title = {Dietary preferences affect the gut microbiota of three snake species (Squamata: Colubridae).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1559646},
pmid = {40469724},
issn = {1664-302X},
abstract = {INTRODUCTION: The gut microbiota is an emerging frontier in animal research, and researchers are increasingly transparent about its importance to animal health. Reptiles, particularly snakes, have not received the same attention given to other vertebrates, and the composition of their wild gut microbiome remains understudied.

METHODS: In this study, the HiSeq high-throughput sequencing platform was used to sequence and analyze the 16S rRNA V4 region of the gut microbiota of three species (Gonyosoma coeruleum, Rhabdophis pentasupralabralis, Rhabdophis tigrinus).

RESULTS: This study investigated alpha diversity analysis and showed that the gut microbiota richness of RP was significantly higher than that of the other two snakes. The dominant genus of Gonyosoma coeruleum (GC) and Rhabdophis tigrinus (RT) is Cetobacterium, while Enterobacteriaceae; g_uncultured is the dominant genus of Rhabdophis pentasupralabralis (RP). Tree clustering based on Bray-Curtis distances and Jaccard similarity coefficients indicated that the gut microbiota composition of RP and RT was more similar. The unique diet of RP promotes a diverse, competitive gut microbiota, while GC and RT displayed more stable networks linked to shared dietary habits. The functional heat map showed that the predicted functions of the gut microbes of the three snake species were different. These findings suggest that dietary preferences exert a stronger influence on gut microbial composition and function than host genetic background, and distantly related species with similar diets exhibit convergent gut microbiota characteristics.},
}

@article {pmid40469670,
year = {2025},
author = {Lopez Leyva, L and Gonzalez, E and Maurice, CF and Koski, KG},
title = {Milk mineral composition is strongly associated with the human milk microbiome.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1550292},
pmid = {40469670},
issn = {2296-861X},
abstract = {INTRODUCTION: Associations between maternal mineral intake, human milk mineral concentrations, and their interactions with the milk microbiota remain understudied, especially in low- and middle-income countries. To understand potential interactions and gain insight into milk composition dynamics, we explored associations of milk mineral concentrations with maternal mineral intakes and the human milk microbiome in an indigenous Guatemalan community.

METHODS: In this cross-sectional study, milk samples were collected from 77 Mam-Mayan mothers and classified into early and established lactation. Concentrations of 9 milk minerals were analyzed, and maternal dietary intake was obtained from two 24-h recalls. Microbiome diversity was assessed by 16S rRNA gene sequencing (V5-V6 region). DESeq2 was used for differential abundance analysis. PCA and Spearman's rank correlation explored relationships among milk minerals, maternal mineral intake, and differentially abundant microbial taxa; results with FDR-adjusted p-values < 0.1 were retained.

RESULTS: Our multifactorial analysis revealed strong associations between milk minerals and the milk microbiome and weak associations with maternal intake. Several maternal intakes (Ca, Se, K, Fe, Mn) and milk mineral concentrations (Ca, Se, K, Mg, Na) were below reference values. In early lactation, milk Fe, Mn, Se, and Cu correlated with differentially abundant taxa, while in established lactation, Fe, Mn, Se, Ca, and Na were correlated. Fe and Mn accounted for 64% of bacterial associations in early lactation and 75% in established lactation. These minerals were correlated with Pseudomonadota (early), Actinomycetota (established), and Bacillota (both), but all species were unique to each stage.

CONCLUSION: Our findings reveal a complex interplay between milk minerals and the microbiome. Iron, manganese, and selenium were consistently associated with milk bacteria across lactation stages. These correlations may reflect microbial responses to mineral availability. Further longitudinal studies with larger samples are needed to clarify how this interaction influences mineral bioavailability and infant growth.},
}

@article {pmid40469523,
year = {2025},
author = {Wang, YC and Wang, S and Lv, YH and Wang, C},
title = {QSCNAS: A platform for quorum sensing and quenching bacteria analysis in global wastewater treatment plants.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70026},
pmid = {40469523},
issn = {2770-596X},
abstract = {This study identifies the potential quorum sensing (QS) bacteria in wastewater treatment plants (WWTPs) and constructs a QS communication network through the establishment of a local QS bacterial database with six languages and the analysis of over 1000 activated sludge microbiome samples collected from 269 WWTPs. The results not only advance the understanding of bacterial communication in WWTPs but also provide a valuable tool for developing regulatory strategies to optimize the functionality of these vital ecosystems.},
}

@article {pmid40469522,
year = {2025},
author = {Wen, T and Liu, YX and Liu, L and Niu, G and Ding, Z and Teng, X and Ma, J and Liu, Y and Yang, S and Xie, P and Zhang, T and Wang, L and Lu, Z and Shen, Q and Yuan, J},
title = {ggClusterNet 2: An R package for microbial co-occurrence networks and associated indicator correlation patterns.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70041},
pmid = {40469522},
issn = {2770-596X},
abstract = {Since its initial release in 2022, ggClusterNet has become a vital tool for microbiome research, enabling microbial co-occurrence network analysis and visualization in over 300 studies. To address emerging challenges, including multi-factor experimental designs, multi-treatment conditions, and multi-omics data, we present a comprehensive upgrade with four key components: (1) A microbial co-occurrence network pipeline integrating network computation (Pearson/Spearman/SparCC correlations), visualization, topological characterization of network and node properties, multi-network comparison with statistical testing, network stability (robustness) analysis, and module identification and analysis; (2) Network mining functions for multi-factor, multi-treatment, and spatiotemporal-scale analysis, including Facet.Network() and module.compare.m.ts(); (3) Transkingdom network construction using microbiota, multi-omics, and other relevant data, with diverse visualization layouts such as MatCorPlot2() and cor_link3(); and (4) Transkingdom and multi-omics network analysis, including corBionetwork.st() and visualization algorithms tailored for complex network exploration, including model_maptree2(), model_Gephi.3(), and cir.squ(). The updates in ggClusterNet 2 enable researchers to explore complex network interactions, offering a robust, efficient, user-friendly, reproducible, and visually versatile tool for microbial co-occurrence networks and indicator correlation patterns. The ggClusterNet 2R package is open-source and available on GitHub (https://github.com/taowenmicro/ggClusterNet).},
}

@article {pmid40469520,
year = {2025},
author = {Yu, L and Chen, Z and Yin, S and Guo, Q and Chen, Y and Li, J and Wang, Y and Liu, X and Xu, Z and Zhang, Y and Zhang, Y and Zheng, Z and Chen, K and Ding, Y and Fan, H and Liu, Z and Ding, Y},
title = {Gut-derived Lactobacillus from exceptional responders mitigates chemoradiotherapy-induced intestinal injury through methionine-driven epigenetic modulation.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70043},
pmid = {40469520},
issn = {2770-596X},
abstract = {Acute chemoradiotherapy-induced intestinal injury (ACRIII) is a common and debilitating complication in patients with colorectal cancer, significantly impairing both quality of life and treatment outcomes. This study aimed to investigate the role of the gut microbiome in mitigating ACRIII. Through bioinformatics analysis of clinical fecal samples and fecal microbiota transplantation (FMT) experiments in mice, we identified a strong association between a high abundance of Lactobacillus species and the absence of ACRIII. From the fecal samples of rectal cancer patients who achieved complete remission without experiencing ACRIII during chemoradiotherapy, 10 novel Lactobacillus strains were isolated and characterized. Among these, Lacticaseibacillus rhamnosus DY801 exhibited a robust capacity to synthesize methionine through metB. This microbial methionine production modulated methionine metabolism in host gut lymphoid tissue inducer (Lti) cells, without diminishing the therapeutic efficacy of chemoradiotherapy. Supplementation with methionine increased intracellular levels of S-adenosylmethionine and enhanced histone H3 lysine 4 trimethylation (H3K4me3) in Lti cells. These epigenetic modifications led to the suppression of pro-inflammatory cytokines interleukin-17A (IL-17A) and interleukin-22 (IL-22), ultimately reducing ACRIII severity. Our findings suggest that specific Lactobacillus strains derived from patients with exceptional treatment responses may offer a novel therapeutic avenue for preventing or alleviating ACRIII. This microbiome-based approach holds significant potential for improving patient outcomes and enhancing the tolerability of chemoradiotherapy in colorectal cancer.},
}

@article {pmid40469508,
year = {2025},
author = {Zhao, S and Zhong, H and He, Y and Li, X and Zhu, L and Xiong, Z and Zhang, X and Zheng, N and Morgavi, DP and Wang, J},
title = {Leveraging core enzyme structures for microbiota targeted functional regulation: Urease as an example.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70032},
pmid = {40469508},
issn = {2770-596X},
abstract = {Microbial communities play critical roles in various ecosystems. Despite extensive research on the taxonomic and functional diversity of microbial communities, effective approaches to regulate targeted microbial functions remain limited. Here, we present an innovative methodology that integrates core enzyme identification, protein structural characterization, regulator virtual screening, and functional validation to achieve precise microbiome functional regulation. As a proof of concept, we focused on the regulation of urea decomposition by the rumen microbiota in ruminants. Through metagenomic analysis, we identified the core urease gene and its corresponding microbial genome (MAG257) affiliated with the unclassified Succinivibrionaceae, and reconstructed its complete gene cluster. Structural analysis of the urease catalytic subunit (UreC) via cryo-electron microscopy (cryo-EM) revealed detailed features of its active site, guiding molecular docking studies that identified epiberberine, a natural compound with potent urease inhibitory activity. Validation in a rumen simulation system demonstrated that epiberberine significantly reduced urea decomposition and enhanced nitrogen utilization. This study establishes a robust framework that combines structural biology and computational screening to achieve targeted microbiome functional regulation, offering a promising tool for microbiome engineering and broader applications in animal productivity, human health, environmental improvement, and biotechnology.},
}

@article {pmid40469507,
year = {2025},
author = {Shen, Y and Qu, W and Song, M and Zhang, T and Liu, C and Shi, X and Xu, X and Jiang, J and Ding, L and Mo, F and Mao, Z and Huang, M and Xu, Z and Chen, J and Shen, E and Ruan, J and Liu, J and Timko, MP and Chen, Y and Fan, L and Zheng, S and Wang, Y},
title = {Single-microbe RNA sequencing uncovers unexplored specialized metabolic functions of keystone species in the human gut.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70035},
pmid = {40469507},
issn = {2770-596X},
abstract = {The human body is inhabited by trillions of microorganisms that play a crucial role in health and diseases. Our understanding of the species and functional composition of the human gut microbiome is rapidly expanding, but it is still mainly based on taxonomic profiles or gene abundance measurements. As such, little is known about the species-function heterogeneity and dynamic activities in human microecosystem niches. By applying a novel gut-specific single-microbe ribonucleic acid (RNA) sequencing and analytical framework on three healthy donors with distinct enterotypes, we created a comprehensive transcriptional landscape of the human gut microbiome and dissected functional specialization in 38,922 single microbes across 198 species. We investigated the functional redundancy and complementarity involved in short-chain fatty acids related central carbon metabolism and studied the heterogeneity and covariation of single-microbe metabolic capacity. Comparing the human gut microbiome at different times throughout the day, we were able to map diurnal dynamic activities of the gut microbiome and discovered its association with sub-population functional heterogeneous. Remarkably, using single-microbe RNA sequencing, we systematically dissected the metabolic function heterogeneity of Megamonas funiformis, a keystone species in Asian populations. Together with in vitro and in vivo experimental validations, we proved M. funiformis can effectively improve mineral absorption through exogenous phytic acid degradation, which could potentially serve as a probiotic that reduces malnutrition caused by deficiency of mineral elements. Our results indicated that species-function heterogeneity widely exists and plays important roles in the human gut microbiome, and through single-microbe RNA sequencing, we have been able to capture the transcriptional activity variances and identify keystone species with specialized metabolic functions of possible biological and clinical importance.},
}

@article {pmid40469504,
year = {2025},
author = {Van Den Bossche, T and Armengaud, J and Benndorf, D and Blakeley-Ruiz, JA and Brauer, M and Cheng, K and Creskey, M and Figeys, D and Grenga, L and Griffin, TJ and Henry, C and Hettich, RL and Holstein, T and Jagtap, PD and Jehmlich, N and Kim, J and Kleiner, M and Kunath, BJ and Malliet, X and Martens, L and Mehta, S and Mesuere, B and Ning, Z and Tanca, A and Uzzau, S and Verschaffelt, P and Wang, J and Wilmes, P and Zhang, X and Zhang, X and Li, L and , },
title = {The microbiologist's guide to metaproteomics.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70031},
pmid = {40469504},
issn = {2770-596X},
abstract = {Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiomes, proteins provide unique insights into the active processes and ecological roles of microbial communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding of microbial ecology, interactions, and functional dynamics. This review, developed by the Metaproteomics Initiative (www.metaproteomics.org), serves as a practical guide for both microbiome and proteomics researchers, presenting key principles, state-of-the-art methodologies, and analytical workflows essential to metaproteomics. Topics covered include experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, and statistical approaches.},
}

@article {pmid40469040,
year = {2025},
author = {Vogel, SC and Murgueitio, N and Huth, N and Sem, K and Knickmeyer, RC and Short, SJ and Mills-Koonce, R and Propper, C and Wagner, NJ},
title = {Longitudinal associations between the infant gut microbiome and negative affect in toddlerhood.},
journal = {Development and psychopathology},
volume = {},
number = {},
pages = {1-13},
doi = {10.1017/S0954579425100229},
pmid = {40469040},
issn = {1469-2198},
abstract = {The role of the gut microbiome in infant development has gained increasing interest in recent years. Most research on this topic has focused on the first three to four years of life because this is a critical period for developing gut-brain connections. Prior studies have identified associations between the composition and diversity of the gut microbiome in infancy and markers of temperament, including negative affect. However, the specific microbes affected, and the directionality of these associations have differed between studies, likely due to differences in the developmental period of focus and assessment approaches. In the current preregistered study, we examined connections between the gut microbiome, assessed at two time points in infancy (2 weeks and 18 months), and negative affect measured at 30 months of age in a longitudinal study of infants and their caregivers. We found that infants with higher gut microbiome diversity at 2 weeks showed more observed negative affect during a study visit at 30 months. We also found evidence for associations between specific genera of bacteria in infancy and negative affect. These results suggest associations between specific features of the gut microbiome and child behavior may differ based on timing of gut microbiome measurement.},
}

@article {pmid40468884,
year = {2025},
author = {Lee, Y and Ko, YM and Kwak, YS},
title = {Genetic and Nutritional Dynamics of SynCom in Suppressing Apple Fire Blight.},
journal = {The plant pathology journal},
volume = {41},
number = {3},
pages = {380-391},
doi = {10.5423/PPJ.OA.03.2025.0040},
pmid = {40468884},
issn = {1598-2254},
support = {RS-2020-RD009282//Rural Development Administration/ ; RS-2025-00516084//National Research Foundation of Korea/ ; },
abstract = {Fire blight disease, caused by Erwinia amylovora, occurs in apples and other Rosaceae plants and is known to cause significant economic damage. The pathogen usually infects flowers during the reproductive growth period of plants, colonizes, and penetrates by producing exopolysaccharides in the stigma. A synthetic microbial community (SynCom) is an artificial community of microorganisms designed to enhance host viability. To construct SynCom, we attempted to identify and utilize the microbial characteristics of apple trees that are not infected with the pathogen compared to those that are infected. In our previous study, we composed SynCom with strains expected to reduce the density of fire blight pathogens through microbiome analysis, strain isolation, and continuous replacement culture. We are able to observe the disease control effect of the constructed SynCom. However, no study has been conducted to clearly determine the genetic mechanism underlying this effect of the SynCom. Here, we present that potential secondary metabolite candidates and nutritional competition with the pathogen were confirmed as biochemical mechanisms through whole genome analysis of SynCom strains. Additionally, by co-cultivating SynCom with the pathogen in limited nutrient conditions, such as apple blossom extracts, which are susceptible to the pathogen, we confirmed the potential of SynCom treatment to reduce the pathogen densities. This study demonstrates that genetic selection using metagenomics can effectively identify microorganisms with potential functional capabilities.},
}

@article {pmid40468702,
year = {2025},
author = {Yoon, SJ and Han, SK and Kim, TS and Suk, KT and Choi, DH and Kim, YD and Kim, MY and Cheon, GJ and Baik, SK and Kim, DJ},
title = {The crosstalk between gut microbiota and microbiota-derived metabolites in hepatocellular carcinoma.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/1040841X.2025.2501590},
pmid = {40468702},
issn = {1549-7828},
abstract = {Hepatocellular carcinoma (HCC), one of the leading causes of death worldwide, is a consequence of persistent liver injury, inflammation, and fibrosis. Recent research has demonstrated that the gut-liver axis plays a crucial role in the pathological mechanisms of HCC development. Given the overall paucity of data available, we examined both clinical and animal studies investigating the influence of gut microbiota and their metabolites on the development of HCC in light of current scientific understanding. In this review, we concentrate on the mechanism by which intestinal dysbiosis facilitates the hepatocarcinogenesis pathway and offer a detailed account of the specific pathways involved in the promotion of HCC by the microbiome and its metabolites. Based on this, researchers might extrapolate which strains would be beneficial or harmful to restore gut homeostasis by targeting gut-liver axis in the pathogenesis of HCC.},
}

@article {pmid40468659,
year = {2025},
author = {Hossain, MS and Seo, H and Lee, KA and Ul-Haq, A and Kim, S and Jo, S and Rahim, MA and Tajdozian, H and Ghorbanian, F and Yoon, Y and Barman, I and Shuvo, MSH and Kim, HS and Song, HY},
title = {Microbiome therapeutic PMC72 through reverse translational research in gout.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {5},
pages = {e2501002},
doi = {10.71150/jm.2501002},
pmid = {40468659},
issn = {1976-3794},
support = {RS-202300219563//National Research Foundation of Korea/ ; //Ministry of Science and ICT/ ; 2020R1I1A-3072680//Ministry of Education/ ; //Soonchunhyang University Research Fund/ ; },
mesh = {Animals ; *Gout/therapy/microbiology/chemically induced ; Humans ; Mice ; *Gastrointestinal Microbiome/drug effects ; Hyperuricemia/chemically induced/therapy ; Uric Acid/blood/metabolism ; Disease Models, Animal ; Translational Research, Biomedical ; Dysbiosis ; Male ; Feces/microbiology ; Febuxostat/therapeutic use ; Oxonic Acid ; Oxidative Stress ; },
abstract = {Gout is an inflammatory arthritis resulting from the deposition of monosodium urate crystals. Urate-lowering therapies for gout have limitations, including side effects and limited efficacy, highlighting the need for novel therapeutic approaches to improve patient outcomes. In this context, our research team conducted a microbiome analysis of fecal samples from healthy individuals and gout patients, identifying Bifidobacterium as a key biomarker. Subsequently, we isolated and identified this strain, B. longum PMC72, and demonstrated its efficacy in a gout mouse model. In potassium oxonate (PO)-induced hyperuricemia mice, PMC72 significantly alleviated nausea, gait disturbances, ankle inflammation, and improved renal health. These effects were associated with marked reductions in oxidative stress markers, including serum uric acid, blood urea nitrogen, hepatic xanthine oxidase, and malondialdehyde (MDA) levels in serum, liver, and joint samples, as well as the downregulation of inflammation and uric acid transport-related gene expression in kidney samples. These benefits were comparable to those treated with Febuxostat, a standard urate-lowering therapy for gout. Furthermore, gut microbiome analysis revealed that PMC72 restored dysbiosis induced by hyperuricemia, contrasting with the reduced microbial diversity observed with febuxostat alone, and showed a complete recovery to eubiosis when combined with Febuxostat. These findings position PMC72 as a promising microbial therapeutic candidate for gout management, demonstrating significant development potential and serving as a benchmark for reverse translational microbiome-based therapeutic research.},
}

Animals
*Gout/therapy/microbiology/chemically induced
Humans
Mice
*Gastrointestinal Microbiome/drug effects
Hyperuricemia/chemically induced/therapy
Uric Acid/blood/metabolism
Disease Models, Animal
Translational Research, Biomedical
Dysbiosis
Male
Feces/microbiology
Febuxostat/therapeutic use
Oxonic Acid
Oxidative Stress

@article {pmid40468650,
year = {2025},
author = {Cha, RR and Sonu, I},
title = {Fecal microbiota transplantation: present and future.},
journal = {Clinical endoscopy},
volume = {58},
number = {3},
pages = {352-359},
doi = {10.5946/ce.2024.270},
pmid = {40468650},
issn = {2234-2400},
support = {//Gyeongsang National University Fund/ ; },
abstract = {Fecal microbiota transplantation (FMT) involves transplanting fecal matter from healthy donors into patients with gut dysbiosis to restore microbial balance. It has been proven to be highly effective in treating recurrent Clostridioides difficile infection (CDI), and United States Food and Drug Administration-approved microbiome-based therapies, such as REBYOTA (fecal microbiota live-jslm) and VOWST (fecal microbiota spores live-brpk), offer promising treatment options. Although FMT is widely used to treat recurrent CDI, its use in gastrointestinal and metabolic diseases remains limited. Future research directions include optimizing donor selection, understanding microbial mechanisms, and exploring the potential of FMT for treating other diseases. Ongoing research not only aims to broaden its indications but also improves its safety and efficacy. Emerging therapies such as VE303 (Vedanta) are being studied to refine treatment approaches and expand the use of microbiota-based therapies. Further studies are needed to standardize guidelines, improve patient outcomes, and better define the role of FMT in the treatment of diseases beyond recurrent CDI.},
}

@article {pmid40468453,
year = {2025},
author = {Hu, F and Gebeyew, K and Wu, Z and Chen, B and Jiao, J and Tan, Z and Tian, D and He, Z},
title = {Fat-rich diet promotes microbiome-dependent ATP synthesis in sheep model.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {81},
pmid = {40468453},
issn = {1674-9782},
support = {XDA26040304//Strategic Priority Research Program/ ; XDA26050102//Strategic Priority Research Program/ ; 32072760//National Natural Science Foundation of China/ ; 2022JJ10054//Natural Science Foundation of Hunan Province of China/ ; },
abstract = {BACKGROUND: The ketogenic diet that forces adenosine triphosphate (ATP) production by beta-oxidation of fatty acids instead of carbohydrate glycolysis, has gained consensus on host metabolism. However, the mechanisms how a ketogenic diet alters gastrointestinal microbiome and its downstream consequences on microbial nutrient availability and energy metabolism remain to be elucidated. Here, we used the sheep model fed with fat-rich diet to evaluate the symbiotic microbiome across three regions of the gastrointestinal tract (rumen, ileum, and colon) to gain a comprehensive understanding of the microbial energy metabolism and microbe-mediated ATP biosynthesis.

RESULTS: Results showed that sheep fed a fat-rich diet had a greater ADG and increased reliance on fat oxidation for fuel utilization. Metagenomics analysis showed the loss of the specialized fiber-degrading bacteria (genus_Fibrobacter) in the rumen and enrichment of genera RUG420 and Eubacterium, which are involved in lipid metabolism and bile acid processing, in the ileum. A significant functional shift related to energy metabolism was shared across three regions of the gastrointestinal microbiomes. These shifts were dominated by glycolysis/gluconeogenesis and TCA cycle in the rumen and by fatty acid degradation and bile acid transformation in the ileum, indicating adaptation to nutrient availability and energy acquisition. Notably, the abundance of substrate-level phosphorylation (SLP) enzymes was significantly increased in the rumen, ileum and colon, while the ATP-producing capacity through electron transport phosphorylation (ETP) by family_Bacteroidaceae in rumen and Acutalibacteraceae in ileum of sheep with fat-rich diet.

CONCLUSIONS: Altogether, the ATP-related microbiome encoding SLP and ETP in rumen, ileum, and colon contributed 36.95% to the host's weight variation. Our study is the first one demonstrating the microbial potential in the ATP synthesis under the shift in dietary energy source, providing a new perspective on the energy metabolism and precise human macronutrients nutrition.},
}

@article {pmid40468444,
year = {2025},
author = {Tang, Q and Yin, X and Wen, G and Luo, Z and Zhang, L and Tan, S},
title = {Unraveling the composition and function of pig gut microbiome from metagenomics.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {60},
pmid = {40468444},
issn = {2524-4671},
support = {No. [2023] 211//2022 Hunan Province Vocational Education "Chuyi" Action High Level Teacher Team Construction Project/ ; No. [2023] 211//2022 Hunan Province Vocational Education "Chuyi" Action High Level Teacher Team Construction Project/ ; },
abstract = {The gut microbiome plays a crucial role in intestinal maturation, metabolism, and immunoregulation, significantly influencing the host's health and growth performance. This review highlights the use of metagenomic techniques to the composition, function, and dynamic changes of the pig gut microbiota. Research has revealed that environmental and host factors, particularly diet, drive significant variations in microbial composition, which in turn shape host epigenetics through microbial components and metabolites. Furthermore, the strong correlation between the gut microbiota and host health presents opportunities for improving growth performance in the livestock industry.},
}

@article {pmid40468436,
year = {2025},
author = {Kilama, J and Islam, MS and Amat, S},
title = {Bovine ocular microbiome: the next frontier in managing Pinkeye in cattle.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {58},
pmid = {40468436},
issn = {2524-4671},
abstract = {Infectious bovine keratoconjunctivitis (IBK), or pinkeye, represents a significant economic challenge to dairy and beef cattle industries resulting in decreased productivity and increased treatment costs. The current IBK prevention and control strategies in cattle face challenges owing to the multifactorial nature of the disease, the rise of antibiotic resistance in IBK pathogens, and inconsistent efficacy of IBK vaccines. Recent efforts in metagenomic characterization of the eye microbiome in humans and animals, including cattle, have revealed that the ocular surface is colonized by relatively diverse and dynamic microbial community that is essential for maintaining ocular health and can be leveraged to enhance resistance against infectious ocular diseases. In this narrative review, we provide comprehensive insights into the ocular microbiota by summarizing the amplicon and metagenomic sequencing- and culture-based studies conducted in cattle, and by reviewing relevant findings from humans and other animal species. We also explore the potential of the ocular microbiome as a new frontier in managing IBK. Finally, we examine the gut-eye-microbiome axis and discuss its potential contribution in improving the resistance of cattle against IBK.},
}

@article {pmid40468269,
year = {2025},
author = {Li, B and Yang, Y and Xu, B and Song, P and Jiang, F and Gao, H and Cai, Z and Gu, H and Zhang, T},
title = {Comparative macrogenomics reveal plateau adaptation of gut microbiome in cervids.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {154},
pmid = {40468269},
issn = {1741-7007},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Deer/microbiology/genetics ; Phylogeny ; Metagenome ; Metagenomics ; *Adaptation, Physiological/genetics ; Energy Metabolism ; Biological Evolution ; },
abstract = {BACKGROUND: Diverse gut microbiota in animals significantly influences host physiology, ecological adaptation, and evolution. However, the specific functional roles of gut microbiota in facilitating host adaptation, as well as the coevolutionary dynamics between microbiota and their hosts, remain largely understudied.

RESULTS: A total of 41,847 metagenome-assembled genomes and 3193 high-quality species-level genome bins were generated, establishing a comprehensive gut microbiome catalog for cervids in this study. Phylogenetic analysis revealed a coevolutionary relationship between cervids and their gut microbiota. Comparative metagenomic analyses further indicated that the gut microbiota of plateau cervids have undergone genome-level adaptations related to energy metabolism. At the genus level, species-level genome bins from the genera Alistipes and Faecousia in plateau cervids exhibit enhanced energy metabolism capabilities. Structural variations analysis revealed that the insertion and duplications structural variations in the gut microbiota of plateau cervids were significantly enriched in energy metabolism pathways. In contrast, the deletions and contractions in structural variations were predominantly enriched with metabolic pathways involved in the biosynthesis of diverse biochemical molecules.

CONCLUSIONS: Our study provides a comprehensive gut microbiome catalog of the cervid gut microbiota, revealing the coevolutionary relationship between cervid gut microbiota and hosts. These findings highlight the adaptive genomic evolution of the gut microbiota in contributing to the plateau adaptability of cervids and offer new insights into the mechanisms by which the gut microbiota help hosts adapt to extreme environments.},
}

*Gastrointestinal Microbiome/genetics
Animals
*Deer/microbiology/genetics
Phylogeny
Metagenome
Metagenomics
*Adaptation, Physiological/genetics
Energy Metabolism
Biological Evolution

@article {pmid40468214,
year = {2025},
author = {Yang, X and Chen, H and Wu, L and Guo, X and Xue, D},
title = {Diversity and correlation analysis of microbiomes and metabolites of Sphagnum palustre in various microhabitats.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {761},
pmid = {40468214},
issn = {1471-2229},
support = {2019QZKK0304//Second Tibetan Plateau Scientific Expedition/ ; QNTS202201//Youth Innovation Program of CIB/ ; 2022376//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 2021JDTD011//Youth Science and Technology Innovation Team Program of Sichuan Province of China/ ; },
mesh = {*Microbiota ; *Sphagnopsida/microbiology/metabolism ; Ecosystem ; Soil Microbiology ; Bacteria/genetics/metabolism ; },
abstract = {BACKGROUND: Sphagnum peat mosses are crucial contributors to global carbon sequestration and are a dominant presence in many northern peatland environments. These mosses host a wide variety of microorganisms, which reside within their tissues and on their surfaces. Despite this close association, the connection between these microorganisms and the production of metabolites across different parts of Sphagnum remains unclear.

RESULTS: This research explored the connection between microbial diversity and metabolite production in various microhabitats of Sphagnum palustre by employing metagenomic and metabolomic techniques. Our results indicate that the S. palustre microbiome composition is more strongly influenced by microhabitat than by geographic location. Microbiome diversity microbiomes related to S. palustre showed a steady decrease from soil to near soil, from X to CAP, and from belowground to aboveground habitats. In contrast, network complexity increased. Species abundance analysis indicated that Proteobacteria was the most prevalent bacterial phylum across CAP, S, Z, and X. Additionally, Ascomycota emerged as the predominant fungal phylum. There were significant differences in nitrogen fixation activity, methane oxidation activity, total nitrogen, and total carbon among different microhabitats. The FAPROTAX analysis revealed differences in the metabolic potential of the carbon (C) and nitrogen (N) cycles across the four microhabitats. LC-MS/MS technology was employed to quantitatively assess metabolites across various S. palustre microhabitats. A total of 3,822 metabolites and 353 differential metabolites were detected, predominantly including lipids, organic acids, and carboxylic acids. The majority of these differential metabolites were associated with metabolic pathways such as carotenoid biosynthesis, steroid biosynthesis, secondary bile acid biosynthesis, as well as the biosynthesis of neomycin, kanamycin, and gentamicin. Correlation analysis revealed both positive and negative relationships between microorganisms and differential metabolites. Methylocystis, which was significantly enriched in X and T, showed a strong positive correlation with differential metabolites in S vs T and Z vs X, but a negative correlation with those in X vs T (p < 0.05).

CONCLUSION: In summary, our study demonstrates that Sphagnum palustre microbiomes are primarily influenced by microhabitats rather than specific environmental conditions at different sites. We identified significant variations in microbial community diversity across various S. palustre microhabitats. Correlation analysis revealed links between microorganisms and differential metabolic processes. This comprehensive investigation of aboveground and belowground microbiomes and metabolites in S. palustre provides new insights into the distribution of microbial communities and metabolites across different microhabitats.},
}

*Microbiota
*Sphagnopsida/microbiology/metabolism
Ecosystem
Soil Microbiology
Bacteria/genetics/metabolism

@article {pmid40468177,
year = {2025},
author = {Yang, B and Yue, C and Guo, C and Zheng, M and Yao, X and Xu, J and Huang, S and Yang, M},
title = {Disease-resistant watermelon variety against Fusarium wilt by remodeling rhizosphere soil microenvironment.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {350},
pmid = {40468177},
issn = {1471-2180},
support = {112024AS0100//Natural Science Foundation of Henan Province/ ; },
mesh = {*Rhizosphere ; *Citrullus/microbiology/genetics ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Fusarium/physiology/pathogenicity ; *Disease Resistance ; Soil/chemistry ; Bacteria/classification/genetics/isolation & purification ; Microbiota ; Fungi/classification/genetics/isolation & purification ; Transcriptome ; },
abstract = {BACKGROUND: Rhizosphere microorganisms and their interactions play a critical role in enhancing plant disease resistance. Here, we found that the disease severity of the resistant variety LW025 showed a decreasing trend with the increase in continuous cropping cycles. However, the mechanisms underlying the reduction in disease severity during the continuous cropping of the resistant watermelon variety LW025, particularly its relationship with the rhizosphere microbiome, remain unclear.

RESULTS: In this study, the transcriptome of different watermelon varieties after continuous planting in pathogen-containing and pathogen-free soils was analyzed. The results showed that only two genes expression showed significant differences in disease-resistant variety between healthy and diseased soils. Subsequently, we analyzed the differences of rhizosphere soil microbial communities after planting different watermelon varieties for three consecutive seasons, as well as the relationship between differential microorganisms and soil physiochemical properties and soil enzyme activity. The results demonstrated continuous cropping of the disease-resistant variety LW025 formed a rhizosphere microbiome different from the initial soil and susceptible variety. Specifically, fungal changes were primarily observed in Ascomycota and Chytridiomycota, while bacterial changes were mainly observed in Cyanobacteria and Gemmatimonadetes. The bacterial functions enriched in the rhizosphere of the resistant variety LW025 after continuous cropping were primarily associated with soil nitrogen cycling. Furthermore, the plant disease index showed a significant positive correlation with the available phosphorus and potassium content in the soil, while exhibiting a significant negative correlation with soil pH and catalase activity.

CONCLUSIONS: Overall, the reduction in disease severity associated with continuous cropping of the disease-resistant variety LW025 was more closely related to changes in the rhizosphere microecological environment. This study explained the mechanism of the resistant variety LW025 against Fusarium infection, and provided new prospects for the development of technologies based on rhizosphere microecological environment modification to improve the resistance of watermelon to Fusarium wilt.},
}

*Rhizosphere
*Citrullus/microbiology/genetics
*Soil Microbiology
*Plant Diseases/microbiology
*Fusarium/physiology/pathogenicity
*Disease Resistance
Soil/chemistry
Bacteria/classification/genetics/isolation & purification
Microbiota
Fungi/classification/genetics/isolation & purification
Transcriptome

@article {pmid40468006,
year = {2025},
author = {Sanz, Y and Cryan, JF and Deschasaux-Tanguy, M and Elinav, E and Lambrecht, R and Veiga, P},
title = {The gut microbiome connects nutrition and human health.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {40468006},
issn = {1759-5053},
abstract = {The gut microbiome has an undeniable role in mediating the health effects of the diet, given its ability to co-digest nutrients and influence nutrient signalling to multiple organ systems. As a suboptimal diet is a major risk factor for and contributor to disease, understanding the multidirectional interactions between the food we eat, the gut microbiome and the different body organ systems is crucial from a public health perspective. Indeed, this research area is leading to the refinement of nutritional concepts and strategies to optimize health through diet. In this Review, we provide an update on how dietary patterns and food intake shape gut microbiome features, the mode of action of diet-microorganism interactions on the immune, nervous and cardiometabolic systems and how this knowledge could explain the heterogeneity of dietary responses, and support food-based dietary guidelines and medical and precision nutrition. Finally, we discuss the knowledge gaps and research efforts needed to progress towards the integration of microbiome science with more precise dietary advice to leverage the role of nutrition in human health.},
}

@article {pmid40467971,
year = {2025},
author = {Smoliński, J and Czyż, K and Kleszcz, A and Trusz, A and Wyrostek, A and Zajfert, K},
title = {A preliminary study on farmed and free-ranging mouflons core microbiome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19555},
pmid = {40467971},
issn = {2045-2322},
mesh = {Animals ; Feces/microbiology ; *Gastrointestinal Microbiome ; Bacteroidetes/genetics/isolation & purification ; *Microbiota ; Firmicutes/genetics/isolation & purification ; Bacteria/genetics/classification ; },
abstract = {The digestive tract of ruminants is populated by a diverse microbiome and is also known as a specific ecosystem. The close relationship between the microbiota and the host digestive system influences development and proper health. The rich microflora of ruminants is often altered by the influence of the environment, diet or individual factors, which in turn affects production rates. The most extensive part of the gastrointestinal tract in terms of microbiology is the large intestine, where bacterial levels increase in the caudal direction. The purpose of this study was to compare the core microbiomes of the feces of farmed and free-ranging mouflons, taking into account differences in housing conditions, as well as their diet and individual variability. The most characteristic clusters for ruminants were studied: Firmicutes and Bacteroidetes, as well as the families Lactobacillaceae and Clostridiaceae. The material for the study consisted of feces collected from 10 farmed and 10 free-ranging mouflons. The experiment was based on demonstrating changes in the levels of the bacteria tested by means of DNA isolation from feces and real-time PCR analysis, taking into account dietary and environmental differences. The results showed that the levels of the Lactobacillaceae and Clostridiaceae families were significantly higher in free-ranging individuals than in farmed ones (p < 0.01). For the Firmicutes and Bacteroidetes phyla, no statistically significant differences were shown. In addition, each mouflon was characterized by an individual composition of the microbiome, which changed through environmental, individual and dietary factors.},
}

Animals
Feces/microbiology
*Gastrointestinal Microbiome
Bacteroidetes/genetics/isolation & purification
*Microbiota
Firmicutes/genetics/isolation & purification
Bacteria/genetics/classification

@article {pmid40467897,
year = {2025},
author = {Wu, Y and Ehlert, B and Metwally, AA and Perelman, D and Park, H and Brooks, AW and Abbasi, F and Michael, B and Celli, A and Bejikian, C and Ayhan, E and Lu, Y and Lancaster, SM and Hornburg, D and Ramirez, L and Bogumil, D and Pollock, S and Wong, F and Bradley, D and Gutjahr, G and Rangan, ES and Wang, T and McGuire, L and Venkat Rangan, P and Ræder, H and Shipony, Z and Lipson, D and McLaughlin, T and Snyder, MP},
title = {Individual variations in glycemic responses to carbohydrates and underlying metabolic physiology.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {40467897},
issn = {1546-170X},
support = {R01 DK110186-01//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; P30DK116074//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; F32DK126287//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01 DK110186-01//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; P30DK116074//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; 11-23-PDF-76//American Diabetes Association (ADA)/ ; 2T15LM007033//U.S. Department of Health & Human Services | NIH | U.S. National Library of Medicine (NLM)/ ; },
abstract = {Elevated postprandial glycemic responses (PPGRs) are associated with type 2 diabetes and cardiovascular disease. PPGRs to the same foods have been shown to vary between individuals, but systematic characterization of the underlying physiologic and molecular basis is lacking. We measured PPGRs using continuous glucose monitoring in 55 well-phenotyped participants challenged with seven different standard carbohydrate meals administered in replicate. We also examined whether preloading a rice meal with fiber, protein or fat ('mitigators') altered PPGRs. We performed gold-standard metabolic tests and multi-omics profiling to examine the physiologic and molecular basis for interindividual PPGR differences. Overall, rice was the most glucose-elevating carbohydrate meal, but there was considerable interindividual variability. Individuals with the highest PPGR to potatoes (potato-spikers) were more insulin resistant and had lower beta cell function, whereas grape-spikers were more insulin sensitive. Rice-spikers were more likely to be Asian individuals, and bread-spikers had higher blood pressure. Mitigators were less effective in reducing PPGRs in insulin-resistant as compared to insulin-sensitive participants. Multi-omics signatures of PPGR and metabolic phenotypes were discovered, including insulin-resistance-associated triglycerides, hypertension-associated metabolites and PPGR-associated microbiome pathways. These results demonstrate interindividual variability in PPGRs to carbohydrate meals and mitigators and their association with metabolic and molecular profiles.},
}

@article {pmid40467859,
year = {2025},
author = {Ferretti, P and Johnson, K and Priya, S and Blekhman, R},
title = {Genomics of host-microbiome interactions in humans.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
pmid = {40467859},
issn = {1471-0064},
abstract = {The human microbiome is a complex ecosystem of microorganisms that inhabit the human body and have a crucial role in human health. Microbiome composition is shaped by its interaction with many factors, including human genetics. Advances in genomic technologies are improving the ability to quantify the effect of human genetics on the microbiome through improved heritability studies and microbiome genome-wide association studies (GWAS). Complementary studies using transcriptomic analyses are providing a more comprehensive view of the bidirectional relationship between host gene expression and the microbiome. The resulting insights into the genetic mechanisms driving host-microbiome interactions will ultimately contribute to the development of personalized medicine and targeted therapies.},
}

@article {pmid40467839,
year = {2025},
author = {Chen, YA and Kawashima, H and Park, J and Mohsen, A and Hosomi, K and Nakagata, T and Murakami, H and Nanri, H and Miyachi, M and Kunisawa, J and Mizuguchi, K},
title = {NIBN Japan Microbiome Database, a database for exploring the correlations between human microbiome and health.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19640},
pmid = {40467839},
issn = {2045-2322},
support = {22AC5002//Ministry of Health, Labour and Welfare/ ; 22AC5002//Ministry of Health, Labour and Welfare/ ; 20AC5004//Ministry of Health, Labour and Welfare/ ; 20AC5004//Ministry of Health, Labour and Welfare/ ; },
mesh = {Humans ; Japan ; *Databases, Factual ; *Gastrointestinal Microbiome ; *Microbiota ; Metadata ; },
abstract = {Recent research has highlighted the substantial impact of gut microbiome on various aspects of human health, such as obesity, inflammation, infectious diseases, and cancer. As a result, gut microbiota composition is increasingly recognized as a potential health indicator and biomarker for disease. Numerous factors, including lifestyle, diet, and physical fitness, are known to shape the composition of the human microbiome. However, a significant challenge in elucidating the relationships between these factors and the gut microbiome lies in needing a comprehensive database that integrates diverse human microbiome profiles with extensive sample metadata. To address this issue, we developed an extensive human microbiome database for healthy individuals. This initiative led to the establishment of the NIBN Japan Microbiome Database (NIBN JMD), one of the largest resources of its kind, encompassing up to 1,000 metadata points and more than 2,000 microbiome samples, including data from longitudinal studies. In this article, we describe the creation and features of NIBN JMD, detailing the data collection, processing, and database implementation. NIBN JMD is publicly accessible at https://jmd.nibn.go.jp/ .},
}

Humans
Japan
*Databases, Factual
*Gastrointestinal Microbiome
*Microbiota
Metadata

@article {pmid40467588,
year = {2025},
author = {Tajadura-Ortega, V and Chai, W and Roberts, LA and Zhang, Y and Di Maio, A and Decout, AC and Pinheiro, BA and Palma, AS and De Nicola, G and Riaposova, L and Gimeno-Molina, B and Lee, YS and Cao, H and Piskarev, V and Akune, Y and Costa, TRD and Amin, H and Sykes, L and Bennett, PR and Marchesi, JR and Feizi, T and Liu, Y and MacIntyre, DA},
title = {Identification and characterisation of vaginal bacteria-glycan interactions implicated in reproductive tract health and pregnancy outcomes.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5207},
pmid = {40467588},
issn = {2041-1723},
mesh = {Female ; Humans ; *Vagina/microbiology/metabolism ; Pregnancy ; *Polysaccharides/metabolism ; Bacterial Adhesion/physiology ; Pregnancy Outcome ; *Reproductive Health ; Chondroitin Sulfates/metabolism ; Escherichia coli/metabolism ; Microbiota ; *Bacteria/metabolism ; Lactobacillus/metabolism ; Streptococcus agalactiae/metabolism ; Epithelial Cells/microbiology/metabolism ; },
abstract = {Lactobacillus displacement from the vaginal microbiome associates with adverse health outcomes and is linked to increased risk of preterm birth. Glycans mediate bacterial adhesion events involved in colonisation and infection. Using customised glycan microarrays, we establish glycan interaction profiles of vaginal bacteria implicated in reproductive health. Glycan binding signatures of the opportunistic pathogens Escherichia coli, Fusobacterium nucleatum and Streptococcus agalactiae to oligomannose N-glycans, galactose-terminating glycans and hyaluronic acid, respectively are highly distinct from Lactobacillus commensals. Binding to sulphated glycosaminoglycans by vaginal bacteria is pH dependent, as is binding to neutral and sialic acid-terminating glycans by F. nucleatum. Adhesion of Lactobacillus crispatus, Lactobacillus iners, Gardnerella vaginalis, S. agalactiae and F. nucleatum to vaginal epithelial cells is partially mediated by chondroitin sulphate. S. agalactiae binding to chondroitin sulphate C oligosaccharides is inhibited by L. crispatus. This study highlights glycans as mediators of vaginal bacterial binding events involved in reproductive health and disease.},
}

Female
Humans
*Vagina/microbiology/metabolism
Pregnancy
*Polysaccharides/metabolism
Bacterial Adhesion/physiology
Pregnancy Outcome
*Reproductive Health
Chondroitin Sulfates/metabolism
Escherichia coli/metabolism
Microbiota
*Bacteria/metabolism
Lactobacillus/metabolism
Streptococcus agalactiae/metabolism
Epithelial Cells/microbiology/metabolism

@article {pmid40467587,
year = {2025},
author = {Xiong, S and Xie, B and Yin, N and Zhu, H and Gao, H and Xu, X and Xiao, K and Cai, X and Sun, G and Sun, X and Cui, Y and Van de Wiele, T and Zhu, Y},
title = {Prenatal exposure to trace elements impacts mother-infant gut microbiome, metabolome and resistome during the first year of life.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5186},
pmid = {40467587},
issn = {2041-1723},
support = {No. L232076//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; Pregnancy ; Infant ; *Trace Elements/adverse effects ; *Metabolome/drug effects ; Feces/microbiology ; *Prenatal Exposure Delayed Effects/microbiology/metabolism ; Adult ; Male ; Metagenomics ; Hair/chemistry ; *Maternal Exposure/adverse effects ; Infant, Newborn ; Bacteria/genetics/classification/drug effects ; Copper ; },
abstract = {Infancy is a critical window for the colonization of gut microbiome. However, xenobiotic impacts on gut microbiome development in early life remain poorly understood. Here, we recruit 146 mother-infant pairs and collect stool samples at 3, 6, and 12 months after delivery for amplicon sequencing (N = 353), metagenomics (N = 65), and metabolomics (N = 198). Trace elements in maternal hair samples (N = 119) affect diversity and composition of the infant gut microbiome. Shannon diversity in 3 month-old infants is correlated positively with selenium and negatively with copper, and relative abundance of Bifidobacterium increases under high exposure to aluminum and manganese. During the first year of life, infants and their paired mothers have distinct microbial diversity and composition, and their bacterial community structures gradually approach. here are 56 differential metabolites between the first and second visit and 515 differential metabolites between the second and third visit. The typical profile of antibiotic resistance genes (ARGs) significantly differs between infants and their mothers. High levels of copper and arsenic exposure may induce the enrichment of ARGs in the infant gut. Our findings highlight the dynamics of the gut microbiome, metabolites, and ARG profiles of mother-infant pairs after delivery, associated with prenatal exposure to trace elements.},
}

Humans
*Gastrointestinal Microbiome/drug effects/genetics
Female
Pregnancy
Infant
*Trace Elements/adverse effects
*Metabolome/drug effects
Feces/microbiology
*Prenatal Exposure Delayed Effects/microbiology/metabolism
Adult
Male
Metagenomics
Hair/chemistry
*Maternal Exposure/adverse effects
Infant, Newborn
Bacteria/genetics/classification/drug effects
Copper

@article {pmid40345399,
year = {2025},
author = {Livingston, DBH and Sweet, A and Chowdary, M and Samuel Demissie, M and Rodrigue, A and Pillagawa Gedara, K and Kishore, L and Mahmoodianfard, S and Power, KA},
title = {Diet alters the effects of lipopolysaccharide on intestinal health and cecal microbiota composition in C57Bl/6 male mice.},
journal = {The Journal of nutritional biochemistry},
volume = {144},
number = {},
pages = {109951},
doi = {10.1016/j.jnutbio.2025.109951},
pmid = {40345399},
issn = {1873-4847},
abstract = {Lipopolysaccharide (LPS), a component of the gram-negative bacteria, induces an inflammatory cascade in mice, negatively impacting aspects of the microbiota gut-brain axis (mGBA). Flaxseed (FS), an oilseed enriched in dietary fiber and n3 poly-unsaturated fatty acids, has been shown to partially attenuate LPS-induced systemic and neuroinflammation. In this study, we investigated the impact of FS and FS oil (FO) diets on microbial dysbiosis, biomarkers of intestinal health, hepatic inflammation and oxidative stress, and metabolic homeostasis in male mice, 24-hours post LPS-exposure. Compared to saline-treated mice, LPS mice showed diet-dependent shifts in the cecal microbiome. Most notably, LPS-treated basal diet (BD)-fed mice had reduced Muribaculaceae and Lachnospiraceae, FS-LPS mice had elevated Akkermansia and Enterobacteriaceae, and both the FS-LPS and FO-LPS mice had increased Bacteroides. LPS increased cecal short-chain fatty acid concentrations, the highest of which were found in FS-fed mice. Intestinal health biomarkers were modulated by LPS in a diet-specific manner such that ileal mucous content was elevated in FS- and FO-fed mice, while LPS-induced inflammation (IL-1β) was attenuated in FS-fed mice. On the other hand, LPS-induced hepatic inflammation and oxidative stress, which were not attenuated by FS or FO diets. Bacteroides abundance and serum Il-10 levels, and cecal butyrate concentrations and hippocampal IL-6 mRNA, were negatively correlated in FS-fed mice only, suggesting a potential role of the microbiome in the anti-inflammatory effects of FS post-LPS treatment. Collectively, LPS exposure negatively impacted the cecal microbiome and markers of intestinal, hepatic, and metabolic health, the former being beneficially altered by FS diet.},
}

@article {pmid40467492,
year = {2025},
author = {Tonomura, S and Hattori, Y and Ishibashi, T and Ikeda, S and Noda, K and Chiba, T and Kato, Y and Asano, R and Fukuma, K and Edamoto-Taira, Y and Motooka, D and Inagaki, T and Okazawa, M and Nakamura, S and Koga, M and Toyoda, K and Nomura, R and Nakano, K and Friedland, RP and Takeda, K and Takahashi, R and Ihara, M and Nakaoka, Y},
title = {Oral Pathobiont Streptococcus Anginosus Is Enriched in the Gut of Stroke Patients and Predicts 2-Year Cardiovascular Outcome.},
journal = {Circulation journal : official journal of the Japanese Circulation Society},
volume = {},
number = {},
pages = {},
doi = {10.1253/circj.CJ-24-0872},
pmid = {40467492},
issn = {1347-4820},
abstract = {BACKGROUND: Several cross-sectional studies have implicated gut dysbiosis caused by an abundance of oral commensals in stroke, but the effect on long-term prognosis is still unknown. Therefore, we longitudinally investigated oral pathobionts in the gut and their clinical relevance to stroke.

METHODS AND RESULTS: We analyzed the salivary and gut microbiomes collected from 189 acute stroke and 55 non-stroke subjects, and found that Streptococcus anginosus was significantly more abundant in both the saliva (median [IQR], 0.01 [0.00-0.14] vs. 0.00 [0.00-0.03], P=0.02) and gut (0.09 [0.00-0.28] vs. 0.00 [0.00-0.02], P<0.001) of the stroke patients compared with their non-stroke counterparts. Network analysis revealed S. anginosus as a central hub in gut dysbiosis. After adjusting for vascular risks, S. anginosus (odds ratio 1.20, 95% confidence interval 1.06-1.36, P<0.01), Anaerostipes hadrus (0.82, [0.73-0.93], P<0.01), and Bacteroides plebeius (0.86, [0.86-0.93], P=0.01) in the gut were independent predictors of stroke. Longitudinally, S. anginosus in the gut was significantly associated with increased rates of death and major cardiovascular events (P=0.04; log-rank test), whereas A. hadrus and B. plebeius were not (P=0.45 and P=0.19). After adjusting for vascular risks, S. anginosus in the gut was a residual risk for increased rates of death and major cardiovascular events (hazard ratio 4.78, 95% confidence interval 1.08-21.18, P=0.04)Conclusions: S. anginosus in the gut may increase the risk of stroke and a poor prognosis.},
}

@article {pmid40467356,
year = {2025},
author = {Messadi, A and Sayhi, S and Ghedira, K and Zaouaoui, C and Arfaoui, B and Khouikhi, S and Rebai, M and Guediche, NEH and Abdelhafidh, N and Louzir, B and Faida, A},
title = {Microbial diversity investigation using 16S metagenomics in Tunisian patients with systemic lupus erythematosus.},
journal = {Revista Argentina de microbiologia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ram.2025.04.002},
pmid = {40467356},
issn = {0325-7541},
abstract = {Systemic lupus erythematosus (SLE) is a multisystemic autoimmune disease associated with significant morbidity and mortality. It is characterized by a loss of self-immune tolerance and autoantibody production, leading to multiple organ damage. Emerging investigations have confirmed the role of gut microbiota dysbiosis in patients with SLE, although the underlying mechanisms remain unclear to date. In this study, we aim to investigate the bacterial profile of SLE including phylum/class/genus relative abundance and diversity, to compare them with healthy controls and to study the correlation of relative abundance of different patterns with clinical/biological parameters. In this case-control study, the bacterial profile was investigated in 7 SLE patients and 7 healthy controls using 16S metagenomics clustering. The present study reported a low abundance of the class Bacilli (0.58% in SLE vs 1.26% in the controls), the genus Lactobacillus (0.43% vs 0.74%), as well as a higher abundance of the genera Gammaproteobacteria (2.37% vs 0.77%) and Escherichia-Shigella (2.04% vs 0.51%) in SLE samples compared to the controls (p<0.05). We also found an association between the class Betaproteobacteria (4.42% vs 1.57%) and the genus Faecalibacterium (11.34% vs 3.35%) and renal manifestations (p<0.05). The phylum Actinobacteria (0.21% vs 3.8%, p=0.036) and the genus Bifidobacterium levels were lower in active SLE compared to the healthy controls. This study is the first report on the gut microbiota of SLE and the first case-control study in Tunisia and North Africa. We obtained a particular profile of bacterial gut microbiota for the SLE group. We found a specific clustering when compared to the healthy controls.},
}

@article {pmid40467241,
year = {2025},
author = {Alegbeleye, O and Boas, DMV and Sant'Ana, AS},
title = {Harnessing the microbiota of vegetables and ready-to-eat (RTE) vegetables for quality and safety.},
journal = {Food research international (Ottawa, Ont.)},
volume = {214},
number = {},
pages = {116667},
doi = {10.1016/j.foodres.2025.116667},
pmid = {40467241},
issn = {1873-7145},
mesh = {*Vegetables/microbiology/virology ; *Food Microbiology ; *Microbiota ; *Food Safety ; *Fast Foods/microbiology ; Humans ; Bacteria/classification/isolation & purification ; Salads/microbiology ; *Food Quality ; },
abstract = {The microbiota of vegetables and Ready-to-Eat (RTE) vegetable salads can have significant implications for quality and safety. Some microbial groups occurring on vegetables can cause foodborne illnesses, while others can potentially influence the shelf life of vegetables and vegetable salad products. The comprehensive assessment of the microbial structure and diversity of vegetables requires sensitive detection and characterization techniques, and this review discusses some of the strengths and limitations of conventional culture dependent approaches and the promise of some contemporary microbial detection/characterization approaches. Some bacterial groups recovered from vegetables have exhibited resistance to important antibiotics and without adequate safeguards, consumption of vegetables and salad products can potentially contribute to the spread and burden of antibiotic resistance. Studies summarised herein indicate that bacterial groups including Pseudomonas, Erwinia, and Lactic Acid Bacteria which contain common spoilage species are predominant in vegetables. Some possible sources of these bacteria to vegetables include agricultural input and post-harvest handling. Viruses and fungi contribute significantly to shaping microbiota of vegetables but also contain some species that are relevant for public health safety and vegetable shelf-life. Inspite of the relevance of these groups on the phylloshpere of vegetables, there is a comparative dearth of data on the incidence and prevalence of fungal and viral groups on vegetablesComprehensive understanding of the microbial profile of vegetables offers a more accurate assessment of potential food safety, and spoilage risks, and studies should aim to assess the total microbiome of vegetables and vegetable salads.},
}

*Vegetables/microbiology/virology
*Food Microbiology
*Microbiota
*Food Safety
*Fast Foods/microbiology
Humans
Bacteria/classification/isolation & purification
Salads/microbiology
*Food Quality

@article {pmid40467108,
year = {2025},
author = {Ghensi, P and Heidrich, V and Bazzani, D and Asnicar, F and Armanini, F and Bertelle, A and Dell'Acqua, F and Dellasega, E and Waldner, R and Vicentini, D and Bolzan, M and Trevisiol, L and Tomasi, C and Pasolli, E and Segata, N},
title = {Shotgun Metagenomics Identifies in a Cross-Sectional Setting Improved Plaque Microbiome Biomarkers for Peri-Implant Diseases.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.14121},
pmid = {40467108},
issn = {1600-051X},
support = {//Italian Society of Periodontology and Implantology (SIdP)/ ; //Eklund Foundation/ ; //International Team for Implantology (ITI)/ ; /ERC_/European Research Council/International ; //CLC Scientific S.r.l./ ; //PreBiomics S.r.l./ ; },
abstract = {AIM: This observational study aimed to verify and improve the predictive value of plaque microbiome of patients with dental implant for peri-implant diseases.

MATERIALS AND METHODS: Patients were included in one of the following study groups according to the health status of their dental implants: (a) healthy, (b) affected by mucositis and (c) affected by peri-implantitis. From each patient, submucosal plaque microbiome samples were collected from the considered dental implant and from a contralateral healthy implant/tooth. After shotgun metagenomic sequencing, the plaque microbiome was profiled taxonomically and functionally with MetaPhlAn 4 and HUMAnN 3, respectively. Taxonomic and functional profiles were fed into machine-learning models, which were then evaluated with cross-validation to assess the extent to which the plaque microbiome could be used to pinpoint peri-implant diseases.

RESULTS: Shotgun metagenomics sequencing was performed for a total of 158 samples spanning 102 individuals. Four-hundred and forty-seven prokaryotic species were identified as part of the peri-implant microbiome, 34% of which were currently uncharacterized species. At the community level, the peri-implant microbiome differed according to the health status of the implant (p ≤ 0.006 for all pairwise comparisons) but this was site-specific, as healthy contralateral sites showed no discriminating microbiome features. Peri-implantitis microbiomes further showed lower inter-subject variability than healthy plaque microbiomes (p < 0.001), while mucositis-associated microbiomes were in the middle of the continuum between health and peri-implantitis. Each health condition was associated with a strong signature of taxonomic and functional microbiome biomarkers (log10 LDA score ≥ 2.5), 30% and 13% of which represented uncharacterized microbial functions and unknown species, respectively. Distinct Fusobacterium nucleatum clades were associated with implant status, highlighting the subspecies F. nucleatum's functional and phenotypic diversity. Machine-learning models trained on taxonomic or functional plaque microbiome profiles were highly accurate in differentiating clinical groups (AUC = 0.78-0.96) and highlighted the extent to which the peri-implant microbiome is associated with peri-implant clinical parameters (AUC = 0.79-0.87).

CONCLUSIONS: Plaque microbiome profiling with shotgun metagenomics revealed consistent associations between microbiome composition and peri-implant diseases. In addition to pointing to peri-implant-associated microbes, warranting further mechanistic studies, we showed high-resolution plaque microbiome evaluation via metagenomics as an effective tool. Its utility within protocols for clinical management of peri-implant diseases should be explored in the future.},
}

@article {pmid40467103,
year = {2025},
author = {Phi Dang, C and Croitoru, K and Turpin, W},
title = {DUOX2-mediated gut barrier dysfunction: a preclinical mechanism in IBD pathogenesis?.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-335565},
pmid = {40467103},
issn = {1468-3288},
}

@article {pmid40466870,
year = {2025},
author = {Gurjar, S and Taliyan, R and Kumari, S and Kesharwani, P},
title = {The interplay of triphala and its constituents with respect to metabolic disorders and gut-microbiome.},
journal = {Fitoterapia},
volume = {},
number = {},
pages = {106642},
doi = {10.1016/j.fitote.2025.106642},
pmid = {40466870},
issn = {1873-6971},
abstract = {Ayurveda is based on natural therapeutic methods that focuses on eliminating toxins from the body and enhancing both physical and mental regeneration using herbal remedies. Medicinal plants have significant elemental and therapeutic value. Triphala (TLP) is a highly potent polyherbal Ayurvedic remedy that is widely regarded as one of the most crucial ayurvedic supplements. This study aims to analyze and comprehend the effectiveness and therapeutic value of TLP and its components by summarizing the pertinent literature based on a selection of publications obtained through a focused search of reliable academic resources. The review primarily emphasizes on the ethnomedical and pharmacological effects of TLP, while also providing a probable explanation of the underlying molecular mechanism. TLP is recognized for its antioxidant, anti-inflammatory, immunomodulatory, antibacterial, antimutagenic, hypoglycemic, antineoplastic, chemoprotective, and radioprotective properties. It is also effective against parasitic infections, and other infectious disorders. Although, the mechanisms are not well explored but these activities are also ascribed to alter the gut microbiota composition. Therefore, it is imperative to undertake rigorous systematic study for TLP in order to identify and assess the chemical ingredients which bring about the change either in gut microbiome composition or increase the number of beneficial gut-microbiota. Hence, this review thoroughly examines the pharmacological advantages of Triphala with special emphasis on molecular mechanisms altering the gut-microbiota prior to its potential utilization in clinical environments.},
}

@article {pmid40466780,
year = {2025},
author = {Yang, Y and Abdelfattah, A and Jia, H and Kumar, V and Jiang, Y and Cheng, L},
title = {Enhanced nitrogen removal by Comamonas 110 colonization and bioaugmentation in sequencing batch activated sludge bioreactor.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132759},
doi = {10.1016/j.biortech.2025.132759},
pmid = {40466780},
issn = {1873-2976},
abstract = {While pure functional strains demonstrate high pollutant removal efficiency, their environmental persistence remains challenging. This study optimized Comamonas 110 inoculation strategies in activated sludge systems, enhancing nitrogen removal efficiency (44 % of nitrogen removal at day 180) and achieving stable colonization (15.22 % abundance at day 180) through 30 % initial dosage combined with operational parameter regulation. Monod modeling and 16S rRNA sequencing revealed Comamonas 110 suppressed Nitrite-Oxidizing Bacteria (NOB) while boosting Ammonia-Oxidizing Bacteria (AOB). Denitrifying enzymes (NAR and NIR) increased significantly in inoculated reactors, attributing to the substantial presence of Comamonas 110. Metagenomics revealed upregulated (tricarboxylic acid) TCA cycle genes and nitrogen metabolism pathways, optimizing electron transfer for denitrification. Concurrently, Extracellular Polymeric Substance (EPS) synthesis-related genes were activated, promoting co-aggregation with native EPS-producing microbes. This study provides new insights into colonization dynamics of bioaugmentation strains through microbiome-environment interplay.},
}

@article {pmid40466732,
year = {2025},
author = {Markey, W and Srinath, H},
title = {The alarming rise of early-onset colorectal cancer.},
journal = {Australian journal of general practice},
volume = {54},
number = {6},
pages = {392-399},
pmid = {40466732},
issn = {2208-7958},
mesh = {Humans ; *Colorectal Neoplasms/epidemiology/diagnosis ; Australia/epidemiology ; Risk Factors ; Incidence ; Age of Onset ; Early Detection of Cancer/methods/trends/statistics & numerical data ; Female ; Mass Screening/methods/trends/statistics & numerical data ; Male ; Middle Aged ; Adult ; },
abstract = {BACKGROUND: Over the past 20 years of the Australian National Bowel Cancer Screening Program, there has been a reduction in Australia's overall rates of colorectal cancer. However, during this same period, there has been a steady rise in the incidence of early-onset colorectal cancer (EOCRC), presenting a new public health issue.

OBJECTIVE: The aim of this study was to evaluate the literature regarding the rising incidence of EOCRC, highlight the importance of the recent reduction in screening age and document what might be done in a primary healthcare setting.

DISCUSSION: The increasing incidence of EOCRC has been largely attributed to risk factors including a Western diet, obesity, tobacco use and alcohol intake, which contribute to microbiome dysgenesis and chronic inflammation from an early age. In response, the initial screening age for colorectal cancer was lowered to 45 years from July 2024 via an opt-in system; however, there is evidence to support a further reduction in screening age to 40 years.},
}

Humans
*Colorectal Neoplasms/epidemiology/diagnosis
Australia/epidemiology
Risk Factors
Incidence
Age of Onset
Early Detection of Cancer/methods/trends/statistics & numerical data
Female
Mass Screening/methods/trends/statistics & numerical data
Male
Middle Aged
Adult

@article {pmid40466498,
year = {2025},
author = {Egea, LG and Jiménez-Ramos, R},
title = {Antibiotic pollution alters the microbiome and reduces primary production and growth in the seagrass Cymodocea nodosa (Ucria) Ascherson.},
journal = {Marine environmental research},
volume = {210},
number = {},
pages = {107242},
doi = {10.1016/j.marenvres.2025.107242},
pmid = {40466498},
issn = {1879-0291},
abstract = {Antibiotics are considered a contaminant of emerging concern that can affect marine plants and their associated microbiome. To date, limited information is available about the effects of antibiotic pollution on seagrasses. Here, we conducted a seven-day mesocosm experiment in which we exposed the seagrass Cymodocea nodosa to a cocktail of ampicillin, streptomycin, and amoxicillin (with two total concentration exposure levels of 20 and 200 μg L[-1]). At the end of the incubation, we assessed phyllosphere and rhizosphere microbiome composition, plant growth, and carbon metabolism. We found that the seagrass community switched from a highly autotrophic in control (19.41 mmol C m[-2] d[-1]) to a moderately heterotrophic in the high-exposure treatment (-2.74 mmol C m[-2] d[-1]). This decrease in net community production was attributed to (i) a reduction in photosynthetic pigments (from 20 % to 41 %) due to antibiotic-induced oxidative stress in the seagrass chloroplasts and (ii) a change in the phyllosphere that showed lower species richness and abundance (from x0.3 to x0.7-fold lower) in exposure treatments compared to control. Although most bacterial families showed a reduced relative abundance under antibiotic stress, some taxa, including Pseudoalteromonadaceae, Halomonadaceae, and Cellvibrionaceae, were markedly enriched in the phyllosphere. Our results show that phyllosphere bacterial community is more sensitive to antibiotic pollution in the seawater column than rhizosphere community. Long-term antibiotic stress may also promote the development of seagrass diseases. Overall, our results suggest that antibiotic exposure may reduce seagrass growth and health and may compromise their function as a blue carbon sink.},
}

@article {pmid40466388,
year = {2025},
author = {Memariani, H and Memariani, M and Eskandari, SE and Ghasemian, A and Nour Neamatollahi, A},
title = {The potential role of probiotics and their bioactive compounds in the management of pulmonary tuberculosis.},
journal = {Journal of infection and public health},
volume = {18},
number = {9},
pages = {102840},
doi = {10.1016/j.jiph.2025.102840},
pmid = {40466388},
issn = {1876-035X},
abstract = {The significance of gut microbiota in human health is well recognized, yet its effects on pulmonary infectious diseases like tuberculosis (TB) are not thoroughly comprehended. While anti-TB drugs and preventive strategies are indispensable, the incorporation of adjunct therapies, including probiotics and their bioactive compounds, could provide potential biotherapeutic benefits. This review strives to collate the recent experimental and clinical investigations into the manipulation of the gut microbiome through probiotics, exploring their potential to sustain eubiosis, enhance recovery from TB, and mitigate the adverse effects of anti-TB therapies. The multi-pronged mechanisms by which probiotics act against M. tuberculosis include their immunomodulatory properties, the promotion of autophagy, direct inhibition of the pathogen growth via bacteriocin production, the reduction of adverse effects from anti-TB drugs, and a diminished risk of comorbidities. Future research should prioritize high-quality randomized controlled trials that integrate omics with personalized microbiome-based therapeutic approaches to combat TB.},
}

@article {pmid40466265,
year = {2025},
author = {Chang, S and Song, M and Lee, J and Kim, S and Song, D and Jeon, K and Kim, H and Yang, J and Kim, H and Cho, J},
title = {Stimbiotics help improve intestinal immunity and positively modulate the gut microbiome in broilers with necrotic enteritis.},
journal = {Poultry science},
volume = {104},
number = {8},
pages = {105315},
doi = {10.1016/j.psj.2025.105315},
pmid = {40466265},
issn = {1525-3171},
abstract = {This experiment was conducted to investigate the effect of stimbiotic (STB) in broilers with necrotic enteritis (NE) on nutrient digestibility and gut health. A total of 200 one-day-old Arbor Acres (initial body weight of 44.03 ± 0.28 g) were used in this experiment for 28 days. All broilers were randomly allocated into four treatments, and each experimental group had 10 replicate cages with five broilers per cage. The experiment was conducted in a 2 × 2 factorial designs consisting of two levels of challenge (challenge and non-challenge) and two levels of STB (0 and 0.05 %). All broilers in challenged groups were orally challenged by overdosing with coccidia vaccines (× 10 recommended doses; Livacox® Q). The NE challenge significantly decreased (P < 0.05) nutrient digestibility, interferon-γ, heterophil levels in blood, and villus height:crypt depth (VH:CD) compared to the non-challenge group. Also, the NE challenge significantly lower (P < 0.05) ZO-1 and higher MUC2 gene expression than the non-challenge group. Supplementation of 0.05 % STB with NE challenge significantly increased (P < 0.05) gross energy digestibility and decreased (P < 0.05) the number of oocysts per gram of feces compared to the NE-challenged group. Supplementation of 0.05 % STB significantly increased (P < 0.05) the VH:CD in ileum compared to the non-supplementation group. Also, supplementation of 0.05 % STB is significantly lower (P < 0.05) MUC2 and TLR4 gene expression in ileum than the non-supplementation group. At the genus level, the supplementation of 0.05 % STB with NE challenge significantly decreased (P < 0.05) the abundance of Muribaculaceae compared to the NE-challenged group on d 21. In conclusion, supplementation of 0.05 % STB in a diet could positively regulate the cecal microflora and gene expression of tight junction protein and alleviate the decline in nutrient digestibility caused by NE.},
}

@article {pmid40466051,
year = {2025},
author = {Montgomery, ST and Carr, PG and Caparrós-Martín, JA},
title = {Optimisation of DNA Extraction from Nasal Lining Fluid to Assess the Nasal Microbiome Using Third-Generation Sequencing.},
journal = {American journal of respiratory cell and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1165/rcmb.2025-0046MA},
pmid = {40466051},
issn = {1535-4989},
abstract = {Sampling nasal lining fluid (NLF) via nasosorption is minimally invasive and well tolerated, but the feasibility of assessing the nasal microbiome using these samples is unknown. However, low biomass makes airway samples particularly susceptible to issues related to contaminant DNA. For this study, we collected nasal swabs and NLF from adult volunteers. DNA was extracted from a mock microbial community and NLF using a column-based kit (ZymoBIOMICS), a precipitation-based kit (Qiagen), or a previously published precipitation-based method. Quality and quantity of DNA was assessed and short-read 16S rRNA sequencing performed to assess feasibility and extraction bias. An optimised methodology was used to extract DNA from NLF and nasal swabs, and long-read 16S rRNA sequencing performed to compare microbial profiles between NLF and nasal swabs. All extraction methods recovered DNA from the mock community, but only precipitation-based methods yielded sufficient DNA from NLF. Extraction methodologies significantly affected microbial profiles, with mechanical lysis needed to minimize bias. Profiles obtained from NLF and swabs were comparable with long-read sequencing. Our findings demonstrate the feasibility of profiling the nasal microbiome using NLF and validated two extraction methodologies as suitable for full-length 16S rRNA sequencing of low-biomass respiratory samples. Our data demonstrate the importance of unbiased DNA extraction methodologies in low-biomass respiratory samples. Additionally, we demonstrated NLF may be an appropriate surrogate for swabs to assess the nasal microbiome.},
}

@article {pmid40465720,
year = {2025},
author = {de Porto, AP and Dylla, NP and Stutz, M and Lin, H and Khalid, M and Mullowney, MW and Little, J and Rose, A and Moran, D and McMillin, M and Burgo, V and Smith, R and Woodson, C and Metcalfe, C and Ramaswamy, R and Lehmann, C and Odenwald, M and Bandealy, N and Zhao, J and Kim, M and Adler, E and Sundararajan, A and Sidebottom, A and Kress, JP and Wolfe, KS and Pamer, EG and Patel, BK},
title = {Fecal metabolite profiling identifies critically ill patients with increased 30-day mortality.},
journal = {Science advances},
volume = {11},
number = {23},
pages = {eadt1466},
doi = {10.1126/sciadv.adt1466},
pmid = {40465720},
issn = {2375-2548},
mesh = {Humans ; *Critical Illness/mortality ; *Feces/microbiology/chemistry ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; Intensive Care Units ; *Metabolome ; Dysbiosis/mortality/microbiology ; Metabolomics/methods ; Prospective Studies ; },
abstract = {Critically ill patients admitted to the medical intensive care unit (MICU) have reduced intestinal microbiota diversity and altered microbiome-associated metabolite concentrations. Metabolites produced by the gut microbiota have been associated with survival of patients receiving complex medical treatments and thus might represent a treatable trait to improve clinical outcomes. We prospectively collected fecal specimens, defined microbiome compositions by shotgun metagenomic sequencing, and quantified microbiota-derived fecal metabolites by mass spectrometry from 196 critically ill patients admitted to the MICU for non-COVID-19 respiratory failure or shock to correlate microbiota features and metabolites with 30-day mortality. Microbiota compositions of the first fecal sample after MICU admission did not independently associate with 30-day mortality. We developed a metabolic dysbiosis score (MDS) that uses fecal concentrations of 13 microbiota-derived metabolites, which predicted 30-day mortality independent of known confounders. The MDS complements existing tools to identify patients at high risk of mortality by incorporating potentially modifiable, microbiome-related, independent contributors to host resilience.},
}

Humans
*Critical Illness/mortality
*Feces/microbiology/chemistry
Male
Female
Middle Aged
*Gastrointestinal Microbiome
Aged
Intensive Care Units
*Metabolome
Dysbiosis/mortality/microbiology
Metabolomics/methods
Prospective Studies

@article {pmid40465653,
year = {2025},
author = {Mengiste, T and Liao, CJ},
title = {Contrasting Mechanisms of Defense Against Biotrophic and Necrotrophic Pathogens, 20 Years Later: What Has Changed?.},
journal = {Annual review of phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-phyto-121823-031139},
pmid = {40465653},
issn = {1545-2107},
abstract = {Significant advances have been made in understanding mechanisms of plant defense against biotrophic and necrotrophic pathogens. Whole-genome sequencing of these pathogens has uncovered the genetic underpinnings of the distinct and common virulence and defense mechanisms. Necrotrophic pathogens produce toxins, necrosis-inducing proteins, secondary metabolites, and hydrolytic enzymes, and their virulence generates endogenous plant peptides. The recognition of these factors triggers broad-spectrum quantitative resistance. Resistance to specialist, host-specific, toxin-producing pathogens is mediated by the absence of host susceptibility proteins, including nucleotide-binding leucine-rich repeats (NLRs), or by detoxification mechanisms. Biotrophic pathogens utilize distinct virulence strategies, and NLR proteins are critical determinants of resistance, interacting synergistically with other quantitative resistance factors. However, NLRs are ineffective against necrotrophs, which exploit canonical immune responses to establish and promote disease. Immune responses such as hypersensitive cell death and the production of reactive oxygen species and accumulation of hormones exhibit distinct or complex roles in defense against biotrophic and necrotrophic pathogens. Lately, the microbiome has become instrumental in uncovering novel pathogen resistance mechanisms. However, further studies are needed to understand the genes involved in recruiting defense-promoting microbes and their impact on pathogens with distinct virulence. Overall, a comprehensive understanding of mechanisms of resistance to biotrophic and necrotrophic pathogens is crucial for activating or suppressing appropriate host responses.},
}

@article {pmid40465497,
year = {2025},
author = {Shin, R and Kashyap, A and Black, TA and Rashid, RM},
title = {Exploring the Gut Microbiome's Role in Drug-Induced Photosensitivity: A Need for Deeper Investigation.},
journal = {Journal of drugs in dermatology : JDD},
volume = {24},
number = {6},
pages = {e40-e41},
pmid = {40465497},
issn = {1545-9616},
}

@article {pmid40465264,
year = {2025},
author = {Liu, M and Geng, J and Jin, S and Hu, P and Wang, X and Liu, X},
title = {Alterations of the Enteric Virome in Vogt-Koyanagi-Harada Disease.},
journal = {Investigative ophthalmology & visual science},
volume = {66},
number = {6},
pages = {15},
doi = {10.1167/iovs.66.6.15},
pmid = {40465264},
issn = {1552-5783},
mesh = {Humans ; *Uveomeningoencephalitic Syndrome/virology/microbiology ; Male ; Female ; *Virome/genetics ; Adult ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Middle Aged ; Bacteria/genetics ; Metagenomics ; Young Adult ; },
abstract = {PURPOSE: This study aims to explore the enteric virome characteristics of Vogt Koyanagi Harada (VKH) disease and its potential role in this disease.

METHODS: Shotgun metagenomic sequencing was used to detect the enteric virome and 16S rRNA to detect the bacteriome in new-onset, untreated patients with VKH (n = 25) and age- and sex-matched healthy controls without autoimmune diseases (n = 25).

RESULTS: Patients with VKH exhibited different enteric viral communities from healthy controls, characterized by decreased richness of core viral communities (present in > 80% of samples) and increased richness of common viral communities (present in 50%-80% of samples). Notably, within the core virus community, bacteriophage richness was markedly reduced, whereas eukaryotic virus richness significantly increased in patients with VKH. The case-control analysis identified 42 differentially abundant viruses, including a decrease in crAss-like phages, the eukaryotic virus Moumouvirus_moumou, and an enrichment of the Chlamydiamicrovirus_CPG1. Most of the differential phages predominantly targeted bacteria from the phyla Pseudomonadota and Firmicutes. The gut virome-bacteria community correlation analysis revealed a shift in the interactions between the core viruses and bacterial communities. Additionally, Wroclawvirus PA5oct (a Pseudomonas phage) correlated with leukotrichia, a clinically relevant symptom of VKH (P = 0.042). The impact of multiple Pseudomonas phages on the host folate biosynthesis was significantly enhanced in patients with VKH. Moreover, the protein (Earp361-372) encoded by VKH-enriched Pseudomonas was identified to share homology with the melanin antigen gp10044-59.

CONCLUSIONS: The gut virome of patients with VKH differs significantly from healthy controls, suggesting its disturbance may contribute to gut microbiome imbalance and VKH development.},
}

Humans
*Uveomeningoencephalitic Syndrome/virology/microbiology
Male
Female
*Virome/genetics
Adult
Case-Control Studies
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome
Middle Aged
Bacteria/genetics
Metagenomics
Young Adult

@article {pmid40465001,
year = {2025},
author = {Ghosh, R and Sil, D and Sharma, R and Kumar, D and Komal, K and Kumar, S and Mahajan, HS and Sharma, M and Kumar, M},
title = {Investigating postbiotics as innovative adjuvants: deciphering the gut-breast connection in breast Cancer therapy, from gut microbiome to personalized medicine.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {547},
pmid = {40465001},
issn = {1573-4978},
mesh = {Humans ; *Breast Neoplasms/therapy/microbiology/immunology ; *Gastrointestinal Microbiome/drug effects ; Precision Medicine/methods ; Female ; *Probiotics/therapeutic use ; },
abstract = {Breast cancer is the most common and deadly cancer affecting women globally. While traditional treatments - surgery, chemotherapeutic agents, radiotherapy - are used, factors damage their effectiveness: tumor heterogeneity, drug resistance, and non-targeted actions on cancer cells. Postbiotics, a newer category of biotics, confer benefits without living microorganisms and show promise against cancer. This review summarizes the link between gut microbiota and BC, postbiotic mechanisms against cancer, and their potential for personalized medicine. Postbiotics modulate the host immune system and inflammation in BC management. They target apoptotic signaling pathways, such as mitochondrial-dependent and death receptor-dependent pathways, interrupt the cell cycle, inhibit cancer cell growth, and regulate immune responses. In cancer, integrative approaches for therapies include microbiome analysis to provide personalized medical treatment, highlighting the microbiome's impact on cancer. Compared to probiotics, postbiotics have advantages, including better bioavailability, stability, and safety profiles. However, research should continue to address clinical evidence and extended studies in their production and application. The use of postbiotics as adjunctive agents in BC treatment has been highlighted for their potential to enhance standard therapy outcomes.},
}

Humans
*Breast Neoplasms/therapy/microbiology/immunology
*Gastrointestinal Microbiome/drug effects
Precision Medicine/methods
Female
*Probiotics/therapeutic use

@article {pmid40464990,
year = {2025},
author = {Peng, Z and Kang, C and Xu, Y and Zhang, C and Zhang, Y and Yan, B and Wang, S and Guo, X and Wan, X and Lv, C and Huang, L and Guo, L and Wang, H},
title = {Effects of Wild and Domesticated Seeds on the Colonization of Rhizosphere Microorganisms in Atractylodes lancea.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {59},
pmid = {40464990},
issn = {1432-184X},
support = {2023YFC3503804//National Key Research and Development Program of China/ ; 2023YFC3503804//National Key Research and Development Program of China/ ; 2023YFC3503804//National Key Research and Development Program of China/ ; 2023YFC3503804//National Key Research and Development Program of China/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; },
mesh = {*Rhizosphere ; *Seeds/microbiology/growth & development ; *Soil Microbiology ; *Atractylodes/microbiology/growth & development ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Seedlings/microbiology/growth & development ; Plant Roots/microbiology ; Domestication ; Endophytes/classification/isolation & purification/genetics ; Plant Leaves/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The domestication of plant species has played a pivotal role in shaping human civilization, yet it has also contributed to a significant reduction in the genetic diversity of crop varieties. This reduction may have profound implications for the formation and establishment of rhizosphere microbial communities in plants. This study systematically investigates microbiome dynamics during seed development in wild and domesticated Atractylodes lancea. The seeds from both wild and domesticated A. lancea exhibited shared microbial genera, while their communities were changed significantly. However, when A. lancea seeds from wild and domesticated germinated into seedlings under identical microbiological conditions, the leaves and root endophytic microbial and rhizosphere microbiome displayed similar genus. Remarkably, the rhizosphere microbial communities of the seedlings consistently enriched Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Paenibacillus, Variovorax, Conexibacter, and norank_f__Micropepsaceae. And this convergence likely arises from the shared chemotype of A. lancea and exposure to identical environmental microbiomes. In summary, this study delineates the transmission processes of A. lancea seed endophytes and identifies the dynamic patterns of microbial shifts during its development from seed to seedling. These findings contribute to a broader understanding of plant-microbe interactions and the role of microbial ecology in crop improvement.},
}

*Rhizosphere
*Seeds/microbiology/growth & development
*Soil Microbiology
*Atractylodes/microbiology/growth & development
*Microbiota
*Bacteria/classification/genetics/isolation & purification
Seedlings/microbiology/growth & development
Plant Roots/microbiology
Domestication
Endophytes/classification/isolation & purification/genetics
Plant Leaves/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid40464955,
year = {2025},
author = {Wang, Y and Li, Z},
title = {Mendelian randomization analysis unveils causal relationships between skin microbiota and osteomyelitis.},
journal = {Archives of dermatological research},
volume = {317},
number = {1},
pages = {797},
pmid = {40464955},
issn = {1432-069X},
mesh = {Humans ; *Osteomyelitis/microbiology/genetics/epidemiology ; Mendelian Randomization Analysis ; *Skin/microbiology ; *Microbiota/genetics ; Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; Skin Microbiome ; },
abstract = {BACKGROUND: Osteomyelitis results principally from endo-/exogenous bacterial infections, whose incidence that complicating bone injuries reaches approximately 30%, with the risk of disability and teratogenicity. Skin microbiota has been found to be clinically linked to osteomyelitis, but substantial evidence is lacking.

METHODS: Mendelian randomization (MR) was applied to unveil the causality between human skin microbiome and osteomyelitis. Genetic data of 1,656 skin microbiota samples were obtained from genome-wide association studies (GWAS), with the outcome of osteomyelitis from UK Biobank (UKB) database.

RESULTS: Two sample MR confirmed 12 skin microbiota strains that possessed significant causality strength with osteomyelitis, in which asv013 [S. epidermidis] (β = 0.061, P = 0.027), Genus propionibacterium (β = 0.065, P = 0.021), Family micrococcaceae (β = 0.086, P = 0.004), asv003 [Staphylococcus (unc.)] (β = 0.065, P = 0.027), and asv004 [Corynebacterium (unc.)] (β = 0.070, P = 0.016) were drivers of osteomyelitis, whilst the leaving asv037 [C. Glutamicum] (β = -0.041, P = 0.004), asv021 [Micrococcus (unc.)] (β = -0.059, P = 0.019), asv063 [Finegoldia (unc.)] (β = -0.037, P = 0.038), Order clostridiales (β = -0.043, P = 0.013), Class betaproteobacteria (β = -0.061, P = 0.004), Family clostridiales (β = -0.061, P = 0.002), and Order clostridiales (β = -0.063, P = 0.023) could be perceived as protective factors. No heterogeneity or pleiotropy in sensitivity analyses were observed, hinting the robustness of the MR findings.

CONCLUSION: This study preliminarily clarified the causal effect of skin microbiome on osteomyelitis. Strains that may significantly trigger or suppress the outcome of osteomyelitis were figured out, which may provide promising insights for the genesis and progression of osteomyelitis, thereby benefiting relevant clinical prevention and treatment.},
}

Humans
*Osteomyelitis/microbiology/genetics/epidemiology
Mendelian Randomization Analysis
*Skin/microbiology
*Microbiota/genetics
Genome-Wide Association Study
Polymorphism, Single Nucleotide
Skin Microbiome

@article {pmid40464915,
year = {2025},
author = {Kim, R and Oh, S and Woo, KA and Shin, CM and Park, KU and Lee, JY},
title = {Blood microbiome signatures in the REM sleep behavior disorder-Lewy body disease continuum.},
journal = {Journal of neural transmission (Vienna, Austria : 1996)},
volume = {},
number = {},
pages = {},
pmid = {40464915},
issn = {1435-1463},
abstract = {Although systemic inflammation triggered by alterations in microbiota from various body sites has been proposed as a potential mechanism underlying Lewy body diseases (LBDs), the association between the blood microbiome and LBDs remains uncertain. This study aimed to investigate the blood microbiome profiles across the REM sleep behavior disorder (RBD)-LBD continuum and to explore their potential as biomarkers reflecting disease phenotypes and clinical severity. Blood samples were collected from 106 patients across the RBD-LBD continuum, including 41 with isolated RBD (iRBD), 45 Parkinson's disease with probable RBD, and 20 dementia with Lewy bodies with probable RBD, as well as from 94 healthy controls. All patients were evaluated with the Movement Disorder Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) and comprehensive neuropsychological tests. Microbiome taxonomic compositions were analyzed using 16 S rRNA metagenomic sequencing. Significant microbial shifts were observed in the RBD-LBD continuum group compared to controls, with reduced microbial alpha diversity and distinct beta diversity patterns. Specifically, the genus Stenotrophomonas was enriched, while the genera Acetobacter, Enhydrobacter, and Lactobacillus were depleted in the RBD-LBD continuum group. The combined model using these genera demonstrated high predictive accuracy for the RBD-LBD continuum, with the area under the receiver-operating-characteristic curve (AUC) of 0.970 (95% confidence interval [CI]: 0.950-0.980). This model also successfully distinguished the iRBD subgroup from controls, achieving an AUC of 0.956 (95% CI, 0.914-0.987). Alpha and beta diversity were significantly associated with MDS-UPDRS Parts I and II scores in the RBD-LBD continuum group. Our findings suggest that patients within the RBD-LBD continuum may share specific blood microbiome signatures.},
}

@article {pmid40464747,
year = {2025},
author = {Zhu, H and Jin, S and Fan, S and Liu, W and Wang, Y and Ha, J and Lu, Y and Li, Z and Mi, M and Zhang, J and Liu, W and Yixi, L and Feng, F and Xu, J},
title = {Compare Phellodendri Chinensis Cortex before and after salt-water processing to ameliorate diabetic nephropathy via metabolomics and microbiome analysis.},
journal = {The Journal of pharmacy and pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jpp/rgaf033},
pmid = {40464747},
issn = {2042-7158},
support = {XZ202401ZR0004//Natural Science Foundation of Tibet Autonomous Region/ ; 300224080210//Tibet University of Tibetan Medicine School-Level Scientific Research Project/ ; 30022506016//2025 Central Support Fund for Local University Development/ ; },
abstract = {OBJECTIVES: The study aims to investigate the therapeutic effects and the underlying mechanisms of Phellodendri Chinensis Cortex (PC) and its salt-water processed form (SPC) on diabetic nephropathy (DN).

METHODS: Histopathological examination, biochemical evaluation immunohistochemistry/immunofluorescence assay were used to compare the effects of PC and SPC on DN. Intestinal microbiota was sequenced by 16S rDNA, serum differential metabolites were identified by UPLC-Q/TOF-MS to elucidate the mechanism.

RESULTS: PC and SPC could improve renal function, reduce blood glucose, proteinuria, inflammation, and oxidative stress, and restoring gut microbiota homeostasis in DN rats, with SPC showing superior efficacy. PC influenced 8 metabolites, primarily in glycerolipid metabolism and pentose and glucuronate interconversions, whereas SPC affected 30 metabolites, predominantly in pathways closely associated with glucose and lipid metabolism, including pentose and glucuronate interconversions, ether lipid metabolism and glycerophospholipid metabolism. Correlation analysis identified specific gut microbiota, such as Enterobacteriaceae, Muribaculaceae, and Lachnospiraceae, as highly correlated with the metabolic effects induced by PC and SPC.

CONCLUSION: The study provides evidence that PC and SPC have a beneficial effect on DN, with SPC exhibiting enhanced therapeutic potential. Furthermore, SPC could better restore gut microbiota diversity and structure, and improved glucose and lipid metabolism.},
}

@article {pmid40464639,
year = {2025},
author = {Zhang, Q and Liu, Y and Li, Y and Bai, G and Pang, J and Wu, M and Li, J and Zhao, X and Xia, Y},
title = {Implications of gut microbiota-mediated epigenetic modifications in intestinal diseases.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2508426},
doi = {10.1080/19490976.2025.2508426},
pmid = {40464639},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Epigenesis, Genetic ; Animals ; Dysbiosis/microbiology/therapy ; DNA Methylation ; Fecal Microbiota Transplantation ; Prebiotics/administration & dosage ; *Intestinal Diseases/microbiology/genetics/therapy ; Probiotics ; Inflammatory Bowel Diseases/microbiology/genetics/therapy ; Colorectal Neoplasms/microbiology/genetics ; },
abstract = {Intestinal diseases are highly prevalent, affecting millions worldwide and significantly contributing to global morbidity. The treatment of complex disorders, such as inflammatory bowel disease (IBD) and colorectal cancer (CRC), remains challenging due to multifactorial etiologies, diverse patient responses, and the limitations of current therapeutic strategies. Although the gut microbiota clearly plays a role in regulating the onset of intestinal diseases, few studies have explored the epigenetic factors by which the microbiota contributes to disease development. Here, the latest insights into the molecular mechanisms underlying the bidirectional influence between gut microbiota and epigenetic modifications are discussed, including DNA methylation, histone modifications, non-coding RNAs, and N6-methyladenosine (m[6]A). Importantly, mechanistic studies based on animal models or human cells have demonstrated that the gut microbiota, and other environmental factors, influence targeted gene expression and activate immune pathways through host epigenetic dysregulation, which are closely associated with the development of IBD and CRC. Furthermore, potential microbiome interventions, including probiotics, prebiotics and postbiotics, fecal microbiota transplantation (FMT), dietary modifications, and phage therapy, have been proposed as innovative therapeutic strategies to correct these abnormal epigenetic patterns associated with the diseases. Overall, addressing microbiome dysbiosis and its epigenetic consequences presents a promising frontier in the treatment of intestinal diseases, offering the potential to not only restore microbial balance but also provide more targeted and personalized therapeutic strategies for better patient outcomes.},
}

Humans
*Gastrointestinal Microbiome
*Epigenesis, Genetic
Animals
Dysbiosis/microbiology/therapy
DNA Methylation
Fecal Microbiota Transplantation
Prebiotics/administration & dosage
*Intestinal Diseases/microbiology/genetics/therapy
Probiotics
Inflammatory Bowel Diseases/microbiology/genetics/therapy
Colorectal Neoplasms/microbiology/genetics

@article {pmid40464558,
year = {2025},
author = {Ruan, Y and Zhu, T and Yang, R and Su, F and An, C and Hu, Z and Li, X and Li, Y and Chen, P and Shao, X and Qin, J and Chen, H and Chen, R},
title = {Donor-derived microbial engraftment and gut microbiota shifts associated with weight loss following fecal microbiota transplantation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0012025},
doi = {10.1128/aem.00120-25},
pmid = {40464558},
issn = {1098-5336},
abstract = {Fecal microbiota transplantation (FMT) is a promising treatment for microbiota dysbiosis and may provide metabolic benefits for obesity. However, its mechanisms and variability in clinical outcomes remain poorly understood. This 12-week multicenter, single-arm study evaluated the efficacy of FMT for weight loss and explored the role of donor-derived microbial engraftment and functional shifts in mediating weight loss among overweight and obese individuals. Twenty-three participants (body mass index ≥24 kg/m[2]) without diabetes received three biweekly FMT sessions via a nasojejunal tube. Fecal samples from participants and donors were analyzed using metagenomic sequencing. By week 12, 52% of participants were classified as responders, achieving significant weight loss of ≥5% from baseline, with an average weight loss of 7.98 ± 2.69 kg (P < 0.001). In contrast, non-responders lost 2.90 ± 1.89 kg (P < 0.001). Responders exhibited a significantly higher proportion of donor-derived microbial strains post-FMT compared to non-responders (37.8% vs 15.2%, P = 0.020). Notably, key taxa, including Phascolarctobacterium (P = 0.034) and Acidaminococcaceae (P = 0.012), increased significantly in abundance in responders post-FMT, indicating successful microbial engraftment as a critical determinant of therapeutic success. These findings suggest that FMT is a viable intervention for weight loss in obese individuals. Successful donor-derived microbial engraftment strongly correlates with weight loss efficacy, highlighting the potential of microbiota-targeted therapies in obesity management and providing insights into the mechanisms underlying FMT outcomes.IMPORTANCEPrior research indicates that fecal microbiota transplantation (FMT) is a promising treatment for diseases related to microbiota imbalance, potentially providing metabolic benefits for obesity. However, the specific role of donor-derived microbial engraftment in driving clinical efficacy has remained unclear. In this study, we evaluated the efficacy of FMT in promoting weight loss and explored the role of donor-derived bacterial strains in this process. Our findings demonstrate that the successful engraftment of specific donor-derived taxa, such as Phascolarctobacterium and Acidaminococcaceae, is strongly associated with significant weight loss. This highlights the critical interplay between donor microbiota and recipient gut environment. These findings underscore the potential of microbiota-targeted therapies as a novel strategy for obesity management.CLINICAL TRIALSThis study is registered with the Chinese Clinical Trial Registry as ChiCTR1900024760.},
}

@article {pmid40464499,
year = {2025},
author = {Zhang, X and Wan, L and Zheng, Y and Ai, Y},
title = {Gut Barrier, Microbial Metabolites, and Immune Homeostasis in Autoimmune Hepatitis: From Molecular Mechanisms to Strategies.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {30},
number = {5},
pages = {27747},
doi = {10.31083/FBL27747},
pmid = {40464499},
issn = {2768-6698},
support = {RCTJ202429//The Youth Talent Support Program of the Anhui Provincial Association for Science and Technology/ ; 8180050//National Natural Science Foundation of China Youth Project/ ; Z2023280/2023PTCM12//Technology project of China Three Gorges University/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Hepatitis, Autoimmune/immunology/microbiology/metabolism/therapy ; *Homeostasis/immunology ; Animals ; Probiotics/therapeutic use ; *Intestinal Mucosa/metabolism/immunology/microbiology ; Dysbiosis ; Bile Acids and Salts/metabolism ; },
abstract = {Autoimmune hepatitis (AIH) is a chronic immune-mediated inflammatory liver disease characterized by recurring immune-triggered hepatic injury. While scientists have yet to fully elucidate the precise triggers of AIH, contemporary research indicates that both gut microbiota and their metabolic products significantly influence AIH progression. These factors contribute to multiple mechanisms, including compromised intestinal barrier function, altered microbial and metabolite trafficking, and disrupted immune balance, leading to inflammatory responses. This review begins by exploring the intestinal microbial populations and their byproducts linked to AIH. It highlights how disrupted gut flora compromises intestinal immune defenses, enables bacterial migration from the gut to hepatic tissue, and induces liver inflammatory responses. Research validates that metabolic products from microbes, such as short-chain fatty acids (SCFAs), bile acids (BAs), and specific amino acids (glutamine, cysteine, tryptophan, and branched-chain variants, among others), interact with immune cell populations. These interactions, coupled with immune cell modifications, contribute to AIH progression. Our review identifies promising treatment strategies, including the use of probiotic supplementation, engineered prebiotic compounds, microbiota transfer procedures, and specific medications targeting gut microorganisms and their byproducts. These approaches could potentially reduce immune-triggered hepatic damage, offering potential new avenues for AIH management.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Hepatitis, Autoimmune/immunology/microbiology/metabolism/therapy
*Homeostasis/immunology
Animals
Probiotics/therapeutic use
*Intestinal Mucosa/metabolism/immunology/microbiology
Dysbiosis
Bile Acids and Salts/metabolism

@article {pmid40464118,
year = {2025},
author = {Zepeda-Rivera, MA and Dewhirst, FE and Bullman, S and Johnston, CD},
title = {Addressing controversy in Fusobacterium nomenclature: what exactly does "F. nucleatum" refer to?.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2514797},
doi = {10.1080/19490976.2025.2514797},
pmid = {40464118},
issn = {1949-0984},
mesh = {*Terminology as Topic ; Humans ; *Fusobacterium/classification/genetics ; *Fusobacterium Infections/microbiology ; *Fusobacterium nucleatum/classification/genetics ; },
abstract = {The F. nucleatum group (sensu lato) is historically composed of four subspecies (F. nucleatum subsp. animalis, F. nucleatum subsp. nucleatum, F. nucleatum subsp. polymorphum, F. nucleatum subsp. vincentii). Although F. nucleatum sensu lato members are typically associated with oral disease, they have recently been shown to disseminate to the gastrointestinal tract and are associated with adverse health conditions such as inflammatory bowel disease and colorectal cancer (CRC). A growing debate over the nomenclature applied to Fusobacterium taxonomy has resulted in different names for these lineages, shifting them from their historic subspecies designations to distinct species names (F. animalis, F. nucleatum, F. polymorphum, F. vincentii). This shift in naming scheme can lead to potentially significant confusion as "F. nucleatum" can now refer to both the group (sensu lato) and a distinct lineage (sensu stricto; historically F. nucleatum subsp. nucleatum). For example, the substantial body of literature documenting the involvement of "F. nucleatum" (sensu lato) in CRC is seemingly contradicted by recent analyses showing that "F. nucleatum" (sensu stricto) is not enriched in CRC. However, this apparent contradiction is due only to changes in the updated Fusobacterium naming scheme. Furthermore, discrepancies arising from this nomenclature shift can obscure the crucial role of other lineages in tumor biology, particularly that of F. nucleatum subsp. animalis/F. animalis. Thus, the adoption of this nomenclature reclassification without careful consideration risks misleading non-experts and sparking misinterpretation of scientific literature and discourse. Here we elaborate on the challenges of the updated Fusobacterium nomenclature scheme, propose tentative suggestions to improve accuracy and clarity, and call for a broader research community effort to discuss and implement a unified approach moving forward.},
}

*Terminology as Topic
Humans
*Fusobacterium/classification/genetics
*Fusobacterium Infections/microbiology
*Fusobacterium nucleatum/classification/genetics

@article {pmid40463962,
year = {2025},
author = {Liu, RP and Senior, A and Bao, Z and Koay, YC and Holmes, A and O'Sullivan, JF},
title = {Multi-organ multi-omic and gut microbiome markers of fat and sucrose dietary oversupply in cardiometabolic disease.},
journal = {iScience},
volume = {28},
number = {4},
pages = {111887},
pmid = {40463962},
issn = {2589-0042},
abstract = {Cardiometabolic disease is the greatest challenge facing global health. Increasingly, evidence suggests that Western diet comprising an over-supply of energy from fat and sucrose leads to obesity, insulin resistance, hypertension, and cardiovascular disease. Traditional preclinical animal studies of cardiometabolic disease often adopt a reductionist approach, focusing on individual components. To overcome this, we comprehensively assessed cardiometabolic phenotypes- anthropometric, physiological, and metabolic- along with the molecular changes consequent upon fat or sucrose dietary oversupply, or both in male C57BL/6J mice. Molecular assessment included measurement of the gut microbiome and several metabolite pools including plasma, heart, liver, and gut contents (cecal and fecal). In these mice, we identified key changes across phenotypes, metabolites, microbiota, and their interrelationship, and synthesized all the data into four distinct phenogroups that explain the variance across cardiometabolic parameters. These phenogroups provide insight into inter-organ regulation of Western diet-dependent cardiometabolic phenotypes, highlighting important avenues for further study.},
}

@article {pmid40463520,
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 = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2022.12.19.22283664},
pmid = {40463520},
abstract = {Children living with HIV (CLWH) are at high risk of colonization and infection by bacterial respiratory pathogens, though this risk can be reduced by other microbes in the upper respiratory microbiome. The impact of HIV infection on development of the upper respiratory microbiome during childhood is poorly understood, and we sought to address this knowledge gap by identifying associations between HIV infection and the nasopharyngeal microbiomes of children in Botswana. 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 the nasopharyngeal microbiomes of children by HIV status. Among the 143 children in this study, HIV infection and HIV-associated immunosuppression were associated with alterations in nasopharyngeal microbiome composition, including lower abundances of Corynebacterium species associated with respiratory health. These findings suggest that the upper respiratory microbiome may contribute to the high risk of bacterial respiratory infections among CLWH.},
}

@article {pmid40463507,
year = {2025},
author = {Seidi, S and Raz, A and Maleki-Ravasan, N and Forouzan, E and Karimian, F and Sebbane, F and Sohrabi, A and Esmaeili, S and Mostafavi, E},
title = {The interplay between species and locations shapes vector fleas microbial communities in plague foci: pathogens rather than symbionts?.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1568103},
pmid = {40463507},
issn = {2235-2988},
mesh = {Animals ; *Siphonaptera/microbiology ; *Plague/transmission/microbiology/epidemiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Symbiosis ; *Insect Vectors/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Iran/epidemiology ; Humans ; Bartonella/isolation & purification/genetics ; High-Throughput Nucleotide Sequencing ; Yersinia pestis ; DNA, Bacterial/genetics ; Phylogeny ; },
abstract = {Besides causing allergies from their bites, fleas transmit the most notorious zoonotic pathogen, Yersinia pestis. They also harbor commensal bacteria in their guts. Here, the microbial communities of fleas were characterized using 16S rRNA Next-Generation Sequencing to understand microbial interactions and functions in areas with historical plague-outbreaks in Iran with the ultimate idea of managing flea-borne diseases. Meriones persicus, Xenopsylla buxtoni and Bartonella spp. were identified as the dominant host, vector and bacterium, respectively. Six bacteria Bartonella, Sphingomonas, Wolbachia, Cardinium, Rickettsia and Ralstonia were identified as the most abundant genera in the microbiome of five flea species. More detailed surveys revealed substantial intrageneric variations (e.g. nine phylotypes for Bartonella) and the diverse nature (from biofilm-forming human pathogens to insect reproductive manipulators, and environmental microbes) for the bacteria studied. The fleas microbiome is largely affected by species and to a lesser extent by location, and circulates by both horizontal and vertical transmissions. The prevalence of Bartonella spp. infection in fleas highlights the potential to explore One Health approaches, particularly in addressing travel-related and zoonotic disease risks. Environmental drivers-such as climate change, habitat alteration, and host dynamics-shape flea microbiomes and influence disease risk, while concerns about antimicrobial resistance further complicate control efforts. Our findings advocate for coordinated strategies that combine public health education, ecological monitoring, and global collaboration to sustainably manage flea-borne diseases.},
}

Animals
*Siphonaptera/microbiology
*Plague/transmission/microbiology/epidemiology
RNA, Ribosomal, 16S/genetics
*Microbiota
Symbiosis
*Insect Vectors/microbiology
*Bacteria/classification/genetics/isolation & purification
Iran/epidemiology
Humans
Bartonella/isolation & purification/genetics
High-Throughput Nucleotide Sequencing
Yersinia pestis
DNA, Bacterial/genetics
Phylogeny

@article {pmid40463443,
year = {2025},
author = {Huang, X and Liu, Y and Jiang, F and Xin, L and Wang, Z and Hua, Z and Wang, C and Zhang, L and Yu, J},
title = {Exploring the research progression and evolutionary trends of gut microbiome and hypertension: a bibliometric analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1530857},
pmid = {40463443},
issn = {1664-302X},
abstract = {Hypertension is one of the most common cardiovascular diseases, with multiple underlying mechanisms. The gut microbiome, as one of the most important microbial communities in the human body, plays a significant role in the development of various diseases, including hypertension. While numerous studies have explored the relationship between gut microbiome and hypertension from different perspectives, there has been no bibliometric study in this field. Therefore, a bibliometric analysis is crucial for accurately assessing and summarizing the current research status. The analysis indicates that the number of publications in this field has steadily increased in recent years, with China and the United States leading in development. The journal Nutrients has the highest number of published papers, and Marques, Francine Z is a prominent figure with significant contributions and influence in this field. Co-occurrence and trend analysis suggest that the main research hotspots include the relationship between gut microbiome and hypertension, mechanisms by which gut microbiome promotes hypertension, and new therapeutic strategies targeting gut microbiome to improve hypertension. Future research trends may focus on expanding new metabolites or measurement techniques, building databases of human and animal gut microbiota and their metabolites, and developing new drugs targeting gut microbiota for hypertension. In summary, this study visually demonstrates the dynamic changes in research hotspots, revealing new patterns and focuses in the field, and aims to provide new insights for clinical work on hypertension.},
}

@article {pmid40463440,
year = {2025},
author = {Deshpande, SP and Sujith, S and Jobby, R and Rajasekharan, SK and Ravichandran, V and Solomon, AP},
title = {The gut microbiome: an emerging epicenter of antimicrobial resistance?.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1593065},
pmid = {40463440},
issn = {1664-302X},
abstract = {The human gut is one of the most densely populated microbial environments, home to trillions of microorganisms that live in harmony with the body. These microbes help with digestion and play key roles in maintaining a balanced immune system and protecting us from harmful pathogens. However, the crowded nature of this ecosystem makes it easier for harmful bacteria to acquire antimicrobial resistance (AMR) genes, which can lead to multidrug-resistant (MDR) infections. The rise of MDR infections makes treatments harder, leading to more extended hospital stays, relapses, and worse outcomes for patients, ultimately increasing healthcare costs and environmental strain. Since many MDR infections are challenging to treat, nosocomial infection control protocols and infection prevention programmes are frequently the only measures in our hands to stop the spread of these bacteria. New approaches are therefore urgently required to prevent the colonization of MDR infections. This review aims to explore the current understanding of antimicrobial resistance pathways, focusing on how the gut microbiota contributes to AMR. We have also emphasized the potential strategies to prevent the spread and colonization of MDR infections.},
}

@article {pmid40463435,
year = {2025},
author = {Strokach, A and Zoruk, P and Boldyreva, D and Morozov, M and Olekhnovich, E and Veselovsky, V and Babenko, V and Selezneva, O and Zakharevich, N and Larin, A and Koldman, S and Koldman, V and Odorskaya, M and Yunes, R and Pavlov, V and Kudryavtseva, A and Danilenko, V and Klimina, K},
title = {Comparative evaluation of sequencing technologies and primer sets for mouse gut microbiota profiling.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1584359},
pmid = {40463435},
issn = {1664-302X},
abstract = {BACKGROUND: Advancements in sequencing technologies, such as Illumina and Oxford Nanopore Technologies (ONT), have significantly improved microbiome research. However, variations in sequencing platforms, primer selection, and DNA quality may influence microbial diversity assessments, particularly in studies of gut microbiota. This study systematically evaluates these factors in mouse gut microbiota analysis, comparing 16S rRNA gene sequencing and metagenome sequencing (MS) across both platforms.

RESULTS: Our findings highlight the critical influence of primer selection on 16S rRNA sequencing results, with certain primer combinations detecting unique taxa that others miss. Despite these variations in taxonomic resolution, all tested primer sets consistently revealed significant differences between experimental groups, indicating that key microbial shifts induced by bacterial cultures remain detectable regardless of primer choice. A comparative analysis of Illumina and ONT 16S rRNA sequencing revealed notable differences in microbial diversity profiling, with ONT capturing a broader range of taxa. In contrast, MS on both platforms showed a high degree of correlation, indicating that ONT sequencing errors have minimal impact on taxonomic diversity estimations. Furthermore, the type of extracted DNA (high molecular weight vs. standard DNA) had little on microbial diversity outcomes, underscoring the robustness of these sequencing technologies.

CONCLUSION: These results highlight the advantages and limitations of different sequencing strategies in microbiota research. While 16S rRNA sequencing remains a cost-effective tool for assessing bacterial diversity, MS provides superior taxonomic resolution and more precise species identification. Our study advocates for a hybrid approach that combines multiple sequencing technologies to achieve a more comprehensive and accurate representation of microbial communities.},
}

@article {pmid40463434,
year = {2025},
author = {Asgharzadeh, S and Pourhajibagher, M and Bahador, A},
title = {The microbial landscape of tumors: a deep dive into intratumoral microbiota.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1542142},
pmid = {40463434},
issn = {1664-302X},
abstract = {Microorganisms in the human body play crucial roles in various health and disease processes. Research indicates that diverse bacterial species are implicated in numerous cancer types. Apart from its involvement in cancer initiation and progression, the microbiome holds promise as a biomarker for diagnosing cancer, assessing risk, and determining prognosis. Intratumoral microbes profoundly impact tumor biology by regulating the initiation and progression of tumors and modulating their response to chemotherapy, radiotherapy, and immunotherapy. A deeper understanding of the role of the intratumoral microbiome in cancer requires further investigation into its effects and underlying mechanisms. This review delves into the significance of intratumoral bacteria in cancer initiation, progression, and metastasis, their impact on cancer treatment outcomes, and Approaches Employed for Profiling the Intratumoral Microbiome.},
}

@article {pmid40463375,
year = {2025},
author = {Fredericks, MN and Kolodner, Z and Waalkes, A and Sawatzki, K and Hao, L and Long, DR and Penewit, K and Midkiff, CC and McCormick, CJ and Beraki, S and Edlefsen, PT and Barrow, J and Greninger, AL and Gale, M and Blair, RV and Salipante, SJ and Fuller, DH and O'Connor, MA},
title = {SIV/SARS-CoV-2 coinfection in rhesus macaques impacts viral shedding, host immunity, the microbiome, and viral evolution.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1587688},
pmid = {40463375},
issn = {1664-3224},
mesh = {Animals ; Macaca mulatta ; *Virus Shedding ; *COVID-19/immunology/virology ; *SARS-CoV-2/immunology/physiology/genetics ; *Simian Immunodeficiency Virus/immunology/physiology ; *Simian Acquired Immunodeficiency Syndrome/immunology/virology ; *Coinfection/immunology/virology ; Disease Models, Animal ; *Microbiota/immunology ; Antibodies, Viral/immunology/blood ; },
abstract = {People living with HIV (PLWH) have an increased risk of severe COVID-19, including prolonged viral shedding and emergence of mutations. To investigate the simian immunodeficiency virus (SIV) macaque model for HIV/SARS-CoV-2 coinfection, seven SIV+ rhesus macaques were co-infected with SARS-CoV-2. COVID-19 in all macaques was mild. SARS-CoV-2 replication persisted in the upper, but not the lower respiratory tract for 14 days post-infection. Animals showed impaired generation of anti-SARS-CoV-2 antibodies and T-cells. Animals also displayed transient changes in microbial communities in the upper airway and gastrointestinal tract. Evidence of SARS-CoV-2 evolution was observed in the upper respiratory tract. This study demonstrates that SIV/SARS-CoV-2 coinfection in rhesus macaques recapitulates aspects of COVID-19 in PLWH. We show that SIV impairs anti-SARS-CoV-2 immunity, potentially leading to prolonged viral shedding, altered pathogenesis, and viral evolution. This highlights the importance of HIV status in COVID-19 and supports the use of this model for HIV/SARS-CoV-2 coinfection.},
}

Animals
Macaca mulatta
*Virus Shedding
*COVID-19/immunology/virology
*SARS-CoV-2/immunology/physiology/genetics
*Simian Immunodeficiency Virus/immunology/physiology
*Simian Acquired Immunodeficiency Syndrome/immunology/virology
*Coinfection/immunology/virology
Disease Models, Animal
*Microbiota/immunology
Antibodies, Viral/immunology/blood

@article {pmid40463287,
year = {2025},
author = {Mahant, AM and Fong, V and Gromisch, M and Hunte, R and Michael, I and Aguilan, JT and Murphy, K and Keller, MJ and Herold, BC},
title = {Neutralizing Activity of Cervicovaginal Secretions against Herpes Simplex Virus is Mediated by Mucosal IgG and Viral Glycoprotein E and Adversely Impacted by Vaginal Dysbiosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.15.654401},
pmid = {40463287},
issn = {2692-8205},
abstract = {Genital herpes simplex virus (HSV) recurrences are more common in women with bacterial vaginosis (BV). Prior studies demonstrated that genital tract secretions exhibit variable neutralizing activity against HSV, independent of serostatus, but the relationship of this activity to the vaginal microbiome and underlying mechanisms have not been defined. To test the hypothesis that cervicovaginal antiviral activity is lower in women with BV, we took advantage of cervicovaginal lavage (CVL) available from two studies conducted among women with symptomatic BV and healthy controls. CVL obtained from women with BV had significantly less antiviral activity than controls (p< 0.001). Inhibitory activity correlated negatively and most strongly with Shannon diversity index (p<0.0001). The innate activity did not differ comparing HSV-seropositive versus seronegative participants and no HSV-specific antibodies were detected in CVL. Activity was enriched in the immunoglobulin fraction but was lost when IgG (but not IgA) was depleted. Increasing doses of an anti-glycoprotein E (gE) monoclonal antibody overcame the neutralizing activity, suggesting that interactions between the Fc region of IgG and gE, a viral Fc gamma receptor (FcγR), contribute. Consistent with this notion, CVL had less HSV inhibitory activity against a gE-null virus. Glycan analysis demonstrated a decrease in mature glycans in IgG from CVL with low antiviral activity and treatment of CVL with peptide N-glycanase F, which cleaves N-glycans in IgG, resulted in a loss of HSV inhibitory activity. We speculate that glycosidases elaborated by anaerobic bacteria cleave Fc glycans, resulting in decreased affinity for gE and a reduction in protective activity. IMPORTANCE: This study provides a mechanistic link for the increased risk of HSV infection and replication in the setting of symptomatic bacterial vaginosis and asymptomatic vaginal dysbiosis. Independent of Fab antigen specificity, the Fc region of mucosal IgG may neutralize HSV by binding to glycoprotein E, a viral Fc receptor. Vaginal dysbiosis leads to a loss of Fc glycans and a concomitant decrease in this innate antiviral activity. These findings suggest that viral Fc receptors, previously thought to function only in immune evasion, may also play a protective role. The results highlight the importance of developing and implementing strategies to protect against vaginal dysbiosis.},
}

@article {pmid40463244,
year = {2025},
author = {Alqudah, S and DeLucia, B and Osborn, LJ and Markley, RL and Bobba, V and Preston, SM and Thambidurai, T and Nia, LH and Fulmer, CG and Sangwan, N and Nemet, I and Claesen, J},
title = {Gut microbial conversion of dietary elderberry extract to hydrocinnamic acid improves obesity-associated metabolic disorders.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.18.654739},
pmid = {40463244},
issn = {2692-8205},
abstract = {Obesity-associated metabolic disorders such as type 2 diabetes mellitus and metabolic dysfunction associated fatty liver disease are major global health concerns, yet current pharmacological treatments often present with major side-effects. Dietary interventions including polyphenol-rich foods offer a promising complementary option for obesity amelioration, but their efficacy is dependent on specific gut microbial metabolism and the underlying molecular mechanisms mostly remain elusive. Here, we demonstrated that dietary elderberry (Eld) extract abrogates the effects of an obesogenic diet in a gut microbiota-dependent manner, by preventing insulin resistance and reducing hepatic steatosis in mice. We developed a targeted, quantitative liquid chromatography-tandem mass spectrometry method for detection of gut bacterial polyphenol catabolites and identified hydrocinnamic acid as a key microbial metabolite, enriched in the portal vein plasma of Eld supplemented animals. Next, we showed that hydrocinnamic acid potently activates hepatic AMP-activated protein kinase α, explaining its role in improved liver lipid homeostasis. Furthermore, we uncovered the metabolic pathway cumulating in hydrocinnamic acid production in the common gut commensal Clostridium sporogenes . Our characterization of hydrocinnamic acid as a diet-derived, and microbiota-dependent metabolite with insulin-sensitizing and anti-steatotic activities will contribute to microbiome-targeted dietary interventions to prevent and treat obesity-associated metabolic diseases.},
}

@article {pmid40463208,
year = {2025},
author = {Mulay, SA and Vishnivetskaya, TA and Hochanadel, LH and Klingeman, DM and Lloyd, KG and Pelletier, DA and Podar, M},
title = {BONCAT-Live for isolation and cultivation of active environmental microbes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.14.654084},
pmid = {40463208},
issn = {2692-8205},
abstract = {UNLABELLED: In diverse environments, microbes drive a myriad of processes, from geochemical and nutrient cycling to interspecies interactions, including in association with plants and animals. Their physiological state is dynamic and impacted by abiotic and biotic conditions, responding to environmental fluctuations by changes in cellular metabolism, according to their genetic potential. Molecular, cellular and genomic approaches can identify and measure microbial responses and adaptation to environmental changes in native communities. However, isolating the individual microbes that respond to specific changes has been difficult. To address that, we implemented BONCAT-Live, by integrating bio-orthogonal non-canonical amino acid tagging (BONCAT) in diverse native communities, with isolation and cultivation of cells responding to specific stimuli, at different time scales. In frozen Arctic permafrost samples, we identified and isolated dormant bacteria that become active after thawing under native or nutrient enriched conditions. From a Populus tree rhizosphere, we isolated strains that thrive under high concentrations of root exudates that act as defense compounds and nutrients. In the human oral microbiome, we identified and isolated bacteria that rapidly proliferated when exposed to metabolites provided by the host or other co-occurring microbes. Further characterization of isolated bacterial strains will provide opportunities for in depth determination of how these microbes adapt to changes in their environments, individually and as part of model communities.

IMPORTANCE: Dynamic microbial activity transforms environments and impacts health and disease in associations with plants and animals, including humans. Identifying the contribution of individual microbes to those processes in real time has not been generally compatible with their selective cultivation. BONCAT-Live tracks which microbes in environmental samples are translationally active and couples it with single cell isolation and cultivation. By studying the response of individual community member to specific natural or induced physical or chemical changes in the environment and culturing those organisms, BONCAT-Live enables further insights into microbial metabolic strategies, community dynamics and environmental adaptations.},
}

@article {pmid40463026,
year = {2025},
author = {Fulcher, JA and Newman, K and Pham, B and Li, F and Cho, GD and Elliott, J and Tobin, NH and Shoptaw, S and Gorbach, PM and Aldrovandi, GM},
title = {Comparison of oral and gut microbiome highlights role of oral bacteria in systemic inflammation in HIV.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.16.654362},
pmid = {40463026},
issn = {2692-8205},
abstract = {BACKGROUND: Chronic HIV-1 infection is associated with increased inflammation-related comorbidities, despite effective viral suppression with antiretroviral therapy. While the role of the gut microbiome in inflammation is well-studied, the contribution of the oral microbiome remains less clear. This study investigates the relationship between the oral and gut microbiomes in driving systemic inflammation in persons with HIV.

METHODS: This cross-sectional study utilized archived samples from 198 participants (99 with HIV and 99 without HIV). Oral microbiome composition was analyzed via 16S rRNA sequencing and systemic inflammatory biomarkers were measured using multiplex assays. Gut microbiome data from previous studies were integrated for comparative analyses. Bacterial inflammatory potential was assessed through in vitro co-culture and epithelial barrier permeability assays.

RESULTS: The oral microbiome in HIV was characterized by increased Veillonella, Capnocytophaga , and Megasphaera , and several decreased genera including Fusobacterium . Using PERMANOVA, we found that the oral microbiome was a significant driver of cytokine variation in HIV compared to the gut microbiome, and identified specific associations with oral Veillonella and Megasphaera . We found no differences in anti- Veillonella parvula serum IgG by HIV status, but IgG titers did correlate with microbial translocation markers sCD14 and LBP in HIV. In vitro studies demonstrated that Veillonella parvula increased oral epithelial barrier permeability and induced monocyte activation.

CONCLUSIONS: The oral microbiome, particularly Veillonella parvula , may contributes to systemic inflammation in HIV through mechanisms involving epithelial barrier disruption, oral translocation, and monocyte activation.},
}

@article {pmid40462952,
year = {2025},
author = {Zhou, H and Chen, J and Zhang, X},
title = {BMDD: A Probabilistic Framework for Accurate Imputation of Zero-inflated Microbiome Sequencing Data.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.08.652808},
pmid = {40462952},
issn = {2692-8205},
abstract = {UNLABELLED: Microbiome sequencing data are inherently sparse and compositional, with excessive zeros arising from biological absence or insufficient sampling. These zeros pose significant challenges for downstream analyses, particularly those that require log-transformation. We introduce BMDD (BiModal Dirichlet Distribution), a novel probabilistic modeling framework for accurate imputation of microbiome sequencing data. Unlike existing imputation approaches that assume unimodal abundance, BMDD captures the bimodal abundance distribution of the taxa via a mixture of Dirichlet priors. It uses variational inference and a scalable expectation-maximization algorithm for efficient imputation. Through simulations and real microbiome datasets, we demonstrate that BMDD outperforms competing methods in reconstructing true abundances and improves the performance of differential abundance analysis. Through multiple posterior samples, BMDD enables robust inference by accounting for uncertainty in zero imputation. Our method offers a principled and computationally efficient solution for analyzing high-dimensional, zero-inflated microbiome sequencing data and is broadly applicable in microbial biomarker discovery and host-microbiome interaction studies. BMDD is available at: https://github.com/zhouhj1994/BMDD .

AUTHOR SUMMARY: Understanding the microbes living in and on our bodies-the microbiome-relies on analyzing complex sequencing data. However, these data often contain many zeros, either because a microbe is truly absent or simply missed due to insufficient sampling. These missing values make it hard to accurately analyze microbial patterns and identify important differences between groups, especially for methods that work on a log scale. To address this, we developed a new method called BMDD that uses a more realistic model to impute the zeros. Unlike existing tools that assume each microbe follows an unimodal abundance distribution, BMDD allows for microbes to follow a bimodal distribution, so they could behave differently in different conditions. It provides not just a single guess, but a range of possible values to better reflect the uncertainty. Our testing shows that BMDD more accurately recovers the true microbial profiles and improves the ability to detect meaningful differences between groups. This method can help researchers gain clearer insights into how the microbiome affects health and disease.},
}

@article {pmid40462927,
year = {2025},
author = {Imes, AM and Pavelsky, MN and Badal, K and Kamp, DL and Briseño, JL and Sakmar, T and Vogt, MA and Nyholm, SV and Heath-Heckman, EAC and Grasse, B and Septer, AN and Mandel, MJ},
title = {Euprymna berryi as a comparative model host for Vibrio fischeri light organ symbiosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.10.632448},
pmid = {40462927},
issn = {2692-8205},
abstract = {UNLABELLED: Functional studies of host-microbe interactions benefit from natural model systems that enable exploration of molecular mechanisms at the host-microbe interface. Bioluminescent Vibrio fischeri colonize the light organ of the Hawaiian bobtail squid, Euprymna scolopes , and this binary model has enabled advances in understanding host-microbe communication, colonization specificity, in vivo biofilms, intraspecific competition, and quorum sensing. The hummingbird bobtail squid, Euprymna berryi, can be generationally bred and maintained in lab settings and has had multiple genes deleted by CRISPR approaches. The prospect of expanding the utility of the light organ model system by producing multigenerational host lines led us to determine the extent to which the E. berryi light organ symbiosis parallels known processes in E. scolopes . However, the nature of the E. berryi light organ, including its microbial constituency and specificity for microbial partners, have not been examined. In this report, we isolate bacteria from E. berryi animals and tank water. Assays of bacterial behaviors required in the host, as well as host responses to bacterial colonization, illustrate largely parallel phenotypes in E. berryi and E. scolopes hatchlings. This study reveals E. berryi to be a valuable comparative model to complement studies in E. scolopes .

IMPORTANCE: Microbiome studies have been substantially advanced by model systems that enable functional interrogation of the roles of the partners and the molecular communication between those partners. The Euprymna scolopes-Vibrio fischeri system has contributed foundational knowledge, revealing key roles for bacterial quorum sensing broadly and in animal hosts, for bacteria in stimulating animal development, for bacterial motility in accessing host sites, and for in vivo biofilm formation in development and specificity of an animal's microbiome. Euprymna berryi is a second bobtail squid host, and one that has recently been shown to be robust to laboratory husbandry and amenable to gene knockout. This study identifies E. berryi as a strong symbiosis model host due to features that are conserved with those of E. scolopes , which will enable extension of functional studies in bobtail squid symbioses.},
}

@article {pmid40462844,
year = {2025},
author = {Morra, M and Marradi, D and Gandini, L and Ivagnes, V and Ottolini, G and Bovio, A and Jabali, G and Maraschi, L and Dada, IA and Chawanda, TV and Gorla, M and Tarasiuk, O and Mocchetti, C and Soluri, MF and Boccafoschi, F and Sblattero, D and Cotella, D},
title = {A non-hypothesis-driven practical laboratory activity on functional metagenomics: "fishing" protein-coding DNA sequences from microbiomes.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1602982},
pmid = {40462844},
issn = {2296-4185},
abstract = {Practical laboratory of the most functional metagenomics courses focuses on activities aimed at providing specific skills in bioinformatics through the analysis of genomic datasets. However, sequence-based analyses of metagenomes should be complemented by function-based analyses, to provide evidential knowledge of gene function. A "true" functional metagenomic approach relies on the construction and screening of metagenomic libraries - physical libraries that contain DNA cloned from metagenomes of various origin. The information obtained from functional metagenomics will help in future annotations of gene function and serve as a complement to sequence-based metagenomics. Here, we describe a simple protocol for the construction of a metagenomic DNA library, optimized and tested by a team of undergraduate biotechnology students. This protocol is based on a technique developed in our laboratory and currently used for research. Using this protocol, libraries of protein domains can be quickly generated, from the DNA of any intron-less genome, such as those of bacteria or phages. Therefore, these libraries provide a valuable platform for training students in various validation tools, including computational methods - for example, metagenome assembly, functional annotation - and proteomics techniques, including protein expression and analysis. By varying the biological source and validation pipeline, this approach offers virtually limitless opportunities for innovative thesis research projects.},
}

@article {pmid40462511,
year = {2025},
author = {Qian, LM and Wang, SX and Zhou, W and Qin, ZX and Wang, YN and Zhao, Q and Xu, RH},
title = {Individualized metagenomic network model for colorectal cancer diagnosis: insights into viral regulation of gut microecology.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {3},
pages = {},
doi = {10.1093/bib/bbaf208},
pmid = {40462511},
issn = {1477-4054},
support = {Y-HR2020QN-0474//Beijing Xisike Clinical Oncology Research Foundation/ ; 84000-31630002//Sun Yat-sen University clinical research 5010 program/ ; CIRP-SYSUCC-0004//Cancer Innovative Research Program of Sun Yat-sen University Cancer Center/ ; 2019-I2M-5-036//CAMS Innovation Fund for Medical Sciences (CIFMS)/ ; 82173128//National Natural Science Foundation of China/ ; 81930065//National Natural Science Foundation of China/ ; 82321003//National Natural Science Foundation of China/ ; },
mesh = {*Colorectal Neoplasms/diagnosis/virology/microbiology/genetics ; Humans ; *Gastrointestinal Microbiome ; *Metagenomics/methods ; *Metagenome ; Dysbiosis/virology ; },
abstract = {The role of gut microbiota, especially viruses, in colorectal cancer (CRC) pathogenesis remains unclear. This study investigated the interplay between gut microbiota and CRC development. We developed a viral/bacterial sequence analysis pipeline to reanalyze gut metagenomic datasets from eight CRC studies. A multisample co-occurrence network was constructed to delineate microbiota species interconnections. Our analysis confirmed dysbiosis in CRC patients and revealed enrichment of viral species, particularly those hosted by Lactococcus and Escherichia. These viruses were identified as central hubs in the multikingdom interaction network. We developed a network-based model using single sample networks (SSN) that distinguished CRC patients from controls with an area under the curve (AUC) of 0.93. Models combining relative abundance and SSN assessment achieved an AUC of 0.97, outperforming SSN-based models without viral data. This study highlights the crucial role of viruses in the gut microbiome network and their potential as targets for CRC prevention and intervention. Our approach offers a new perspective on noninvasive diagnostic criteria for CRC.},
}

*Colorectal Neoplasms/diagnosis/virology/microbiology/genetics
Humans
*Gastrointestinal Microbiome
*Metagenomics/methods
*Metagenome
Dysbiosis/virology

@article {pmid40462354,
year = {2025},
author = {Li, X and Xu, L and Demaree, B and Noecker, C and Bisanz, JE and Weisgerber, DW and Modavi, C and Turnbaugh, PJ and Abate, AR},
title = {Microbiome Single Cell Atlases Generated with a Commercial Instrument.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2409338},
doi = {10.1002/advs.202409338},
pmid = {40462354},
issn = {2198-3844},
support = {//Florida State University Start-up fund/ ; COA7000-138420-7030928-45-A73H5//UCSF Benioff Center for Microbiome Medicine (BCMM) Trainee Pilot Award/ ; R01HG008978//Foundation for the National Institutes of Health/ ; U01AI129206//Foundation for the National Institutes of Health/ ; R01AI149699//Foundation for the National Institutes of Health/ ; R01EB019453//Foundation for the National Institutes of Health/ ; R01HL122593//Foundation for the National Institutes of Health/ ; R01AT011117//Foundation for the National Institutes of Health/ ; F32GM140808//Foundation for the National Institutes of Health/ ; },
abstract = {Single-cell sequencing is useful for resolving complex systems into their composite cell types and computationally mining them for unique features that are masked in pooled sequencing. However, while commercial instruments have made single-cell analysis widespread for mammalian cells, analogous tools for microbes are limited. Here, EASi-seq (Easily Accessible Single microbe sequencing) is presented. By adapting the single-cell workflow of the commercial Mission Bio Tapestri instrument, this method allows for efficient sequencing of individual microbial genomes. EASi-seq allows tens of thousands of microbes to be sequenced per run and, as it is shown, can generate detailed atlases of human and environmental microbiomes. The ability to capture large genome datasets from thousands of single microbes provides new opportunities in discovering and analyzing species subpopulations. To facilitate this, a companion bioinformatic pipeline is developed that clusters genome by sequence similarity, improving whole genome assembly, strain identification, taxonomic classification, and gene annotation. In addition, the integration of metagenomic contigs with the EASi-seq datasets is demonstrated to reduce capture bias and increase coverage. EASi-seq enables high-quality single-cell genomic sequencing for microbiome samples using a simple workflow run on a commercially available platform.},
}

@article {pmid40462248,
year = {2025},
author = {García-Sánchez, JC and Rovito, SM},
title = {Differences in composition and potential function of the bacterial communities of cave- and surface-dwelling Mexican salamanders.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {56},
pmid = {40462248},
issn = {2524-4671},
support = {Problemas Nacionales FOINS 2015 #721//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; Problemas Nacionales FOINS 2015 #721//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; },
abstract = {Caves are a challenging environment for many organisms to inhabit, and many cave-dwelling animals are endemic to particular cave systems. Microorganisms in caves have been shown to have a high biosynthetic capacity, likely as a result of intense biological interactions to deal with resource scarcity. Although cave salamanders have been studied extensively in other parts of the world, they have received relatively little attention in Mexico. Declines of some cave-dwelling species may be due to outbreaks of fungal disease, and a better understanding of their cutaneous microbiome could help with future conservation efforts in the face of disease outbreaks. We characterized the cutaneous microbiome of 11 cave-dwelling Mexican salamanders and their relatives from surface environments using high-throughput 16S amplicon sequencing. We expected cave salamanders to have a more diverse microbiome containing more bacteria with potential antifungal capacity compared to forest salamanders. We also estimated networks of associations between bacteria to test the hypothesis that there are more positive associations in caves. Finally, we used a bioinformatic approach to see if bacteria in caves potentially have more metabolic pathways associated with microbial communication as a result of more intense biological interactions in caves. Although we do not find higher skin bacterial diversity in caves compared to forests, we do find differences in microbiome composition between environments, more positive associations between bacteria, and a slightly higher number of metabolic pathways associated with microbial communication in caves. Our results provide some support for an impact of the cave environment on the skin microbiome of Mexican salamanders.},
}

@article {pmid40462245,
year = {2025},
author = {Min, X and Aldar, and Jian, G},
title = {Dietary Supplementation With Mannitol Regulates the Rumen and Intestinal Microbiome, Immune Function, and Antioxidant Capacity of Grazed Mongolian Sheep.},
journal = {Animal science journal = Nihon chikusan Gakkaiho},
volume = {96},
number = {1},
pages = {e70074},
doi = {10.1111/asj.70074},
pmid = {40462245},
issn = {1740-0929},
support = {2020LH03011//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; 2023LHMS03047//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; 2022JBQN088//Fundamental Research Funds for the Inner Mongolia Normal University/ ; },
mesh = {Animals ; *Mannitol/administration & dosage/pharmacology ; *Rumen/microbiology/metabolism/immunology ; Sheep/immunology/microbiology/metabolism/physiology ; *Gastrointestinal Microbiome/drug effects ; *Antioxidants/metabolism ; *Dietary Supplements ; *Diet/veterinary ; *Animal Nutritional Physiological Phenomena ; Animal Feed ; Fermentation/drug effects ; *Intestines/microbiology ; },
abstract = {This study aimed to investigate the short-term effects of mannitol supplementation on grazing Mongolian sheep, including ruminal and intestinal microbiome, serum biochemical parameters, and immune and antioxidant functions. Ten sheep were randomly divided into control and experimental groups (n = 5) receiving without or with 10 g/kg mannitol, respectively. After 20 days, including a 5-day adaptation, mannitol did not affect the average daily gain and rumen fermentation but significantly altered microbial composition, as evidenced by principal coordinates' analysis. The abundances of genera including Rikenellaceae_RC9_gut_group increased notably in the rumen, and those of Alistipes and Norank_f_Muribaculaceae increased in intestine with mannitol supplementation. Mannitol increased the serum concentrations of total protein, albumin, retinol-binding protein, paraoxonase, and total cholesterol and decreased alanine aminotransferase levels. Mannitol also increased the levels of immunoglobulins, interleukins, tumor necrosis factor, interferon, and complements and antioxidant enzyme activities while reducing malondialdehyde and hydrogen peroxide concentrations. The serum total protein positively correlated with Rikenellaceae_RC9_gut_group and Alistipes while negatively correlated with superoxide dismutase and specific microbial genera. Taken together, mannitol supplementation reshapes ruminal and intestinal microbial communities, improving serum biomarkers, immune responses, and antioxidant defenses in grazing Mongolian sheep. These findings offer insights into novel feeding strategies for the management of grazing sheep.},
}

Animals
*Mannitol/administration & dosage/pharmacology
*Rumen/microbiology/metabolism/immunology
Sheep/immunology/microbiology/metabolism/physiology
*Gastrointestinal Microbiome/drug effects
*Antioxidants/metabolism
*Dietary Supplements
*Diet/veterinary
*Animal Nutritional Physiological Phenomena
Animal Feed
Fermentation/drug effects
*Intestines/microbiology

@article {pmid40462143,
year = {2025},
author = {Kindtler, NL and Sheikh, S and Zervas, A and Ellegaard-Jensen, L and Feld, L and Scheel, M and Jiménez, FC and da Fonseca, RR and Laursen, KH and Jacobsen, CS and Ekelund, F},
title = {Small sample amounts from rhizosphere of barley maintain microbial community structure and diversity revealed by total RNA sequencing.},
journal = {Plant methods},
volume = {21},
number = {1},
pages = {79},
pmid = {40462143},
issn = {1746-4811},
abstract = {Total RNA sequencing is a crucial technique in microbial ecology for profiling active microbial communities in various environments, including the rhizosphere. Since total RNA sequencing yields both 16 S and 18 S ribosomal RNA (rRNA), it is effective for taxonomic profiling of the full microbial community in a sample. However, the effectiveness of this approach with limited initial sample amounts remains unclear. In this study, we grew barley in a growth system designed for highly controlled plant experiments using an inert growth medium inoculated with a soil microbiome. Our objectives were two-fold: firstly, to test the feasibility of extracting total RNA from the rhizosphere of barley grown in an inert growth medium consisting of sand and perlite. Secondly, we aimed to address the challenge of extracting comprehensive taxonomic information from minimal amounts of rhizosphere samples from barley plants, using three different amounts of freeze-dried rhizosphere material: 10, 40, and 200 mg. We showed that although smaller sample amounts yielded lower concentrations of extracted RNA, this did not significantly influence the diversity or composition of the rhizosphere microbiome as indicated by SSU rRNA. Our results demonstrate that total RNA sequencing, focusing on SSU rRNA, robustly captures the taxonomic diversity of active rhizosphere microbial communities, even in small initial sample amounts. Effective use of smaller samples opens new possibilities for detailed studies in environments where sample quantity is limited. We also conclude that the growth system applied in this experiment is suitable for highly controlled plant experiments focusing on total RNA extraction from the rhizosphere.},
}

@article {pmid40462080,
year = {2025},
author = {Kobayashi, Y and Fujiwara, N and Murakami, Y and Ishida, S and Kinguchi, S and Haze, T and Azushima, K and Fujiwara, A and Wakui, H and Sakakura, M and Terayama, K and Hirawa, N and Isozaki, T and Yasuzaki, H and Takase, H and Yano, Y and Tamura, K},
title = {Visualizing fatigue mechanisms in non-communicable diseases: an integrative approach with multi-omics and machine learning.},
journal = {BMC medical informatics and decision making},
volume = {25},
number = {1},
pages = {204},
pmid = {40462080},
issn = {1472-6947},
mesh = {Humans ; *Machine Learning ; Female ; *Noncommunicable Diseases ; Male ; Middle Aged ; *Fatigue/metabolism/etiology/genetics/microbiology ; Saliva/chemistry ; Adult ; *Metabolomics ; Microbiota ; Biomarkers ; Aged ; Multiomics ; },
abstract = {BACKGROUND: Fatigue is a prevalent and debilitating symptom of non-communicable diseases (NCDs); however, its biological basis are not well-defined. This exploratory study aimed to identify key biological drivers of fatigue by integrating metabolomic, microbiome, and genetic data from blood and saliva samples using a multi-omics approach.

METHODS: Metabolomic, microbiome, and single nucleotide polymorphisim analyses were conducted on saliva and blood samples from 52 patients with NCDs. Fatigue dimensions were assessed using the Multidimensional Fatigue Inventory and correlated with biological markers. LightGBM, a gradient boosting algorithm, was used for fatigue prediction, and model performance was evaluated using the F1-score, accuracy, and receiver operating characteristic area under the curve using leave-one-out cross-validation. Statistical analyses included correlation tests and multiple comparison adjustments (p < 0.05; false discovery rate <0.05). This study was approved by the Yokohama City University Hospital Ethics Committee (F230100022).

RESULTS: Plasmalogen synthesis was significantly associated with physical fatigue in both blood and saliva samples. Additionally, homocysteine degradation and catecholamine biosynthesis in the blood were significantly associated with mental fatigue (Holm p < 0.05). Microbial imbalances, including reduced levels of Firmicutes negativicutes and Patescibacteria saccharimonadia, correlated with general and physical fatigue (r = - 0.379, p = 0.006). Genetic variants in genes, such as GPR180, NOTCH3, SVIL, HSD17B11, and PLXNA1, were linked to various fatigue dimensions (r range: -0.539-0.517, p < 0.05). Machine learning models based on blood and salivary biomarkers achieved an F1-score of approximately 0.7 in predicting fatigue dimensions.

CONCLUSION: This study provides preliminary insights into the potential involvement of alterations in lipid metabolism, catecholamine biosynthesis disruptions, microbial imbalances, and specific genetic variants in fatigue in patients with NCDs. These findings lay the groundwork for personalized interventions, although further validation and model refinement across diverse populations are needed to enhance the prediction performance and clinical applicability.},
}

Humans
*Machine Learning
Female
*Noncommunicable Diseases
Male
Middle Aged
*Fatigue/metabolism/etiology/genetics/microbiology
Saliva/chemistry
Adult
*Metabolomics
Microbiota
Biomarkers
Aged
Multiomics