@article {pmid40577235,
year = {2025},
author = {Mazinani, S and Aghazadeh, M and Poortahmasebi, V and Arafi, V and Hasani, A},
title = {Cervical cancer pathology and vaginal and gut microbiota: conception of the association.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf088},
pmid = {40577235},
issn = {1472-765X},
abstract = {The role of gut and vaginal microbiota has been examined as potential markers in the progression of cervical cancer and inspired heightened attention. We attempted to identify the current status, the influence of changing trends in the gut and vaginal microbiota, and their impact on cervical cancer. All publications were searched in online databases such as PubMed, Scopus, Medline, and Google Scholar using the keywords "cervical cancer," "vaginal microbiota," "gut microbiota," "dysbiosis," "cervical intraepithelial neoplasia," and "HPV." Growing evidence that gut microbiota dysbiosis is involved in many diseases has attracted many researchers. The vaginal microbiome is a micro-ecosystem complex that undergoes continuous fluctuations throughout a woman's life. Decrease in Lactobacilli spp. Levels can lead to an overgrowth of anaerobic bacteria, resulting in bacterial vaginosis that accounts for adverse health outcomes, including increased susceptibility to sexually transmitted infections, including human papillomavirus, and cervical intraepithelial neoplasia, leading to cervical cancer. Thus, dysbiosis, characterized by an imbalance of beneficial and harmful bacteria, can negatively affect health. Understanding the intricate interactions between the microbiota and cervical cancer can provide valuable insights into potential therapeutic strategies and the development of preventive measures.},
}

@article {pmid40577168,
year = {2025},
author = {Bergmann, KC and Zuberbier, T},
title = {Effect of the Multi-Strain Probiotic SYN-53 in the Management of Allergic Rhinoconjunctivitis.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16634},
pmid = {40577168},
issn = {1398-9995},
support = {//Synformulas/ ; },
abstract = {Dysbiosis is increasingly linked to allergy development. This study evaluates the efficacy of the multi-strain probiotic SYN-53 in the management of allergic rhinoconjunctivitis (ARC). Eighty-four subjects with confirmed grass pollen allergy underwent up to three bi-weekly 3-day intake cycles with SYN-53 or placebo. After each cycle, subjects were exposed to grass pollen in an allergen exposure chamber. ARC symptoms were assessed using the Total Symptom Score (TSS) before and after each use of SYN-53. After one intake cycle, SYN-53 already showed a trend towards greater efficacy over placebo, which became significant after two cycles (ΔTSSMAX: -3.44 ± 0.42 vs. -1.87 ± 0.37; p = 0.0067), with 38% vs. 24% symptom relief. In subjects with moderate to severe symptoms, SYN-53 was already significantly superior after one single intake cycle and improved further after two cycles (ΔTSSMAX: -4.78 ± 0.51 vs. -2.43 ± 0.47; p = 0.0014), with 45% vs. 26% symptom relief. SYN-53 is effective in the management of ARC, highlighting the role of bacterial diversity and dosage in probiotic nutritional supplements.},
}

@article {pmid40576768,
year = {2025},
author = {Sima, S and Jeffries, T and Sial, A and Sharma, S and De La Lande, R and Chopra, N and Kohan, S and Khong, P and Diwan, A},
title = {Microbiome impacts surgical outcomes- comparison of gut microbiome dysbiosis in patients undergoing lumbar microdiscectomy: results from the MISO pilot study.},
journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society},
volume = {},
number = {},
pages = {},
pmid = {40576768},
issn = {1432-0932},
}

@article {pmid40576748,
year = {2025},
author = {Gupta, MK and Chauhan, K and Bhardwaj, S and Srivastava, R},
title = {Innovative Interventions: Postbiotics and Psychobiotics in Neurodegenerative Disease Treatment.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40576748},
issn = {1867-1314},
abstract = {Neurodegenerative disorders, including Huntington's disease, Amyotrophic lateral sclerosis, Alzheimer's disease, and Parkinson's disease, create more challenges as the population gets older and there are no curative therapies available. Recent advances in gut microbiome research have spotlighted postbiotics and psychobiotics as innovative therapeutic strategies targeting the gut-brain axis to alleviate neurodegenerative symptoms and slow disease progression. Postbiotics, which are metabolites and cellular components released by probiotic bacteria, and psychobiotics, a class of probiotics with potential mental health benefits, offer novel approaches to neuroprotection. This chapter examines the ways in which postbiotics and psychobiotics modulate inflammation, oxidative stress, neurotrophic factors, and gut barrier integrity to provide neuroprotective effects. We review scientific research that highlights the efficacy of specific microbial strains and their metabolites in enhancing cognitive function and reducing neurodegeneration. In addition, we explore the consequences of diet and specific nutrition on strengthening the therapeutic results of these medications. The purpose of this chapter is to provide a detailed analysis of the existing data supporting the use of postbiotics and psychobiotics in both the prevention and management of neurological diseases. By integrating perspectives from microbiology, neurology, and clinical nutrition, we highlight the potential of these interventions to enhance patient outcomes and quality of life. In addition, we discuss the translational limitations and future research approaches required to successfully transition these microbiome-based treatments from the laboratory to clinical practice, emphasizing the importance of a holistic and personalized approach in combating neurodegenerative diseases.},
}

@article {pmid40576702,
year = {2025},
author = {Shtrozberg, S and Bazzichi, L and Sarzi-Puttini, P and Aloush, V and Ablin, JN},
title = {Is the gut microbiome of importance in fibromyalgia? A critical review of emerging evidence.},
journal = {Clinical and experimental rheumatology},
volume = {43},
number = {6},
pages = {990-998},
doi = {10.55563/clinexprheumatol/pmajsv},
pmid = {40576702},
issn = {0392-856X},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Fibromyalgia/microbiology/physiopathology/therapy/diagnosis ; Animals ; Probiotics/therapeutic use ; Nutritional Status ; Dysbiosis ; Prebiotics ; Fecal Microbiota Transplantation ; },
abstract = {Fibromyalgia (FM) is a multifaceted chronic pain syndrome, predominantly affecting women, and characterised by a constellation of symptoms including diffuse musculoskeletal pain, fatigue, cognitive impairment and poor sleep quality. Its complex pathophysiology likely involves genetic, environmental and psychosocial factors. Recent studies have raised the possibility that the gut microbiome may influence FM symptoms via the gut-brain axis, although this hypothesis remains unconfirmed. This review aims to explore potential associations between gut microbiome alterations, nutrition, and FM, with particular attention to the limitations of current evidence. While certain studies have reported differences in the gut microbiota composition of patients with FM, these findings are preliminary and often derive from small, heterogeneous cohorts. Likewise, faecal microbiota transplantation studies in animals and limited human trials suggest a possible link to pain sensitivity, but further validation is needed.Nutritional interventions, including prebiotics, probiotics and specific dietary strategies, have shown early promise in modulating gut microbiota and alleviating FM symptoms. Nutrients such as magnesium, selenium and omega-3 fatty acids, as well as antioxidant compounds, may influence pain and inflammation pathways, but definitive clinical recommendations are lacking. Given the emerging nature of this field, larger and better-controlled studies are required to clarify the role of the gut microbiome and nutrition in FM. A multidisciplinary management strategy, integrating nutritional approaches cautiously and based on individual profiles, may offer benefits, although no standard therapeutic guidelines currently exist.},
}

Humans
*Gastrointestinal Microbiome
*Fibromyalgia/microbiology/physiopathology/therapy/diagnosis
Animals
Probiotics/therapeutic use
Nutritional Status
Dysbiosis
Prebiotics
Fecal Microbiota Transplantation

@article {pmid40576634,
year = {2025},
author = {Figueiredo, JC and Redwood, D and Li, L and Donato, E and Fort, D and Fox, EE and Grady, WM and Green, H and Harrison, TA and Haupt, C and Hsu, L and Hullar, MAJ and Huyghe, JR and Johnson, W and Koehne, AL and LaBrie, SD and Lakey, MA and Lin, M and Loroña, NC and Maresh, GA and Matrana, M and Mizrahi, JD and Nash, SH and Nguyen, NT and Paruch, JL and Phipps, AI and Qu, C and Randolph, TW and Romo, S and Thomas, CE and Thomas, S and Tiesinga, J and Whitlow, C and Yeung, CCS and Yin, H and Zibilich, CM and Li, CI and Thomas, TK and Peters, U},
title = {The Translational Research Program in Cancer Differences across Populations.},
journal = {Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology},
volume = {},
number = {},
pages = {},
doi = {10.1158/1055-9965.EPI-24-1711},
pmid = {40576634},
issn = {1538-7755},
abstract = {BACKGROUND: Colorectal cancer (CRC) incidence and mortality vary substantially across populations. The Translational Research Program in Cancer Differences across Populations (TRPCDP) was established in 2020 to address differences in CRC incidence and mortality rates within the United States.

METHODS: TRPCDP centralized data acquisition and harmonization across three sites in the U.S. to create a well-annotated resource of CRC tumors across four populations: African American/Black, Alaska Native, Hispanic/Latino/a, and non-Hispanic White. Using a case-control framework, patients with lethal CRC were matched to two controls with non-lethal CRC. Formalin-fixed paraffin-embedded tumor and normal tissue were retrieved and sent for centralized pathology review, followed by DNA and RNA extraction and tissue microarray development. Multi-omics and spatial profiling are underway to evaluate the transcriptome, proteome, and microbiome. Patient demographic and clinical data were obtained by medical record review, patient self-report, or linkage to cancer registries. Additional health-related factors were assessed using geospatial linkage.

RESULTS: The virtual biorepository includes 7,181 patients [African American (n=1,345), Alaska Native (n=1,640), Hispanic (n=1,659), and non-Hispanic White (n=2,537)]. Tissue blocks (1,594 tumor, 728 normal colon) were selected for 938 patients. To date, DNA and RNA have been extracted (n=831) and tissue microarrays have been constructed (n=414). Transcriptomic, spatial tumor profiling (multiplex immunofluorescence, PhenoCycler, GeoMx) and microbiome data (16S rRNAseq, ddPCR) are available.

CONCLUSION: The TRPCDP has developed a clinically annotated biorepository for future molecular epidemiology studies.

IMPACT: TRPCDP is a unique program that supports collaborative research, community engagement, and pipeline development for the next generation of scientists.},
}

@article {pmid40576627,
year = {2025},
author = {Marlicz, W and Skonieczna-Żydecka, K and Łoniewski, I and Koulaouzidis, A},
title = {Rethinking iron therapy in IBD: integrating the microbiota perspective.},
journal = {Scandinavian journal of gastroenterology},
volume = {},
number = {},
pages = {1-3},
doi = {10.1080/00365521.2025.2525909},
pmid = {40576627},
issn = {1502-7708},
abstract = {Iron deficiency and anemia are common in patients with inflammatory bowel disease (IBD), requiring effective and well-tolerated iron replacement strategies. While oral iron is widely used, growing evidence suggests it can disrupt the gut microbiota by reducing beneficial commensal bacteria and promoting pro-inflammatory shifts in the intestinal environment. These changes may exacerbate mucosal inflammation and contribute to gastrointestinal side effects, often resulting in poor adherence. Intravenous iron, by bypassing the gastrointestinal tract, appears to have a less disruptive effect on the microbiota and may more reliably restore iron stores, particularly in patients with active disease or intolerance to oral formulations. Current expert recommendations support intravenous iron as the first-line option in such cases, though oral iron remains a practical choice for selected patients with mild anemia and inactive disease. Emerging research also raises concerns about the safety of oral iron in vulnerable populations, as it may promote dysbiosis and expansion of potentially pathogenic bacteria. In response, adjunctive strategies are being explored to support the microbiota and improve the tolerability and efficacy of oral iron. Incorporating microbiota-related considerations into treatment decisions may enhance outcomes and reduce side effects. Future clinical guidelines should reflect the evolving understanding of the gut microbiome's role in iron metabolism and inflammation, promoting more personalized, microbiota-conscious approaches to iron therapy in IBD.},
}

@article {pmid40576466,
year = {2025},
author = {Bacińska, Z and Strub, DJ and Balcerzak, L},
title = {Antibacterial potential of essential oils against oral pathogenic bacteria: A literature and clinical review.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf161},
pmid = {40576466},
issn = {1365-2672},
abstract = {The human oral microbiome is a complex ecosystem, comprising diverse microbial species in symbiotic relationships. Environmental factors such as diet, immune response, and inflammation can disrupt the balance of the oral microbiome, leading to increased activity and proliferation of pathogenic species associated with oral diseases. In response to global dental problems, there is a burgeoning interest in exploiting the antibacterial properties of essential oils (EOs) for clinical applications, being promising alternative to traditional antiseptics. This review synthesizes literature on the Minimum Inhibitory Concentration (MIC) of plant-derived EOs and their effectiveness against key oral pathogenic bacteria, which belong to the so-called 'red', 'orange', 'purple', 'yellow', and 'green' complexes, and includes newly discovered oral bacteria. Furthermore, it examines clinical investigations into oral hygiene products infused with EOs, evaluating their antiplaque, antigingivitis properties, and effectiveness in reducing tartar formation and gingival bleeding. Overall, this review highlights the high antibacterial efficacy of EOs against oral bacteria and their potential therapeutic abilities. It is expected that they will be used as a potential alternative for chemical preservatives in oral care products in the future. Based on the searched clinical studies, EO-based oral care products seem to be effective in the treatment of dental problems, such as e.g. dental plaque, gingivitis, and caries.},
}

@article {pmid40576342,
year = {2025},
author = {Napier, EG and Cinco, IR and Wagner, SB and Stuart, EV and Qiao, Q and Taylor, J and Stevenson, B and Messaoudi, I},
title = {Borreliosis and doxycycline treatment disrupt gut microbiota and immune responses in nonhuman primates.},
journal = {mBio},
volume = {},
number = {},
pages = {e0143725},
doi = {10.1128/mbio.01437-25},
pmid = {40576342},
issn = {2150-7511},
abstract = {Borrelia burgdorferi (Bb) is the spirochete that causes Lyme disease (LD). Transmission to humans occurs via bites of infected Ixodes spp. ticks. Doxycycline is often used to treat LD patients, which is sometimes delayed due to current diagnostic challenges. Recently, several lines of evidence show dysbiosis of the gut microbiome in LD patients, which may be a host factor contributing to pathogenesis and symptomology but is still an understudied area in the field. To address this knowledge gap, we longitudinally compared the immune response and gut microbial composition of Japanese macaques after intradermal infection with Bb strain 297 with or without doxycycline treatment. Immunological and microbial changes were monitored longitudinally using enzyme-linked immunosorbent assay, flow cytometry, single-cell genomics, and 16S amplicon sequencing assays. All Bb-inoculated animals seroconverted to produce Bb-specific antibodies. Borrelial DNA was undetected by real-time quantitative PCR in the skin, blood, and cerebrospinal fluid. Levels of CXCL13, a B cell chemoattractant, increased following infection but reached a nadir after treatment. The frequency of circulating immune cells remained constant over the course of the study, but gene expression analysis showed downregulation of antimicrobial genes in monocytes, dendritic cells, and B cells until late in infection, regardless of treatment. Infection and antibiotic treatment led to a loss of gut commensals important for maintaining gut integrity. Finally, untreated infected animals showed mononuclear myocarditis along with sporadic detection of borrelial DNA. Data from this study suggest aberrant B cell activity, myocarditis, and loss of important commensal microbes as factors contributing to symptoms of untreated Lyme disease.IMPORTANCELyme disease (LD) is caused by Borrelia burgdorferi (Bb) transmitted via tick bite. The incidence of LD is expanding in North America and Southeast Asia. LD patients are frequently misdiagnosed or receive delayed treatment due to the lack of sensitive diagnostic strategies. The pathophysiology of LD remains poorly understood because of challenges with clear infection timelines in clinical studies. Here, we utilize Japanese macaques to provide an in-depth longitudinal investigation into the host immunological and gut microbial changes in response to Bb infection. This work highlights CXCL13 as a potential Bb diagnostic marker, as well as host factors such as aberrant B cell activity, mononuclear myocarditis, and gut dysbiosis as potential therapeutic targets.},
}

@article {pmid40576334,
year = {2025},
author = {Lee, EM and Srinivasan, S and Purvine, SO and Fiedler, TL and Leiser, OP and Proll, SC and Minot, SS and Djukovic, D and Raftery, D and Johnston, C and Fredricks, DN and Deatherage Kaiser, BL},
title = {Syntrophic bacterial and host-microbe interactions in bacterial vaginosis.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf055},
pmid = {40576334},
issn = {1751-7370},
abstract = {Bacterial vaginosis (BV) is a common, polymicrobial condition of the vaginal microbiota that is associated with symptoms such as malodor and excessive discharge, along with increased risk of various adverse sequelae. Host-bacteria and bacteria-bacteria interactions are thought to contribute to the condition, but many of these functions have yet to be elucidated. Using untargeted metaproteomics, we identified 1068 host and 1418 bacterial proteins in a set of cervicovaginal lavage samples collected from 20 participants with BV and 9 who were negative for the condition. We identified Dialister micraerophilus as a major producer of malodorous polyamines and identified a syntrophic interaction between this organism and Fannyhessea vaginae that leads to increased production of putrescine, a metabolite characteristic of BV. Although formate synthesis has not previously been noted in BV, we discovered diverse bacteria associated with the condition express pyruvate formate-lyase enzymes in vivo and confirm these organisms secrete formic acid in vitro. Sodium hypophosphite efficiently inhibited this function in multiple taxa. We also found that the fastidious organism Coriobacteriales bacterium DNF00809 can metabolize formic acid secreted by Gardnerella vaginalis, representing another syntrophic interaction. We noted an increased abundance of the host epithelial repair protein transglutaminase 3 in the metaproteomic data, which we confirmed by enzyme-linked immunosorbent assay. Other proteins identified in our samples implicate Finegoldia magna and Parvimonas micra in the production of malodorous trimethylamine. Some bacterial proteins identified represent novel targets for future therapeutics to disrupt BV communities and promote vaginal colonization by commensal lactobacilli.},
}

@article {pmid40576243,
year = {2025},
author = {Omeir, K and Ancira, J and Gabrilska, R and Tipton, C and Miller, C and Noe, A and Subasinghe, K and Rowe, M and Phillips, N and Wolcott, J and Philips, CD},
title = {Heritable Tissue-Specific Gene Expression Associates With Chronic Wound Microbial Species.},
journal = {Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society},
volume = {33},
number = {4},
pages = {e70055},
doi = {10.1111/wrr.70055},
pmid = {40576243},
issn = {1524-475X},
support = {R15GM141973-01/NH/NIH HHS/United States ; },
mesh = {Humans ; *Microbiota/genetics ; Female ; Male ; *Wound Healing/genetics ; Middle Aged ; Chronic Disease ; *Wound Infection/microbiology/genetics ; *Wounds and Injuries/microbiology/genetics ; Aged ; Gene Expression Profiling ; Adult ; Transcriptome ; Genome-Wide Association Study ; },
abstract = {The reasons for interpatient variability in chronic wound microbiome composition are thought to be complex but are poorly known. To investigate how patients' genetically regulated tissue expression may influence chronic wound bacterial composition, we performed a microbiome-transcriptome-wide association study. This approach involved estimating for 509 patients their tissue-specific gene expression from DNA genotypes, followed by associating gene expression to the relative abundances of species detected in their wounds as provided on clinical reports to the physician. Comparisons to artery, blood, fibroblast, skeletal muscle, skin, subcutaneous fat, and nerve tissue resulted in 251 transcriptional differences at 109 genes significantly explaining abundances of 39 different species. Overall, these species were detected in ~63% of wounds. A similar number of associations per tissue was observed (range 31-39), and many genes were associated at multiple tissues in distinct ways. The cumulative variance across loci for species relative abundance explained ranged from ~5%-36%, depending on species. Although the same gene was almost never associated with more than one species, ~14% of enriched pathways were independently enriched for multiple species, which may reflect the diversity of ways microbes interact with partially overlapping attributes of the wound bed. Commonly enriched pathways pertained to collagen formation and modification, cell signalling, cytoskeletal dynamics, interactions with extracellular matrix, transmembrane proteins, amongst others. This work expands the new perspective that individual genetics may partially determine microbial colonisation and infection.},
}

Humans
*Microbiota/genetics
Female
Male
*Wound Healing/genetics
Middle Aged
Chronic Disease
*Wound Infection/microbiology/genetics
*Wounds and Injuries/microbiology/genetics
Aged
Gene Expression Profiling
Adult
Transcriptome
Genome-Wide Association Study

@article {pmid40575713,
year = {2025},
author = {Masri, MTA and Al-Deeb, MA},
title = {A systematic review of the microbiome of Hyalomma Koch, 1844 ticks using next-generation sequencing of the 16S ribosomal RNA gene.},
journal = {Veterinary world},
volume = {18},
number = {5},
pages = {1090-1100},
pmid = {40575713},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: Ticks are critical vectors of pathogens affecting humans and livestock globally. The microbiome of ticks, comprising diverse bacterial communities, plays a crucial role in tick biology and vector competence. Hyalomma ticks are prominent in the Middle East and North Africa (MENA) region and are known carriers of significant pathogens. This study aimed to systematically evaluate existing literature regarding the microbiome composition of Hyalomma ticks in the MENA region, identify predominant bacterial genera, and highlight knowledge gaps.

MATERIALS AND METHODS: A systematic literature search was conducted using four databases: ScienceDirect, PubMed, Google Scholar, and Scopus. The search covered studies published between 2014 and 2024 employing 16S ribosomal RNA gene sequencing to analyze microbiomes of Hyalomma ticks within the MENA region. Studies not fulfilling these criteria were excluded through independent assessment by two authors.

RESULTS: Out of 1,220 screened articles, seven studies met inclusion criteria, involving five Hyalomma species: Hyalomma dromedarii, Hyalomma anatolicum, Hyalomma excavatum, Hyalomma marginatum, and Hyalomma scupense. Most studies (57.14%) focused on H. dromedarii, primarily collected from camels. The geographical distribution of studies included the United Arab Emirates (42.86%), Saudi Arabia (28.57%), Iran (14.29%), and Tunisia (14.29%). Common bacterial genera identified across multiple studies included Acinetobacter, Bacillus, Flavobacterium, Francisella, Rickettsia, Staphylococcus, Pseudomonas, and Corynebacterium. However, substantial gaps were noted, particularly concerning variations related to tick lifecycle stages, host interactions, temporal dynamics, and extensive geographic coverage within the MENA region.

CONCLUSION: This systematic review underscores the presence of key bacterial genera within Hyalomma ticks across the MENA region, revealing their potential roles in tick biology and pathogen transmission. Major research gaps identified include limited geographical scope, insufficient exploration of microbiome variation across tick life stages, host-specific interactions, and the environmental factors influencing microbial communities. Addressing these gaps through comprehensive, longitudinal, and multi-regional studies is imperative for improving public health strategies and developing targeted tick-control methods.},
}

@article {pmid40575647,
year = {2025},
author = {Tüsüz Önata, E and Özdemir, Ö},
title = {Microbiome, dysbiosis and use of probiotics in various diseases.},
journal = {World journal of virology},
volume = {14},
number = {2},
pages = {99574},
pmid = {40575647},
issn = {2220-3249},
abstract = {The community of microorganisms that colonize certain areas of the human body is called microbiota. Microorganisms such as bacteria, fungi and viruses make up the microbiota. The sum of the genomes of these microorganisms and microorganisms refers to the microbiome. It has been shown that microbiota has important effects such as protecting the organ from pathogens, contributing to metabolic functions (such as vitamin synthesis, carbohydrate digestion) and providing immunoregulation. Dysbiosis refers to compositional and functional changes in the microbiota. At the beginning of the 21[st] century, numerous studies have investigated the human microbiota and its imbalance in relation to various diseases and found that dysbiosis is associated with many diseases. The aim of this mini-review article is to provide brief information about dysbiosis and its care and to raise awareness.},
}

@article {pmid40575486,
year = {2025},
author = {Nieves, L and Roach, A and Hunter, J and Smeh, S and Islas, A and Islas, A and Blattman, J and Di Palma, M},
title = {Harnessing the microbiome to improve clinical outcomes for cancer, transplant, and immunocompromised patients in the intensive care unit (ICU).},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1577108},
pmid = {40575486},
issn = {2235-2988},
mesh = {Humans ; *Intensive Care Units ; *Neoplasms/microbiology/therapy/immunology ; *Immunocompromised Host ; *Microbiota ; Dysbiosis/microbiology ; *Transplant Recipients ; Treatment Outcome ; },
abstract = {In recent decades, there has been a growing emphasis on understanding how the architecture of the human microbiome can impact typical biological processes and patient clinical outcomes. In fact, microbiome modifications and modulations have not only been associated with impacts on general health and well-being but have also been shown to yield differences in patient responsiveness to vaccines, medications, and chemotherapeutic regimens. Much of this influence likely stems from how changes in the microbiome result in differences in microbial communities and the subsequent release of microbial-derived metabolites that can alter typical immunological processes. Understanding how microbial composition can impact patient responsiveness can be particularly important in the intensive care unit (ICU), where the efficacy of medications and treatments can result in negative patient outcomes if unsuccessful. Clinical scientists have further developed the concept of the pathobiome, a disease-promoting microbiome whose development can be associated with dysbiosis. Understanding how the microbiome and its associated components can impact patient responsiveness, especially in the ICU, must be further researched and understood. Here, we analyze what causes variances in the microbiome and pathobiome in significant immunocompromised populations, including cancer patients and transplant recipients, and how variances in the microbiome can impact patient outcomes in the ICU. Further, we detail potential future applications of how our understanding of what impacts the human microbiome during the treatment of these populations may be exploited to improve patient prognosis.},
}

Humans
*Intensive Care Units
*Neoplasms/microbiology/therapy/immunology
*Immunocompromised Host
*Microbiota
Dysbiosis/microbiology
*Transplant Recipients
Treatment Outcome

@article {pmid40575430,
year = {2025},
author = {Brar, AS and Vemula, SL and Yanamaladoddi, V and Sodhi, S and Hatwal, J and Sohal, A and Batta, A},
title = {Impact of gut microbiome on atrial fibrillation: Mechanistic insights and future directions in individualized medicine.},
journal = {World journal of cardiology},
volume = {17},
number = {6},
pages = {107386},
pmid = {40575430},
issn = {1949-8462},
abstract = {Atrial fibrillation (AF) is a growing global health burden, with a prevalence of over 52.55 million cases. Rising disability-adjusted life-years, increasing age, and disparities in care have contributed to the worsening severity and mortality of AF. Modifiable risk factors, such as hypertension, obesity, and diabetes mellitus, are associated with alterations in gut microbiota, making the gut-heart axis a potential therapeutic target. Gut dysbiosis influences AF pathogenesis through inflammation, metabolic disruption, and autonomic dysfunction. Key mechanisms include gut barrier dysfunction, short-chain fatty acid (SCFA) depletion, lipopolysaccharides (LPS)-induced inflammation, and ferroptosis-mediated atrial remodeling. Trimethylamine N-oxide, bile acids, and tryptophan metabolites contribute to arrhythmogenic remodeling. Emerging evidence suggests that dietary interventions, including prebiotics and probiotics, as well as gut surveillance, may help mitigate AF progression. Clinical implications of gut modulation in AF include personalized dietary strategies, microbiome assessment through metagenomic sequencing, and targeted interventions such as SCFA-based therapies and ferroptosis inhibition. Metabolite surveillance, including LPS and indoxyl sulfate monitoring, may influence the effectiveness of anticoagulant and antiarrhythmic therapy. Despite growing mechanistic evidence linking gut dysbiosis to AF, clinical applications remain unexplored. This review summarizes the current understanding of the gut microbiome's role in AF.},
}

@article {pmid40575364,
year = {2025},
author = {Bangolo, A and Amoozgar, B and Habibi, M and Simms, E and Nagesh, VK and Wadhwani, S and Wadhwani, N and Auda, A and Elias, D and Mansour, C and Abbott, R and Jebara, N and Zhang, L and Gill, S and Ahmed, K and Ip, A and Goy, A and Cho, C},
title = {Exploring the gut microbiome's influence on cancer-associated anemia: Mechanisms, clinical challenges, and innovative therapies.},
journal = {World journal of gastrointestinal pharmacology and therapeutics},
volume = {16},
number = {2},
pages = {105375},
pmid = {40575364},
issn = {2150-5349},
abstract = {BACKGROUND: Anemia is a prevalent and challenging complication in patients with hematologic and solid malignancies, which stems from the direct effects of malignancy, treatment-induced toxicities, and systemic inflammation. It affects patients' survival, functional status, and quality of life profoundly. Recent literature has highlighted the emerging role of the gut microbiome in the pathogenesis of cancer-associated anemia. The gut microbiota, through its intricate interplay with iron metabolism, inflammatory pathways, and immune modulation, may either exacerbate or ameliorate anemia depending on its composition, and functional integrity. Dysbiosis, characterized by disruption in the gut microbial ecosystem, is very common in cancer patients. This microbial imbalance is implicated in anemia causation through diminished iron absorption, persistent low-grade inflammation, and suppression of erythropoiesis.

AIM: To consolidate current evidence regarding the interplay between gut microbiome and anemia in the setting of malignancies. It aims to provide a detailed exploration of the mechanistic links between dysbiosis and anemia, identifies unique challenges associated with various cancer types, and evaluates the efficacy of microbiome-focused therapies. Through this integrative approach, the review seeks to establish a foundation for innovative clinical strategies aimed at mitigating anemia and improving patient outcomes in oncology.

METHODS: A literature search was performed using multiple databases, including Google Scholar, PubMed, Scopus, and Web of Science, using a combination of keywords and Boolean operators to refine results. Keywords included "cancer-associated anemia", "gut microbiome", "intestinal microbiota", "iron metabolism", "gut dysbiosis", "short-chain fatty acids", "hematopoiesis", "probiotics", "prebiotics", and "fecal microbiota transplantation". Articles published in English between 2000 and December 2024 were included, with a focus on contemporary and relevant findings.

RESULTS: Therapeutic strategies aimed at restoration of gut microbial homeostasis, such as probiotics, prebiotics, dietary interventions, and fecal microbiota transplantation (FMT), can inhibit anemia-causing pathways by enhancing microbial diversity, suppressing detrimental flora, reducing systemic inflammation and optimizing nutrient absorption.

CONCLUSION: Gut dysbiosis causes anemia and impairs response to chemotherapy in cancer patients. Microbiome-centered interventions, such as probiotics, prebiotics, dietary modifications, and FMT, have shown efficacy in restoring microbial balance, reducing inflammation, and enhancing nutrient bioavailability. Emerging approaches, including engineered probiotics and bacteriophage therapies, are promising precision-based, customizable solutions for various microbiome compositions and imbalances. Future research should focus on integrating microbiome-targeted strategies with established anemia therapies.},
}

@article {pmid40575334,
year = {2025},
author = {Bhagavathula, AS and Al Qady, AM and Aldhaleei, WA},
title = {Diagnostic accuracy and quality of artificial intelligence models in irritable bowel syndrome: A systematic review.},
journal = {World journal of gastroenterology},
volume = {31},
number = {23},
pages = {106836},
pmid = {40575334},
issn = {2219-2840},
mesh = {Humans ; *Irritable Bowel Syndrome/diagnosis/microbiology ; *Artificial Intelligence/standards ; Biomarkers/analysis ; Sensitivity and Specificity ; Gastrointestinal Microbiome ; Feces/microbiology ; Observational Studies as Topic ; },
abstract = {BACKGROUND: Irritable bowel syndrome (IBS) affects approximately 9%-12% of the global population, presenting substantial diagnostic challenges due to symptom subjectivity and lack of definitive biomarkers.

AIM: To systematically examine the diagnostic accuracy of artificial intelligence (AI) models applied to various biomarkers in IBS diagnosis.

METHODS: A comprehensive search of six databases identified 18053 articles published up to May 31, 2024. Following screening and eligibility criteria, six observational studies involving 1366 participants from the United Kingdom, China, and Japan were included. Risk of bias and reporting quality were assessed using quality assessment of diagnostic accuracy studies-2, prediction model risk of bias assessment tool-AI, and transparent reporting of a multivariable prediction model for individual prognosis or diagnosis-AI tools. Key metrics included sensitivity, specificity, accuracy, and area under the curve (AUC).

RESULTS: The included studies applied AI models such as random forests, support vector machines, and neural networks to biomarkers like fecal microbiome composition, gas chromatography data, neuroimaging features, and protease activity. Diagnostic accuracy ranged from 54% to 98% (AUC: 0.61-0.99). Models using fecal microbiome data achieved the highest performance, with one study reporting 98% sensitivity and specificity (AUC = 0.99). While most studies demonstrated high methodological quality, significant variability in datasets, biomarkers, and validation methods limited meta-analysis feasibility and generalizability.

CONCLUSION: AI models show potential to improve IBS diagnostic accuracy by integrating complex biomarkers which will aid the development of algorithms to direct treatment strategies. However, methodological inconsistencies and limited population diversity underscore the need for standardized protocols and external validation to ensure clinical applicability.},
}

Humans
*Irritable Bowel Syndrome/diagnosis/microbiology
*Artificial Intelligence/standards
Biomarkers/analysis
Sensitivity and Specificity
Gastrointestinal Microbiome
Feces/microbiology
Observational Studies as Topic

@article {pmid40575111,
year = {2025},
author = {Cheng, P and Jia, R and Jin, B and Zhou, F and Xu, H and Wang, B},
title = {IBS May Have a Causal Effect on Increased Tryptophan Metabolites Levels: Insights from a Bidirectional Two-Sample Mendelian Randomization Study.},
journal = {International journal of tryptophan research : IJTR},
volume = {18},
number = {},
pages = {11786469251327399},
pmid = {40575111},
issn = {1178-6469},
abstract = {BACKGROUND: Irritable Bowel Syndrome (IBS) is a chronic functional gastrointestinal disorder characterized by abdominal pain and altered bowel habits. Tryptophan, an essential amino acid derived from dietary proteins, can be metabolized into various compounds by the gut microbiome. Emerging evidence suggests that tryptophan metabolites play a role in functional gastrointestinal disorders. However, the causal relationship between tryptophan metabolites and IBS remains to be fully elucidated.

OBJECTIVE: This study aims to evaluate the potential causal relationship between tryptophan metabolites and IBS using Mendelian randomization (MR).

METHODS: Instrumental variables (IVs) were selected from summary data of genome-wide association studies (GWAS) for tryptophan and IBS. SNPs potentially influencing MR results were excluded through outlier detection using MR-PRESSO. Bidirectional two-sample MR analyses were conducted using the inverse-variance weighted (IVW), MR-Egger regression, weighted median, weighted mode, and simple mode methods. The MR-Egger intercept test was employed to assess pleiotropy and heterogeneity among IVs, with visualization of the MR results through scatter plots, funnel plots, and forest plots.

RESULTS: Genetically predicted tryptophan metabolites were not associated with the risk of IBS. In the reverse direction, genetically predicted IBS was associated with increased levels of tryptophan, serotonin, and kynurenine in the IVW analysis. Sensitivity and replication analyses confirmed these findings.

CONCLUSION: The findings of this Mendelian randomization study suggest that IBS may lead to elevated levels of tryptophan, serotonin, and kynurenine. These results have important implications for understanding the interplay between tryptophan metabolism and IBS in clinical settings. Further research is warranted to explore the underlying mechanisms.},
}

@article {pmid40575011,
year = {2025},
author = {Pilmer, L and Woolley, L and Lymbery, A and Salini, M and Dam, C and Foysal, MJ and Partridge, G},
title = {Sustainable Fishmeal Alternatives: Impact of Partially Defatted Black Soldier Fly (Hermetia illucens) Meal on Growth and Health of Yellowtail Kingfish (Seriola lalandi).},
journal = {Aquaculture nutrition},
volume = {2025},
number = {},
pages = {1804215},
pmid = {40575011},
issn = {1365-2095},
abstract = {Reducing fishmeal (FM) in aquaculture diets is essential for improving sustainability and reducing reliance on marine resources. Black soldier fly (BSF; Hermetia illucens) larvae meal is a promising alternative protein source. This study evaluated the effects of replacing FM with BSF meal on the growth and health of juvenile yellowtail kingfish (YTK) (Seriola lalandi, initial weight ~22 g). Fish were reared in 24 tanks (three replicates per treatment) and fed for 33 days under controlled conditions. Eight diets were tested: a control (40% FM) and seven diets with BSF meal replacing FM at 25%, 50%, or 75%, with or without garlic and tuna hydrolysate additives. Fish fed 25% and 50% BSF diets showed growth and feed conversion comparable to the control, while 75% BSF significantly reduced growth due to decreased feed intake. Additives did not improve feed intake. Histological analysis indicated good gut health and nutrient absorption. Serum cholesterol decreased with BSF inclusion, and urea levels varied. No significant changes in gene expression were observed in the gut, liver, or brain. Microbiome analysis showed increased diversity and compositional shifts at higher BSF levels. These results support the use of BSF meal as a sustainable FM replacement at moderate inclusion levels, with further research needed to address palatability at higher levels.},
}

@article {pmid40574876,
year = {2025},
author = {Odenwald, MA and Ramaswamy, R and Lin, H and Lehmann, C and Moran, A and Mullowney, MW and Sidebottom, AM and Hernandez, A and McMillin, M and Rose, A and Moran, D and Little, J and Sulakhe, D and D'Souza, M and Woodson, C and Tanveer, T and de Porto, A and Dylla, N and Sundararajan, A and Burgo, V and Cantoral, J and Jadczak, C and Adler, E and Aronsohn, A and Pamer, EG and Rinella, ME},
title = {Fecal Butyrate and Deoxycholic Acid Concentrations Correlate With Mortality in Patients With Liver Disease.},
journal = {Gastro hep advances},
volume = {4},
number = {8},
pages = {100695},
pmid = {40574876},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: The intestinal microbiome produces metabolites, including short chain fatty acids (SCFAs) and secondary bile acids (BAs), that impact host physiology. Loss of intestinal microbiome diversity is associated with cirrhosis progression, but the impact of microbiome-associated metabolites on liver disease remains largely undefined. We aimed to correlate fecal metabolite concentrations with the severity and progression of liver disease.

METHODS: In this cross-sectional study, fecal samples from patients hospitalized with liver disease were analyzed by shotgun metagenomic sequencing to determine microbiome compositions and targeted mass spectrometry to quantify SCFAs and BAs. Random survival forest and logistic regression models identified clinical, metagenomic, and metabolomic features associated with rehospitalization and survival.

RESULTS: This cross-sectional study included 24 chronic liver disease, 18 compensated cirrhosis, 225 decompensated cirrhosis and 40 acute-on-chronic liver failure patients and 27 control fecal donors. Microbiome sequencing and metabolite profiling correlated microbial diversity and SCFA and BA concentrations with liver disease severity. Butyrate and deoxycholic acid (DCA) were more important features than individual microbial species in random survival forest models predicting 30-day transplant-free survival, and low butyrate and DCA were associated with 30-day mortality (P < .0001). After controlling for model for end stage liver disease (MELD)-sodium score, disease stage, age and gender, low fecal concentrations of butyrate and DCA remained significant risk factors for death (Cox 1.38, P = .027). Bacterial species associated with butyrate and DCA concentrations included Bifidobacterium spp. and F. prausnitzii.

CONCLUSION: Mass spectrometry rapidly identifies patients with low fecal butyrate and DCA concentrations who are at increased risk of 30-day mortality. These findings set the stage for clinical trials of microbiome reconstitution with butyrate and DCA-producing bacterial species.},
}

@article {pmid40574855,
year = {2025},
author = {Mo, Y and He, X and Shi, P and Ning, Y and Zhou, M and Cui, H and Zhang, T},
title = {Hematopoietic effects of Fufang E'jiao Jiang revealed by microbiome, metabolome and transcriptome analyses: a multi-omics strategy.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1561477},
pmid = {40574855},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Metabolome/drug effects ; Mice ; *Anemia/chemically induced/drug therapy/metabolism/microbiology ; *Transcriptome/drug effects ; Gene Expression Profiling ; Metabolomics/methods ; Male ; *Hematopoiesis/drug effects ; Cyclophosphamide ; Feces/microbiology ; Multiomics ; },
abstract = {INTRODUCTION: Fufang E'jiao Jiang has been extensively utilized to replenish qi and nourish blood as the homology of medicine and food.

METHODS: We analyzed the effects of FEJ on cyclophosphamide and acetylphenylhydrazine-induced anemia mice through gut microbiome analysis, fecal metabolomics, and transcriptome sequencing.

RESULTS: FEJ markedly alleviated the anemia symptoms in the mice. FEJ markedly alleviated the anemia symptoms caused by cyclophosphamide and acetylphenylhydrazine induction. FEJ improved the gut microbiome imbalance by inhibiting the proliferation of harmful bacteria Turicibacter, Akkermansia and Tuzzerella. Fecal metabolomic data showed that FEJ regulated metabolic disorders in anemia mice and was probably associated with L-leucine, L-proline, glycine, phenylalanine, propanoic acid and butanoic acid. Transcriptome analysis indicated the amelioration of anemia was predominantly associated with the hematopoietic cell lineage, osteoclast formation and B cell receptor signaling pathway. According to Spearman's correlation analysis, there was a strong link between gut microbiota and hematopoietic index, metabolites and genes.

DISCUSSION: Our study supports the application of FEJ in anemia treatment.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Metabolome/drug effects
Mice
*Anemia/chemically induced/drug therapy/metabolism/microbiology
*Transcriptome/drug effects
Gene Expression Profiling
Metabolomics/methods
Male
*Hematopoiesis/drug effects
Cyclophosphamide
Feces/microbiology
Multiomics

@article {pmid40574831,
year = {2025},
author = {Guo, X and Wang, K and Liu, Q and Baran, N and Ma, W},
title = {The gut-immune axis in primary immune thrombocytopenia (ITP): a paradigm shifts in treatment approaches.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1595977},
pmid = {40574831},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Purpura, Thrombocytopenic, Idiopathic/therapy/immunology/microbiology ; Dysbiosis/immunology ; Fecal Microbiota Transplantation ; Animals ; Blood Platelets/immunology ; Probiotics/therapeutic use ; },
abstract = {Primary immune thrombocytopenia (ITP) is an autoimmune disorder characterized by platelet destruction and impaired production, leading to bleeding risk. While immunosuppressive therapies are standard, many patients experience relapses or refractory disease, highlighting the need for novel approaches. Emerging evidence suggests the gut microbiota plays a role in immune regulation, yet its impact on ITP remains unclear. Dysbiosis has been linked to immune dysfunction in other autoimmune diseases, but whether it drives or results from immune dysregulation in ITP is debated. This review explores the gut-immune axis in ITP, focusing on microbiota-driven immune modulation, cytokine signaling, and platelet homeostasis. We assess microbiota-targeted interventions, including fecal microbiota transplantation (FMT), probiotics, and dietary modifications, while addressing key controversies and knowledge gaps. Advances in microbiome sequencing and artificial intelligence may facilitate personalized interventions. Standardizing microbiota-based diagnostics and validating their efficacy in clinical trials are crucial for their integration into ITP management. Bridging these gaps may lead to microbiota-driven strategies that enhance immune regulation and improve patient outcomes.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Purpura, Thrombocytopenic, Idiopathic/therapy/immunology/microbiology
Dysbiosis/immunology
Fecal Microbiota Transplantation
Animals
Blood Platelets/immunology
Probiotics/therapeutic use

@article {pmid40574696,
year = {2025},
author = {Biada, I and Tiezzi, F and Ibáñez-Escriche, N and Luz García, M and Argente, MJ and Santacreu, MA},
title = {Differential intestinal microbiome response to heat stress in two rabbit maternal lines: A comparative analysis using Random Forest, BayesC, and PLS-DA.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf206},
pmid = {40574696},
issn = {1525-3163},
abstract = {Heat stress affects livestock productivity and health, particularly in rabbits, due to their physiological vulnerabilities. This study explores the relationship between environmental conditions, genetic lines backgrounds, and soft fecal microbiota. A 2×2 factorial design was used, involving two maternal rabbit lines: A (standard longevity line) and LP (high longevity line), exposed to heat stress and thermal comfort. Samples were analyzed with multiple models to assess the impact of heat stress on microbiota by comparing microbial diversity and evaluating the classification performance of Random Forest, Partial Least Squares Discriminant Analysis (PLS-DA), and Bayesian Regression (BayesC). Heat stress influenced microbial diversity in both lines, increasing alpha diversity and driving significant beta-diversity shifts (2.3% variance, p < 0.001). This could be due to intestinal barrier disruption, which facilitate pathogen proliferation. The high longevity line LP exhibited higher richness under thermal comfort, whereas heat stress equalized these differences between lines, possibly due to increased pathogen proliferation in the low longevity line A. These differences in response to heat stress may be influenced by the crosstalk between microbiota and host genetics, shaping distinct adaptive mechanisms in each line. Prediction accuracy and key selected variables distinguishing between lines A and LP varied across thermal conditions, with the Area Under the Curve (AUC) exceeding 0.92 under heat stress and 0.87 in thermal comfort. This reflects different microbiome regulations between the two lines under heat stress. Potential stress-associated taxa such as Erysipelatoclostridium and Monoglobus were more abundant in the low longevity line A. These results highlight LP's higher longevity and expected resilience, while line A's susceptibility is reflected in a higher abundance of heat stress-associated taxa in the latter. This underscores soft fecal microbiota as a potential biomarker for heat stress resilience and emphasizes the role of host-microbiota interactions in mediating genetic-environmental responses. Additionally, this study highlights the value of combining modeling approaches, which enhance accuracy and reveal key taxa driving heat stress responses. Among the models tested, PLS-DA achieved the highest accuracy, while Random Forest identified a smaller yet biologically relevant subset of taxa, providing valuable phylogenetic and taxonomic insights.},
}

@article {pmid40574683,
year = {2025},
author = {},
title = {Correction to: Human microbiome: Impact of newly approved treatments on C. difficile infection.},
journal = {American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajhp/zxaf137},
pmid = {40574683},
issn = {1535-2900},
}

@article {pmid40574533,
year = {2025},
author = {Baker, EJ and Cumberford, G and Hanaway, P},
title = {Recognizing the Health Benefits of Plant-Sourced Omega-3 Stearidonic Acid: Exploring Its Complementary Role to Preformed EPA/DHA.},
journal = {Lipids},
volume = {},
number = {},
pages = {},
doi = {10.1002/lipd.12452},
pmid = {40574533},
issn = {1558-9307},
abstract = {Very-long chain (VLC) omega-3 polyunsaturated fatty acids (PUFAs) like eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA) are crucial for optimal development, healthy aging, and disease management. Traditionally sourced from fatty fish, these omega-3 PUFAs face sustainability challenges, prompting increased exploration of plant-based alternatives, such as stearidonic acid (SDA). Recent studies highlight the efficient conversion of SDA to EPA, meaning that SDA may offer similar health benefits to EPA, including immune, joint, cognitive, and gut microbiome modulation (with distinct SDA-derived metabolites). This mini-review explores new research on SDA and its potential to deliver human health benefits. SDA-rich oils, notably Buglossoides arvensis oil (RBO; also known as Ahiflower oil) provide an eco-friendly, sustainable alternative to fish-derived omega-3 PUFAs. As concerns about marine omega-3 PUFA sources grow, SDA-rich oils present a viable option for clinicians and consumers seeking effective omega-3 PUFA supplementation.},
}

@article {pmid40574493,
year = {2025},
author = {Sun, J and Ren, C and Liu, N and Cao, X and Wang, C and Yao, S and Li, X and Wang, Z},
title = {Can Rhizosphere Effects Mitigate the Threat from Nanoplastics and Plastic Additives to Tomato (Solanum lycopersicum L.)?.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01842},
pmid = {40574493},
issn = {1520-5851},
abstract = {Nanoplastics (NPs) and plastic additives inevitably coexist to threaten soil health and plant growth. Herein, in a root-box system isolating the rhizosphere and bulk soils, we explored the combined effects of NPs and a kind of typical plastic additive di-(2-ethylhexyl)phthalate (DEHP) on soil health via combining the evidence from in situ zymography, the microbiome, and metabolism. The plastic additive dominated the risks of plastic pollution to plants, and the coexistence of NPs did not mitigate the DEHP threat to microorganisms and increased that to food safety. Compared to single DEHP, combined NPs and DEHP inhibited β-glucosidase activity to limit soil organic carbon (C) decomposition and stimulated acid phosphatase activity to increase P uptake by tomato roots and enriched the relative abundance of C-fixed bacteria and P-dissolution bacteria, while inhibiting that of chemical heterotrophic bacteria in rhizosphere soils, which further stimulated the synthesis and metabolism of phospholipid and fatty acid and triphosphate cycle and increased nutrients bioavailability for plants. Therefore, rhizosphere effects optimized the root nutrient acquisition strategy, microbial community structure, and their metabolic processes to reduce the threat from NPs and plastic additives to plants. This study provides new insights for environmental risk control and agricultural management under plastic pollution.},
}

@article {pmid40574415,
year = {2025},
author = {Liu, X and Liang, Y and Li, Z and Xie, C and Zhang, Y and Wang, W and Ge, S and Li, J},
title = {Nano-Toothbrush for Noninvasive Control of Periodontitis.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345251335922},
doi = {10.1177/00220345251335922},
pmid = {40574415},
issn = {1544-0591},
abstract = {Periodontitis is a prevalent oral disease, and current clinical management remains limited to mechanical debridement of subgingival plaque and adjunctive antibiotic therapy. In this study, we introduced a piezocatalytic nanoparticle-constructed "nano-toothbrush" as a noninvasive strategy for oral biofilm removal. The dextran-mediated biofilm affinity of the nano-toothbrush induced localized oxidative stress under ultrasound irradiation, effectively disrupting biofilms and inhibiting pathogenic bacteria. This efficacy was evidenced by the removal of ex vivo biofilms from periodontitis patients. Importantly, the selective action of the nano-toothbrush minimized the damage to mouse fibroblasts and human immortalized oral epithelial cells, affirming its biosafety. In vivo studies showed that the nano-toothbrush significantly inhibited the cell viability of Porphyromonas gingivalis, effectively suppressed alveolar bone resorption, and alleviated inflammatory responses in a rat periodontitis model while concurrently preserving the diversity of the oral microbiome. This study presents a promising noninvasive and precise method for the removal of oral biofilms, offering new perspectives on the application of nanotherapeutics in the treatment of periodontitis and other plaque-induced diseases.},
}

@article {pmid40574306,
year = {2025},
author = {Shen, G and Xu, X and Li, M and Sun, Z and Wei, L and Deng, Z and Lin, Z and Huang, J and Qi, W and Xu, J},
title = {The Clinical Trials Landscape for Alzheimer's Disease.},
journal = {CNS neuroscience & therapeutics},
volume = {31},
number = {6},
pages = {e70492},
doi = {10.1111/cns.70492},
pmid = {40574306},
issn = {1755-5949},
support = {202201010823//Guangzhou Science and Technology Program Project/ ; 2024A1515013041//Natural Science Foundation of Guangdong Province/ ; Y-zai2022/qn-0250//Beijing Xisike Clinical Oncology Research Foundation/ ; },
mesh = {*Alzheimer Disease/therapy/drug therapy ; Humans ; *Clinical Trials as Topic/methods ; },
abstract = {INTRODUCTION: Not only drug and non-drug development but also non-therapeutic research in Alzheimer's disease (AD) clinical trials is unclear.

METHODS: The participants were AD clinical trials obtained from the clinicaltrials.gov registry. The research objectives and interventions of those trials were analyzed. Bibliometric network analysis of those published articles in PubMed was also conducted.

RESULTS: A total of 1681 clinical trials and 565 corresponding published articles in the past 20 years were included in the analysis. "Safety", "dose", "adverse events", and "biomarker" were the most frequently used words that appeared in the title or abstract of published articles. The top three classes of 362 drugs were anti-Amyloid, enhancing acetylcholine, neurotransmitter, or targeting its receptor. The physical therapy, diet, and cognitive training ranked as the first three classes of non-drug therapy. Imaging, risk factors, and molecular biomarkers were the three most abundant categories in non-therapeutic research, and three fields of prevention, risk factors, and the dental or intestinal microbiome showed an escalated trend (All Ptrend < 0.05).

DISSUSION: The results described a comprehensive landscape for the clinical studies of AD. Although most drugs treated AD abortively, the success of lecanemab and decanemab provides confidence for us to further study the pathogenesis of AD and explore new therapeutic targets to develop anti-AD drugs. Rising non-drug and non-therapeutic research will provide more possible methods for the treatment and prevention of AD in thefuture.},
}

*Alzheimer Disease/therapy/drug therapy
Humans
*Clinical Trials as Topic/methods

@article {pmid40573904,
year = {2025},
author = {Yang, H and Zhou, Y and Cheng, X and Qiu, C and Wang, S and Xia, Y and Huai, X and Xiu, Z and Wang, J and He, Y and Cao, G and Wei, Q and Wang, J and Ai, J and Zhang, H and Zhang, Y and Zhang, J and Zhang, W and Wang, B},
title = {Safety, Tolerability, and Immunogenicity of a DNA Vaccine (pGX9501) Against SARS-CoV-2 in Healthy Volunteers: A Single-Center, Randomized, Double-Blind, Placebo-Controlled, and Dose-Ranging Phase I Trial.},
journal = {Vaccines},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/vaccines13060573},
pmid = {40573904},
issn = {2076-393X},
support = {92169212//National Natural Science Foundation of China/ ; HS2021SHZX001//Shanghai Municipal Science and Technology Major Project/ ; },
abstract = {Background: pGX9501 is a prophylactic DNA vaccine encoding the spike protein of SARS-CoV-2 and can induce immune response in the human body so as to prevent COVID-19. With respect to non-clinical studies, pGX9501 has been demonstrated to induce both cellular and humoral immune responses in various animal models. It was found that the level of antibody titers following a two-dose regimen was higher than that following a single-dose regimen in nonhuman primate challenge model. Methods: In China, a phase I, randomized, double-blind, placebo-controlled clinical trial has been conducted in Huashan Hospital, Shanghai, China to evaluate the safety, tolerability, and immunogenicity of DNA vaccine pGX9501 administered intradermally (ID) followed by electroporation (EP) in 45 Chinese healthy volunteers aged 18 to 59 years old. Results: No adverse events of special interest (AESIs), death, or treatment-related SAEs occurred in this study. All the treatment-related (vaccine or EP) adverse events (TRAEs) were of grade 1 and 2 in severity. The solicited AEs were reported in thirty-two (32/36, 88.9%) and nine (9/9, 100.0%) subjects, respectively, in the DNA vaccine and placebo group. The frequency of solicited AEs did not increase with vaccine dose level and frequency. The DNA vaccine pGX9501 effectively enhanced both humoral and cellular immune responses in a dose-dependent manner, with increased antibody GMTs and peak seroconversion rates observed on day 42. The significant rise in IFN-γ levels confirmed the vaccine's ability to induce cellular immune responses. Variations in the microbiome structure suggested a tangible impact of the gut microbiota on vaccine immunogenicity. Conclusions: The findings from this study confirm the immunogenicity and safety of the DNA vaccine pGX9501 and point to the potential role of the gut microbiota in vaccine immune responses. These insights provide practical references for the future design and development of DNA vaccines.},
}

@article {pmid40573878,
year = {2025},
author = {Ullah, F and Ali, S and Siraj, M and Akhtar, MS and Zaman, W},
title = {Plant Microbiomes Alleviate Abiotic Stress-Associated Damage in Crops and Enhance Climate-Resilient Agriculture.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/plants14121890},
pmid = {40573878},
issn = {2223-7747},
abstract = {Plant microbiomes, composed of a diverse array of microorganisms such as bacteria, fungi, archaea, and microalgae, are critical to plant health and resilience, playing key roles in nutrient cycling, stress mitigation, and disease resistance. Climate change is expected to intensify various abiotic stressors, such as drought, salinity, temperature extremes, nutrient deficiencies, and heavy metal toxicity. Plant-associated microbiomes have emerged as a promising natural solution to help mitigate these stresses and enhance agricultural resilience. However, translating laboratory findings into real-world agricultural benefits remains a significant challenge due to the complexity of plant-microbe interactions under field conditions. We explore the roles of plant microbiomes in combating abiotic stress and discuss advances in microbiome engineering strategies, including synthetic biology, microbial consortia design, metagenomics, and CRISPR-Cas, with a focus on enhancing their practical application in agriculture. Integrating microbiome-based solutions into climate-smart agricultural practices may contribute to long-term sustainability. Finally, we underscore the importance of interdisciplinary collaboration in overcoming existing challenges. Microbiome-based solutions hold promise for improving global food security and promoting sustainable agricultural practices in the face of climate change.},
}

@article {pmid40573860,
year = {2025},
author = {Luo, D and Liao, D and Han, T and Ji, C and He, C and Li, X},
title = {Regulatory Effects of Companion Plants (Maize (Zea mays) and Perilla frutescens) on American Ginseng Growth and Microbiome in Root Rot-Infested Field.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/plants14121871},
pmid = {40573860},
issn = {2223-7747},
support = {2022YFC3501501//National Key R&D Program of China/ ; },
abstract = {American ginseng (AG) cultivation suffers from severe diseases, requiring heavy pesticide use. This study aimed to explore whether companion planting with maize (AG-maize) or Perilla frutescens (AG-perilla) could enhance AG growth and alter rhizosphere/root microbiomes in a root rot-infested field. Compared to monoculture (CK), companion planting significantly improved AG growth and survival rate at wither stage, with AG-maize showing the superior efficacy- increasing root length and fresh weight, and plant height by 39.04%, 46.10%, and 48.69%, respectively, while raising survival rate from 1.51% to 14.54%. Microbial analysis revealed that companion planting increased microbiome diversity and network complexity. At green fruit stage, AG-perilla increased rhizosphere fungal Chao1 index by 42.6%, while AG-maize and AG-perilla elevated endophytic fungal Shannon indices by 46.68% and 74.84%, respectively. At wither stage, AG-maize notably enriched beneficial microbes (e.g., soil Pseudomonas +108.49%, Bacillus +200.73%) while reducing pathogens (soil Fusarium -20.04%, root endophytic Alternaria -54.55%). Structural equation model indicated AG-maize improved AG survival via core species-driven antibiosis and nutrient regulation, with keystone species Lysobacter sp. RHLT3-4 and Verrucomicrobium sp. IMCC25902 significantly correlating with AG health. The AG-maize system fostered synergistic microbial networks, enriching beneficial taxa and suppressing pathogens. These findings provide a foundation for developing eco-friendly disease management and high-yield AG cultivation strategies.},
}

@article {pmid40573793,
year = {2025},
author = {Li, Y and Xiao, Y and Zhao, W and Kang, J and Yang, K and Fu, J},
title = {Characteristic Functional Genera (CFG) Mediate Nitrogen Priming Effect in the Microbiome of Saline-Alkaline Farmland.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/plants14121806},
pmid = {40573793},
issn = {2223-7747},
support = {LJGXCG2022-107//Heilongjiang Province "Double First-Class" Discipline Collaborative Innovation Achievement Construction Project "Green and Low-Carbon for Food Crops"/ ; YQJH2024171//Program for Young Talents of Basic Research in Universities of Heilongjiang Province/ ; YQ2024C043//Nature Scientific Foundation of Heilongjiang Province/ ; XDA28130103//Strategic Priority Research Program of the Chinese Academy of Science/ ; },
abstract = {This study aimed to investigate the impact of nitrogen priming effect on the makeup of the maize rhizosphere microbial community structure in saline-alkali agriculture, focusing on characteristic functional genera. In 2020, three nitrogen levels of 60 kg·ha[-1] (N1), 180 kg·ha[-1] (N2), and 300 kg·ha[-1] (N3), along with a control group, were established in the meadow saline-alkali soil farmland of Daqing in Heilongjiang Province. The maize cultivar was Xianyu 335. Rhizosphere soil was taken for nutritional analysis and high-throughput sequencing of the microbial population. The findings indicated that the bacterial community structure in the N1 and N2 treatment groups was comparable; however, the N3 treatment dramatically altered the community structure (p < 0.01). A notable disparity existed between the fungal nitrogen application group and the control group. Screening identified ten genera, including Lysobacter and Coniophora, as characteristic functional genera, with their habitats and functions dramatically altered during nitrogen priming effect. Nitrogen priming effect enhanced bacterial functionality for nitrogen source augmentation but diminished the capacity for nitrogen transformation, while also altering the nutritional preferences of fungus. Soil nitrogen and organic matter content showed distinct responses to different nitrogen application rates and exhibited significant interactions with the microbial community. The impacts of low, medium, and high nitrogen treatments on microbial and soil indicators varied, suggesting that effective nutrient management necessitates the regulation of microbial community function and accurate nitrogen administration. The research findings hold substantial importance and promotional potential for the sustainable advancement of saline-alkali agriculture.},
}

@article {pmid40573780,
year = {2025},
author = {Zhang, S and Luo, Z and Peng, J and Wu, X and Meng, X and Qin, Y and Zhu, F},
title = {Analysis of Cadmium Accumulation Characteristics Affected by Rhizosphere Bacterial Community of Two High-Quality Rice Varieties.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/plants14121790},
pmid = {40573780},
issn = {2223-7747},
support = {2024YFD2301400//the National Key Research and Development Program of China/ ; 2024CX09//the Agricultural Science and Technology Innovation Project of Hunan Province, China/ ; },
abstract = {Cadmium-contaminated rice poses serious health risks through the bioaccumulation of Cd (cadmium) from soil to edible grains. Cd contamination disrupts soil microbial ecology and alters microbial diversity. However, the role of cultivar-specific rhizosphere microbial communities in modulating Cd uptake remains unclear. In this study, we aimed to elucidate the mechanism underlying variety-dependent rhizosphere microecological remodeling and Cd accumulation in two independently selected late rice varieties, Yuzhenxiang (YZX) and Xiangwanxian 12 (XWX12). Combining physiological and metagenomic analyses, we revealed variety-specific correlations between root Cd accumulation and dynamic changes in soil pH, soil available phosphorus, and rhizosphere bacteria. The key bacterial genera (Variibacter, Nitrospira) showed differential enrichment patterns under Cd stress. In contrast, Galella and Anaeromyxobacter likely reduce Cd bioavailability by modulating phosphorus availability. Overall, this study elucidates that rice cultivars indirectly shape Cd accumulation patterns via rhizosphere microbial remodeling, providing novel insights for microbial remediation strategies in Cd-contaminated farmland.},
}

@article {pmid40573741,
year = {2025},
author = {Kruščić, K and Jelušić, A and Hladnik, M and Janakiev, T and Anđelković, J and Bandelj, D and Dimkić, I},
title = {The Influence of Bacterial Inoculants and a Biofertilizer on Maize Cultivation and the Associated Shift in Bacteriobiota During the Growing Season.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/plants14121753},
pmid = {40573741},
issn = {2223-7747},
support = {451-03-136/2025-03/200178//Ministry of Education, Science and Technological Development of Serbia/ ; TERRA_MADRE 7455//Program PRISMA of the Science Fund of the Republic of Serbia/ ; },
abstract = {Maize (Zea mays L.) relies heavily on nitrogen and phosphorus inputs, typically supplied through organic and inorganic fertilizers. However, excessive agrochemical use threatens soil fertility and environmental health. Sustainable alternatives, such as poultry manure (PM) and plant growth-promoting rhizobacteria (PGPR), offer promising solutions. This study examines the effects of a phytobiotic bacterial formulation (PHY), composed of Bacillus subtilis and Microbacterium sp., applied alone and in combination with PM, on maize's rhizosphere bacteriobiome across key growth stages. Field trials included four treatments: a control, PHY-coated seeds, PM, and combined PHY_PM. The results show that early in development, the PM-treated rhizospheres increased the abundance of beneficial genera such as Sphingomonas, Microvirga, and Streptomyces, though levels declined in later stages. The PHY_PM-treated roots in the seedling phase showed a reduced abundance of taxa like Chryseobacterium, Pedobacter, Phyllobacterium, Sphingobacterium, and Stenotrophomonas, but this effect did not persist. In the PM-treated roots, Flavisolibacter was significantly enriched at harvesting. Overall, beneficial bacteria improved microbial evenness, and the PHY_PM treatment promoted bacterial diversity and maize growth. A genome analysis of the PHY strains revealed plant-beneficial traits, including nutrient mobilization, stress resilience, and biocontrol potential. This study highlights the complementarity of PM and PGPR, showing how their integration reshapes bacteriobiome and correlates with plant parameters in sustainable agriculture.},
}

@article {pmid40573190,
year = {2025},
author = {Ruiz-Álvarez, BE and Cattero, V and Desjardins, Y},
title = {Prebiotic-like Effects of Proanthocyanidin-Rich Aronia Extract Supplementation on Gut Microbiota Composition and Function in the Twin-M-SHIME[®] Model.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {18},
number = {6},
pages = {},
doi = {10.3390/ph18060793},
pmid = {40573190},
issn = {1424-8247},
support = {NSERC-Symrise Industrial Chair on prebiotic Effects of Fruits and Vegetables//Symrise/ ; },
abstract = {Background: Phenolic compounds, particularly anthocyanins and proanthocyanidins (PACs), are poorly absorbed in the upper digestive tract and reach the colon largely intact, where they may influence gut microbiota (GM) composition and, in turn, impact host health. We hypothesized that a PAC-rich aronia extract would beneficially modulate the GM, promote the growth of health-associated bacteria, and enhance short-chain fatty acid (SCFA) production across different colon sections, with partial reversion effects after supplementation ends. Methods: The Twin-M-SHIME[®] system was used to simulate the digestion and colonic fermentation in two donors with contrasting microbiota profiles. The experimental design included four phases: stabilization (14 days), control (7 days), treatment with 500 mg/day PAC-rich aronia extract (21 days), and wash-out (10 days). SCFA production was monitored, and changes in microbiome composition were assessed using 16S rRNA gene sequencing. Results: PAC-rich aronia extract significantly modulated SCFA levels, increasing butyrate and reducing acetate, with some inter-donor variability. SCFA concentrations tended to return to baseline after the wash-out (WO) period. Metagenomic analysis revealed a decrease in Collinsella, Sutterella, Selenomonas, and Parabacteroides-genera linked to low-fiber diets and gut inflammation-while promoting Proteobacteria (e.g., Escherichia-Shigella, Klebsiella) and butyrate-associated Firmicutes such as Lactiplantibacillus. Although some microbial shifts partially reverted during the wash-out (e.g., Akkermansia, Bacteroides, and Bifidobacterium), other changes persisted. Conclusions: These findings suggest that PAC-rich aronia extract beneficially modulates GM and SCFA production, but continuous intake may be necessary to maintain these effects over time.},
}

@article {pmid40573134,
year = {2025},
author = {Wu, H and Witt, BL and van der Pol, WJ and Morrow, CD and Duck, LW and Tollefsbol, TO},
title = {Combined Phytochemical Sulforaphane and Dietary Fiber Inulin Contribute to the Prevention of ER-Negative Breast Cancer via PI3K/AKT/MTOR Pathway and Modulating Gut Microbial Composition.},
journal = {Nutrients},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/nu17122023},
pmid = {40573134},
issn = {2072-6643},
support = {R01CA178441/NH/NIH HHS/United States ; },
mesh = {Animals ; *Isothiocyanates/pharmacology/administration & dosage ; *Inulin/pharmacology/administration & dosage ; Sulfoxides ; Female ; *Gastrointestinal Microbiome/drug effects ; *Dietary Fiber/administration & dosage/pharmacology ; Mice ; TOR Serine-Threonine Kinases/metabolism ; Proto-Oncogene Proteins c-akt/metabolism ; *Breast Neoplasms/prevention & control ; Mice, Transgenic ; Phosphatidylinositol 3-Kinases/metabolism ; Signal Transduction/drug effects ; Receptors, Estrogen/metabolism ; Phytochemicals/pharmacology/administration & dosage ; Prebiotics ; Anticarcinogenic Agents ; },
abstract = {Background: Breast cancer (BC) is the second most common cancer among women in the United States. It has been estimated that one in eight women will be diagnosed with breast cancer in her lifetime. Various BC risk factors, such as age, physical inactivity, and smoking, play a substantial role in BC occurrence and development. Early life dietary intervention with plant-based bioactive compounds has been studied for its potential role in BC prevention. Sulforaphane (SFN), an isothiocyanate, is an antioxidant and anti-inflammatory agent extracted from broccoli sprouts (BSp) and other plants. Dietary supplementation of SFN suppresses tumor growth by inducing protective epigenetic changes and inhibiting cancer cell proliferation. Inulin, as a dietary fiber, has been studied for alleviating GI discomfort and weight loss by promoting the growth of beneficial bacteria in the gut. Objective: Early-life combinatorial treatment with both phytochemical SFN and potential prebiotic agent inulin at lower and safer dosages may confer more efficacious and beneficial effects in BC prevention. Methods: Transgenic mice representing estrogen receptor-negative BC were fed 26% (w/w) BSp and 2% (w/v) inulin supplemented in food and water, respectively. Results: The combinatorial treatment inhibited tumor growth, increased tumor onset latency, and synergistically reduced tumor weight. Gut microbial composition was analyzed between groups, where Ruminococcus, Muribaculaceae, and Faecalibaculum significantly increased, while Blautia, Turicibacter, and Clostridium sensu stricto 1 significantly decreased in the combinatorial group compared with the control group. Furthermore, combinatorial treatment induced a protective epigenetic effect by inhibiting histone deacetylases (HDACs) and DNA methyltransferases (DNMTs). Intermediates in the AKT/PI3K/MTOR pathway were significantly suppressed by the combinatorial treatment, including PI3K p85, p-AKT, p-PI3K p55, MTOR, and NF-κB. Cell cycle arrest and programmed cell death were induced by the combinatorial treatment via elevating the expression of cleaved-caspase 3 and 7 and inhibiting the expressions of CDK2 and CDK4, respectively. Orally administering F. rodentium attenuated tumor growth and induced apoptosis in a syngeneic triple-negative breast cancer (TNBC) mouse model. Conclusions: Overall, the findings suggest that early-life dietary combinatorial treatment contributed to BC prevention and may be a potential epigenetic therapy that serves as an adjunct to other traditional neoadjuvant therapies.},
}

Animals
*Isothiocyanates/pharmacology/administration & dosage
*Inulin/pharmacology/administration & dosage
Sulfoxides
Female
*Gastrointestinal Microbiome/drug effects
*Dietary Fiber/administration & dosage/pharmacology
Mice
TOR Serine-Threonine Kinases/metabolism
Proto-Oncogene Proteins c-akt/metabolism
*Breast Neoplasms/prevention & control
Mice, Transgenic
Phosphatidylinositol 3-Kinases/metabolism
Signal Transduction/drug effects
Receptors, Estrogen/metabolism
Phytochemicals/pharmacology/administration & dosage
Prebiotics
Anticarcinogenic Agents

@article {pmid40573129,
year = {2025},
author = {Ferrer, MF and Retuerto, M and Thavamani, A and San Valentin, EM and Sferra, TJ and Ghannoum, M and Sankararaman, S},
title = {Clinical and Gut Microbiome Characteristics of Medically Complex Patients Receiving Blenderized Tube Feeds vs. Standard Enteral Feeds.},
journal = {Nutrients},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/nu17122018},
pmid = {40573129},
issn = {2072-6643},
support = {none//Fellowship Research Award Program, Rainbow Children's Foundation./ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Enteral Nutrition/methods/adverse effects ; Male ; Female ; Adolescent ; Child ; Child, Preschool ; Infant ; Young Adult ; Vomiting/etiology/epidemiology ; *Food, Formulated ; },
abstract = {Background: Diet is known to influence the composition of the gut microbiome. For patients who require enteral feeding, there has been a growing popularity of using blenderized tube feeds (BTFs) as an alternative to standard enteral formula (SEF). There is limited literature exploring the impact of BTFs on the gut microbiome. Methods: Twenty-eight patients 1 to 22 years of age who received their nutrition via gastrostomy tube for over 4 weeks were included and participants were divided into BTF and SEF groups. Demographics and clinical information were collected from the medical records, and all legal guardians completed a semi-structured interview using a questionnaire. 16SrRNA sequencing was used for bacteriome analysis. Results: Eleven patients in the BTF group and seventeen in the SEF group were included. No significant differences in the demographics were noted. Patients on BTFs had no emesis compared to seven (41%) in the SEF group, p = 0.02. There were no significant differences in other clinical characteristics and comorbidities. No significant differences in the gut microbiome between the groups were noted for alpha and beta diversities, richness, and evenness (at both genus and species levels). Differential abundance analysis showed only a few significant differences between the groups at all reported taxonomic levels. Conclusions: Patients on BTFs had a significantly decreased prevalence of emesis compared to the SEF group. No significant differences in the microbiome between the groups were noted for alpha and beta diversities, richness, and evenness. Prospective studies are recommended to verify our preliminary data and further evaluate the implications of our study results.},
}

Humans
*Gastrointestinal Microbiome
*Enteral Nutrition/methods/adverse effects
Male
Female
Adolescent
Child
Child, Preschool
Infant
Young Adult
Vomiting/etiology/epidemiology
*Food, Formulated

@article {pmid40573072,
year = {2025},
author = {Wakino, S and Hasegawa, K and Tamaki, M and Minato, M and Inagaki, T},
title = {Kidney-Gut Axis in Chronic Kidney Disease: Therapeutic Perspectives from Microbiota Modulation and Nutrition.},
journal = {Nutrients},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/nu17121961},
pmid = {40573072},
issn = {2072-6643},
mesh = {Humans ; *Renal Insufficiency, Chronic/microbiology/therapy/physiopathology ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/therapy/microbiology ; Probiotics/therapeutic use ; Prebiotics/administration & dosage ; *Kidney/physiopathology ; Synbiotics/administration & dosage ; Fecal Microbiota Transplantation ; Uremia/microbiology ; *Nutrition Therapy/methods ; },
abstract = {Chronic kidney disease (CKD) has a high prevalence worldwide, with an increasing incidence. One of the mechanisms of CKD progression involves a disordered inter-organ relationship between the kidneys and the intestine, known as the kidney-gut axis. In CKD, two pathological gut conditions-disturbed gut microbiota composition called uremic dysbiosis and leaky gut-contribute to the progression of CKD. Dysbiosis is associated with the increased production of gut-derived uremic toxins, leaky gut, and chronic systemic inflammation, leading to worsening uremia, which in turn aggravates the gut condition. This vicious cycle should be a target of the therapeutic strategy against CKD. The modulation of uremic dysbiosis, including prebiotics, probiotics, and synbiotics, has been a typical treatment approach, although clinical evidence for their efficacy has been insufficient. Some non-antibiotic drugs have an impact on human gut bacteria that are believed to play a role in their clinical efficacy on kidney function. Nutrition therapies, including a low-protein diet, dietary fiber, a Mediterranean diet, and whole grains, positively influence gut microbiota composition and have been linked to a decreased risk of CKD. Novel strategies are currently being explored, involving the use of postbiotics, microbiome sequencing techniques, and fecal microbiota transplantation, although clinical application remains to be tested. Human trials investigating the above-mentioned interventions remain inconclusive due to several limitations, including dietary variability and genetic factors. Future research should focus on the development of more effective probiotics, prebiotics, and microbial metabolism-modifying drugs, not only for CKD but for other systemic diseases as well.},
}

Humans
*Renal Insufficiency, Chronic/microbiology/therapy/physiopathology
*Gastrointestinal Microbiome/physiology
*Dysbiosis/therapy/microbiology
Probiotics/therapeutic use
Prebiotics/administration & dosage
*Kidney/physiopathology
Synbiotics/administration & dosage
Fecal Microbiota Transplantation
Uremia/microbiology
*Nutrition Therapy/methods

@article {pmid40572802,
year = {2025},
author = {Mackawy, AMH and Alturky, FS and Mohammed, AH and Alharbi, BF and Huq, M and Wasti, AZ and Ahmed, MAA and Alharbi, HOA},
title = {A Comparative Analysis of Feeding Practices and Oral Immunity in Infants.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {6},
pages = {},
pmid = {40572802},
issn = {1648-9144},
mesh = {Humans ; Infant ; Female ; *Breast Feeding/statistics & numerical data ; Male ; Interleukin-17/analysis ; Infant Formula ; Mouth Mucosa/microbiology/immunology ; },
abstract = {Background and Objectives: Infant feeding practices play a crucial role in shaping the oral microbiome, modulating inflammatory responses, and maintaining epithelial health during the first year of life. Breastfeeding promotes the growth of beneficial bacteria and supports a diverse, stable microbial community. In contrast, formula feeding is associated with increased colonization by potentially pathogenic bacteria, such as Staphylococcus and Escherichia coli, which may elevate the risk of infections, oral diseases, and inflammation. This study investigates the effects of breastfeeding versus formula feeding on oral bacterial growth, epithelial cell integrity, and interleukin-17 (IL-17) expression in infants aged 1-12 months. Materials and Methods: A total of 60 infants (30 breastfed and 30 formula-fed) were recruited from pediatric clinics in the Qassim region. Microbial cultures quantified bacterial colony-forming units (CFUs), and epithelial cell morphology was assessed through the microscopic analysis of mucosal scrapings. IL-17 concentrations were quantified from the oral mucosa through enzyme-linked immunosorbent assay. Statistical analyses, including t-tests and chi-square tests, compared bacterial loads, IL-17 levels, and indicators of epithelial health between groups. Adjustment for potential confounders was achieved through multivariate statistical analysis. Results: Formula-fed infants showed significantly higher IL-17 levels than breastfed infants (p < 0.001), indicating a stronger pro-inflammatory profile. Breastfed infants exhibited lower inflammation, improved epithelial health, and reduced cellular debris compared to formula-fed infants, who had higher bacterial loads. A significant correlation was found between epithelial health and bacterial clustering, with clearer epithelial cells associated with lower bacterial colonization. Conclusions: Formula feeding was associated with increased salivary IL-17 levels, greater bacterial colonization, and compromised epithelial integrity, indicating a heightened pro-inflammatory state and potential vulnerability to mucosal irritation or infection. Breastfeeding appeared to confer protective effects by promoting healthier microbial balance, epithelial integrity, and reducing inflammatory responses. These findings underscore the immunological and microbial benefits of breastfeeding in supporting oral health during infancy.},
}

Humans
Infant
Female
*Breast Feeding/statistics & numerical data
Male
Interleukin-17/analysis
Infant Formula
Mouth Mucosa/microbiology/immunology

@article {pmid40572315,
year = {2025},
author = {Kim, B and Lee, S and Lee, YJ and Kang, YM and Rhee, MH and Kwak, D and Yeo, YG and Kang, JW and Kim, T and Seo, MG},
title = {Preliminary Insights into the Gut Microbiota of Captive Tigers in Republic of Korea: Influence of Geographic and Individual Variation.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572315},
issn = {2076-2607},
support = {none//Baekdudaegan National Arboretum (Korean Tiger Conservation Center)./ ; },
abstract = {The gut microbiome plays a crucial role in the health and physiology of tigers (Panthera tigris), influencing digestion, immune function, and overall well-being. While numerous studies have characterized the gut microbiota of domestic carnivores and some wild felids, comparative analyses across different tiger subspecies under varying environmental contexts remain limited. In this exploratory study, we investigated the gut microbiome diversity and composition of 15 captive tigers, including both Siberian (P. tigris altaica) and Bengal (P. tigris tigris) subspecies, housed in two different regions in Korea. Using 16S rRNA gene sequencing of fecal samples, we analyzed microbial diversity across multiple taxonomic levels. Preliminary analyses revealed significant differences in microbial composition between geographic locations, whereas sex-based differences appeared minimal. Alpha and beta diversity metrics demonstrated substantial inter-individual variability, likely influenced by regional and environmental factors. Given the small sample size and the confounding between subspecies and housing location, the findings should be regarded as preliminary and not generalized beyond this specific cohort. Nevertheless, these insights highlight the potential utility of gut microbiome profiling for health monitoring and management in captive-tiger populations. Future research incorporating larger, more diverse cohorts will be essential to validate these trends and clarify the roles of diet, health status, and enrichment in shaping the gut microbiota.},
}

@article {pmid40572314,
year = {2025},
author = {Kim, MJ and Yoo, J and Yoo, S and Kwon, MY and Lee, S and Kim, M},
title = {The Clinically Significant Changes in the Composition and Functional Diversity of the Vaginal Microbiome in Women with Type 2 Diabetes Mellitus.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572314},
issn = {2076-2607},
support = {BCMC20LH03//Clinical Medicine Research of Bucheon St. Mary's Hospital/ ; },
abstract = {Type 2 diabetes mellitus (T2DM) significantly influences the composition and diversity of the vaginal microbiome, with implications for mucosal immunity, infection risk, and genitourinary health. This study aimed to investigate the vaginal microbiome profiles in women with T2DM, with a focus on differences according to menopausal status and associations with Candida colonization and the use of sodium-glucose cotransporter 2 (SGLT2) inhibitors. Compared to healthy controls, women with T2DM exhibited a decreased abundance of Lactobacillus species and increased microbial diversity. Community state of type (CST) IV, characterized by low Lactobacillus abundance and dominance of anaerobic taxa, was prevalent in the T2DM group. Among Candida-positive patients, Lactobacillus iners-dominant CST III was frequently observed, along with elevated levels of total and L-lactic acid. SGLT2 inhibitor users exhibited a different CST distribution pattern and slightly lower microbial richness and diversity, although these differences were not statistically significant. These findings underscore the impact of T2DM and its treatment on vaginal microbial composition and highlight the importance of considering vaginal health as part of comprehensive diabetes management in women.},
}

@article {pmid40572300,
year = {2025},
author = {Zhang, J and Tang, S and Wei, H and Yao, L and Chen, Z and Han, H and Ji, M and Yang, J},
title = {Reducing Cd Uptake by Wheat Through Rhizosphere Soil N-C Cycling and Bacterial Community Modulation by Urease-Producing Bacteria and Organo-Fe Hydroxide Coprecipitates.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572300},
issn = {2076-2607},
support = {42377039//National Natural Science Foundation of China/ ; },
abstract = {The bioavailability of heavy metals is profoundly influenced by their interactions with active soil components (microorganisms, organic matter, and iron minerals). However, the effects of urease-producing bacteria combined with organo-Fe hydroxide coprecipitates (OFCs) on Cd accumulation in wheat, as well as the mechanisms underlying these effects, remain unclear. In this study, pot experiments integrated with high-throughput sequencing were employed to investigate the impacts of the urease-producing bacterial strain TJ6, ferrihydrite (Fh), and OFCs on Cd enrichment in wheat grains, alongside the underlying soil-microbial mechanisms. The results demonstrate that the strain TJ6-Fh/OFC consortium significantly (p < 0.05) reduced (50.1-66.7%) the bioavailable Cd content in rhizosphere soil while increasing residual Cd fractions, thereby decreasing (77.4%) Cd accumulation in grains. The combined amendments elevated rhizosphere pH (7.35), iron oxide content, and electrical conductivity while reducing (14.5-21.1%) dissolved organic carbon levels. These changes enhanced soil-colloid-mediated Cd immobilization and reduced Cd mobility. Notably, the NH4[+] content and NH4[+]/NO3[-] ratio were significantly (p < 0.05) increased, attributed to the ureolytic activity of TJ6, which concurrently alkalinized the soil and inhibited Cd uptake via competitive ion channel interactions. Furthermore, the relative abundance of functional bacterial taxa (Proteobacteria, Gemmatimonadota, Enterobacter, Rhodanobacter, Massilia, Nocardioides, and Arthrobacter) was markedly increased in the rhizosphere soil. These microbes exhibited enhanced abilities to produce extracellular polymeric substances, induce phosphate precipitation, facilitate biosorption, and promote nutrient (C/N) cycling, synergizing with the amendments to immobilize Cd. This study for the first time analyzed the effect and soil science mechanism of urease-producing bacteria combined with OFCs in blocking wheat's absorption of Cd. Moreover, this study provides foundational insights and a practical framework for the remediation of Cd-contaminated wheat fields through microbial-organic-mineral collaborative strategies.},
}

@article {pmid40572296,
year = {2025},
author = {Schmidt, JE and Flores, J and Barragan, L and Amores, F and Khalsa, SDS},
title = {Optimizing Cocoa Productivity Through Soil Health and Microbiome Enhancement: Insights from Organic Amendments and a Locally Derived Biofertilizer.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572296},
issn = {2076-2607},
support = {n/a//Mars Wrigley/ ; },
abstract = {Despite growing interest in improving soil health on cocoa farms, applied research on the impacts of specific amendments on soil and plant outcomes is lacking. An integrated assessment of the impacts of two different organic amendments (compost and vermicompost) and a microbial biofertilizer on soil physical, chemical, and biological properties, as well as cocoa flowering, fruit set, and yield, was conducted in Guayaquil, Ecuador. Complementary culture-dependent and culture-independent methods were used to assess the impacts of amendments on microbial diversity, community composition, and specific taxa. Compost or vermicompost application affected soil chemical properties, including potassium, phosphorus, and sodium, and had small but significant effects on fungal beta diversity. Biofertilizer application slightly lowered soil pH and altered the total abundance of specific taxonomic groups including Azotobacter sp. and Trichoderma sp., with borderline significant effects on Azospirillum sp., Lactobacillus sp., Pseudomonas sp., calcium-solubilizing bacteria, and phosphorus-solubilizing bacteria. Amplicon sequencing (16S, ITS) identified 15 prokaryotic and 68 fungal taxa whose relative abundance was influenced by organic amendments or biofertilizer. Biofertilizer application increased cherelle formation by 19% and monthly harvestable pod counts by 11% despite no impact on flowering index or annual pod totals. This study highlights the tangible potential of microbiome optimization to simultaneously improve on-farm yield and achieve soil health goals on cocoa farms.},
}

@article {pmid40572287,
year = {2025},
author = {Dai, H and Jia, M and Xue, J and Liu, Z and Zhou, D and Hou, Z and Yu, J and Lu, S},
title = {Complementary Rhizosphere Microbial Strategies Drive Functional Specialization in Coastal Halophyte Succession: Differential Adaptation of Suaeda glauca and Phragmites communis to Saline-Alkali Stress.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572287},
issn = {2076-2607},
support = {BE2022306//Special Fund on Technology Innovation of Carbon Dioxide Peaking and Carbon Neutrality of Jiangsu Province/ ; LYKJ[2022]02//Jiangsu Provincial For-estry Science and Technology Innovation and Promotion Project/ ; JSPKLB202511//Scientific Fund of Nanjing Botanical Garden Mem Sun Yat-Sen/ ; },
abstract = {While rhizosphere microbiome functions in saline soils are well documented, complementary microbial strategies between pioneer and late-successional halophytes remain unexplored. Here, we used 16S rRNA sequencing and FAPROTAX functional prediction to compare the rhizosphere bacterial communities of two key halophytes-Suaeda glauca and Phragmites communis-in a reclaimed coastal wetland. The results demonstrate that both plants significantly restructured microbial communities through convergent enrichment of stress-tolerant taxa (Firmicutes, Pseudomonas, Bacillus, and Planococcus) while suppressing sulfur-oxidizing bacteria (Sulfurovum and Thiobacillus). However, they exhibited distinct microbial specialization: S. glauca uniquely enriched organic-matter-degrading taxa (Promicromonospora and Zhihengliuella) and upregulated aromatic compound degradation (2.29%) and ureolysis (0.86%) according to FAPROTAX analysis, facilitating carbon mobilization in early successional stages. Notably, P. communis selectively recruited nitrogen-cycling Serratia, with increased nitrate respiration (3.51% in P. communis vs. 0.91% in S. glauca) function, reflecting its higher nitrogen demand. Environmental factors also diverged: S. glauca's microbiome correlated with potassium and sodium, whereas P. communis responded to phosphorus and chloride. These findings uncover distinct microbial recruitment strategies by halophytes to combat saline stress-S. glauca-P. communis synergy through microbial carbon-nitrogen coupling-offering a template for consortia design in saline soil restoration.},
}

@article {pmid40572280,
year = {2025},
author = {Wang, Y and Diao, K and Li, H and Zhang, C and Zhang, G and Guo, C},
title = {Effects of Dietary Protein Levels on Production Performance, Meat Quality Traits, and Gut Microbiome of Fatting Dezhou Donkeys.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572280},
issn = {2076-2607},
support = {Grant Nos. 2019YFE0107700 and NRF-2019K1A3A1A20081146//This research was supported by the National Key R&D Program of China-Korea Cooperative Project/ ; Grant No. SDAIT-30-02//the Shandong Province Modern Agricultural Technology System Donkey Industry Innovation Team/ ; Grant No. 2022TZXD0018//the Key R&D Program of Shandong Province/ ; },
abstract = {This study aimed to investigate the effects of varying dietary protein levels on growth performance, meat quality traits, amino acid and fatty acid compositions, and hindgut microbiota in Dezhou donkeys. Eighteen 12-month-old male donkeys, weighing 188 ± 9 kg, were randomly allocated into three groups and fed diets containing 11.03% (LP), 12.52% (MP), and 14.06% (HP) protein. The average daily gain (ADG) was significantly higher (p < 0.05) in the HP and MP groups, while the feed conversion ratio (FCR) was lower (p < 0.05) compared to the LP group. The MP group exhibited superior performance in terms of serum albumin (ALB) and high-density lipoprotein (HDL) levels, as well as protein digestibility (p < 0.05). Improvements in meat tenderness, as well as increased levels of leucine, flavor amino acids (FAAs), and non-essential amino acids (NEAAs) (p < 0.05), were observed in the MP group compared to those in the LP and HP groups. The levels of total fatty acids (TFAs), saturated fatty acids (SFAs), unsaturated fatty acids (UFAs), and monounsaturated fatty acids (MUFAs) were higher (p < 0.05) in the LP and MP groups than in the HP group, with no significant differences (p > 0.05) observed between the LP and MP groups. The genera Prevotella, Clostridium_sensu_stricto_1, NK4A214_group, Oscillospiraceae_UCG-002, and Oscillospiraceae_UCG-005 in the rectum were identified as differential microbes associated with varying dietary protein levels. In conclusion, this study indicates that a dietary protein level of 12.52% could enhance the growth performance, dietary nutrient digestibility, slaughter performance, and meat quality of Dezhou donkeys by modulating hindgut microbial communities.},
}

@article {pmid40572254,
year = {2025},
author = {Park, Y and Kyung, S and Mun, S and Yu, BS and Yun, K and Baek, C and Lee, DG and Kang, S and Kim, SR and Kim, JH and Lee, Y and Park, BC and Han, K},
title = {Comparative Analysis of Bacteriome in Hair Follicle Layers of Patients with Female Pattern Androgenic Alopecia.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572254},
issn = {2076-2607},
abstract = {Androgenetic alopecia (AGA) is the most common form of patterned hair loss, exhibiting gender-specific clinical features. Recent studies highlight the importance of the skin microbiome in maintaining skin health, but the relationship between the hair follicle microbiome and hair loss, particularly AGA, remains understudied. Hair follicle layer samples were collected directly from the crown region of female pattern hair loss (FPHL), male pattern hair loss (MPHL), and healthy adult women (control) groups. Microbial DNA was extracted and analyzed using Illumina 16S rRNA V3-V4 gene amplicon sequencing. Alpha-diversity and beta-diversity analyses and taxonomic and functional profiling were conducted through relative abundance, LEfSe, and PICRUSt2 analyses. The alpha-diversity analysis showed a significant decrease in microbial richness in the hair loss groups. Unweighted UniFrac-based beta-diversity analysis revealed significant clustering between the control group and the FPHL group. Taxonomic profiling and LEfSe analysis identified differences in microbial composition and biomarkers. PICRUSt2 analysis further revealed altered pathways related to porphyrin metabolism, fatty acid biosynthesis, and steroid hormone metabolism. Additionally, differences in microbiome composition and potential functions were found between the FPHL and MPHL groups. This study provides comprehensive insights into the hair follicle microbiome, revealing unique microbial patterns and functional alterations associated with FPHL. Understanding these microbiome characteristics may contribute to targeted approaches for addressing AGA. Further research is warranted.},
}

@article {pmid40572244,
year = {2025},
author = {Roy, S and Alizadeh Bahmani, AH and Davids, M and Herrema, H and Nieuwdorp, M},
title = {Modulating the Gut-Muscle Axis: Increasing SCFA-Producing Gut Microbiota Commensals and Decreasing Endotoxin Production to Mitigate Cancer Cachexia.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572244},
issn = {2076-2607},
abstract = {Cancer cachexia is a multi-organ and multifactorial syndrome characterized by muscle wasting (with or without adipose tissue loss) and systemic inflammation in patients with advanced malignancies. Gut microbiota dysbiosis, particularly the depletion of short-chain fatty acid (SCFA)-producing bacteria, may contribute to the progression of cancer cachexia. Studies in both murine models and humans consistently associate cachexia with a decline in SCFA-producing gut microbiota commensals and an overgrowth of pro-inflammatory pathobionts. These microbial imbalances may lead to reduced levels of SCFAs and branched-chain amino acids (BCAAs) and alter the normal bile acid profile. BCAAs and the maintenance of a normal bile acid profile are associated with muscle synthesis and decreased breakdown. While SCFAs (acetate, propionate, and butyrate), contribute to intestinal barrier integrity and immune regulation. SCFA depletion may increase gut permeability, allowing bacterial endotoxins, such as lipopolysaccharide (LPS), to enter the bloodstream. This may lead to chronic inflammation, muscle catabolism, and impairment of anabolic pathways. Interventions targeting gut microbiota in preclinical models have mitigated inflammation and muscle loss. While clinical data are limited, it suggests an improvement in immune functions and better tolerance to anticancer therapies. Current evidence is predominantly derived from cross-sectional studies suggesting associations without causality. Thus, future longitudinal studies are needed to identify biomarkers and optimize personalized therapy.},
}

@article {pmid40572228,
year = {2025},
author = {Yue, C and Chai, Z and Li, F and Shang, L and Hu, Z and Deng, Y and Tang, YZ},
title = {Transitions of the Bacteria-Fungi Microbiomes Associated with Different Life Cycle Stages of Dinoflagellate Scrippsiella acuminata.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572228},
issn = {2076-2607},
support = {42376138//National Natural Science Foundation of China/ ; 42176207//National Natural Science Foundation of China/ ; },
abstract = {Dinoflagellates significantly contribute to the carbon fixation and microbial loop in the ocean with high ecological diversity. While the microbial communities associated with the HABs of dinoflagellates have attracted intensive attention in recent years, little attention has been paid to the microbiomes associated with resting cysts, an important stage in the life cycle and bloom initiation dynamics of dinoflagellates. Using Scrippsiella acuminata as a representative of cyst producers and cyst-relevant research in dinoflagellates, we surveyed the bacteria and fungi microbiomes long associated with different life cycle stages of the dinoflagellate culture through 16S and ITS rRNA amplicon sequencing, and predicted their possible functions using the PICRUSt2 algorithm. The results found high species diversity of the associated bacteria-fungi microbiomes, and species featured with diverse and flexible metabolic capabilities that have stably co-occurred with the laboratory culture of S. acuminata. The host-attached and the free-living groups of bacteria-fungi microbiomes, as operationally defined in the context, showed significant differences in terms of their nutritional preferences. The bacteria-fungi species diversity and community structure associated with cysts are also distinguished significantly from that with vegetative cells, with the latter attracting more bacteria-fungi species specializing in phosphate solubilization. These results suggest that the relative species abundance and thus the community structure of the host-associated microbiome shift with the transition of life cycle stages and environmental conditions. Our findings show the association tightness between bacteria-fungi microbiomes and dinoflagellate hosts and the different life stages of hosts shaping the bacteria-fungi communities, which result in dynamic and specific interactions between bacteria-fungi microbiomes and their hosts.},
}

@article {pmid40572225,
year = {2025},
author = {Jiang, Y and Li, W and Li, J and Hu, J and Wei, Y and Wang, Y and Yang, H and Zhou, Y and Wu, Y and Zhang, S},
title = {Co-Inoculating Burkholderia vietnamiensis B418 and Trichoderma harzianum T11W Reduced Meloidogyne incognita Infestation of Tomato Plants.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572225},
issn = {2076-2607},
support = {ZR2021MC085//Shandong Provincial Natural Science Foundation/ ; 2022TSGC2370//Shandong Provincial Innovation Capability Promotion Project for Sci-tech Small and Medium-sized Enterprises/ ; 2024GH15//Innovation Pilot Project of Integration of Science, Education, and Industry of Shandong Academy of Sciences (International Scientific and Technology Cooperation)/ ; },
abstract = {Root-knot nematodes (RKNs; Meloidogyne incognita) pose a significant threat to tomato crops, necessitating sustainable control methods. This study investigated the inoculation efficacy of co-cultured Burkholderia vietnamiensis B418 and Trichoderma harzianum T11W compared with single-strain treatments for RKNs suppression and their influence on the structure and function of the rhizosphere microbiome. Co-inoculation with B418 + T11W achieved a 71.42% reduction in the disease index, significantly outperforming single inoculations of B418 (54.46%) and T11W (58.93%). Co-inoculation also increased plant height by 38.51% and fresh weight by 76.02% compared to the RKNs infested plants control, promoting robust tomato growth. Metagenomic analysis reveals that co-inoculation enhanced bacterial diversity, with 378 unique bacterial species and a high Shannon index, while fungal diversity decreased with Trichoderma dominance (83.31% abundance). Actinomycetota (46.42%) and Ascomycota (97.92%) were enriched in the co-inoculated rhizosphere, showing negative correlations with RKNs severity. Functional analysis indicates enriched metabolic pathways, including streptomycin and unsaturated fatty acid biosynthesis, enhancing microbial antagonism. Single inoculations altered pathways like steroid degradation (B418) and terpenoid biosynthesis (T11W), but co-inoculation uniquely optimized the rhizosphere microenvironment. These findings highlight co-inoculation with B418 + T11W effectively suppressing RKNs and fostering plant health by reshaping microbial communities and functions, offering a promising approach for sustainable agriculture.},
}

@article {pmid40572215,
year = {2025},
author = {Ning, W and Luo, X and Zhang, Y and Li, S and Yang, X and Wang, X and Chen, Y and Xu, Y and Zhang, D and Zhang, S and Liu, Y},
title = {Comparative Analysis of Nano-Bactericides and Thiodiazole-Copper on Tomato Rhizosphere Microbiome.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572215},
issn = {2076-2607},
support = {2024AQ2036//2024AQ2036/ ; 2024CX04//2024CX04/ ; RCZ202505//RCZ202505/ ; },
abstract = {Vegetable crops such as tomato are highly susceptible to various pathogens. Nanoparticles (NPs) are emerging as effective nano-bactericides for managing plant pathogens. Communities of rhizosphere bacteria are essential for plant physiological health and also serve as a critical factor in evaluating the environmental compatibility of NPs. We evaluated the effects of a nano-bactericide (Cu-Ag nanoparticles) and a commercial bactericide (thiodiazole-copper) on the rhizosphere microbiome of tomato. The results show that low and high doses of the two bactericides induced alterations in the bacterial community structure to differing extents. Cu-Ag nanoparticles increased the relative abundance of potentially beneficial bacteria, including Bacteroidota, Gemmatimonadota, Acidobacteriota, and Actinobacteriota. Functional prediction revealed that Cu-Ag nanoparticles may affect the metabolic pathways of tomato root rhizosphere microorganisms and regulate the lacI/galR family, which controls virulence factors and bacterial metabolism. This study provides insight into the influence of metal nanoparticles on plant rhizosphere microbiomes and may lay a foundation for the application of nano-bactericides for the environmentally friendly control of plant diseases.},
}

@article {pmid40572205,
year = {2025},
author = {Chen, YC and Chiang, YF and Huang, KC and Wang, KL and Huang, YJ and Shieh, TM and Ali, M and Hsia, SM},
title = {The Vaginal Microbiome: Associations with Vaginal pH, Menopause and Metabolic Parameters.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572205},
issn = {2076-2607},
abstract = {The vaginal microbiota, a critical determinant of women's health, is influenced by hormonal and metabolic parameters across the lifespan. While Lactobacillus species are beneficial markers of vaginal health, microbial composition undergoes pronounced alterations after menopause. This study aimed to elucidate the associations between vaginal microbiota composition, vaginal pH, menopausal status, and metabolic parameters in Asian women. Vaginal secretion samples were collected from 40 women (20 premenopausal, 20 postmenopausal). Full-length 16S rRNA gene sequencing was used to characterize the microbiota, categorized into Community State Types (CSTs): CST-I + II (Lactobacillus crispatus/gasseri, protective), CST-III (Lactobacillus iners, neutral), and CST-IV (anaerobic bacteria, harmful). Vaginal pH and clinical data were assessed in relation to microbial profiles. CST distribution differed significantly by menopausal status and vaginal pH. Harmful-type CST-IV was more prevalent in postmenopausal women (70% vs. 40%, p < 0.05), while CST-III was dominant in premenopausal women (45% vs. 5%). CST-IV was associated with elevated pH (median 6.00, p = 0.026) and increased abundance of anaerobes including Bacteroides, Fusobacterium, Porphyromonas, Prevotella, and Streptococcus. Oral antibiotic use reduced both beneficial and harmful CSTs, shifting toward neutral CST-III (75%, p = 0.048). Use of sodium-glucose cotransporter-2 (SGLT2) inhibitors in postmenopausal women was associated with a higher prevalence of protective CST-I + II (57.14% vs. 8.33%, p < 0.05), though no significant impact on pathogen presence was observed. This study highlights the dynamic interplay between menopausal status, metabolic interventions, and vaginal microbiota composition. Findings may inform targeted strategies to maintain vaginal health in aging populations.},
}

@article {pmid40572201,
year = {2025},
author = {Bukša, A and Petrović, F and Maglica, Ž},
title = {Fungal β-Glucans Enhance Lactic Acid Bacteria Growth by Shortening Their Lag Phase and Increasing Growth Rate.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572201},
issn = {2076-2607},
support = {Uniri-prirod-18-302//University of Rijeka/ ; },
abstract = {The gut microbiome has a significant role in general health and well-being. Novel types of prebiotics, such as fungal polysaccharides, show potential for the formulation of new synbiotic formulations. However, little is known about the underlying mechanisms of the prebiotic effects of such compounds. This study investigated the prebiotic properties of fungal glucan extracts from Pleurotus ostreatus, Lentinula edodes, and Saccharomyces cerevisiae, employing a novel high-throughput method based on optical density measurements. This approach enabled the simultaneous screening of the effects of multiple extracts on six different strains of probiotic bacteria. Experiments were conducted to evaluate the effect of the extracts on the growth dynamics (the duration of the lag phase and the growth rate) of probiotic strains of the genera Lactobacillus and Lacticaseibacillus and on pathogenic bacteria. Fungal polysaccharide supplementation, particularly with their β-glucans, significantly shortened the lag phase by an average of 7-8 h in all tested strains and increased the growth rate by 2-fold in four strains of lactic acid bacteria. Different magnitudes of effects were observed across the various strain-extract combinations. This study lays the groundwork for elucidating the mechanism by which fungal β-glucans stimulate growth in probiotic bacteria and for the rapid screening of optimal combinations for formulating innovative synbiotics.},
}

@article {pmid40572188,
year = {2025},
author = {Asao, K and Hashida, N},
title = {Overview of Microorganisms: Bacterial Microbiome, Mycobiome, Virome Identified Using Next-Generation Sequencing, and Their Application to Ophthalmic Diseases.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572188},
issn = {2076-2607},
support = {23K15906 [to K.A.]//the Japan Society for the Promotion of Science/ ; 21K09695 [to N.H.]//the Japan Society for the Promotion of Science/ ; },
abstract = {This review outlines technological advances in pathogen identification and describes the development and evolution of next-generation sequencers that can be applied to the ocular microbiome. Traditional methods such as culture and PCR have limitations in detecting the full spectrum of resident microorganisms, prompting a transition toward metagenomic analysis. As microbiome research expands across body systems, the comprehensive identification of ocular bacteria, fungi, and viruses has become possible. The commensal ocular microbiome may influence disease development through changes in the immune system and ocular environment. Next-generation sequencing enables detailed microbial profiling, aiding in disease diagnosis and treatment selection. Alterations in the microbiome may also induce metabolic changes, offering insights into novel treatment methods. This review outlines the evolution of next-generation sequencing technology, summarizes current knowledge of microorganisms found on the ocular surface and in intraocular fluid, and discusses future challenges and prospects. However, the large volume of microbiome data obtained must be interpreted with caution due to possible analytical biases. Furthermore, determining whether the microbiome is truly pathogenic requires comprehensive interpretation beyond the clinical findings and results of traditional identification methods.},
}

@article {pmid40572181,
year = {2025},
author = {Hansen, LHB and Lauridsen, C and Nielsen, B and Jørgensen, L and Schönherz, A and Canibe, N},
title = {Early Inoculation of a Multi-Species Probiotic in Piglets-Impacts on the Gut Microbiome and Immune Responses.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572181},
issn = {2076-2607},
support = {7038-00168B//Innovation Foundation, Denmark/ ; },
abstract = {Intestinal diseases in nursery pigs harm health and performance and drive antimicrobial resistance. This study evaluated whether early probiotic inoculation helps piglets to cope with weaning-related gut challenges. The probiotic, containing Lacticaseibacillus rhamnosus, Enterococcus lactis, Bifidobacterium longum subsp. infantis, and Bifidobacterium breve, was given orally to newborn piglets daily until day 4 and then every other day until weaning at day 28 (at 4 × 10[9] CFU/dose). The control piglets received a placebo. The results showed that the probiotic pigs had reduced fecal alpha-diversity on day 7 but greater Shannon diversity on day 28 (feces) and day 23 (intestinal contents) compared to those of the control pigs. Beta-diversity analysis showed microbial differences between the groups on day 35. Most zOTUs (zero-radius operational taxonomic units) found to significantly differentiate the two treatment groups were found pre weaning. Bifidobacterium breve, Ligilactobacillus salivarius, as well as Clostridium ramosum were significantly more abundant in the feces of the probiotic pigs more than once. The probiotic pigs had higher expression levels of mucin 2 (MUC2); solute carrier family 5, member 8 (SLC5A8); and interleukin 8 (IL-8) post weaning. In the early post-weaning period, the probiotic pigs had less diarrhea as well as lower cadaverine levels in digesta than the control pigs. In conclusion, early probiotic inoculation may induce lasting immunomodulation via microbial antigen changes, enhancing resilience during challenges, like weaning. Notably, the effects persisted beyond weaning and probiotic cessation.},
}

@article {pmid40572178,
year = {2025},
author = {Maniscalco, I and Bartochowski, P and Priori, V and Iancau, SP and De Francesco, M and Innamorati, M and Jagodzinska, N and Giupponi, G and Masucci, L and Conca, A and Mroczek, M},
title = {The Effects of Fecal Microbial Transplantation on the Symptoms in Autism Spectrum Disorder, Gut Microbiota and Metabolites: A Scoping Review.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572178},
issn = {2076-2607},
abstract = {The bilateral interaction between the brain and the gut has recently been on the spectrum of researchers' interests, including complex neural, endocrinological, and immunological signaling pathways. The first case reports and clinical studies have already reported that delivering microbes through fecal microbial transplantation (FMT) may alleviate symptoms of psychiatric disorders. Therefore, modifying the gut microbiota through FMT holds promise as a potential treatment for psychiatric diseases. This scoping review assessed studies from PubMed related to FMT in autism spectrum disorder and attention deficit hyperactivity disorder. The evaluation included nine clinical studies and case reports. The beneficial and persistent effect on the autism spectrum disorder (ASD) symptoms has been reported. Also, an increased microflora diversity and altered levels of neurometabolites in serum were identified, albeit with a tendency to return to baseline over time. The microbiome-gut-brain axis could provide new targets for preventing and treating psychiatric disorders. However, a recent large randomized clinical trial has shed light on the previously collected data and suggested a possible contribution of the placebo effect. This highlights the necessity of large randomized double-blind studies to reliably assess the effect of FMT in ASD.},
}

@article {pmid40572172,
year = {2025},
author = {Wiącek, J and Skonieczna-Żydecka, K and Łoniewski, I and Deli, CK and Fatouros, IG and Jamurtas, AZ and Moszczyńska, D and Karolkiewicz, J},
title = {Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 Supplementation: An Exploratory, Randomized, Placebo-Controlled Trial of Endocannabinoid and Inflammatory Responses in Female Dancers.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572172},
issn = {2076-2607},
support = {Development of Young Researchers (Doctoral school of J. Wiącek)//Poznan University of Physical Education/ ; },
abstract = {The anandamide (AEA) and lipopolysaccharide (LPS) interaction is gaining attention, but evidence on the influence of probiotics on endocannabinoid system (ECS) biomarkers remains limited. This study (NCT05567653) investigated the effects of 12-week supplementation with Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 on AEA (main outcome) and inflammatory biomarkers in female dancers. Fifteen participants (5 probiotic, 10 placebo) were included in the final analysis. Serum levels of AEA, LPS, and cytokines (tumor necrosis factor-alpha-TNF-α, interleukin-1 beta-IL-1β, and interleukin-10-IL-10) were measured using an ELISA (enzyme-linked immunosorbent assay), and the psychological stress responses were evaluated using the Mini-COPE questionnaire. At the baseline, a correlation between AEA and LPS was observed (Spearman's r = 0.9677, p < 0.05). After 12 weeks, no statistically significant differences in the AEA, LPS, cytokine levels, or stress-coping strategies were observed between the probiotic and placebo groups (LPS-probiotic: +3.48 EU/L, p = 0.9361; placebo: +56.98 EU/L, p = 0.0694; AEA-probiotic: -1.11 ng/mL, p = 0.9538; placebo: +14.08 ng/mL, p = 0.4749). The direction of change may indicate a trend toward increased inflammation in the absence of probiotics, consistent with patterns described in previous literature. However, these results should be viewed as hypothesis generating and warrant confirmation in larger trials.},
}

@article {pmid40572124,
year = {2025},
author = {LaPoint, P and Banks, K and Bacorn, M and Prasad, R and Romero-Soto, HN and Namasivayam, S and Chen, Q and Patel, A and Levy, S and Hourigan, SK},
title = {Can Vaginal Seeding at Birth Improve Health Outcomes of Cesarean Section-Delivered Infants? A Scoping Review.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572124},
issn = {2076-2607},
abstract = {Although Cesarean section (C-section) delivery is often a necessary medical intervention, it also increases the risk of the infant developing chronic inflammatory, metabolic, and neurodevelopmental disorders. The association of C-section with the development of these conditions is thought to be partially mediated by the effects of the C-section on the infant's microbiome development and subsequent immune regulation. C-section-delivered infants acquire a different set of microbes compared with infants who are vaginally delivered. "Vaginal seeding" exposes C-section-delivered infants to the maternal vaginal microbiome directly after birth, partly replicating the microbial exposures they would have received during a vaginal delivery. Studies have shown that vaginal seeding at birth partially restores the infant microbiome towards that of a vaginally delivered infant. More recently, preliminary studies have shown a potential benefit of vaginal seeding on health outcomes. Here, we examine the evidence from observational studies and randomized controlled trials that have evaluated microbiome restoration after C-section, and we discuss new research assessing the potential impact of vaginal seeding on immune, metabolic, and neurodevelopmental outcomes and the underlying mechanisms. Collectively, we review the potential health benefits, safety risks, regulatory implications, and future directions for the use of vaginal seeding in infants delivered by C-section.},
}

@article {pmid40572122,
year = {2025},
author = {Fu, R and Zhu, M and Zhang, Y and Li, J and Feng, H},
title = {Harnessing the Rhizosphere Microbiome for Selenium Biofortification in Plants: Mechanisms, Applications and Future Perspectives.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572122},
issn = {2076-2607},
support = {242300421100; 242300421586//the Natural Science Foundation of Henan Province/ ; 242102320358//the Science and Technology Research Project of Henan Province/ ; 2024HYTP008//the Project for Youth Talent Lifting of Henan Province/ ; },
abstract = {The rhizosphere microbiome plays a critical role in promoting crop health and productivity. Selenium (Se), a beneficial trace element for plants, not only enhances resistance to both abiotic and biotic stresses but also modulates soil microbial communities. Se biofortification of crops grown in seleniferous soils using selenobacteria represents an eco-friendly and sustainable biotechnological approach. Crops primarily absorb selenium from the soil in its oxidized forms, selenate and selenite, and subsequently convert it into organic Se compounds. However, the role of Se-oxidizing bacteria in soil Se transformation, bioavailability, and plant uptake remains poorly understood. In this review, systematic collection and analysis of research on selenobacteria, including both Se-oxidizing and Se-reducing bacteria, are therefore essential to elucidate their functions in enhancing crop growth and health. These insights can (i) deepen our mechanistic understanding of microbially mediated Se cycling and stress resilience and (ii) offer a novel framework for nanomicrobiome engineering aimed at promoting sustainable food production.},
}

@article {pmid40572111,
year = {2025},
author = {Lucero, J and Nishiguchi, MK},
title = {Host-Associated Biofilms: Vibrio fischeri and Other Symbiotic Bacteria Within the Vibrionaceae.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572111},
issn = {2076-2607},
support = {1T32GM141862-24S3/NH/NIH HHS/United States ; DBI 2214038//National Science Foundation/ ; },
abstract = {Biofilm formation is important for microbial survival, adaptation, and persistence within mutualistic and pathogenic systems in the Vibironaceae. Biofilms offer protection against environmental stressors, immune responses, and antimicrobial treatments by increasing host colonization and resilience. This review examines the mechanisms of biofilm formation in Vibrio species, focusing on quorum sensing, cyclic-di-GMP signaling, and host-specific adaptations that influence biofilm structure and function. We discuss how biofilms differ between mutualistic and pathogenic species based on environmental and host signals. Recent advances in omics technologies such as transcriptomics and metabolomics have enhanced research in biofilm regulation under different conditions. Horizontal gene transfer and phase variation promote the greater fitness of bacterial biofilms due to the diversity of environmental isolates that utilize biofilms to colonize host species. Despite progress, questions remain regarding the long-term effects of biofilm formation and persistence on host physiology and biofilm community dynamics. Research integrating multidisciplinary approaches will help advance our understanding of biofilms and their implications for influencing microbial adaptation, symbiosis, and disease. These findings have applications in biotechnology and medicine, where the genetic manipulation of biofilm regulation can enhance or disrupt microbiome stability and pathogen resistance, eventually leading to targeted therapeutic strategies.},
}

@article {pmid40572102,
year = {2025},
author = {Fan, J and Yin, Y and Liu, Y and Chen, Y and Long, W and Liao, C},
title = {Age-Dependent Composition and Diversity of the Gut Microbiome in Endangered Gibbon (Nomascus hainanus) Based on 16S rDNA Sequencing Analysis.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572102},
issn = {2076-2607},
support = {31960703//The National Natural Science Foundation of China/ ; U22A20363//the National Natural Science Foundation of China/ ; ZDKJ2021035//The Major Science and Technology Plan of Hainan Province/ ; },
abstract = {The Hainan gibbon (Nomascus hainanus) is one of the most endangered primates globally, threatened by habitat destruction, genetic diversity loss, and ecological competition. In this study, given the critical role of the gut microbiota in host immune regulation and nutrient metabolism, we investigated the composition of and age-related variations in the gut microbiota in Hainan gibbons. Using 16S rRNA sequencing, we systematically investigated the gut microbial diversity of Hainan gibbons. We collected 41 fecal samples from Hainan Tropical Rainforest National Park, covering three age groups: juveniles (4-6 years), subadults (7-10 years), and elderly animals (≥13 years). This study found that microbiota composition changed significantly with age. Juveniles had higher microbial diversity and complexity, while subadults showed an increased abundance of Fibrobacter and Prevotella in their microbial communities, along with a Tax4Fun-predicted enrichment of functional genes related to energy metabolism, cell motility, and nervous system functions. LEfSe analysis identified statistically significant microbial taxa among different age groups, with Bacteroidota and Firmicutes being the dominant phyla across all groups with varying proportions. These results highlight the critical role of the gut microbiota in the health and adaptability of Hainan gibbons, offering insights for conservation strategies. The findings of this study are significant for understanding the changes in gut microbiota and their ecological functions across different life stages of endangered primates.},
}

@article {pmid40572090,
year = {2025},
author = {Jayasekera, V and Han, Y and Du, L},
title = {Identification of Pyrrole-2-Carboxylic Acid from the Biocontrol Agent Lysobacter Involved in Interactions with Fusarial Fungi.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572090},
issn = {2076-2607},
support = {P20 GM113126/GM/NIGMS NIH HHS/United States ; NA//University of Nebraska Collaboration Initiative Seed Grant/ ; },
abstract = {Lysobacter, a genus of Gram-negative bacteria, is known for producing antibiotic compounds, making it a promising biocontrol agent against crop pathogens. As part of the soil microbiome, Lysobacter species cooccur with a variety of microorganisms in the ecosystem. However, little is known about bioactive natural products involved in Lysobacter's interactions with other organisms. This study investigated interactions between Lysobacter sp. 3655 and two economically important fungal pathogens, Fusarium graminearum and Fusarium verticillioides. We discovered a Lysobacter molecule that is dramatically suppressed when co-culturing with the fungi, and the structure of this molecule was determined to be pyrrole-2-carboxylic acid (P2C). Chitin, a primary component of fungal cell walls, also suppressed P2C production in Lysobacter. Exogenous P2C addition promoted formation of Lysobacter biofilms within a range of concentrations, suggesting its potential role as a signaling molecule. Previously reported result showed that the mutation of the global regulator Clp in Lysobacter enzymogenes led to drastic increase of biofilm formation. Intriguingly, while P2C increased the biofilm formation in the wildtype of L. enzymogenes, it reduced the biofilms in the Clp mutant. Together, these findings reveal P2C as a novel signaling molecule mediating the interaction between Lysobacter and surrounding fungal species, highlighting its role in Lysobacter adaptation in response to environmental conditions.},
}

@article {pmid40572088,
year = {2025},
author = {Mauri, C and Giubbi, C and Consonni, A and Briozzo, E and Meroni, E and Luzzaro, F and Tonolo, S},
title = {The Emergence of Bacteroides pyogenes as a Human Pathogen of Animal Origin: A Narrative Review.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572088},
issn = {2076-2607},
abstract = {Bacteroides pyogenes is a Gram-negative obligate anaerobe rod. It is naturally found in the oral microbiome of cats and dogs, which represents a primary source of disease for humans. The present review provides an update on the role of B. pyogenes as a pathogen responsible for infections in humans. Indeed, an increasing number of B. pyogenes infections have been reported in recent years, including skin and soft tissue infections as well as severe diseases like osteomyelitis, Lemierre's syndrome, and bloodstream infection. Pre-analytical and analytical phases are crucial to guarantee the isolation of anaerobic bacteria, including B. pyogenes. Moreover, the introduction of MALDI-TOF mass spectrometry and 16S rRNA sequencing in clinical microbiology laboratories may be partially responsible for the increasing number of reports of B. pyogenes infections. However, the mechanisms underlying the pathogenicity of B. pyogenes remain poorly understood and require further investigations. Indeed, despite common antimicrobial susceptibilities, infections frequently persist and require multiple courses of antibiotics. In addition, based on literature data, this review indicates that treatment of skin and soft tissue infections often necessitates surgical procedures and hospitalization.},
}

@article {pmid40572084,
year = {2025},
author = {Vieira de Lima, R and Blanco, KC and Bagnato, VS},
title = {Control of Methicillin-Resistant Staphylococcus aureus Using Photodynamic Therapy in Synergy with Staphylococcus epidermidis: Role of Mixed Cultures in Developing Strategies to Inhibit Infections.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572084},
issn = {2076-2607},
support = {88887.928185/2023-00//CAPES/ ; 2013-07276-1//CEPOF-CEPID Program/ ; },
abstract = {Staphylococcus aureus is a Gram-positive bacterium living abundantly on our skin and mucous membranes. When there is an imbalance in microbiota, they are the main protagonists of various infections, such as soft tissue infections and bacteremia. However, Staphylococcus epidermidis also colonizes this microbiome, is able to compete with pathogenic bacteria, including methicillin-resistant Staphylococcus aureus (MRSA), and can contribute to treatments such as photodynamic inactivation (PDI) by inhibiting infection progression and restoring a healthy microbiota. In vitro photodynamic inactivation experiments were carried out using synthetic curcumin at a concentration of 5 μM as a photosensitizer and varying light doses (1, 2 and 5 J/cm[2]) at a wavelength of 450 nm, on pure cultures (S. aureus, S. epidermidis and MRSA) and mixed cultures, in which bacteria were placed together proportionally. This study revealed that pure cultures of these bacteria obtained statistically significant results with varying light doses of 2 and 5 J/cm[2]. In addition, in an attempt to bring infections closer to reality, experiments were carried out on mixed cultures. The results were not only significant but also increased reduction of bacteria, including resistant bacteria. Study offers new perspectives on the importance of themicrobiota for treatment of infections caused by the Staphylococcus genus.},
}

@article {pmid40572081,
year = {2025},
author = {Dietz, MW and Hsu, BY and van der Velde, M and Tieleman, BI},
title = {Gut Microbiome Development in Rock Pigeons: Effects of Food Restriction Early in Life.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572081},
issn = {2076-2607},
support = {Scolarship of overseas studies//Ministry of Education, Taiwan/ ; Personal Grant ot Prof A.G.G. Groothuis//University of Groningen/ ; },
abstract = {The developmental period is a critical phase in birds, influencing even lifetime reproductive success. The gut microbiome (GM) is important herein, affecting digestive capacity and immune function. Diet impacts the GM, but wild nestlings may experience resource limitations, which may also affect the GM. We investigated the effects of a week of food restriction early in life on the GM in captive rock pigeon nestlings (Columba livia). We sampled the GM at 0, 2, 4, 7, 8, 12, 20, 27, and 38 days and in foster parents. Alpha diversity varied only with age. However, differences in alpha diversity between nestlings and adults were larger during food restriction. Beta diversity varied with age, food treatment, and their interaction term. Four of the eleven major genera varied with age, while four others did not vary with age or food treatment. Major genera that contained potential pathogens (Escherichia-Shigella and Clostridium sensu stricto 1) were more abundant under food restriction. Food restriction thus affected GM development. The increase in alpha diversity and potential pathogens suggest that suppressed immune function may mediate the impact of food restriction on the GM. The effect diminished when food restriction was ended, suggesting that in wild nestlings, the impact of food restriction on the GM may be short-term.},
}

@article {pmid40572077,
year = {2025},
author = {Saha, P and Hartmann, P},
title = {Impact of Gut Microbiome on Gut Permeability in Liver and Gut Diseases.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572077},
issn = {2076-2607},
support = {K12 HD105271/GF/NIH HHS/United States ; KL2TR001444//University of California San Diego Altman Clinical and Translational Research Institute (ACTRI)/NIH grant/ ; #PNC22-159963//AASLD Pinnacle Research Award in Liver Diseases/ ; P30 DK120515/DK/NIDDK NIH HHS/United States ; },
abstract = {Hepatobiliary and gastrointestinal conditions, including chronic liver diseases and inflammatory bowel disease, are associated with significant morbidity and mortality globally. While the pathophysiology and symptoms vary from one disease to another, aberrations of the gut microbiome with deleterious microbial products affecting the intestinal barrier are common in patients suffering from these diseases. In this review, we summarize changes in the gut microbiome associated with various disease states and detail their role in gut barrier disruption and in modulating disease progression. Further, we discuss therapeutic interventions and precision medicine approaches targeting the microbiome, which have shown promise in alleviating these chronic illnesses in mouse models and patients.},
}

@article {pmid40572065,
year = {2025},
author = {Souza, DT and Moreira, ACS and Quevedo, HD and May, A},
title = {Evaluation of Microbial Transplantation from High-Productivity Soil to Improve Soybean Performance in Less Productive Farmland.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572065},
issn = {2076-2607},
abstract = {Microbial transplantation represents a sustainable strategy to address productivity gaps in agricultural soils by transferring microbiomes that enhance nutrient cycling, pathogen suppression, and stress tolerance. This study evaluates whether probiotic consortia from high-yield soybean soils (donor soil) could improve crop performance in less productive fields (recipient soil). We developed a host-adapted inoculant from soybean rhizospheres grown in donor soil and applied it to seeds at five concentrations (0.25-10 g/kg seed) in recipient soil, with untreated controls for comparison. To assess crop-specific microbial recruitment, we prepared a parallel bean-derived inoculant under identical conditions. Through 16S rRNA sequencing and growth/yield analysis, we found the following: (1) Distinct bacteriome assemblies between soybean- and bean-derived inoculants, confirming host specificity; (2) Successful enrichment of beneficial taxa (Enterobacteriaceae increased by 15-22%, Rhizobiaceae by 7-12%) despite native community resilience; and (3) Consistent yield improvement trends (4.8-6.2%), demonstrating potential to bridge productivity gaps. These results show that transplanted microbiomes can effectively modulate rhizosphere communities while maintaining ecological balance. This work establishes a scalable approach to address soil productivity limitations through microbiome transplantation. Future research should optimize (a) inoculant composition for specific productivity gaps; (b) delivery systems; and (c) compatibility with resident microbiomes, particularly in systems where niche-specific processes govern microbial establishment.},
}

@article {pmid40572063,
year = {2025},
author = {Shi, J and Su, H and He, S and Dai, S and Mao, H and Wu, D},
title = {Pan-Genomic Insights into Rumen Microbiome-Mediated Short-Chain Fatty Acid Production and Regulation in Ruminants.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572063},
issn = {2076-2607},
abstract = {The rumen microbiome represents a cornerstone of ruminant digestive physiology, orchestrating the anaerobic fermentation of plant biomass into short-chain fatty acids (SCFAs)-critical metabolites underpinning host energy metabolism, immune function, and environmental sustainability. This comprehensive review evaluates the transformative role of pan-genomics in deciphering the genetic and metabolic networks governing SCFA production in the rumen ecosystem. By integrating multi-omics datasets, pan-genomic approaches unveil unprecedented layers of microbial diversity, enabling precise identification of core functional genes and their dynamic contributions to carbohydrate degradation and SCFA biosynthesis. Notable advancements include the following: mechanistic insights into microbial community assembly and metabolic pathway regulation, highlighting strain-specific adaptations to dietary shifts; precision interventions for optimizing feed efficiency, such as rationally designing microbial consortia and screening novel feed additives through pan-genome association studies; and sustainability breakthroughs, demonstrating how targeted modulation of rumen fermentation can simultaneously enhance production efficiency and mitigate methane emissions. This synthesis underscores the potential of pan-genomics to revolutionize ruminant nutrition, offering a blueprint for developing next-generation strategies that reconcile agricultural productivity with environmental stewardship. The translational applications discussed herein position pan-genomics as a critical tool for advancing animal science and fostering a resilient livestock industry.},
}

@article {pmid40572060,
year = {2025},
author = {Dong, W and Zang, Q and Wang, Y and Ma, E and Ding, W and Yan, L and Hao, F},
title = {Synergistic Effects of Paenibacillus polymyxa NBmelon-1 Inoculation and Grafting Restructure of Rhizosphere Microbiome and Enhanced Disease Resistance in Melon Self-Rootstocks.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572060},
issn = {2076-2607},
support = {2021Z006//Development of Specific Germplasm and Breeding of New Multi-resistant Melon Rootstock Varieties/ ; CARS-25//National Watermelon and Melon Industry Technology System Construction Project/ ; },
abstract = {Rhizosphere microorganisms play pivotal roles in mitigating the challenges associated with continuous cropping in melon cultivation. While grafting and plant growth-promoting rhizobacteria (PGPR) independently influence rhizosphere microbial communities, their combined effects remain largely unexplored. This study investigates the synergistic regulation of Paenibacillus polymyxa NBmelon-1 inoculation and grafting on rhizosphere microbiome assembly, plant performance, and disease resistance in melon self-rootstocks. Field experiments demonstrated that NBmelon-1 inoculation significantly enhanced rootstock stem diameter (95.3% increase in spring) and root development, achieving a graft survival rate exceeding 95%. The combined treatment (NB+GJ) increased scion fruit yield by 29.8% in autumn and 36.5% in spring, as well as the single-fruit weight by 22.5% in autumn and 37.3% in spring, while maintaining fruit morphology. Integrated 16S rRNA and ITS sequencing revealed that the NB+GJ treatment selectively enriched antagonistic bacterial phyla (e.g., Firmicutes and Actinobacteriota) and suppressed pathogenic fungi (e.g., Fusarium and Melanconiella). Seasonal shifts in microbial diversity and functional gene profiles underscored the dynamic interplay between treatments and environmental factors. These findings establish a novel strategy for optimizing melon self-rootstock grafting systems and sustainably managing soil-borne diseases.},
}

@article {pmid40572023,
year = {2025},
author = {Silva, APV and Moloney, GM and Sequeira, AM and Liber, M and Bastiaanssen, T and Rea, K and Fitzgerald, P and Golubeva, A and Rodriguez-Aburto, M and Renes, IB and Knol, J and Dinan, T and Cryan, JF},
title = {Targeting the Microbiota Reverses C-Section-Induced Effects on Intestinal Permeability, Microbiota Composition, and Amygdala Gene Expression in the Mouse.},
journal = {Neurogastroenterology and motility},
volume = {},
number = {},
pages = {e70107},
doi = {10.1111/nmo.70107},
pmid = {40572023},
issn = {1365-2982},
support = {/SFI_/Science Foundation Ireland/Ireland ; },
abstract = {BACKGROUND: The microbiome significantly influences the development of the gastrointestinal and immune systems. The delivery method, whether Caesarean section (CS) or vaginal birth (VB), plays a crucial role in shaping microbiota composition, with CS babies exhibiting differences. Early-life nutritional interventions using probiotics or prebiotics may help restore this imbalance in CS infants. Our study aimed to assess gut permeability in CS mice compared to VB mice and explore whether prebiotics or probiotics could mitigate any deficiencies.

METHODS: Using a mouse model (NIH Swiss) for CS delivery, we measured plasma levels of a 4 kDa macromolecule (FITC) at PND7, 14, 23, and 35. We evaluated ileal gene expression of tight junction proteins, profiled intestinal microbiome composition, and examined the expression of genes involved in neurotransmitter physiology in the amygdala. Additionally, we studied the impact of administering Bifidobacterium breve in drinking water and dietary administration of GOS/FOS on these outcomes.

KEY RESULTS: At PND7, CS-born mice exhibited increased ileal permeability, along with reduced expression of Tjp1, Occludin, Claudin 3, and Epcam compared to VB mice. Administration of B. breve or GOS/FOS alleviated changes in Epcam expression. During the pre-weaning period, beta diversity differed between VB and CS. Post-weaning, β-diversity increased following probiotic and prebiotic intervention. Additionally, CS mice showed changes in neurotransmitter gene expression in the amygdala, which were also mitigated by B. breve or GOS/FOS.

DISCUSSION: Our findings indicate that targeted microbiota-associated interventions can reverse deficits in intestinal permeability induced in CS mice.},
}

@article {pmid40571832,
year = {2025},
author = {Viswanathan, L and Moshiree, B},
title = {Advances in Diagnostics for the Evaluation of Neurogastroenterology & Motility Disorders: Are They Ready for Prime Time?.},
journal = {Current gastroenterology reports},
volume = {27},
number = {1},
pages = {45},
pmid = {40571832},
issn = {1534-312X},
}

@article {pmid40571722,
year = {2025},
author = {Toit, AD},
title = {A misplaced microbiome.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40571722},
issn = {1740-1534},
}

@article {pmid40571157,
year = {2025},
author = {Zhou, W and Ring, NG and Caldwell, R and Milstone, LM and Oh, J},
title = {Genotype-environment-driven dysbiosis in the skin microbiome of ichthyosis.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2025.06.1568},
pmid = {40571157},
issn = {1523-1747},
abstract = {Many factors might be expected to influence the cutaneous microbiome, especially on diseased skin. Yet few studies account for the complex interactions between host and environmental factors. To shed light on such interactions, we characterized the skin microbiome from seven types of ichthyosis and confirmed previous reports of genotype-related and barrier-related effects. We then focused on the TGM1 genotype and assessed the association between the microbiome features and the ichthyosis genotype and phenotype while adjusting for contextual host covariables, including clinical treatments. We showed that the ichthyosis genotype and phenotype interact - sometimes antagonistically - with treatment to influence the composition and metabolic potential of the skin microbiome at species, strain, and metabolic pathway levels. Notable interactions with the TGM1 genotype included transepidermal water loss (TEWL) and emollient and retinoid use. Larger groups of patients and additional measurements will be needed to unravel the complex interactions that impact host and environmental influences on skin microbiome.},
}

@article {pmid40571154,
year = {2025},
author = {Zhou, R and Chaskar, P and Patrick, MT and Wang, K and Piketty, C and Julia, V and Gudjonsson, JE and Krishnaswamy, JK and Tsoi, LC},
title = {Nemolizumab treatment normalizes dysregulated microbiome in lesional prurigo nodularis.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2025.06.1575},
pmid = {40571154},
issn = {1523-1747},
}

@article {pmid40571109,
year = {2025},
author = {Chen, H and Qiu, X and Lei, S and Zhao, Y and Zhang, M and Gao, M and Guo, R and Di, H and Huang, J and Yu, Z},
title = {Gut vs. Vaginal Microbiome in Diabetes Progression: Key Microbial Shifts and Implications.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107833},
doi = {10.1016/j.micpath.2025.107833},
pmid = {40571109},
issn = {1096-1208},
abstract = {BACKGROUND: Dysiosis in gut and vaginal microbiome is implicated in type 2 diabetes (T2D) pathogenesis, but their contributions remain unclear. This study aims to compare their alterations and clinical relevance in diabetes development.

METHODS: Metagenomic sequencing was performed on vaginal and fecal samples from T2D patients. Differential feature selection and correlation model were used to dissect microbial contributions to diabetic markers.

RESULTS: Gut microbiota exhibited reduced diversity in T2D patients, with enrichment of Desulfovibrio desulfuricans and Adlercreutzia equolifaciens validated in public cohorts. Vaginal microbiota diversity remained unaffected. Furthermore, structural equation modeling revealed stronger gut microbiota associations with blood glucose and HbA1c. Notably, Romboutsia ilealis-derived pgm was enriched in the diabetes group, which could catalyze the production of glucose, suggesting that it may be involved in the progression of T2D.

CONCLUSION: Our findings establish the gut microbiome as the dominant driver of T2D progression, with R. ilealis emerging as a potential therapeutic target. This highlights the priority of gut-centric microbiota interventions in diabetes management.},
}

@article {pmid40571107,
year = {2025},
author = {Chen, J and Chen, Z and Xu, B and Huang, Z and Zhang, C},
title = {Skin microbiome of Asian elephants with skin diseases during seasonal transitions.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107832},
doi = {10.1016/j.micpath.2025.107832},
pmid = {40571107},
issn = {1096-1208},
abstract = {INTRODUCTION: Wild Asian elephants (Elephas maximus), which are an endangered species, often suffer from skin diseases during seasonal transitions, which seriously affect their health. Understanding the pathogenesis of such skin diseases is critical for their prevention and treatment. It is known that skin microorganisms are closely related to host skin health.

OBJECTIVE: To compare the microbiotas and microbiomes of diseased and healthy skin of Asian elephants.

METHODS: DNA was extracted from skin swab samples from diseased and healthy Asian elephants for metagenomic sequencing. Various bioinformatic tools were used to process the raw sequencing data and identify gene sequences for functional annotation and species identification as well as to determine species abundance. Antibiotic resistance genes and virulence factors were also identified using DIAMOND.

RESULTS: Staphylococcus was highly enriched in the microbiota of diseased skin, whereas Leuconostoc predominated in that of healthy skin. Moreover, substantial differences existed between the two elephant skin groups in terms of metabolic pathways related to ATP-binding cassette transporters and TCSs and the abundance of antibiotic resistance genes and Staphylococcus-associated toxins. The substantial difference in Staphylococcus-related virulence factors was likely due to the significant enrichment of Staphylococcus in the diseased skin samples, suggesting that this bacterial genus is the causative agent of skin diseases in Asian elephants. Additionally, Leuconostoc mesenteroides, which was enriched in the healthy skin samples, has anti-inflammatory, antimicrobial, and other beneficial effects that have promising applications in the prevention, diagnosis, and treatment of skin diseases.

CONCLUSION: This study reveals the cause of skin diseases in Asian elephants and provides a theoretical basis for improving the skin health of wild animals and expanding wildlife conservation methods and technologies.},
}

@article {pmid40571019,
year = {2025},
author = {Wang, Y and Zhang, Z and Chen, S and Zhang, Y and Cao, Y and Zhao, J and Chen, A and Wu, Y},
title = {Integrated microbiome and metabolome analyses reveal effects of sodium alginate on the growth of Meretrix meretrix.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {145431},
doi = {10.1016/j.ijbiomac.2025.145431},
pmid = {40571019},
issn = {1879-0003},
abstract = {Sodium alginate (SA) has diverse biological activities, and its effects on the growth and intestinal health of Meretrix meretrix were evaluated over a 60-day feeding trial. The study tested five SA concentrations: 0 mg/L (SA0), 5 mg/L (SA5), 10 mg/L (SA10), 15 mg/L (SA15), and 20 mg/L (SA20). Results showed that 10 mg/L SA (SA10) significantly improved clam growth and intestinal health, enhancing villus length, goblet cell distribution, and digestive enzyme activity. However, higher SA concentrations (SA15 and SA20) degraded growth and intestinal health. Integrated microbiome-metabolome analysis revealed that sodium alginate at 10 mg/L could activate phenylalanine metabolism, tryptophan metabolism and lysine degradation pathway by optimizing the microbial community structure and specifically enriching functional bacteria (such as Xylanibacter, Achromobacter and Escherichia-Shigella), thus generating key metabolites such as phenaceturic acid, indole-3-acetamide and succinate, thus synergistically strengthening the intestinal barrier function, regulating the immune microenvironment and improving the energy metabolism efficiency. In a word, the appropriate concentration of sodium alginate (10 mg/L) can reshape the intestinal flora structure and metabolic network of M. meretrix, and then promote the growth of the clams.},
}

@article {pmid40571003,
year = {2025},
author = {Zhu, F and Xi, T and Liu, Q and Yu, N and Wang, F and Wen, Y and Wang, W},
title = {Asparagus polysaccharide attenuates atherosclerosis by modulating gut microbiota and metabolites.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {145492},
doi = {10.1016/j.ijbiomac.2025.145492},
pmid = {40571003},
issn = {1879-0003},
abstract = {Atherosclerosis remains a critical driver of cardiovascular morbidity; however, therapeutic strategies for halting its progression remain suboptimal. To date, there are no reports of asparagus polysaccharide (AP)-the active component of Asparagus cochinchinensis (Lour.) Merr.-promoting human health by modulating the gut microbiota. In the present study, we provided a high-fat diet (HFD) to an ApoE[-/-] murine model to investigate the mechanisms by which AP mitigates atherosclerotic pathogenesis. Our results demonstrated that AP significantly alleviated HFD-induced aortic lesions, decreased serum lipid levels (p < 0.01), and markedly decreased the mRNA levels of inflammatory factors in the aorta (p < 0.001). Using 16S rRNA sequencing, we observed that AP reversed HFD-induced alterations in the relative abundances of Bacteroidetes and Firmicutes at the phylum level, and remarkably increased the abundance of Actinobacteria (p < 0.01). Using untargeted metabolomics analysis, we identified 10 key metabolites associated with atherosclerosis. Furthermore, while L-glutaminyl-L-tryptophan levels increased in the faeces and decreased in the blood following HFD induction, AP treatment reversed this trend. This study provides the first evidence that AP exerts its anti-atherosclerotic effects through the gut microbiota-metabolite axis, with L-glutaminyl-L-tryptophan emerging as a potential, novel translational biomarker for therapeutic monitoring.},
}

@article {pmid40570997,
year = {2025},
author = {Liu, W and Lan, Z and Lin, Z and Zhao, Y and Lian, J and Yu, G},
title = {The microbiome-immune cell interaction network: Advancing tumor immunotherapy.},
journal = {Seminars in cancer biology},
volume = {114},
number = {},
pages = {128-137},
doi = {10.1016/j.semcancer.2025.06.009},
pmid = {40570997},
issn = {1096-3650},
abstract = {Tumor immunotherapy has achieved revolutionary advancements; however, owing to the complex interplay of multiple intrinsic and extrinsic tumor factors, the patient response rate remains suboptimal. Recent research has emphasized the pivotal role of microbiome in tumor progression. Under normal physiological conditions, microbiome enter orally and colonize sites such as the oral and intestinal mucosa, establishing a dynamic microbiome equilibrium that participates in essential physiological processes, including host metabolism and immune regulation. However, in pathological states, including dysbiosis, tumor initiation, or compromised mucosal barrier function, the microbiome can penetrate the mucosal barrier, infiltrate tumor tissues, and engage in intricate direct or indirect interactions with immune cells. These interactions play a pivotal role in reshaping the tumor immune microenvironment and modulating the host's anti-tumor immune response. This review elaborate the regulatory mechanisms involved in direct and indirect interactions between microbiome and immune cells within tumors, and their implications for tumor immunotherapy. We discuss the external factors that impact these interactions and outline the potential use of engineered bacteria in cancer treatment. From the perspective of the interaction network between microbiomes and immune cells, this review elucidates the mechanisms and potential of microbiomes in tumor immunotherapy, offering new insights and potential targets for innovative strategies in tumor prevention and treatment.},
}

@article {pmid40570852,
year = {2025},
author = {Janssen, E and Das, M and Butts, J and Alasharee, M and Mukherjee, S and Lozano, GL and Rao, C and Livingston, AF and Woods, B and Smith, E and Peters, Z and Milin, E and Beamer, MA and Wilkie, H and Leyva-Castillo, JM and Kam, C and Sobh, A and Dasouki, M and Wakim, RH and Dbaibo, G and Al-Herz, W and Chatila, TA and Finkelman, FD and Rakoff-Nahoum, S and Geha, RS},
title = {DOCK8 in T cells promotes Th17 and Treg cell functionality to restrain mucosal mast cells and limit susceptibility to oral anaphylaxis.},
journal = {Immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.immuni.2025.06.004},
pmid = {40570852},
issn = {1097-4180},
abstract = {Immunoglobulin E (IgE)-mediated release of mediators from mast cells (MCs) drives food allergy, and intestinal MC load is an important determinant of disease severity. Dedicator of cytokinesis 8 (DOCK8)-deficient patients are highly susceptible to food allergy. We found that they exhibited elevated serum MC tryptase levels, suggesting increased MC load. Dock8[-/-] mice also had exaggerated IgE-mediated oral anaphylaxis, expansion of jejunal mucosal MCs (MMCs), and elevated serum levels of MMC-derived tryptase. This resulted in increased intestinal permeability, which promoted antigen absorption and thereby oral anaphylaxis. Mechanistically, these events were driven by an intestinal cascade in which reduced interleukin (IL)-17 cytokines led to dysbiosis, which drove IL-25 production. Increased IL-25 enhanced T helper (Th)2 production of IL-4 that expanded MMCs and exaggerated oral anaphylaxis. Furthermore, the failure of DOCK8-deficient T regulatory (Treg) cells to suppress intestinal IL-4 production and MC expansion left the exaggerated anaphylaxis unrestrained. These results suggest multi-faceted coordination between the microbiome, mucosal T cells, and MCs to restrict oral anaphylaxis.},
}

@article {pmid40570789,
year = {2025},
author = {Liu, W and Bo, T and Zhao, N and Hu, B and Li, G and Xiao, Z},
title = {Small mammal activities structure fine-scale soil microbial communities and coordinate rodenticide effects in the typical steppes of China.},
journal = {Ecotoxicology and environmental safety},
volume = {302},
number = {},
pages = {118560},
doi = {10.1016/j.ecoenv.2025.118560},
pmid = {40570789},
issn = {1090-2414},
abstract = {Soil microbial community is a diverse combination of microbial species that is influenced by soil moisture, physicochemical properties, biological activities, and other factors. Brandt's vole (Lasiopodomys brandtii) is a small rodent distributed in the typical steppes of China, Mongolia, and Russia, which often causes serious pest to the local areas when its population outbreaks. Yet the impacts of rodenticides on soil microbial diversity and ecosystem functions in Brandt's vole habitats are not well-known. In this study, we compared the microbial community composition and functional genes between the central and peripheral areas of undisturbed cave communities, as well as grasslands with and without rodenticides. The results showed that the activity of field voles and rodenticides had a significant impact on soil microbial communities, antibiotic resistance genes, and soil element cycling. The use of rodenticides reduces the activity of rodents, reduces pathogenic bacteria in the soil. The use of rodenticides inhibits N cycling, while rodent activity promotes the N cycling. Relative abundance of dissimilatory nitrate reduction nitrate (narGHI or napA), denitrification nitrous oxide (nosZ), nitrogen fixation nitrogen (nifH), denitrification nitric oxide (norB) were significantly decreased in rodenticide soil. The activity of rodents increases the abundance of specific antibiotic resistance genes (ARGs), while rodenticides reduce the abundance of AGRs in the soil. Our study for the first time explores the interaction effects of rodent activity and rodenticide use on soil, providing a reference for understanding the multifunctionality of soil ecosystems and the response of microbial communities to external disturbances (rodents and humans) in the future.},
}

@article {pmid40570762,
year = {2025},
author = {Pateriya, D and Malwe, AS and Sharma, VK},
title = {CRCpred: An AI-ML tool for colorectal cancer prediction using gut microbiome.},
journal = {Computers in biology and medicine},
volume = {195},
number = {},
pages = {110592},
doi = {10.1016/j.compbiomed.2025.110592},
pmid = {40570762},
issn = {1879-0534},
abstract = {Colorectal cancer (CRC) is a leading cause of death worldwide. A plethora of research shows the alteration of the gut microbiome and the association of bacterial taxa with CRC. Gaining insights into the health status through microbiome-based diagnosis is a rapidly growing area of research. Many studies have utilized machine learning (ML) to leverage gut microbial dysbiosis for CRC screening, yet most have been limited by their training data and algorithms. Here, using 1728 publicly available metagenomic samples from 11 studies across eight countries, we developed a web-based tool, "CRCpred," employing ML and deep learning-based hybrid algorithms for CRC prediction. The XGBoost algorithm demonstrated the highest performance, achieving an average area under the curve (AUC) of 0.90 on the test and 0.91 on the validation datasets. Our results highlight the utility of CRCpred in predicting CRC and healthy status using gut bacterial species relative abundance profile. CRCpred is publicly available at https://metabiosys.iiserb.ac.in/crcpred.},
}

@article {pmid40570700,
year = {2025},
author = {Chan, AA and Caron, C and Navarrete, M and Lee, CK and Noguti, J and Bui, JD and Lee, DJ},
title = {Mammary tissue microbiome analysis in PyMT mice reveals Methylobacteria as a commensal organism with potential therapeutic applications.},
journal = {Translational oncology},
volume = {59},
number = {},
pages = {102451},
doi = {10.1016/j.tranon.2025.102451},
pmid = {40570700},
issn = {1936-5233},
abstract = {Studies have reported differences in specific bacteria comparing the tissue microbiome in human breast cancer versus normal breast tissue, prompting hypotheses for potential therapies or theragnosis. To test these hypotheses using controlled experiments animal models are needed. Therefore, we investigated the microbiome in the gut and mammary tissue in a mouse model of breast cancer. C57BL/6 mice expressing the polyoma middle T antigen in the mammary gland (PyMT) develop spontaneous multifocal breast tumors. Microbiota in the gut and mammary tissue were studied prior to and after development of mammary gland tumors by amplicon and shotgun DNA sequencing. In parallel, RNA sequencing was performed on tumor and normal tissue to measure differences in gene expression associated with breast cancer. Bacteria identified in these studies were administered to mice to test their effects on cancer progression. Bacterial community composition in the gut of healthy or tumor-bearing mice showed wide fluctuation over time and did not organize into discrete clusters. In tumor versus healthy mammary gland tissue, relative abundances of six bacteria were significantly different: Ralstonia, Methylobacterium, Pelomonas, Staphylococcus and Tepidimonas. Methlyobacterium sequences were significantly higher (PERMANOVA, P = 0.013) in healthy tissue when compared to tumor, leading to a hypothesis that Methylobacterium may promote health. When co-transplanted with breast tumor cells, Methylobacterium reduced growth in immune competent mice. Here we describe the gut and mammary tissue microbial composition of healthy and breast tumor-bearing animals, identifying Methylobacterium sp as a commensal bacteria that might have therapeutic potential to reduce breast cancer progression.},
}

@article {pmid40570605,
year = {2025},
author = {Wu, Y and Liu, C and Shao, C and Huang, Q},
title = {Astaxanthin alleviates the microcystin-LR-induced intestinal inflammatory toxicity in zebrafish.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {286},
number = {},
pages = {107462},
doi = {10.1016/j.aquatox.2025.107462},
pmid = {40570605},
issn = {1879-1514},
abstract = {Astaxanthin (AST), a potent natural antioxidant, has demonstrated promising therapeutic potential in mitigating inflammation. However, the precise anti-inflammatory mechanisms of AST, particularly in whole-organism contexts, remain incompletely understood. Given the zebrafish (Danio rerio)'s remarkable genomic, physiological, and immunological similarities to humans, it offers a uniquely advantageous vertebrate model for biomedical research. Therefore, in this study, we utilized adult zebrafish to investigate AST's capacity to attenuate microcystin-LR (MC-LR)-induced inflammatory toxicity and attempted to elucidate underlying mechanistic pathways. AST administration significantly alleviated intestinal inflammation, as evidenced by preservation of normal intestinal morphology, reduced intestinal permeability, and modulation of gene expression profiles linked to inflammation and intestinal homeostasis. Transcriptome sequencing coupled with bioinformatics analysis revealed that AST primarily suppressed inflammatory responses through regulation of peroxisome proliferator-activated receptor (PPAR) signaling axis. Notably, AST did not merely inhibit pro-inflammatory pathways but also enhanced the expression of genes critical for maintaining intestinal barrier integrity and metabolic homeostasis. Furthermore, the 16S rRNA gene amplicon sequencing of zebrafish microbiota revealed that AST treatment restructured the gut microbial community in the MC-LR-exposed fish. Specifically, AST promoted the expansion of beneficial flora, including Lactobacillus rhamnosus GG (LGG), which correlated with improved inflammatory outcomes. Collectively, these findings establish AST as an effective modulator of MC-LR-induced intestinal inflammation in zebrafish, acting via dual mechanisms: PPAR-mediated transcriptional regulation and optimization of the gut microbiome. These insights provide a robust preclinical rationale for exploring AST-based therapies in inflammatory disorders.},
}

@article {pmid40570459,
year = {2025},
author = {Qi, J and Li, J and Xi, Y and Yang, Z and Guo, S and Han, X and Wang, R and Li, L and Bai, L and Han, C and Wang, J and Liu, H},
title = {Multi-omics analysis provides new insights into molecular mechanisms for waterfowl fatty liver formation.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105398},
doi = {10.1016/j.psj.2025.105398},
pmid = {40570459},
issn = {1525-3171},
abstract = {Waterfowl fatty liver has high nutritional value and offers benefits to human health. While previous research on fatty liver has focused on individual organs, this study explored fatty liver by examining the cecum, serum metabolites, and liver gene expression. This study integrated transcriptomic, metabolomic, and 16S rRNA microbiome analyses to analyze the molecular mechanism of waterfowl fatty liver formation. We identified seven core genes, five core metabolites, and three core microorganisms, which were significantly correlated. Overfeeding increased the abundance of Mucispirillum in the cecum, while Prevotella and Olsenella decreased. These microbial shifts, mediated by metabolites such as phthalic acid, influenced lipid metabolism, which induced changes in liver gene expression, including upregulation of ACBD4 and downregulation of HSP90B1 and HSPA5, thereby supporting fatty liver development. Additionally, ABC transporters, protein processing in the endoplasmic reticulum, and amino acid metabolism were important in fatty liver development. Our research findings provide new insights into the molecular mechanism of fatty liver with overfeeding in waterfowl from the perspective of the gut-liver axis.},
}

@article {pmid40570156,
year = {2025},
author = {Pyles, MB and Fowler, AL and Crum, AD and Hayes, SH and Schendel, RR and Lawrence, LM},
title = {Dietary nonstructural carbohydrates influence synthesis of mare milk carbohydrates and yield.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf213},
pmid = {40570156},
issn = {1525-3163},
abstract = {Mare milk is the primary source of nutrients for neonatal foals and contains various carbohydrates. Milk oligosaccharides are complex carbohydrates that are resistant to enzymatic digestion and provide support for the immune system and developing microbiome in the neonate. However, factors influencing the synthesis of milk carbohydrates in the mare are not well understood. This study aimed to determine the effects of dietary non-structural carbohydrate (NSC) on mare milk composition and yield. Thoroughbred mares were paired by age and last breeding date then randomly assigned to one of two dietary treatments at 319 d of gestation: a High NSC concentrate (43.9% NSC; n=9; HC) or a Low NSC concentrate (17.8% NSC; n=7; LC). The mares were fed the concentrate feeds in addition to forage. Colostrum and milk samples were collected at the following time points postpartum: at parturition, 12 h, 3 d, 7 d, 14 d, and 21 d. Total milk carbohydrates (lactose and oligosaccharides) were analyzed using an infrared-based milk analyzer (MilkoScan FT+, Foss, Denmark). Milk oligosaccharides were separately quantified following defatting and deproteinization with chloroform and methanol, purification by solid phase extraction, and correction for residual lactose. Daily milk yield was measured at 6 and 7 d postpartum. Mixed model ANOVA with repeated measures was used to evaluate the effect of diet and time on milk components and total milk yield. Mares fed the HC concentrate tended to have higher total milk carbohydrates than mares fed the LC concentrate (P=0.059). There was no main effect of diet on milk oligosaccharides (P=0.34), however, this study was the first to report a change over time in total oligosaccharide concentrations in mare milk, which were highest after foaling and decreased over time (P=0.002). Daily milk yield, on a body weight (BW) basis, was higher in mares fed the HC concentrate (2.30% of BW) compared to the mares fed the LC concentrate (2.04% of BW; P=0.035). These results demonstrate the importance of the maternal diet to milk composition and production, and ultimately, the nutrients provided to the foal.},
}

@article {pmid40570071,
year = {2025},
author = {Savelieva, EI and Shachneva, MD},
title = {Problems and prospects of metabolomic studies in the alteration of the gut microbiome.},
journal = {Biomeditsinskaia khimiia},
volume = {71},
number = {3},
pages = {195-208},
doi = {10.18097/PBMCR1556},
pmid = {40570071},
issn = {2310-6972},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolomics/methods ; *Metabolome ; Animals ; Bile Acids and Salts/metabolism ; *Renal Insufficiency, Chronic/microbiology/metabolism ; Fatty Acids, Volatile/metabolism ; },
abstract = {The review summarizes existing knowledge on the relationship between certain diseases and alteration (degeneration) of the intestinal microbiome. We consider major microbial metabolites firmly recognized as signaling molecules acting in communication between the microbiome and the host organism. These include short-chain fatty acids, bile acids, amines, amino acids, and their metabolites. Special attention is paid to metabolomic studies of the microbiome in chronic kidney diseases, in particular, immunoglobulin A nephropathy. The arguments supporting a concept of the microbiome of blood, previously considered an exclusively sterile environment in healthy humans, are considered. Metagenomic methods plays a key role in characterization of both the composition and potential physiological effects of microbial communities. The advantages and limitations of metabolomic analysis of blood serum/plasma and feces have been analyzed. Since the potential of clinical studies of the mutual impact of the microbiome-metabolome is limited by genetic and external factors, preclinical studies still employ both germ-free models and models based on the effects of antibiotics. The review considers the problems and prospects of metabolomics in studying the nature and mechanisms of the mutual impact of the microbiome and metabolome.},
}

Humans
*Gastrointestinal Microbiome
*Metabolomics/methods
*Metabolome
Animals
Bile Acids and Salts/metabolism
*Renal Insufficiency, Chronic/microbiology/metabolism
Fatty Acids, Volatile/metabolism

@article {pmid40569902,
year = {2025},
author = {Belheouane, M and Kalsdorf, B and Niemann, S and Gaede, KI and Lange, C and Heyckendorf, J and Merker, M},
title = {Serratia sp. traits distinguish the lung microbiome of patients with tuberculosis and non-tuberculous mycobacterial lung diseases.},
journal = {PloS one},
volume = {20},
number = {6},
pages = {e0325362},
pmid = {40569902},
issn = {1932-6203},
mesh = {Humans ; *Microbiota/genetics ; Male ; Middle Aged ; *Lung/microbiology ; RNA, Ribosomal, 16S/genetics ; Female ; Adult ; *Serratia/genetics/isolation & purification/classification ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Mycobacterium Infections, Nontuberculous/microbiology ; Nontuberculous Mycobacteria/genetics ; *Tuberculosis, Pulmonary/microbiology ; *Lung Diseases/microbiology ; },
abstract = {BACKGROUND: Pathogenic mycobacteria, such as Mycobacterium tuberculosis complex (Mtbc), and non-tuberculous mycobacteria (NTMs) can cause severe chronic pulmonary infections. However, not all infected patients develop active disease, and it remains unclear whether key lung microbiome taxa play a role in the pathogenesis of tuberculosis (TB) and NTM lung diseases (LD). Here, we aim to further define the lung microbiome composition in TB, and NTM-LD prior to the initiation of therapy.

STUDY DESIGN: We employed 16S rRNA amplicon sequencing to characterize the baseline microbiome in bronchoalveolar lavage fluid (BALF) from patients diagnosed with TB (n = 23), NTM-LD (n = 19), or non-infectious inflammatory disease (n = 4). We applied depletion of human cells, removal of extracellular DNA, implementation of a decontamination strategy, and exploratory whole-metagenome sequencing (WMS) of selected specimens.

RESULTS: Genera Serratia and unclassified Yersiniaceae dominated the lung microbiome of most patients with a mean relative abundance of >15% and >70%, respectively. However, at the sub-genus level, as determined by amplicon sequence variants (ASVs), TB-patients exhibited increased community diversity, and distinct signatures of ASV_7, ASV_21 abundances which resulted in a significant association with disease state. Exploratory WMS, and ASV similarity analyses suggested the presence of Serratia liquefaciens, Serratia grimesii, Serratia myotis and/or Serratia quinivorans in TB and NTM-LD patients.

CONCLUSIONS: The lung microbiome of TB-patients harbored a distinct, and heterogenous structure, with specific occurrences of certain Serratia traits. Some of these traits may play a role in understanding the microbial interactions in the lung microbiome of patients infected with Mtbc.},
}

Humans
*Microbiota/genetics
Male
Middle Aged
*Lung/microbiology
RNA, Ribosomal, 16S/genetics
Female
Adult
*Serratia/genetics/isolation & purification/classification
Bronchoalveolar Lavage Fluid/microbiology
Aged
*Mycobacterium Infections, Nontuberculous/microbiology
Nontuberculous Mycobacteria/genetics
*Tuberculosis, Pulmonary/microbiology
*Lung Diseases/microbiology

@article {pmid40466811,
year = {2025},
author = {Healy, HG and Pawluk, E and Dieter, L and Roberts, SC and Tanner, W and Mathew, T and Peaper, D and Martinello, RA and Peccia, J},
title = {Bacterial recolonization of hospital sink biofilms.},
journal = {The Journal of hospital infection},
volume = {162},
number = {},
pages = {95-105},
doi = {10.1016/j.jhin.2025.05.013},
pmid = {40466811},
issn = {1532-2939},
abstract = {BACKGROUND: Hospital sink drains are known reservoirs for many pathogens that cause healthcare-associated infections (HAIs). Drain bacteria can migrate up to the drain cover and then spread to surrounding surfaces and patients through droplet dispersal during sink use. Therefore, cleaning sink surfaces represents a key intervention strategy to limit transmission between drains and patients.

AIMS: In this study, we aimed to: (1) characterize microbial community taxonomy and abundance in sink components and (2) evaluate the kinetics and sources of bacterial recolonization onto sink surfaces after cleaning.

METHODS: Drainpipes, drain covers, sink basins, drinking water, and p-trap liquid from hospital sinks in New Haven, CT, USA were sampled before and after intervention surface cleaning/disinfection (N = 251). Bacterial abundance and taxonomy were assessed via culture counts, digital droplet PCR, MALDI-ToF, and 16S rRNA gene amplicon sequencing.

FINDINGS: Drain biofilms had median bacterial abundance of 1.80 × 10[8] 16S rRNA gene copies/cm[2] and 2.06 × 10[6] cfu/cm[2], which correlated with bacterial abundance on sink surfaces. Hallway sinks, which were used more frequently than patient room sinks, had higher bacterial abundance. Drain microbial communities largely consisted of novosphingobium and sphingobium, with detection of acinetobacter, pseudomonas, legionella, and stenotrophomonas. Sink surfaces had abundant mycobacterium, methylobacterium-methylorubrum, and sphingobium, as well as genera common to skin microbiomes (e.g., corynebacterium, staphylococcus, streptococcus). Immediately after cleaning/disinfection, culturable bacteria were generally undetectable on drain covers; bacterial gene copies were reduced but rebounded to over 80% of pre-cleaning levels within 24 h. After seven days, 9.2% of recolonizing bacteria were derived from drains, and 15.7% were from tap water.

CONCLUSION: This study contributes to our understanding of factors that influence pathogen abundance on hospital sink surfaces and limitations of routine cleaning and disinfection.},
}

@article {pmid40569810,
year = {2025},
author = {Márquez, FJ and Granados, JE and Canet, LM and de Rojas, M and Caruz, AJ and Pérez, JM},
title = {The microbiome of the sucking louse Linognathus stenopsis (Phthiraptera, Anoplura, Linognathiidae).},
journal = {Journal of medical entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jme/tjaf060},
pmid = {40569810},
issn = {1938-2928},
support = {1380336//PAIDI/ ; },
}

@article {pmid40569694,
year = {2025},
author = {Kasmanas, JC and Magnúsdóttir, S and Zhang, J and Smalla, K and Schloter, M and Stadler, PF and de Leon Ferreira de Carvalho, ACP and Rocha, U},
title = {Integrating comparative genomics and risk classification by assessing virulence, antimicrobial resistance, and plasmid spread in microbial communities with gSpreadComp.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf072},
pmid = {40569694},
issn = {2047-217X},
support = {2019/03,396-9//São Paulo Research Foundation/ ; 2022/03,534-5//São Paulo Research Foundation/ ; //Deutsche Forschungsgemeinschaft/ ; //International Development Research Centre/ ; },
mesh = {*Plasmids/genetics ; Humans ; *Genomics/methods ; Virulence/genetics ; *Drug Resistance, Bacterial/genetics ; Gastrointestinal Microbiome/genetics ; Virulence Factors/genetics ; Computational Biology/methods ; Software ; Genome, Bacterial ; *Bacteria/genetics/pathogenicity/drug effects ; },
abstract = {BACKGROUND: Comparative genomics, genetic spread analysis, and context-aware ranking are crucial in understanding microbial dynamics' impact on public health. gSpreadComp streamlines the path from in silico analysis to hypothesis generation. By integrating comparative genomics, genome annotation, normalization, plasmid-mediated gene transfer, and microbial resistance-virulence risk-ranking into a unified workflow, gSpreadComp facilitates hypothesis generation from complex microbial datasets.

FINDINGS: The gSpreadComp workflow works through 6 modular steps: taxonomy assignment, genome quality estimation, antimicrobial resistance (AMR) gene annotation, plasmid/chromosome classification, virulence factor annotation, and downstream analysis. Our workflow calculates gene spread using normalized weighted average prevalence and ranks potential resistance-virulence risk by integrating microbial resistance, virulence, and plasmid transmissibility data and producing an HTML report. As a use case, we analyzed 3,566 metagenome-assembled genomes recovered from human gut microbiomes across diets. Our findings indicated consistent AMR across diets, with diet-specific resistance patterns, such as increased bacitracin in vegans and tetracycline in omnivores. Notably, ketogenic diets showed a slightly higher resistance-virulence rank, while vegan and vegetarian diets encompassed more plasmid-mediated gene transfer.

CONCLUSIONS: The gSpreadComp workflow aims to facilitate hypothesis generation for targeted experimental validations by the identification of concerning resistant hotspots in complex microbial datasets. Our study raises attention to a more thorough study of the critical role of diet in microbial community dynamics and the spread of AMR. This research underscores the importance of integrating genomic data into public health strategies to combat AMR. The gSpreadComp workflow is available at https://github.com/mdsufz/gSpreadComp/.},
}

*Plasmids/genetics
Humans
*Genomics/methods
Virulence/genetics
*Drug Resistance, Bacterial/genetics
Gastrointestinal Microbiome/genetics
Virulence Factors/genetics
Computational Biology/methods
Software
Genome, Bacterial
*Bacteria/genetics/pathogenicity/drug effects

@article {pmid40569658,
year = {2025},
author = {Yan, H and Wang, E and Wei, GS and Xu, X and Hurst, MRH and Zhang, B},
title = {Microbial dynamics across tri-trophic systems: insights from plant-herbivore-predator interactions.},
journal = {FEMS microbiology ecology},
volume = {101},
number = {7},
pages = {},
doi = {10.1093/femsec/fiaf065},
pmid = {40569658},
issn = {1574-6941},
support = {6222052//Beijing Natural Science Foundation/ ; 32070402//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Microbiota ; *Tetranychidae/microbiology/physiology ; *Food Chain ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Herbivory ; Predatory Behavior ; *Mites/microbiology/physiology ; *Plants/microbiology ; },
abstract = {Microbes play a critical role in regulating tri-trophic interactions among plants, herbivores, and their natural enemies, influencing key ecological and evolutionary processes. To fully understand these interactions through the food chain, a well-defined tri-trophic system is required. We investigated microbial dynamics involving plants (beans, cucumbers, and eggplants), spider mites (Tetranychus urticae), and predatory mites (Phytoseiulus persimilis) through 16S rRNA gene sequencing. The results revealed significant variations in microbiota across different trophic levels. Source tracking analysis indicated that microbiota at each trophic level were rarely inherited from the previous one, and deterministic processes played a key role in shaping the endosphere communities of these levels. Most shared zero-radius operational taxonomic units across each trophic level belonged to Pseudomonas, Bacillus, and Staphylococcus. Leaf microbiota differed among plants, while spider mites harbored similar microbiota. Notably, the microbiota of predatory mites on eggplants differed significantly from those on the other two plants. Biomarker selection and correlation analyses revealed that the abundance of Methylobacterium and Stenotrophomonas was strongly correlated with the improved fitness of predatory mites across different plants. Our study highlights the complex and dynamic nature of microbial communities across different trophic levels in a well-defined plant-herbivore-predator system.},
}

Animals
*Microbiota
*Tetranychidae/microbiology/physiology
*Food Chain
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
*Herbivory
Predatory Behavior
*Mites/microbiology/physiology
*Plants/microbiology

@article {pmid40569514,
year = {2025},
author = {Villanueva-Millan, MJ and Leite, G and Mathur, R and Rezaie, A and Fajardo, CM and de Freitas Germano, J and Morales, W and Sanchez, M and Rivera, I and Parodi, G and Weitsman, S and Rashid, M and Hosseini, A and Brimberry, D and Barlow, GM and Pimentel, M},
title = {Hydrogen Sulfide and Methane on Breath Test Correlate with Human Small Intestinal Hydrogen Sulfide Producers and Methanogens.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {40569514},
issn = {1573-2568},
abstract = {BACKGROUND: Evidence indicates that 3 gas breath testing (BT) correlates with stool microbial populations. Breath methane (CH4) levels correlate with stool Methanobrevibacter smithii levels and constipation, while hydrogen sulfide (H2S) levels correlate with stool H2S producers and diarrhea. However, their relationships to small bowel microbes are unknown.

AIMS: To assess relationships between small bowel microbes and breath gases.

METHODS: REIMAGINE study subjects completed a fasting single-sample BT for CH4 and H2S. During esophagogastroduodenoscopy without colon preparation, duodenal aspirates were obtained using double-lumen sterile aspiration catheters. Microbial DNAs underwent shotgun sequencing (NovaSeq6000).

RESULTS: Duodenal bacterial profiles differed significantly in subjects with breath H2S ≥ 1.5 ppm vs. those with < 1.5 ppm, with 2.08-log2fold greater prevalence of phylum Thermodesulfobacteriota. Higher breath H2S levels correlated with greater duodenal prevalences of H2S producers, including Proteus mirabilis (P = 0.002), Desulfosarcina widdelii (P = 0.027), and Desulfobulbus oligotrophicus (P = 0.041); co-occurrence of all 3 species correlated with ~ 50% higher breath H2S levels (P = 0.0001). Duodenal archaeal profiles differed significantly in subjects with intestinal methanogen overgrowth (IMO, CH4 ≥ 10 ppm), with 2.94-log2fold greater prevalence of family Methanobacteriaceae vs. non-IMO subjects. Higher breath CH4 correlated with greater prevalences of methanogens including M. smithii (P = 0.02), Halarchaeum sp. CBA1220 (P = 0.003), Desulfurococcus mucosus (P = 0.046), and Halobaculum rubrum (P = 0.049). IMO was more common in subjects with co-occurrence of all 4 species (P = 0.04). In IMO-positive subjects, CH4 levels correlated with greater constipation severity (P = 0.019); P. mirabilis (P = 0.021) and D. oligotrophicus (P = 0.003) correlated with looser stool in IMO-negative subjects. M. smithii prevalence correlated with known hydrogen-producing syntrophs, e.g., Christensenella minuta (P < 0.001).

CONCLUSION: This study demonstrates that duodenal prevalences of H2S-producing bacteria and methanogenic archaea contribute to H2S and CH4 levels, respectively, on BT.},
}

@article {pmid40569502,
year = {2025},
author = {Mortezaee, K},
title = {Microbiota interaction with Tregs: a target for colitis.},
journal = {Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico},
volume = {},
number = {},
pages = {},
pmid = {40569502},
issn = {1699-3055},
abstract = {Gut-resident microbiota associate with host immune system to promote homeostasis, and regulatory T cells (Tregs) are critical in the maintenance of immune balance. Tregs have immunosuppressive activity, and their presence hampers the development of inflammatory diseases. This review aims to unravel microbiome impact on Tregs in bowel inflammation and harnessing such interaction to combat colitis as a separate disease or a consequence of immune checkpoint inhibitor (ICI) therapy of cancer. Short-chain fatty acids (SCFAs) are microbial-derived metabolites associated positively with Treg generation and maintenance and being effective for hampering bowel inflammation. Treg induction shapes gut microbiota profile and support microorganism colonization in their niche and protect the host from inflammation, while suppression of Treg differentiation and activity directs microbiota-induced Th17 expansion and inducing inflammation. Thus, balancing Treg representation with Th17 cells and Treg reprogramming through manipulation of gut microbiota can offer therapy. Microbiota epithelial attachment/detachment and interaction with antigen-presenting cells (APCs) are important for the final fate of T cell signature. Fecal microbial transplantation (FMT) is a strategy for promoting normobiosis and represents a navel approach to targeting colitis. FMT with appropriate microbiota from healthy donors can reinforce microbial diversity, density and persistence to enrich their environment with transforming growth factor (TGF)-β, induce IL-10 producing APCs and reinforce gut barrier, with all these being effective for recovering Tregs, restoring intestinal homeostasis and hampering colitis. ICI therapy of cancer may predispose subjects to colitis due to the impact on microbiome and reducing Treg population. FMT promotes local Treg reorchestration, being advantageous in cancer patients.},
}

@article {pmid40569263,
year = {2025},
author = {Darlington, DN and Berger, RB and Keesee, JD and Nicholson, SE and Wu, X},
title = {Trauma and Hemorrhage Lead to an Elevation in Fecal Short-Chain Fatty Acids.},
journal = {Shock (Augusta, Ga.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/SHK.0000000000002645},
pmid = {40569263},
issn = {1540-0514},
abstract = {INTRODUCTION: Severe trauma and hemorrhage in rats lead to changes in the beta diversity of the commensal bacteria found in the gut. Because Short-Chain Fatty Acids (SCFA) are produced by these bacteria, SCFA concentration may also change following trauma and hemorrhage and reflect these alterations in the microbiome.

OBJECTIVE: To determine whether changes in SCFA occur after trauma and hemorrhage in the feces and plasma of rodents.

MATERIALS AND METHODS: Polytrauma was induced in isoflurane-anesthetized Sprague-Dawley rats by damage to the small intestine, liver, right leg skeletal muscle, and femur, followed by 20% hemorrhage. Whole blood resuscitation was performed at 1 hour (20%). Rats were euthanized at 2 hours and feces and plasma were analyzed for short-chain fatty acids (SCFA) by liquid chromatography tandem mass spectroscopy.

RESULTS: Of twenty-one SCFA analyzed in the feces and plasma, 11 were measurable. In feces, five demonstrated a significant elevation after 2 hours of severe trauma and hemorrhage (n-8) including propionic (37775 ± 8919 vs. 146591 ± 46734 nM/mg protein: mean ± SEM), pentanoic (10975 ± 2981 vs. 41828 ± 10645), 2-methyl propionic (2621 ± 523 vs. 13798 vs. 2083), 4-methyl pentanoic (1134 ± 302 vs. 4320 ± 1029) and 3-phenyl propionic acid (42194 ± 4863 vs. 153024 ± 38473). The addition of whole blood resuscitation did not change these responses, but led to an additional significant elevation in butyric (68551 ± 10786 vs. 369951 ± 79515) and hexanoic acid (24548 ± 6791 vs. 102002 ± 32069). There was no change in SCFA after trauma, hemorrhage or resuscitation in the plasma (n = 6).

CONCLUSION: Two hours of severe trauma and hemorrhage lead an elevation in many SCFAs in rat feces. No change in SCFA was found in plasma. Because SCFA are primarily derived from commensal bacteria in the gut, these data suggest that the measurement of SCFA could be used as an index of changes in the gut microbiome in pathological condition including trauma and hemorrhage.},
}

@article {pmid40569166,
year = {2025},
author = {Agudelo, FAG and Leblanc, N and Bourdeau-Julien, I and St-Arnaud, G and Dahhani, F and Flamand, N and Veilleux, A and Di Marzo, V and Raymond, F},
title = {Dietary Manganese Modulates Microbiota and Intestinal N-Acylethanolamines in a Sex-Specific Manner in Mice With Diet-Induced Obesity.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {13},
pages = {e70763},
pmid = {40569166},
issn = {1530-6860},
support = {//Canada Excellence Research Chairs, Government of Canada (CERC)/ ; RGPIN 03922//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; //Canadian Government | Canadian Institutes of Health Research (CIHR)/ ; //UL | Sentinelle Nord, Universit Laval (Sentinel North)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Female ; Male ; Mice ; *Obesity/metabolism/etiology/microbiology ; *Manganese/pharmacology/administration & dosage ; Mice, Inbred C57BL ; *Ethanolamines/metabolism ; Diet, High-Fat/adverse effects ; Endocannabinoids/metabolism ; Sex Factors ; Intestines/microbiology ; Diet ; },
abstract = {Obesity is characterized by low-grade inflammation, changes in gut microbiota, and increased tone of the expanded endocannabinoid system (eCBome). The gut is a complex ecosystem that serves as an interface between the diet and its ultimate conversion to nutrients and energy for all cells of the organism. Manganese (Mn) is an essential micronutrient from the diet required for normal cell function and physiological processes. Moreover, it is an indispensable trace mineral for some microbial species since it is a cofactor in several metabolic enzymes. Therefore, we aimed to identify possible interactions between gut microbiota composition and the eCBome during dietary variations of Mn in the context of diet-induced obesity. Female and male mice were fed Mn-depleted and Mn-enriched diets in combination with Low Fat-Low Sucrose (LFLS) or High Fat-High Sucrose (HFHS) diets for 28 days to assess intestinal microbiota and eCBome levels. Mn-enriched diets enhanced the circulating levels of N-docosapentaenoyl-ethanolamine (DPEA) and anandamide (AEA), while they reduced the intestinal concentrations of other N-acylethanolamines, particularly in the caecum. Besides, we found a strong sex effect of Mn on the intestinal levels of 2-monoacylglycerols (2-MAGs), which were lower in females. Other endocannabinoid-like molecules involved in the immune response were impacted by dietary Mn enrichment, such as N-palmitoyl-glycine and N-oleoyl-L-serine. Concomitantly, Mn enrichment promoted segment-specific changes in the relative abundance of several taxa in intestinal microbiota following the HFHS diet. Microbial families such as Peptostreptococcaceae, Muribaculaceae, and Erysipelotrichaceae responded differentially to dietary variations in Mn. This study hints at potential interactions between Mn levels and diet composition with the eCBome and intestinal bacteria during dietary Mn variations within HFHS-induced dysmetabolic processes in a sex-dependent manner. These results will eventually contribute to identifying members of the gut microbiome and mediators of the eCBome useful for improving metabolic health.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Female
Male
Mice
*Obesity/metabolism/etiology/microbiology
*Manganese/pharmacology/administration & dosage
Mice, Inbred C57BL
*Ethanolamines/metabolism
Diet, High-Fat/adverse effects
Endocannabinoids/metabolism
Sex Factors
Intestines/microbiology
Diet

@article {pmid40569073,
year = {2025},
author = {Kobiałka, M and Świerczewski, D and Walczak, M and Urbańczyk, W},
title = {Extremely distinct microbial communities in closely related leafhopper subfamilies: Typhlocybinae and Eurymelinae (Cicadellidae, Hemiptera).},
journal = {mSystems},
volume = {},
number = {},
pages = {e0060325},
doi = {10.1128/msystems.00603-25},
pmid = {40569073},
issn = {2379-5077},
abstract = {UNLABELLED: Among the Hemiptera insects, a widespread way of feeding is sucking sap from host plants. Due to their nutrient-poor diet, these insects enter into obligate symbiosis with their microorganisms involved in the synthesis of components essential for host survival. However, within the Cicadellidae family, there is a relatively large group of mesophyll feeders-Typhlocybinae-that is considered to be devoid of obligate symbiotic companions. In this work, we examine the composition of microorganisms in this subfamily and compare the results with their close relatives-the Eurymelinae subfamily. To study the microbiome, we used high-throughput next-generation sequencing (NGS, Illumina) and advanced microscopic techniques, such as transmission electron microscopy (TEM) and fluorescence in situ hybridization (FISH), in a confocal microscope. In the bodies of Typhlocybinae insects, we did not detect the presence of microorganisms deemed to be obligate symbionts. Their microbial communities consist of facultative symbionts, mainly alphaproteobacteria such as Wolbachia or Rickettsia as well as others that can be considered as facultative, including Spiroplasma, Acidocella, Arsenophonus, Sodalis, Lariskella, Serratia, Cardinium, and Asaia. On the other hand, the Eurymelinae group is characterized by a high diversity of microbial communities, both obligate and facultative, similar to other Cicadomorpha. We find co-symbionts involved in the synthesis of essential amino acids such as Karelsulcia, betaproteobacteria Nasuia, or gammaproteobacteria Sodalis. In other representatives, we observed symbiotic yeast-like fungi from the family Ophiocordycipitaceae or Arsenophonus bacteria inhabiting the interior of Karelsulcia bacteria. Additionally, we investigated some aspects of symbiont transmission and the phylogeny of symbiotic organisms and their hosts.

IMPORTANCE: The Typhlocybinae and Eurymelinae leafhoppers differ significantly in their symbiotic communities. They have different diets, as Typhlocybinae insects feed on parenchyma, which is richer in nutrients, while Eurymelinae, like most representatives of Auchenorrhyncha, consume sap from the phloem fibers of plants. Our work presents comprehensive studies of 42 species belonging to the two above-mentioned, and so far poorly known, Cicadomorpha subfamilies. Phylogenetic studies indicate that the insects from the studied groups have a common ancestor. The diet shift in the Typhlocybinae leafhoppers contributed to major changes in the composition of microorganisms inhabiting the body of these insects. Research on the impact of diet on the microbiome and the subsequent consequences on the evolution and adaptation of organisms plays an important role in the era of climate change.},
}

@article {pmid40569063,
year = {2025},
author = {Bolino, M and Duman, H and Avcı, İ and Kayili, HM and Petereit, J and Zundel, C and Salih, B and Karav, S and Frese, SA},
title = {Proteomic and N-glycomic comparison of synthetic and bovine whey proteins and their effect on human gut microbiomes in vitro.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0020025},
doi = {10.1128/spectrum.00200-25},
pmid = {40569063},
issn = {2165-0497},
abstract = {UNLABELLED: Advances in food production systems and customer acceptance have led to the commercial launch of dietary proteins produced via modern biotechnological approaches as alternatives to traditional agricultural sources. At the same time, a deeper understanding of how dietary components interact with the gut microbiome has highlighted the importance of understanding the nuances underpinning diet-microbiome interactions. Novel food proteins with distinct post-translational modifications resulting from their respective production systems have not been characterized, nor how they may differ from their traditionally produced counterparts. Here, we have characterized the protein composition and N-glycome of a yeast-synthesized and commercially available whey protein ingredient and compared this novel ingredient to whey protein isolate powder derived from bovine milk. Despite strong similarities in protein composition, we found that the N-glycome significantly differs between the two protein sources, reflecting the biosynthetic machinery of the production systems. Furthermore, the diversity of proteins found in yeast-synthesized whey protein were lower relative to bovine whey protein, despite both being predominantly β-lactoglobulin. Finally, to understand whether these differences in N-glycome profiles may affect the human gut microbiome, we compared these proteins in an in vitro fecal fermentation model. The two whey protein sources generated significant differences among three representative gut microbiomes in vitro, most likely due to differences in N-glycan composition and degradation by these representative microbial communities. This work highlights the need to understand how differences in novel biotechnological systems affect the bioactivity of synthesized proteins and how these differences impact the human gut microbiome.

IMPORTANCE: Recent advances in food technology have led to the production of animal-free products from yeast that are traditionally derived from animals, such as milk proteins. These new processes raise important questions about the use of synthetic proteins as a replacement for traditionally sourced protein, especially in the context of the gut microbiome. Importantly, yeast produce N-glycans comprised primarily of mannose, while animals synthesize structurally and compositionally complex N-glycan structures. Given these differences, we characterized a new, yeast-derived whey protein ingredient and compared it to bovine whey protein. We found that yeast-derived whey protein differs in its impact on human gut microbiomes because of differences in N-glycan structures, despite similarity in protein composition. These findings raise important questions as to whether these differences in synthetic proteins lead to significant changes to the gut microbiome in vivo, and whether this may impact the utility of these novel ingredients.},
}

@article {pmid40569025,
year = {2025},
author = {Celik, E and Ozcan, G and Vatansever, C and Paerhati, E and Uygur, L and Unal, C and Guler Cekic, S and Ozten, MA and Gürsoy, A and Keskin, Ö and Turgal, M and Gursoy, T and Can, F},
title = {Alterations in vaginal microbiome in women with short cervix: longitudinal study of microbial diversity and impact of vaginal progesterone treatment.},
journal = {Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1002/uog.29269},
pmid = {40569025},
issn = {1469-0705},
support = {119S463//Türkiye Bilimsel ve Teknolojik Araştırma Kurumu/ ; },
abstract = {OBJECTIVES: A short cervix is a known risk factor for preterm birth, and imbalances in the vaginal microbiome, such as low relative abundance of Lactobacillus, may be associated with an increased risk of preterm birth. The aim of this study was to evaluate differences in the vaginal microbiome between women with a short cervix and those with normal cervical length in the second trimester. Additionally, we aimed to assess longitudinal changes in microbial diversity during pregnancy, as well as the impact of vaginal progesterone treatment on vaginal microenvironment in women with a short cervix.

METHODS: This was a prospective, longitudinal study conducted at Koc University Hospital between January 2020 and May 2023, in women with a singleton pregnancy with a short cervical length (≤ 25 mm) in the second trimester (20 + 0 to 24 + 6 weeks' gestation). After diagnosis of short cervix, administration of 200 mg vaginal progesterone daily was initiated. The control group comprised women with a normal cervical length (> 25 mm) in the second trimester, matched for age and body mass index (BMI). Cervicovaginal swabs were collected from the posterior fornix at three gestational-age ranges: in the first trimester (11 + 0 to 13 + 6 weeks), the second trimester (20 + 0 to 24 + 6 weeks) and the third trimester (28 + 0 to 34 + 6 weeks), and cervical length was measured following sample collection. DNA was extracted and the 16S rRNA bacterial gene was sequenced to analyze and compare the vaginal microbiome between women with a short cervix and controls. We also assessed the microbiome longitudinally in each group, across the first, second and third trimesters. In the short-cervix group, we also compared the microbiome before initiation of progesterone treatment in the second trimester and 4 weeks after its initiation.

RESULTS: Among 490 pregnant women who underwent first-trimester screening during the study period and had vaginal swabs collected, short cervical length was detected in 31 at the second-trimester scan. These women formed the study group. A further 27 women, with a normal cervical length, were matched for BMI and age and assigned to the control group. During the second trimester, women with a short cervix exhibited greater species diversity compared with the control group; this was suggested by the higher Shannon index (0.45 vs 0.33; P = 0.135), which reflects species richness and evenness, and further demonstrated by the higher Chao index (20.2 vs 13.8; P = 0.018), which estimates species richness. In the second trimester, Lactobacillus was less abundant in women with a short cervix than in the control group, although the difference did not reach significance (86.8% vs 95.5%; P = 0.091). At the phylum level, in women with a short cervix compared to those with normal cervical length, the relative abundance of Firmicutes, to which the genus Lactobacillus belongs, was significantly lower (90.7% vs 97.6%; P = 0.041), while the relative abundances of both Bacteroidota (1.73% vs 0.4%; P = 0.004) and Proteobacteria (0.2% vs 0.01%; P = 0.007) were higher. In the second trimester, the relative abundance of Lactobacillus gasseri was significantly lower in women with a short cervix compared to controls (4.7% vs 13.8%; P = 0.023). In the longitudinal analysis of the vaginal microbiome, there were no significant differences among the trimesters in the control group. In contrast, in those with a short cervix, there was a notable decrease in the amount of Lactobacillus crispatus, from 55.0% in the first trimester to 36.1% in the second trimester (P = 0.052). In women with a short cervix, there was no significant difference in bacterial diversity after vs before progesterone treatment (Chao index, 22.6 vs 20.5; P = 0.609).

CONCLUSION: These findings highlight the significant alterations in the vaginal microbiome of pregnant women with a short cervix in comparison to those with normal cervical length, particularly in terms of higher species diversity and distinct community composition. The study also shows that vaginal progesterone treatment in women with a short cervix does not alter the vaginal microbiome, suggesting that it is a safe and effective intervention without disrupting the vaginal microbial balance. Understanding the relationship between cervical length and the vaginal microbiome is essential for developing strategies to reduce the risk of preterm birth in high-risk populations. © 2025 The Author(s). Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.},
}

@article {pmid40568872,
year = {2025},
author = {Han, J and Fan, DJ and Jiang, LC and Lu, Z and Ye, T and Wei, Z and Feng, YQ},
title = {In Situ Dynamic Molecular Monitoring of Single Seed Exudates by Induced Electrospray Ionization Mass Spectrometry.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c01437},
pmid = {40568872},
issn = {1520-6882},
abstract = {Seed exudates are essential for seed germination and shaping the microbiome. However, analyzing single seed exudates in situ is challenging due to their low volume and complexity. This study utilized tapered glass capillary emitters as miniature Petri dishes as well as induced electrospray ionization mass spectrometry (iESI-MS) for in situ collection and real-time analysis of single seed exudates. Through this innovative platform, we observed dynamic changes in amino acids (AAs) and organic acids (OAs) in the central carbon metabolism pathway of single Arabidopsis seed exudates during the imbibition process. Quantitative results revealed that the levels of AAs and OAs exhibited a pattern of an initial increase followed by a decrease. Furthermore, the onset and peak levels of AAs occurred earlier than those of OAs, suggesting that the seeds may adopt a two-step defense mechanism to regulate the composition of the microbiome. This study provides a valuable tool for gaining insight into seed exudates and microbiome interactions.},
}

@article {pmid40568744,
year = {2025},
author = {Sabu Kattuman, EE and Teegala, LR and Darzi, S and Thodeti, CK and Paruchuri, S},
title = {Leukotrienes: Bridging the Inflammatory Gap in Asthma and Inflammatory Bowel Diseases (IBD).},
journal = {Comprehensive Physiology},
volume = {15},
number = {3},
pages = {e70022},
pmid = {40568744},
issn = {2040-4603},
support = {R01AI144115/NH/NIH HHS/United States ; R01HL148585/NH/NIH HHS/United States ; 25PRE1373953//American Heart Association/ ; 971237//American Heart Association/ ; },
mesh = {Humans ; *Inflammatory Bowel Diseases/metabolism/immunology ; *Asthma/metabolism/immunology ; *Leukotrienes/metabolism ; Animals ; Inflammation/metabolism ; Gastrointestinal Microbiome ; },
abstract = {Leukotrienes are potent inflammatory lipid mediators produced primarily by immune cells. Inflammation, being the center stone of two major disease conditions, namely, asthma and inflammatory bowel disease (IBD), has led researchers to study the role of leukotrienes (LTs) in both these disease settings extensively. Several studies indicate a crucial role for LTs in the development and progression of IBD, whereas LTs, especially cysteinyl leukotrienes (cys-LTs), have been identified as the major contributors to asthma initiation and progression for over three decades. Additionally, the lungs and the gut share several common characteristics, including their exposure to the external environment, similar microbiome composition, and inflammatory responses. These similarities suggest a bidirectional relationship, supported by the increased risk of IBD in asthma patients and vice versa. However, the specific role of LTs in this lung-gut connection remains unclear. This review will examine how several common factors, such as physiology, microbiome, environment, and inflammatory mediators, especially LTs, modulate this crosstalk. The review also highlights in detail how altered leukotriene biosynthesis and signaling contribute to the pathogenesis of both asthma and IBD. Furthermore, we will consider the therapeutic implications of targeting leukotriene pathways for patients with concurrent asthma and IBD in the hope of developing more efficient treatment outcomes for these interconnected conditions. Finally, this review will very briefly explore the involvement of neuronal connections in mediating the lung-gut crosstalk.},
}

Humans
*Inflammatory Bowel Diseases/metabolism/immunology
*Asthma/metabolism/immunology
*Leukotrienes/metabolism
Animals
Inflammation/metabolism
Gastrointestinal Microbiome