@article {pmid41522435,
year = {2025},
author = {Zalila-Kolsi, I},
title = {Engineered bacteria as living therapeutics: Next-generation precision tools for health, industry, environment, and agriculture.},
journal = {AIMS microbiology},
volume = {11},
number = {4},
pages = {946-962},
pmid = {41522435},
issn = {2471-1888},
abstract = {Synthetic biology has revolutionized precision medicine by enabling the development of engineered bacteria as living therapeutics, dynamic biological systems capable of sensing, responding to, and functioning within complex physiological environments. These microbial platforms offer unprecedented adaptability, allowing for real-time detection of disease signals and targeted therapeutic delivery. This review explores recent innovations in microbial engineering across medical, industrial, environmental, and agricultural domains. Key advances include CRISPR-Cas systems, synthetic gene circuits, and modular plasmid architectures that provide fine-tuned control over microbial behavior and therapeutic output. The integration of computational modeling and machine learning has further accelerated design, optimization, and scalability. Despite these breakthroughs, challenges persist in maintaining genetic stability, ensuring biosafety, and achieving reproducibility in clinical and industrial settings. Ethical and regulatory frameworks are evolving to address dual-use concerns, public perception, and global policy disparities. Looking forward, the convergence of synthetic biology with nanotechnology, materials science, and personalized medicine is paving the way for intelligent, responsive, and sustainable solutions to global health and environmental challenges. Engineered bacteria are poised to become transformative tools not only in disease treatment but also in diagnostics, biomanufacturing, pollution mitigation, and sustainable agriculture.},
}

@article {pmid41522308,
year = {2025},
author = {Henry, GD and Diaz, N and Phillips, CD and Lentz, AC and Perito, P and Natale, R and Bennett, N and Stuart, AR and Henry, CJ and Chung, PH},
title = {Methods and early findings from a study comparing next-generation sequencing versus traditional cultures for penile implants concerning for low-grade infection.},
journal = {Translational andrology and urology},
volume = {14},
number = {12},
pages = {3945-3951},
pmid = {41522308},
issn = {2223-4691},
abstract = {Microbial culture is the current standard of care to choose therapeutic antibiotics for infection occurring with inflatable penile prostheses (IPPs). However, next-generation sequencing (NGS) of DNA has proven beneficial for analysis of biofilm composition and relative abundance of specific microorganisms. The main goal of this study is to evaluate whether NGS compared to microbial culture can better guide the management and antibiotic selection and device survival rates. We hypothesize that identifying microbial composition with NGS, as compared with traditional culture, will lead to better therapeutic strategies resulting in improved patient outcomes and device survival. In this present manuscript, we describe the overall study methodology and analyze device survival rates, classify clinical presentations of IPP infections, and determine infected implant microbial composition and antibiotic resistance among an early patient cohort. These early results included 18- to 80-year-old consecutive male patients who received antimicrobial treatment without surgical replacement for at least 7 days since identification of infected IPPs. Subjects were randomized into two analytic arms: traditional culture and NGS. Throughout the study, investigators and patients completed questionnaires to provide data for comparison. To date, of the 9 patients enrolled in the study, 6 eventually underwent device removal due to worsening infection within 7 days of initiating empiric antibiotic treatment. Six patients were seen in a clinic setting, while 3 were seen in the hospital/emergency department: 7 implants were primary, while 2 were secondary. All subjects received a Coloplast IPP but had differing reservoirs and reservoir locations. In cases where penile shaft tenderness was present, the implanted IPP was more often removed within 7 days. In contrast, when no tenderness was reported, the device remained viable for at least 10 days. As of this report, 11 active sites have participated in the study, with ongoing patient enrollment aimed at reaching sufficient sample sizes for statistical comparison. Penile shaft tenderness was a common presentation among patients whose early antibiotic treatment for IPP infection failed. Recruitment of additional patients to this prospective, randomized controlled trial will help to identify favorable presentations of IPP infection. Additional data will allow comparison of implantation outcomes between NGS and traditional culture.},
}

@article {pmid41521788,
year = {2026},
author = {Hernandez-Rovira, B and Villamaria, E and Oh, J and Ozarslan, B and Wyles, S},
title = {Topical Carboxytherapy Modulates the Skin Microbiome Following CO2 Laser Resurfacing: A Pilot Study.},
journal = {Journal of cosmetic dermatology},
volume = {25},
number = {1},
pages = {e70668},
doi = {10.1111/jocd.70668},
pmid = {41521788},
issn = {1473-2165},
support = {//Lumisque Skincare, LLC/ ; },
}

@article {pmid41521690,
year = {2026},
author = {Bailey, AM and Hofseth, LJ},
title = {Microplastics in Early Onset Carcinogenesis.},
journal = {Carcinogenesis},
volume = {},
number = {},
pages = {},
doi = {10.1093/carcin/bgaf093},
pmid = {41521690},
issn = {1460-2180},
abstract = {Plastics have become integral to modern life, but their persistence has generated vast quantities of microplastics (MPs, <5 mm) and nanoplastics (NPs, <1 µm) that now contaminate food, water, air, and human tissues. Although not yet classified as carcinogens by the International Agency for Research on Cancer, accumulating experimental and epidemiologic evidence raises concern that MPs may contribute to cancer development. Global plastic production has risen from 2 megatons in 1950 to more than 450 megatons annually in 2022, leaving behind pervasive waste that fragments into MPs and NPs. These particles act as xenobiotics, carrying toxic additives and adsorbed pollutants, provoking oxidative stress, chronic inflammation, DNA damage, and microbiome disruption; all processes central to carcinogenesis. MPs have been detected in human cancers, and animal studies show tissue accumulation, fibrosis, and genomic instability following exposure. Importantly, the proliferation of plastics parallels a global rise in early-onset cancers (diagnosed before age 50), suggesting a possible, though unproven, temporal association. Individuals born after the 1950s plastic boom have experienced continuous MP exposure beginning in utero, potentially predisposing them to carcinogenic pathways later in life. In this review, we integrate human biomonitoring data, experimental findings, and clinical observations to evaluate the emerging hypothesis that chronic MP exposure contributes to cancer risk. While causality has not been established, the biological plausibility and mounting evidence underscore the urgent need for mechanistic and epidemiologic studies to clarify the role of MPs and NPs in cancer development. It also underscores an urgent need for research into causal pathways and preventive mechanisms.},
}

@article {pmid41521588,
year = {2026},
author = {Alolod, GAL and Guzman, JPMD and Bermeo-Capunong, MRA and Konishi, K and Koiwai, K and Kondo, H and Hirono, I},
title = {Metagenomic Insights on the Progression of White Muscle Disease in Kuruma Shrimp (Penaeus japonicus) Caused by Photobacterium damselae subsp. damselae.},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e70117},
doi = {10.1111/jfd.70117},
pmid = {41521588},
issn = {1365-2761},
support = {22H00379//Japan Society for the Promotion of Science/ ; JPMJSA1806//Japan Science and Technology Agency/ ; },
abstract = {Kuruma shrimp (Penaeus japonicus) is an economically important shrimp perennially affected by diseases. In 2022, White Muscle Disease (WMD) was first characterised in this Penaeid species, caused by Photobacterium damselae subsp. damselae (Pdd). In this study, muscular and gut microbiome dynamics and their function in the disease progression are investigated by 16S rRNA metagenome sequencing using Illumina sequencing technologies. Alpha diversity indices showed that Pdd infection in the muscle, stomach, and intestine did not significantly change bacterial diversity between control and infected groups at all time points observed (Days 0, 1, 3, 5, 7 and 10). In the infected samples, the Shannon and Simpson indices increased starting Day 5 (D5), in congruence with the first observation of muscle whitening. Bacterial composition for the infected group at the genus level revealed that Photobacterium and Vibrio have increased their relative abundance in the muscle at Day 5 (D5) until Day 7 (D7), but declined at Day 10 (D10). As for stomach samples, Photobacterium declined in abundance and later increased significantly at Day 7 (D7). Photobacterium in the intestinal samples from the infected group increased at Day 5 (D5) but later decreased at Day 7 (D7). Meanwhile, linear discriminant analysis Effect Size (LEfSe) identified that most taxa belong to phylum Pseudomonadota, which can be potential markers for WMD. Moreover, the temporal dynamics of the amplicon sequencing variant ASV2, confirmed to be 100% homologous to the WMD-P3 strain used in this study, were characterised. For all tissues, the logarithmic relative abundance is considered high and very apparent in infected samples collected at Day 7 (D7). Overall, our study provides an understanding of the muscle and gut microbial community, specifically at the genus level, distinguished between WMD-infected and healthy Kuruma shrimps.},
}

@article {pmid41521409,
year = {2025},
author = {Lindsay, J and Yeoh, D and Teh, BW and Reynolds, GK and Henden, A and McQuilten, Z and Wheeler, M and Hamilton, A and Nelson, A and Nakagaki, M and Sandhu, S and Slavin, MA and , },
title = {Consensus guidelines for antibacterial prophylaxis in patients with neutropenia.},
journal = {Internal medicine journal},
volume = {55 Suppl 7},
number = {},
pages = {115-135},
doi = {10.1111/imj.70250},
pmid = {41521409},
issn = {1445-5994},
mesh = {Humans ; *Antibiotic Prophylaxis/standards/methods ; *Neutropenia/drug therapy/chemically induced ; *Anti-Bacterial Agents/therapeutic use ; *Consensus ; Australia/epidemiology ; Neoplasms/drug therapy ; *Practice Guidelines as Topic/standards ; },
abstract = {Since the publication of the Australian consensus guidelines in 2011, the routine use of prophylactic antibiotics in patients with neutropenia has remained controversial, because of concern that the risks of promoting antimicrobial resistance outweighed the level of evidence that their use reduced mortality. Populations at risk have changed over this period and now include a multitude of new cancer therapies, such as targeted cancer therapies and immunotherapies. Emerging understanding about the importance and role of the microbiome in defining treatment response and patterns of antibiotic resistance has also expanded. In addition, the management of neutropenic fever has improved significantly through the development and routine implementation of sepsis pathways. These updated consensus guidelines review recent evidence for the use of antibacterial prophylaxis in adults and children receiving cancer therapies associated with neutropenia. Recommendations presented in these guidelines were based on evaluating current evidence for the benefits and harms of antibacterial prophylaxis while considering the current Australian and New Zealand healthcare setting. In most circumstances, the potential harm of antibiotic resistance, adverse effects of antibiotics and disruption to the microbiome, outweighed the benefit of reducing the incidence of infection, without a benefit in mortality.},
}

Humans
*Antibiotic Prophylaxis/standards/methods
*Neutropenia/drug therapy/chemically induced
*Anti-Bacterial Agents/therapeutic use
*Consensus
Australia/epidemiology
Neoplasms/drug therapy
*Practice Guidelines as Topic/standards

@article {pmid41521406,
year = {2025},
author = {Douglas, AP and Cooley, L and McMullan, B and Kinsella, P and Laundy, N and Yap, N and Bupha-Intr, O and Alcorn, K and Bajel, A and Weinkove, R and Legg, A and Roberts, JA and Trubiano, JA and Conyers, R and Thursky, KA and , },
title = {Consensus guidelines for initial management of neutropenic fever.},
journal = {Internal medicine journal},
volume = {55 Suppl 7},
number = {},
pages = {43-67},
doi = {10.1111/imj.70248},
pmid = {41521406},
issn = {1445-5994},
mesh = {Humans ; *Consensus ; *Neutropenia/therapy/diagnosis ; *Anti-Bacterial Agents/therapeutic use ; *Fever/diagnosis/therapy/etiology/drug therapy ; *Disease Management ; *Practice Guidelines as Topic/standards ; Adult ; },
abstract = {This update of the Australasian consensus guidelines for the initial empiric management of neutropenic fever occurs in the context of major changes in cancer treatment paradigms, as well as advances in the management of sepsis and new models of care for infections since the last version of these guidelines in 2011. Acknowledging the important role of antimicrobials in the disruption of the gut microbiome and emerging antimicrobial resistance, as well as the changing epidemiology of antimicrobial resistance more broadly, these guidelines address current evidence for optimal empiric neutropenic fever therapy. A writing group - including adult and paediatric representatives across infectious diseases, microbiology, haematology, transplant and oncology, as well as across craft groups, including medicine, nursing and pharmacy - was developed to produce and address key management questions. This was overseen by a steering committee, which included consumer representation. Using an extensive review of the literature, these guidelines provide consensus recommendations with evidence grading for initial empiric management of neutropenic fever in adults and children, including recommended investigations, antimicrobial therapy and approach to patients with beta-lactam allergy or risk factors for multidrug-resistant infection. Management beyond the first 72 h is discussed in separate chapters of this issue: the Subsequent Management (for high-risk neutropenic fever) and Ambulatory Management (for low-risk neutropenic fever) chapters.},
}

Humans
*Consensus
*Neutropenia/therapy/diagnosis
*Anti-Bacterial Agents/therapeutic use
*Fever/diagnosis/therapy/etiology/drug therapy
*Disease Management
*Practice Guidelines as Topic/standards
Adult

@article {pmid41521300,
year = {2026},
author = {Deng, W and Chen, D and Wei, Y and Chen, W and Chen, K and Zhong, H and He, X},
title = {Washed microbiota transplantation relieves atopic dermatitis via gut-skin microbiome rebalancing.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04717-1},
pmid = {41521300},
issn = {1471-2180},
support = {2022B1111070006//Key-Area Research and Development Program of Guangdong Province/ ; 82300440//National Natural Science Foundation of China Youth Program/ ; },
abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic, relapsing inflammatory skin disease in which dysbiosis of gut and skin microbiota contributes to pathogenesis and severity. Washed microbiota transplantation (WMT)-an improved form of fecal microbiota transplantation with enhanced safety and microbiota quality control-has shown efficacy in a single reported adolescent case. However, clinical data on WMT in AD and its effects on the skin and gut microbiota remain limited.

METHODS: Twenty-three patients with moderate-to-severe AD received at least two courses of WMT between January 2022 and December 2023. Disease activity was evaluated using the SCORing Atopic Dermatitis (SCORAD) index, the Eczema Area and Severity Index (EASI), the Numeric Rating Scale (NRS) for itch, and the Dermatology Life Quality Index (DLQI). Peripheral blood counts, cytokine profiles, lymphocyte subsets, and gut and skin microbiota were assessed before and after treatment.

RESULTS: WMT was well tolerated (58 sessions; 5.2% mild adverse events) and significantly improved SCORAD, EASI, DLQI, and NRS scores, with greater EASI reductions in adults than in children. Absolute basophil counts decreased significantly after treatment, whereas other hematologic and cytokine parameters remained stable. Gut microbiota showed an increased Gut Microbiome Health Index, a decreased Microbial Dysbiosis Index, and enrichment of short-chain fatty acid-producing taxa, including the Eubacterium coprostanoligenes group, Lachnospiraceae, and Coprococcus. Skin microbiota shifted from Staphylococcus dominance to higher abundances of Acinetobacter, Perlucidibaca, and other potentially protective genera, inversely correlating with disease severity and systemic inflammation.

CONCLUSIONS: WMT appears safe and effective in alleviating clinical manifestations of AD while reshaping both gut and skin microbiota. These parallel microbial shifts support the gut-skin axis as a therapeutic target and highlight WMT as a promising microbiota-centered intervention for immune-mediated skin diseases.},
}

@article {pmid41521238,
year = {2026},
author = {Zhoua, J and Leia, K and Zhang, P and Wang, Z and Wang, W},
title = {Probiotics regulate the intestinal microbiome to promote growth in juvenile Salmo trutta fario.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-35054-y},
pmid = {41521238},
issn = {2045-2322},
support = {CARS-46//China Agriculture Research System of Specialty Freshwater Fish/ ; },
}

@article {pmid41521228,
year = {2026},
author = {Sharma, S and Seekatz, A and Alizadeh, M and Hassan, H and Yitabrek, A and Pratt, S and Abdelaziz, K},
title = {Early-life supplementation of poultry-derived lactobacilli drives microbial succession and gut immune modulation in broiler chickens.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-35177-2},
pmid = {41521228},
issn = {2045-2322},
support = {SC-1700628//USDA National Institute of Food and Agriculture Hatch Project/ ; 2016204//South Carolina Department of Agriculture (ACRE CGP)/ ; },
abstract = {While probiotic supplementation via feed or drinking water is well known to improve poultry gut health by modulating the microbiota and enhancing immune function, the effects of in ovo supplementation remain largely unexplored. In this study, we investigated the effects of administering a lactobacilli cocktail in ovo (embryonic day 18), post-hatch, and in combination on gut immunity and the succession of the cecal microbiota in broilers over 5 weeks. 16S rRNA gene-based sequencing of cecal contents revealed a steady increase in Shannon diversity during the first 2 weeks (PERMANOVA, p < 0.005), with community structure stabilizing by week 3 across all groups. In ovo administration of lactobacilli improved early hatch rates and modulated microbial composition during early succession, including reductions in Klebsiella and Enterococcus, and enrichment of Lactobacillus, during the first two weeks (MaAsLin2, q < 0.25). These microbiome shifts were accompanied by a reduction in the expression of the pro-inflammatory cytokines, including interferon gamma (IFN-γ), interleukin-1β (IL-1β), and IL-8 in the cecal tonsils. These findings highlight the transient yet critical role of early-life probiotic interventions in shaping gut microbial colonization and immune response in broiler chickens. More importantly, a single in ovo lactobacilli dose yielded effects comparable to weekly oral or combined administration.},
}

@article {pmid41521189,
year = {2026},
author = {Vardeman, ET and Cheng, HP and Vandebroek, I and Kennelly, EJ},
title = {The effects of the Caribbean medicinal plant Argemone mexicana on Gardnerella vaginalis using a co-culture method with vaginal Lactobacillus spp.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-26731-5},
pmid = {41521189},
issn = {2045-2322},
support = {F31AT011471//National Institutes of Health, NCCIH/ ; },
abstract = {Bacterial vaginosis (BV) is caused by vaginal microbiome dysbiosis, when beneficial Lactobacillus species are no longer dominant and are replaced by harmful anaerobic bacteria such as Gardnerella vaginalis. In Caribbean cultures, women use plants topically, such as Argemone mexicana, to treat several vaginal infections, including BV. There has been little research into how traditional botanical extracts affect the vaginal microbiota, especially as these extracts are often prepared in different ways for the same condition. This study aims to evaluate the effect of botanical preparations using an in vitro co-culture assay with beneficial Lactobacillus species and BV-causing Gardnerella vaginalis. This is an application of an in vitro co-culture assay to assess the effect of botanical preparations on the vaginal microbiota. We hypothesized that variations in the chemical composition of these preparations would affect the composition of vaginal microbiota. Argemone mexicana extractions were tested using an in vitro co-culture method with Gardnerella vaginalis and one of three vaginal Lactobacillus species and evaluated by UPLC-qToF-MS for metabolomic chemical analysis. Aqueous extractions that did not have significant antibacterial effect compared to the control in monoculture suppressed the growth of Gardnerella vaginalis in co-culture with Lactobacillus, supporting the traditional Dominican use of this plant. These results are likely related to the presence of berberine and polysaccharides in the aqueous extractions.},
}

@article {pmid41521071,
year = {2026},
author = {Kwon, ES},
title = {Integrating Perspectives on Aging: From Mechanistic Causes to Therapeutic Interventions.},
journal = {BMB reports},
volume = {},
number = {},
pages = {},
pmid = {41521071},
issn = {1976-670X},
abstract = {Aging poses one of the most urgent biomedical challenges of the 21st century, increasing vulnerability to chronic diseases and limiting healthspan in aging populations. Recent advances in aging research are transforming our understanding of aging from an inevitable decline to a multidimensional and potentially modifiable biological process. This special issue presents five invited reviews that collectively illustrate the recent progress in aging research. These articles introduce emerging concepts that shed light on the fundamental causes of aging, including the genetic architecture underlying human aging, senescence-driven fibrotic scarring arising from imperfect tissue repair, and the progressive erosion of epigenetic information in the brain. They further highlight promising avenues for intervention-such as epigenetic rejuvenation, the bidirectional interplay between the aging gut microbiome and host physiology, and the emergence of precision geronutrition. By integrating genetic, molecular, cellular, microbial, and nutritional perspectives, this collection emphasizes a future where extending human healthspan is both realistic and scientifically attainable.},
}

@article {pmid41520913,
year = {2026},
author = {Yang, X and Liu, Y and Miao, K},
title = {Microbiome-Modulated Immunotherapy in Oncology: Current Applications and Future Prospects.},
journal = {Seminars in cancer biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.semcancer.2026.01.001},
pmid = {41520913},
issn = {1096-3650},
abstract = {Cancer immunotherapy has transformed oncology, yet therapeutic efficacy remains heterogeneous and frequently limited by primary or acquired resistance. Increasing evidence demonstrates that both intra- and extratumoral microbiota critically modulate antitumor immunity, influencing clinical responses of immunotherapy and immune-related adverse events (irAEs). Microbial communities regulate the tumor immune microenvironment through multiple mechanisms, including microbe-associated molecular patterns, microbial metabolites, and outer membrane vesicles, acting on tumor or immune cells. These insights have fostered the development of microbiome-based applications in oncology, ranging from predictive biomarkers to therapeutic interventions such as engineered bacteria, fecal microbiota transplantation, probiotics, prebiotics, outer membrane vesicles, bacteriophages, and dietary modulation. Early-phase clinical studies indicate that microbiota-targeted strategies can enhance immunotherapy efficacy or mitigate irAEs, although strain specificity, interindividual variability, and safety remain significant challenges. Future progress will require mechanistic elucidation, integration of multi-omics analyses, standardization of methodologies, and personalized intervention frameworks to translate microbiome modulation into clinically actionable, precision immunotherapy.},
}

@article {pmid41520880,
year = {2026},
author = {Tham, TN and Huong, NTL and Kim, QN and Kieu, NTD and Huy, NT},
title = {The Role of the Gut Microbiome in Childhood Obesity: Mechanistic Insights and Community-Based Interventions.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {102911},
doi = {10.1016/j.clnesp.2026.102911},
pmid = {41520880},
issn = {2405-4577},
abstract = {Childhood obesity remains a critical issue, yet traditional efforts focusing on diet and exercise have failed. This review proposes that gut microbiota dysbiosis is not an association, but rather a potentially causal and actionable mechanism underlying childhood obesity. An altered gut microbiome, defined by diminished diversity and specific changes, such as a higher Firmicutes/Bacteroidetes ratio, is a primary contributor to excess weight because of its ability to enhance energy overconsumption, dysregulate production of short-chain fatty acids, regulate appetite, and induce chronic low-grade inflammation. This overview seeks to provide a synthesis of mechanistic evidence and controversies of the gut microbiome as a targetable leverage point, by assessing the microbial signatures of obesity and reflect on the evidence to date and what it implies about the effort: A quest for a singular "obesity microbe" is unlikely to provide success. The unexplained complexity of the host and environment, the lack of a high-quality standard, and evidence of functional microbial pathways and metabolites provide a more fruitful focus. Among other things, this article suggests using high-fiber, whole food dietary strategies to modify the microbiome, the targeted use of evidence-based multi-strain probiotics, and designing school and public health policies to create protective microbiome public health policies. The childhood obesity demands that future efforts focus on the integration of large, multi-omic, longitudinal studies, and the implementation of high-fidelity long-term randomized controlled trial designs that establish the causative relationships, uniform structure to the protocols and enable the implementation of high-impact, equity-based, scalable precision nutrition methodologies.},
}

@article {pmid41520868,
year = {2026},
author = {Bajinka, O and Jallow, L and Ozdemir, G},
title = {A multi-target therapeutic framework for Alzheimer's disease: an integrative mechanistic review.},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2026.01.010},
pmid = {41520868},
issn = {1873-7544},
abstract = {BACKGROUND: Alzheimer's disease (AD) is increasingly recognized as a multifactorial network disorder in which amyloid and tau pathology interact with mitochondrial dysfunction, neuroinflammation, metabolic impairment, vascular dysregulation, and synaptic failure. This review provides an integrative, systems-level synthesis of these mechanisms with emphasis on diagnostic and therapeutic implications.

METHODS: A structured narrative review was conducted using PubMed, Scopus, Web of Science, and Embase (2010-2025). Eligible studies included clinical trials, biomarker validation studies, cohort analyses, and mechanistic investigations. Evidence was synthesized by mechanistic domain with focus on cross-system interactions and translational relevance.

FINDINGS: Convergent data indicate that soluble Aβ species, tau propagation, glial dysregulation, insulin resistance, mitochondrial bioenergetic failure, lipid imbalance, and BBB dysfunction form a self-reinforcing neurodegenerative network. Diagnostic advances-including plasma p-tau181/217, Aβ42/40 ratio, GFAP, sTREM2, neuronal exosomes, and multimodal machine-learning models-enable earlier staging and refinement of therapeutic selection. Therapeutic development is shifting from linear amyloid removal to multi-target strategies incorporating anti-tau agents, glial-modulating compounds, metabolic and microbiome interventions, medical nutrition, and multidomain lifestyle programs. Across trials, combined strategies targeting interacting mechanisms demonstrate stronger biomarker and cognitive effects than single-axis approaches.

CONCLUSIONS: AD management requires a systems-oriented therapeutic architecture in which interventions are selected based on mechanistic dominance, biomarker stage, and potential synergy. We outline a multi-target strategy integrating amyloid/tau modulation, neuroimmune regulation, metabolic-vascular stabilization, and synaptic support. Future work should prioritize biomarker-guided stratification, treatment sequencing, and prevention-oriented combination designs.},
}

@article {pmid41520514,
year = {2026},
author = {Kharb, A and Zhu, X},
title = {Unlocking therapeutic impacts of the gut microbiota with computational tools.},
journal = {Current opinion in biotechnology},
volume = {97},
number = {},
pages = {103431},
doi = {10.1016/j.copbio.2025.103431},
pmid = {41520514},
issn = {1879-0429},
abstract = {The human gut microbiota, particularly the intestinal microbiota, shapes host physiology, disease risk, and therapeutic outcomes through complex metabolic and enzymatic activities. Recent advances in molecular omics, metabolomics, enzyme bioinformatics, and artificial intelligence (AI) have created unprecedented opportunities to elucidate its therapeutic roles to further enable precision microbiome medicine for personalized prevention, diagnosis, and treatment. In this review, we highlight emerging applications that leverage molecular omics and metabolomics technologies to dissect gut microbial functions, along with developments in enzyme bioinformatics and AI tools that reveal gut microbial species, enzymes, and metabolic pathways impacting human health. Finally, we discuss perspectives on data standardization, functional annotation, and interpretability, and how emerging tools are accelerating translational microbiome research.},
}

@article {pmid41520466,
year = {2026},
author = {Rapaka, D and Saniotis, A and Thatayaone, M and Bitra, VR},
title = {Neuroendocrine signaling as a pathological seed for the female bias of Alzheimer's disease and the concept of estrobolome.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {195},
number = {},
pages = {118999},
doi = {10.1016/j.biopha.2026.118999},
pmid = {41520466},
issn = {1950-6007},
abstract = {The prevalence of Alzheimer's disease (AD) is anticipated to escalate with the global increase in life expectancy. Although sex-based differences in AD have been previously documented, doubts persist regarding the relationship between sex and pathophysiological pathways. Sex hormones may contribute to these disparities, with a heightened risk of AD-related dementia associated with oophorectomy before menopause. We cannot ascertain if estrogens alone are solely accountable for this accelerated pathological progression of the disease. Estrogens are regulated by the gut microbiota. Thus, the gut-estrogen-brain axis appears to be implicated as a potential new influencer in the pathophysiology of AD, as the female microbiome differs from the male gut microbiome. This suggests it could be a risk factor for the higher prevalence of AD in women. This review speculates on the possible mechanisms for AD prevalence in women, including both anatomical and neuroendocrinological perspectives.},
}

@article {pmid41520335,
year = {2026},
author = {Sang, J and Li, S and Xu, C and Pan, X and Zhu, Y and Li, Y and Ma, C and Zhang, Y and Chen, S and Qiu, Q and Si, H and Huang, Z and Wang, J and Jiao, J and Li, Z},
title = {Rumen microbiome biogeography and ventral epithelial architecture in three ruminant species.},
journal = {Cell reports},
volume = {45},
number = {1},
pages = {116779},
doi = {10.1016/j.celrep.2025.116779},
pmid = {41520335},
issn = {2211-1247},
abstract = {Ruminants thrive in diverse ecosystems by leveraging their rumen microbiome to ferment fibrous plants. However, the spatial biogeography of rumen microbiome and the genetic diversity of the ventral rumen epithelium remain unknown. Here, we present a multi-omics study in roe deer, sika deer, and sheep, integrating region-resolved microbiome and metabolome across 11 ruminal sacs, as well as single-cell RNA sequencing (scRNA-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and bulk RNA sequencing (RNA-seq) of ventral epithelium. We reveal species-specific microbial compositions and metabolic capacities contributing to differences in short-chain fatty acid and vitamin B production. We uncover functional divergence, genomic specialization, and metabolic changes across the microbiome of distinct ruminal sacs. Single-cell profiling reveals changes of immune responses and structural remodeling of the ruminal ventral epithelium. We demonstrate that vitamin B12 promotes epithelial growth and we identify genes enhancing stem cell differentiation. Our results highlight variation in microbial ecology and epithelial architecture among three ruminant species, offering insights to improve livestock productivity.},
}

@article {pmid41520334,
year = {2026},
author = {Peng, Z and Zhang, H and Ding, Y and Liu, Z and Xie, M},
title = {Prior high fiber intake impinges on the cellular responses of mesenteric adipose and intestinal tissues to subsequent high fat feeding.},
journal = {Cell reports},
volume = {45},
number = {1},
pages = {116801},
doi = {10.1016/j.celrep.2025.116801},
pmid = {41520334},
issn = {2211-1247},
abstract = {While high-fiber diets (HfiDs) promote weight loss, their long-term efficacy is limited by rapid weight regain upon returning to high-fat diets (HFDs). Using C57BL/6J mice in diet-switching paradigms, we characterized tissue-specific responses to HfiD-to-HFD transitions through single-nucleus and spatial transcriptomics. HfiD pre-feeding enhanced mesenteric white adipose tissue progenitor/adipocyte sensitivity to subsequent HFD exposure. In the intestine, HfiD prevented HFD-induced immune-enterocyte expansion in the duodenum and reversed the enterocyte-to-goblet cell shift in the colon while maintaining persistent epigenetic reprogramming. Although HfiD-induced microbiome changes were largely reversed by HFD, we identified sexually dimorphic remodeling of adipose cell populations during diet transitions. Our findings demonstrate that prior HfiD feeding fundamentally reprograms adipose and intestinal responses to subsequent HFD challenge, providing mechanistic insights into dietary intervention outcomes. This work establishes a spatiotemporal resource for understanding tissue plasticity during dietary changes, offering new perspectives for obesity management strategies.},
}

@article {pmid41520313,
year = {2026},
author = {Chai, Y and Zhou, Y and Peng, H and Jiang, Y and Dai, J and Liu, J},
title = {Comparative efficacy of hyperthermic chemotherapy and BCG instillation in non-muscle invasive bladder cancer: a systematic review and meta-analysis.},
journal = {International urology and nephrology},
volume = {},
number = {},
pages = {},
pmid = {41520313},
issn = {1573-2584},
support = {2023YFS0257//Science & Technology Department of Sichuan Province/ ; },
abstract = {OBJECTIVE: To systematically evaluate the comparative efficacy and safety of hyperthermic intravesical chemotherapy (HIVEC) versus bacillus Calmette-Guérin (BCG) instillation in patients with non-muscle-invasive bladder cancer (NMIBC).

METHODS: A systematic literature search was conducted across PubMed, Embase, the Cochrane Library, and CBM from inception to June 30, 2025, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The study protocol was registered in the International Prospective Register of Systematic Reviews (PROSPERO) under registration number CRD420251075299. Randomized controlled trials and cohort studies comparing HIVEC with BCG in NMIBC patients were included. Primary outcomes were 24-month recurrence-free survival (RFS), progression-free survival (PFS), and overall survival (OS). Secondary outcomes included adverse events. Risk ratios (RRs) or hazard ratios (HRs) with 95% confidence intervals (CIs) were pooled using fixed- or random-effects models.

RESULTS: Seven studies involving 820 patients were included. The meta-analysis showed no significant differences between HIVEC and BCG in 24-month RFS (RR = 1.01, 95% CI: 0.90-1.12), PFS (RR = 1.00, 95% CI: 0.95-1.05), or OS (RR = 0.99, 95% CI: 0.91-1.09). However, BCG was associated with a significantly higher incidence of dysuria (RR = 1.38, 95% CI: 0.57-3.37). No significant differences were observed in other adverse events such as urinary tract infection, hematuria, or pain.

CONCLUSION: HIVEC demonstrates comparable oncological efficacy to BCG in terms of 24-month RFS, PFS, and OS for NMIBC patients, while offering a better tolerability profile with a significantly lower risk of dysuria. These findings support HIVEC as a valuable alternative treatment option, particularly in the context of BCG shortages or for BCG-intolerant patients.},
}

@article {pmid41520283,
year = {2026},
author = {Duquesnoy, M and Chassaing, B},
title = {MBRA 3.0: integrating the mucus environment for advanced high-throughput in vitro intestinal microbiome modeling.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2612804},
doi = {10.1080/19490976.2026.2612804},
pmid = {41520283},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Mucus/microbiology/metabolism ; *Intestinal Mucosa/microbiology/metabolism ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Feces/microbiology ; Fatty Acids, Volatile/metabolism ; Models, Biological ; Colon/microbiology ; High-Throughput Screening Assays/methods ; },
abstract = {The colonic mucus layer is a dynamic barrier that plays central roles in intestinal health, and recent studies highlight that it harbors a distinct and functionally critical microbial community. However, most in vitro gut models fail to recapitulate this mucosal niche, limiting mechanistic investigation of microbiota-mucus interactions. Here, we developed the MBRA 3.0 system, a next-generation chemostat engineered to integrate mucus-coated carriers and enable high-throughput dissection of spatial microbiome dynamics. Using fecal microbiota from eight human donors, we report that mucus addition does not impact total bacterial density but selectively shapes microbial community structure, metabolic output, and pro-inflammatory potential in a donor-dependent manner. Notably, MBRA 3.0 resolves stable, compositionally distinct mucus-associated and luminal communities, mirroring in vivo spatial heterogeneity. Integration of this mucosal niche also modulates short-chain fatty acid (SCFA) profiles and inflammatory signatures, highlighting the relevance of the spatial context for intestinal microbiota research. Hence, MBRA 3.0 offers a scalable and customizable platform to model mucus-microbiota interactions, advancing our understanding of gut ecology and supporting translational discovery in gastrointestinal health and disease.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Mucus/microbiology/metabolism
*Intestinal Mucosa/microbiology/metabolism
*Bacteria/classification/genetics/isolation & purification/metabolism
Feces/microbiology
Fatty Acids, Volatile/metabolism
Models, Biological
Colon/microbiology
High-Throughput Screening Assays/methods

@article {pmid41520282,
year = {2026},
author = {Yin, Q and Gupta, S and Muller, E and Almeida, A},
title = {The human gut microbiome in enteric infections: from association to translation.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2612836},
doi = {10.1080/19490976.2026.2612836},
pmid = {41520282},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Bacteria/genetics/classification/isolation & purification ; Host-Pathogen Interactions ; Animals ; },
abstract = {Enteric infections remain a leading global cause of morbidity, mortality and economic loss, increasingly compounded by the rise of antimicrobial resistance. The gut microbiome - spanning bacteria, archaea, fungi, protists and viruses - is now recognized as an important mediator that shapes susceptibility to infection, pathogen expansion and disease severity through mechanisms such as colonization resistance, resource competition and immune modulation. Conversely, the gut microbial community can facilitate enteric infection through other processes such as cross-feeding and horizontal gene transfer. In this review, we synthesize correlative and mechanistic evidence currently available on microbiome-pathogen interactions; outline host, environmental and socioeconomic modifiers that affect disease risk across the life course; and evaluate current clinical applications. We highlight key limitations in the field and identify priority areas for future research to refine causal models of microbiome-pathogen ecology and enable targeted diagnostics and therapeutics for preventing and managing enteric infections.},
}

Humans
*Gastrointestinal Microbiome
Bacteria/genetics/classification/isolation & purification
Host-Pathogen Interactions
Animals

@article {pmid41520281,
year = {2026},
author = {Tang, TWH and Ullah, K and Lee, JJ and Chen, HC and Hsieh, PCH},
title = {Comparative insights into the gut-heart axis: cross-species and cross-population perspectives.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611617},
doi = {10.1080/19490976.2025.2611617},
pmid = {41520281},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Cardiovascular Diseases/microbiology ; *Heart/physiology ; Swine ; Bacteria/classification/metabolism/genetics/isolation & purification ; Host Microbial Interactions ; Species Specificity ; *Gastrointestinal Tract/microbiology ; Disease Models, Animal ; },
abstract = {Gut microbiota research has rapidly expanded our understanding of host-microbe interactions in cardiovascular diseases, yet translation of these insights remains challenged by species-specific differences and substantial population heterogeneity. In this review, we synthesize current evidence across rodents, swine, non-human primates, and multi-ethnic human cohorts to delineate conserved versus context-dependent features of the gut-heart axis. Rodent models remain indispensable for mechanistic discovery, enabling causal testing through germ-free, antibiotic-treated, and humanized microbiota platforms, whereas large-animal models better replicate human cardiac anatomy, physiology, and microbial ecology. Human studies provide essential clinical relevance, demonstrating that patients with myocardial infarction, coronary artery disease, atrial fibrillation, and heart failure harbor distinct microbial and metabolite signatures. However, these findings vary across populations due to differences in diet, lifestyle, host genetics, medication exposure, and environmental transitions. Despite taxonomic variability, several functional pathways, most notably short-chain fatty acid production, bile acid biotransformation, and aromatic amino acid metabolism generating molecules such as trimethylamine-N-oxide and phenylacetylglutamine, consistently associate with cardiovascular risk. At the same time, population-specific features, including glycan-microbe interactions shaped by ABO and FUT2 genotypes, diet-responsive metabolite profiles, and variable drug-microbiome interactions, highlight the importance of genetic and environmental context. By integrating cross-species and cross-population evidence, this review outlines a framework for identifying robust microbial pathways, clarifying their translational boundaries, and guiding the development of microbiota-informed diagnostics and interventions that account for biological, cultural, and environmental diversity.},
}

Humans
*Gastrointestinal Microbiome/physiology
Animals
*Cardiovascular Diseases/microbiology
*Heart/physiology
Swine
Bacteria/classification/metabolism/genetics/isolation & purification
Host Microbial Interactions
Species Specificity
*Gastrointestinal Tract/microbiology
Disease Models, Animal

@article {pmid41520196,
year = {2026},
author = {Verburgt, CM and Dunn, KA and Bielawski, JP and Otley, AR and Heyman, MB and Sunseri, W and Shouval, DS and Boneh, RS and de Meij, T and Hyams, JS and Denson, LA and Kugathasan, S and Benninga, MA and de Jonge, WJ and Van Limbergen, JE},
title = {Timing is Everything: Lessons Learned for Building Microbiome-Based Models in Pediatric Crohn's Disease.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf313},
pmid = {41520196},
issn = {1536-4844},
support = {//CIHR-SPOR-Chronic Diseases/ ; //Canadian Institutes of Health Research [CIHR]-Canadian Association of Gastroenterology-Crohn's Colitis Canada New Investigator Award [2015-2019] Crohn/ ; 585718//Colitis Foundation of America, Pro-Kiids/ ; TKI-LSH-ADT-2021-AMC-26344//Health Holland TKI grant/ ; },
}

@article {pmid41520073,
year = {2026},
author = {Alam, N and Yaseen, G and Chandio, MA and Khan, RA and Nasir, MF and Shenawa, E},
title = {Discordance between preoperative urine culture and intraoperative stone/pelvis culture as a predictor of post-PCNL sepsis: a single-center retrospective analysis for targeted antibiotic stewardship.},
journal = {International urology and nephrology},
volume = {},
number = {},
pages = {},
pmid = {41520073},
issn = {1573-2584},
abstract = {PURPOSE: To evaluate the diagnostic accuracy of preoperative midstream urine culture (PMUC) against intraoperative stone and pelvic urine cultures, and to determine if culture discordance independently predicts sepsis following percutaneous nephrolithotomy (PCNL).

METHODS: This retrospective cohort study analyzed 250 adult patients undergoing PCNL between January 2023 and October 2025. All participants had both PMUC and intraoperative stone/pelvic urine cultures. The primary outcome was post-PCNL sepsis defined by Sepsis-3 criteria. Diagnostic performance metrics were calculated, and the association between discordance and sepsis was assessed using multivariable logistic regression, LASSO penalization, and propensity-score matching to adjust for confounders.

RESULTS: Culture discordance was observed in 30% (75/250) of patients. The sensitivity of PMUC for detecting upper urinary tract colonization was only 48%. Sepsis occurred in 6.8% of the total cohort but was significantly more frequent in the discordant group (17.3 vs 2.3%, p < 0.0001). In multivariable analysis, discordance remained the strongest independent predictor of sepsis (adjusted OR 6.23, 95% CI 2.20-17.62, p < 0.001), displacing stone burden and operative time. Notably, patients with sterile preoperative urine but positive intraoperative cultures accounted for 92.3% of sepsis events within the discordant group.

CONCLUSION: PMUC is an unreliable surrogate for the upper tract microbiome, failing to detect colonization in over half of cases. Culture discordance is a robust predictor of post-PCNL sepsis, driven by untreated bacterial biofilms within stones. Routine intraoperative culturing is essential for targeted antibiotic stewardship to mitigate septic complications.},
}

@article {pmid41519984,
year = {2026},
author = {Cronin, B and Kandel, S and McElroy, T and Syed, S and Swinton, C and Corley, C and Sridharan, V and Robeson, MS and Allen, AR},
title = {Changes in gut, microbiome, and cognition after doxorubicin, cyclophosphamide, and paclitaxel chemotherapy treatment.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-33903-w},
pmid = {41519984},
issn = {2045-2322},
support = {1R01CA258673/GF/NIH HHS/United States ; },
abstract = {Over 317,000 new cases of breast cancer will be diagnosed in 2025, making it the most diagnosed cancer among women in the United States. Advancements in treatment options such as chemotherapy and radiation have resulted in a 5-year survival rate of 91%. Upwards of 78% of the 4.1 million breast cancer survivors currently living in the United States report chemotherapy induced cognitive impairment (CICI), or "chemobrain". CICI defined as an impairment in memory, learning, executive function, and attention following chemotherapy treatment. There is a need for a better understanding of the long-term side effects of these treatments and the impact these may have on the quality of life for these survivors. In this study, we used a translational mouse model to study cognitive decline via intraperitoneal injections of the combination chemotherapy AC-T: Doxorubicin (DOX), Cyclophosphamide (CYP), and Paclitaxel (PTX). Mice underwent behavior tests to assess social memory and anxiety 30 days after the last AC-T injection. AC-T treated mice revealed behavioral deficits in social memory and an increase in anxiety-like behavior. RNA-sequencing and western blot analysis revealed negatively altered expression of transcripts associated with neurogenesis, axonal guidance, neurotransmission, and protein IEGs such as Arc, c-Fos, and Egr-1, respectively. Proteomics indicated increases in inflammatory markers in intestinal tissue, which also coincided with changes in intestinal morphology of AC-T treated mice. The gut microbiota of AC-T treated mice showed became dysbiotic. This study provides a multi-omic overview of the effects of AC-T treatment on cognition and intestinal inflammation and morphology.},
}

@article {pmid41519975,
year = {2026},
author = {Christoffersen, SN and Østergaard, SK and de Jonge, N and Pertoldi, C and Sørensen, JG and Noer, NK and Kristensen, TN and Nielsen, JL and Bahrndorff, S},
title = {Arctic Insects Show a Highly Dynamic Microbiome Shaped by Abiotic and Biotic Variables.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02685-z},
pmid = {41519975},
issn = {1432-184X},
abstract = {Arctic regions are inhabited by terrestrial ectotherms that have adapted to an extreme environment where food resources are limited. The host associated microbiome may partly explain their ability to live under these conditions, but very little is known about the microbiome of Arctic ectotherms. We investigate how the bacterial community of the Greenlandic seed bug (Nysius groenlandicus) and damsel bug (Nabis flavomarginatus) is affected by different abiotic and biotic factors (time, acclimation temperature, humidity, and diet) under both field and laboratory conditions. We found large differences in the bacterial composition and diversity between the two species including species-specific presence of potentially symbiotic bacteria. The bacterial community of both species changed across the season, which may be explained by the changing climatic conditions, such as temperature and humidity. This was further supported by results from the laboratory experiments. We also found that diet changed the bacterial composition in both species and that bacteria could be transferred from prey to predator. Together, these results show that the bacterial community of some Arctic insects are highly dynamic and modulated by different abiotic and biotic factors, suggesting that the microbiome plays an important role for these organisms to persist in an extreme and resource-limited Arctic environment.},
}

@article {pmid41519950,
year = {2026},
author = {Ye, X and Zhang, T and Zhou, J and Zhao, C and Wu, J},
title = {The gut microbial profile and circulating metabolism are associated with functional constipation in children.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {41519950},
issn = {1530-0447},
abstract = {BACKGROUND: A growing body of evidence highlights the link between gut microbiome imbalances and constipation. However, the role of gut microbiota and its metabolic interactions in pediatric functional constipation (FC) remains incompletely understood.

METHODS: We recruited a total of 40 children with FC and 40 healthy children (CONT). 16SrRNA and metagenomic sequencing were used to evaluate the changes in the gut microbiota structure and gene function in FC patients. Differences in serum metabolite levels were analyzed via targeted metabolomic sequencing.

RESULTS: The FC group exhibited a decrease in gut microbiota diversity, an increase in Bacteroides and Prevotella abundances, depletion of genera such as Lactobacillus and Bifidobacterium and an imbalance of related metabolic activities. Metabolomic analysis revealed that the levels of several metabolites, including taurine and glycochenodeoxycholic acid, which are involved in bile acid (BA) metabolic pathways, differed between the FC and CONT groups. Differences in metabolite levels were associated with changes in the abundances of specific bacteria and with intestinal dysfunction in FC patients.

CONCLUSION: FC in children is associated with distinct gut microbiota alterations and dysregulated BA metabolism. These findings provide potential therapeutic targets for modulating the gut microbiome and metabolic pathways in FC management.

IMPACT: This study offers a comprehensive perspective on the intricate relationship between microbial composition and metabolic pathways in the context of functional constipation in children. This study focuses on children, highlighting how disruptions in bile acid metabolism due to gut microbiota disorders are linked to the occurrence of functional constipation. These findings suggest that disturbances in bile acid metabolism may play a role in the mechanisms underlying functional constipation by impairing intestinal secretion and transport functions. This study offers a new way to study the effects of the gut microbiota, bile acid metabolism, and the gut‒brain axis.},
}

@article {pmid41519893,
year = {2026},
author = {Schaefer-Dreyer, P and Behrens, W and Winkel, A and Pott, PC and Paulsen, M and Stanislawski, N and Tanisik, F and Melk, A and Schmidt, BMW and Lucas, H and Heiden, S and Klopp, N and Illig, T and Blume, H and Blume, C and Yang, I and Stiesch, M},
title = {Effects of cigarette smoking on the oral microbiome in adolescents.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {1348},
pmid = {41519893},
issn = {2045-2322},
mesh = {Humans ; Adolescent ; *Microbiota ; Male ; Female ; *Mouth/microbiology ; *Cigarette Smoking/adverse effects ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Young Adult ; },
abstract = {Smoking, a risk factor for periodontitis and peri-implantitis, is associated with shifts in the oral microbiome (OM) composition. Although smoking habits are almost always established before adulthood, data on effects of smoking on the OM in adolescents is rare. The aim of this study was to investigate the early impact of smoking on the OM composition in pupils. The adolescent cohort, aged 14-20, comprised 98 smokers and 98 non-smokers matched for several physiological co-variates. Buccal swabs were analysed for OM composition using high-throughput sequencing of the full-length 16 S rRNA gene targeting species-level resolution. Parameters of bacterial diversity and abundance of individual bacterial taxa were related to information on smoking. The microbiome dataset contained 733 species-level taxa. Streptococcus, Rothia, and Haemophilus dominated both groups, smokers and non-smokers. Smoking exerted a discernible influence on the overall microbial composition as measured by weighted UniFrac distances. The number of species-level bacterial taxa was significantly higher in individual smokers compared to non-smokers. Furthermore, several taxa, including known pathogens, exhibited significant differences in abundance between the two groups. The genera Veillonella, and Actinomyces, as well as and multiple Actinomyces species, Dialister invisus, Atopobium parvulum, Streptococcus mutans and Prevotella melaninogenica were significantly more abundant in smokers. Our findings indicated an early onset of smoking-related changes already in the oral microbiome of adolescents.},
}

Humans
Adolescent
*Microbiota
Male
Female
*Mouth/microbiology
*Cigarette Smoking/adverse effects
*Bacteria/genetics/classification
RNA, Ribosomal, 16S/genetics
Young Adult

@article {pmid41519453,
year = {2026},
author = {Combs, MP and Shaver, CM},
title = {Emerging from the shadows: reading between the lines to illuminate the microbiome's role in CLAD.},
journal = {The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.healun.2026.01.001},
pmid = {41519453},
issn = {1557-3117},
}

@article {pmid41519378,
year = {2026},
author = {Jeong, H and Eppel, PS and Kaelber, DC and Singh, RP and Talcott, KE},
title = {Malabsorption Syndromes and Risk of Age-Related Macular Degeneration: Evidence from Real-World Data.},
journal = {Ophthalmology. Retina},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.oret.2026.01.002},
pmid = {41519378},
issn = {2468-6530},
abstract = {PURPOSE: Despite mechanistic links connecting malnutrition and gut microbiome with retinal health, clinical research exploring the relationship between malabsorption syndromes and age-related macular degeneration (AMD) remains limited. This study compared the risks of AMD diagnosis in patients with and without various malabsorption syndrome diagnoses.

DESIGN: Retrospective cohort study of aggregated, de-identified patient data from multiple healthcare organizations across the United States using the TriNetX U.S. Collaborative Research Network in 11/2025.

PARTICIPANTS: Adults with a cataract-related International Classification of Diseases (ICD) encounter diagnosis codes and no baseline AMD ICD encounter diagnosis codes were divided into groups based on the presence of ICD encounter diagnosis codes for celiac disease (CeD), ulcerative colitis (UC), Crohn's disease (CrD), chronic pancreatitis (CP), and short bowel syndrome (SBS). Within the CP cohort, patients with pancreatic enzyme replacement therapy (PERT) prescription orders were subanalysis. For each cohort, a corresponding control cohort of patients without the respective ICD encounter diagnosis codes was created.

METHODS: The study and control cohorts were propensity-matched 1:1 on demographic factors, comorbidities, and disease-related conditions and prescription orders. The matched cohorts were compared on the risk of having AMD ICD encounter diagnoses.

MAIN OUTCOME MEASURE: Risk ratios (RR) and 95% confidence intervals (CI) of having an AMD ICD encounter diagnosis code with an accompanying retinal optical coherence tomography Common Procedural Terminology code. Significance was defined as CI ≤0.9 or ≥1.1.

RESULTS: Compared to controls without IBD, the CrD cohort (n=9,537, RR=1.42, CI=1.16-1.74), but not the UC cohort (n=15,039, RR=1.28, CI=1.09-1.51), had a higher risk of having early/intermediate AMD. CP was associated with an increased risk of AMD (n=12,856, RR=1.82, CI=1.53-2.16), even in the PERT subset (n=3,812, RR=1.83, CI=1.35-2.48). SBS (n=3,747) was associated with an increased risk of advanced/exudative AMD (RR=1.98, CI=1.31-2.98), but not early/intermediate AMD (RR=1.28, CI=0.96-1.71). CeD was not associated with increased AMD risk (n=9,315, RR=1.09, CI=0.88-1.35).

CONCLUSIONS: Chronic non-infectious causes of malabsorption syndromes-CrD, CP, and SBS-may represent underrecognized risk factors of AMD. This explorative study adds clinical evidence for a potential role of the gut-retina axis in the pathogenesis of AMD.},
}

@article {pmid41519280,
year = {2026},
author = {Yan, T and Rong, L and Wang, S and Song, X and Hu, B and Wang, Z and Wang, X and Ding, X and Guan, R and Yu, H and Niu, D and Zhang, Y},
title = {Alterations in cardiovascular biomarkers and gut microbiome associated with night shift work: Insights from the Chinese Platform Workers Study.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123735},
doi = {10.1016/j.envres.2026.123735},
pmid = {41519280},
issn = {1096-0953},
abstract = {The expansion of the gig economy has been marked by an increase in platform workers, including ride-hailing drivers, who typically work non-standard schedules, with night shifts being common. Although night shift work was known to disrupt circadian rhythms and elevate cardiovascular risks, the interplay between early alteration in cardiovascular biomarkers and gut microbiome remain unclear. To investigate these associations in the platform worker groups, we conducted a cross-sectional study comparing 66 night shift and 175 day shift ride-hailing drivers in Beijing, China. All participants underwent health examinations, provided blood tests for the assessment of four key cardiovascular biomarkers (hs-cTnI, ET-1, NT-pro-BNP, and FABP-3), and submitted fecal samples for gut microbiome profiling via 16S rDNA sequencing. Bioinformatics, linear regression, and mediation analyses were conducted to evaluate the associations between night shift work, biomarkers, and microbial taxa, with adjustments for key sociodemographic and lifestyle factors. Night shift drivers exhibited significantly higher levels of NT-pro-BNP (median 49.8 vs. 41.3 pg/ml, P = 0.044), an association that remained significant after adjustment for covariates (β = 0.195, P = 0.004). Twenty differentially abundant taxa were identified, four of which were significantly associated with hs-cTnI. No significant mediation effect was observed. This study found that night shift work in ride-hailing drivers was significantly associated with adverse cardiovascular biomarker profiles and distinct gut microbiome alterations. Correlation analysis further suggested that gut microbial changes were linked to the observed cardiovascular risk. This study reported associations between night-shift work and alterations in early cardiovascular injury biomarkers as well as the gut microbiota, suggesting a potential link between gut microbiota and night-shift-related cardiovascular injury.},
}

@article {pmid41519271,
year = {2026},
author = {Nicholas, JC and Alkis, T and Bis, JC and Boerwinkle, E and Brody, JA and Clish, CB and de Vries, PS and Gao, Y and Gerzsten, RE and Guo, X and Johnson, AD and Larson, MG and Lemaitre, RN and Psaty, BM and Ramachandran, V and Reiner, AP and Rich, SS and Rodriguez, B and Rong, J and Rotter, JI and Simino, J and Smith, NL and Wilson, J and Yao, J and Morrison, AC and Yu, B and Raffield, LM},
title = {Fibrinogen-Associated Plasma Metabolites and Implications for Coagulation, Inflammation, and Vascular Diseases.},
journal = {Journal of thrombosis and haemostasis : JTH},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtha.2025.12.016},
pmid = {41519271},
issn = {1538-7836},
abstract = {BACKGROUND: Fibrinogen is a critical coagulation factor that plays an essential role in thrombosis and is elevated in individuals with chronic inflammation. Here, we used fibrinogen as a representative quantitative measure of pro-coagulant risk and evaluated metabolites associated with fibrinogen levels through non-targeted plasma metabolomic profiling (Broad and Metabolon platforms).

METHODS: Our analysis included 10,533 individuals across six U.S. based cohorts representing diverse population groups. The cross-sectional relationship between each of 789 tested metabolites and plasma fibrinogen concentration was assessed with adjustment for relevant covariates such as age, sex, body mass index, and circulating lipoprotein levels.

RESULTS: Meta-analysis of per-cohort results revealed 270 metabolites significantly associated with fibrinogen level (FDR adjusted p-value < 0.05). Lipid species such as glycerophospholipids, sphingolipids, and fatty acyls were prevalent among significantly associated metabolites; some of these may capture effects of inflammation, as supported by sensitivity analyses adjusted for C-reactive protein. Significant associations between fibrinogen levels and serotonin, thyroxine, and sex-hormone derivatives may capture endogenous influences on fibrinogen levels. Exogenous compounds and microbial co-metabolites significantly associated with fibrinogen also implicate lifestyle and microbiome risk-factors. Only a portion of fibrinogen-associated metabolites (30%) have been associated with a cardiovascular disease outcome in a prior study, suggesting the associations discovered here may provide insights on vascular biology which case-control studies may not yet be powered to detect.

CONCLUSIONS: These findings contribute to a growing list of metabolite biomarkers that may influence coagulation and inflammation pathways and may thereby contribute to vascular risk.},
}

@article {pmid41519234,
year = {2026},
author = {Holdaway, CM and Vo, A and Leonard, KA and Nelson, R and Thiesen, A and Fan, Y and Marcolla, CS and Clugston, RD and Willing, BP and Jacobs, RL},
title = {Dietary Ethanolamine Increases Hepatic Lipid Accumulation in Mice Fed a High Fat Diet.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101348},
doi = {10.1016/j.tjnut.2025.101348},
pmid = {41519234},
issn = {1541-6100},
abstract = {BACKGROUND: Ethanolamine (Etn), a precursor of phosphatidylethanolamine (PE), may alter hepatic lipid homeostasis and gut health; its dietary effects remain undefined.

OBJECTIVE: To determine the effects of dietary Etn on lipid and glucose metabolism and liver/gut health in high-fat diet (HFD)-fed mice, complemented by in vitro hepatocyte assays.

METHODS: Ten-week-old C57BL/6 mice (20 male, 18 female) were fed ad libitum HFD (45% energy from fat) with (ES) or without (CON) Etn (8 g/kg diet) for 10 weeks. Outcomes included body/liver weight, glucose tolerance (GTT), plasma PC/CE/TG, hepatic TG/PC/PE, hepatic ER-stress and inflammation markers, jejunal morphology/barrier/inflammation genes, and fecal microbiota (α/β diversity). HuH7 cells received 20 μM or 5 mM Etn to assess TG/PC/PE synthesis.

STATISTICS: repeated-measures ANOVA (GTT), t-test or Wilcoxon (other endpoints), PERMANOVA (β diversity); α=0.05.

RESULTS: ES increased hepatic TG in females by 230% vs CON (p = 0.001), and trended higher in males (p = 0.054); hepatic PC and PE masses were unchanged. In ES-males, GTT AUC decreased by 22.6% (p = 0.037), and plasma PC, CE, and TG were reduced by: PC - 16.6%, CE - 24.5%, TG - 25.9% (all p < 0.05). ES males showed higher hepatic Tnf and Cd68 and increased CHOP protein (all p < 0.05). In vitro, Etn did not alter hepatocellular TG, PC, or PE synthesis (all p > 0.05). Female ES mice exhibited altered fecal β-diversity (PERMANOVA p = 0.006) with early jejunal inflammatory signals (Tnf ↑; p = 0.055).

CONCLUSIONS: Dietary Etn modifies hepatic lipid storage and gut microbiota in a sex-dependent manner and improves glucose tolerance in males, whereas in vitro data indicate no direct effect on hepatocyte lipid synthesis.},
}

@article {pmid41519187,
year = {2026},
author = {Zhang, Z and Tao, H and Mao, K and Meng, F and Jiang, S and Chen, J and He, X and Tian, X},
title = {The Central Qi Theory in Traditional Chinese Medicine: Gut Microbiota Modulation as a Strategic Target for Hepatocellular Carcinoma Therapy.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121147},
doi = {10.1016/j.jep.2025.121147},
pmid = {41519187},
issn = {1872-7573},
abstract = {Patients with intermediate and advanced hepatocellular carcinoma (HCC) often derive limited benefit from systemic therapy and experience a substantial symptom burden with deterioration in quality of life. These challenges underscore the need for safe, effective adjunctive or alternative therapies. The traditional Chinese medicine concept of Central Qi shows conceptual contemporary with contemporary understanding of the gut-liver axis and microbiome biology. Chinese herbal medicines centered on tonifying the central and replenishing qi (Buzhong Yiqi) are considered adjunctive or alternative therapeutic options for alleviating symptoms, improving quality of life, and enhancing tolerance and adherence to standard treatments.

AIM OF THIS REVIEW: To delineate links among the interrelations among Central Qi, the gut microbiota, and HCC, to synthesize evidence on how Buzhong Yiqi medicines modulate the gut microbiota, and to elucidate the proposed mechanistic bases for their potential adjunctive effects in HCC. This review aims to provide a biologically plausible framework to inform microbiome-based mechanistic research and clinical translation.

METHODS: Databases including PubMed, Web of Science, Elsevier ScienceDirect, CNKI, and Google Scholar were searched using predefined terms related to hepatocellular carcinoma, gut microbiota, and the gut-liver axis, nutrient absorption, metabolic regulation, immune modulation, and Buzhong Yiqi medicines, as well as their representative herbs. In vivo, in vitro, and clinical studies published from 2000 to October 2025 were included.

RESULTS: Dysbiosis disrupts the metabolic pathways of bile acid, short-chain fatty acid, and tryptophan metabolic pathways, while compromising the intestinal barrier. This disruption can worsen appetite regulation and energy imbalance, as well as weaken antitumor immunity. Buzhong Yiqi medicines have been reported to enrich beneficial taxa, reduce pathogens and pathobionts, and improve microbial metabolite profiles, restoration of barrier integrity, improvements in nutrient intake and energy homeostasis. These findings are heterogeneous and largely derived from non-HCC models, but collectively suggest potential support of metabolic and immune homeostasis, with possible influence on the tumor immune microenvironment. Early exploratory data also indicate a potential interaction with immune checkpoint inhibitors, although its clinical significance remains uncertain.

CONCLUSION: Central Qi deficiency provides a biologically plausible conceptual framework linking impaired digestion, disrupted energy metabolism, microbial dysbiosis, and reduced immune responsiveness in HCC. Modulation of the GM through Buzhong Yiqi medicines may offer supportive metabolic and immunological benefits, but current evidence is preliminary, based mainly on associative findings, and requires cautious interpretation. Key uncertainties remain regarding causal relationships, HCC-specific mechanisms, and the consistency of clinical effects. Future research should prioritize standardized preparations, mechanistic validation, biomarker-guided stratification, and rigorously designed clinical trials to clarify the clinical relevance of these proposed pathways and to advance global acceptance of integrative therapy.},
}

@article {pmid41519162,
year = {2026},
author = {Olmstead, M and Van Nest, K and Swistek, S and Cohnstaedt, LW and Oppert, B and Shults, P},
title = {Microbial communities in filth flies collected from dairy and poultry farms for supplemental animal feed.},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toaf283},
pmid = {41519162},
issn = {1938-291X},
support = {NP104- 3020-32000-20-00D//USDA/ ; },
abstract = {Alternative protein sources are needed due to the rising demand and increasing cost of protein ingredients in livestock diets. Mass collection of wild-caught flies from locations with high insect pressure may be an economical and environmentally sustainable approach to supplement livestock feed, but there may be feed safety issues from microbes found in field-caught insects. Therefore, we evaluated a sequencing-based approach to accurately identify potential pathogens in wild-caught flies captured on 2 different livestock farms. In this study, we combined whole-genome shotgun metagenomic sequencing with total RNA-seq to identify a broad range of microbial taxa present in and on wild-caught flies. We describe several databases tailored to the host insect, host animals, and pathogens associated with livestock and humans. Sequences were identified from potentially pathogenic bacteria including Escherichia coli, Gallibacterium anatis, Helicobacterium pullorum, Morganella morganii, Proteus mirabilis, and Providencia alcalifaciens. In addition, sequences from the pathogenic fungi Aspergillus fumigatus and viruses such as the fly pathogen Musca hytrosavirus were found. Despite the limitations of current database curation, a combination of metagenomics and total RNA-seq approaches to taxa identification can provide insight into a broad spectrum of potential pathogens in insects used as supplemental livestock feed.},
}

@article {pmid41519109,
year = {2026},
author = {Hoedt, EC and Talley, NJ},
title = {Toward a personalized diet-microbiome strategy in inflammatory bowel disease: Matching donor, diet, and patient.},
journal = {Med (New York, N.Y.)},
volume = {7},
number = {1},
pages = {100918},
doi = {10.1016/j.medj.2025.100918},
pmid = {41519109},
issn = {2666-6340},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/therapy/diet therapy ; *Fecal Microbiota Transplantation/methods ; *Precision Medicine/methods ; *Gastrointestinal Microbiome ; *Diet ; },
abstract = {Fecal microbiota transplant plus dietary change to restore the imbalance of an individual's microbiome to relieve disorders such as inflammatory bowel disease has not been established but has promise. In this commentary, we suggest the need to embrace a more nuanced, personalized approach, one that considers microbial functionality, dietary context, and host compatibility.},
}

Humans
*Inflammatory Bowel Diseases/microbiology/therapy/diet therapy
*Fecal Microbiota Transplantation/methods
*Precision Medicine/methods
*Gastrointestinal Microbiome
*Diet

@article {pmid41518932,
year = {2026},
author = {Du, B and Yang, Y and He, L and Tang, Y},
title = {Microbiota and infertility: a translational review of mechanisms and clinical applications in assisted reproduction.},
journal = {European journal of obstetrics, gynecology, and reproductive biology},
volume = {318},
number = {},
pages = {114941},
doi = {10.1016/j.ejogrb.2026.114941},
pmid = {41518932},
issn = {1872-7654},
abstract = {Infertility constitutes a major global health concern, affecting approximately 17.5% of couples of reproductive age. Although advances in assisted reproductive technologies (ART) have expanded treatment options, success rates remain highly variable due to host-specific and biological determinants. This review synthesizes current evidence on the reproductive impact of the human microbiota and its translational relevance to ART outcomes. Vaginal microbial communities dominated by Lactobacillus, particularly L. crispatus, are associated with improved conception and implantation, whereas genital or intestinal dysbiosis correlates with infertility and suboptimal treatment responses. The microbiota modulates reproductive competence through intertwined immune, endocrine-metabolic, and mucosal barrier pathways that regulate inflammation, hormonal balance, and epithelial integrity. Emerging findings indicate that gut microbial alterations linked to polycystic ovary syndrome (PCOS) and endometriosis are accompanied by insulin resistance and chronic inflammation, impairing ovulation, endometrial receptivity, and embryo viability. Interventions such as probiotics and synbiotics yield heterogeneous efficacy; individualized antimicrobial strategies, metabolic modulation, and lifestyle optimization may offer complementary benefit, while microbiota reconstruction remains experimental. Methodological limitations, including contamination in low biomass samples, variations in sequencing workflows, and population heterogeneity, still hinder data comparability and mechanistic interpretation. Future research should prioritize adequately powered randomized controlled trials using standardized microbiome metrics and live birth as a primary endpoint. Integrating microbiome profiling into ART workflows may refine patient stratification and inform precision adjuvant therapies. However, clinical implementation requires stronger causal evidence, validated biomarkers, and harmonized methodological frameworks to translate microbiome discoveries into reproducible reproductive gains.},
}

@article {pmid41518832,
year = {2025},
author = {Hellwig, P and Seick, I and Meinusch, N and Benndorf, D and Wiese, J and Reichl, U and Heyer, R},
title = {Molecular community data meets anaerobic digestion Model 1 (ADM1) - a study about the correlation between metagenome-centric metaproteomics data of a two-step full-scale anaerobic digester and its corresponding mathematical model.},
journal = {Water research},
volume = {292},
number = {},
pages = {125272},
doi = {10.1016/j.watres.2025.125272},
pmid = {41518832},
issn = {1879-2448},
abstract = {Advanced models, such as the Anaerobic Digestion Model No 1 (ADM1), are essential for operating, planning, and optimizing renewable energy production in anaerobic digester plants (AD-P)s. In this study, the ADM1da model was employed to simulate a two-step AD-P in an industrial setting. The ADM1da model is an extended ADM1 model for mixed substrates, accounting for substrate-specific disintegration, temperature effects, biogas-related mass reduction, and mineral solids content. ADM1 models can represent the anaerobic digestion processes, although the biological assumptions are coarse and reflect the knowledge and available tools for microbial communities at the time of development. Meanwhile, metagenome-centric metaproteomics provides deeper insight into the metabolic activities of microbial communities in AD-Ps. Until now, this data has not been integrated with ADM1 models. The objective of this study is to assess the feasibility of incorporating metagenome-centric metaproteome data into the ADM1 model. In a novel approach, 49 high-quality metagenome-assembled genomes (MAGs) with associated protein abundances were systematically classified into the trophic groups defined by the ADM1 model using specifically developed grouping rules. Abundances of MAGs were more variable than the process parameter-dependent dynamics of ADM1. Depending on the grouping rules, 32%-78% of all high-quality MAGs were successfully categorized into ADM1 trophic groups. However, some MAGs, e.g., Methanotrix, were multifunctional (acetoclastic and hydrogenotrophic methanogenesis) and required assignment to multiple groups. Unfortunately, more precise grouping rules resulted in greater discrepancies between metaproteomics data and the model. Additionally, 22% of the MAGs could not be assigned. The metagenome-centric metaproteome data imply that ADM1 probably needs extension to cover the observed microbial function of syntrophic acetate oxidizers, hydrolytic bacteria, lactate- and ethanol-fermenting bacteria, and mortality by phages. It was also observed that changes in process parameters, such as those caused by seasonal feeding, led to significant changes in the protein abundance Integrating metagenome-centric metaproteomic data into ADM1 trophic groups was shown to be feasible.Some trophic groups detected in protein data but not implemented in ADM1 imply the need for data-driven model enhancement and approval. In the future, more accurate models considering molecular data could support a deeper understanding of microbial community dynamics in AD-Ps.},
}

@article {pmid41518828,
year = {2025},
author = {Wu, Z and Liang, F and Zhu, N and Han, C and Wang, Z and Wang, W and Wang, L and Guo, Y and Luo, W and Wang, Y},
title = {Codonopsis pilosula regulates pathogen defense mechanisms through collaboration of root volatile compounds and microbial interactions.},
journal = {Plant physiology and biochemistry : PPB},
volume = {231},
number = {},
pages = {110974},
doi = {10.1016/j.plaphy.2025.110974},
pmid = {41518828},
issn = {1873-2690},
abstract = {Codonopsis pilosula responds to pathogen infection by modulating root volatile organic compounds (VOCs) and reshaping the rhizosphere microbiome. GC-IMS analysis linked root VOCs with microbial community composition, showing positive correlations with Bradyrhizobium and beneficial fungi, and negative associations with Alternaria pathogens. Representative VOCs-benzothiazole, linalool, and (E,E)-2,4-heptadienal-showed significant antifungal activity against Fusarium oxysporum. Molecular docking and qPCR analyses indicate that these compounds may interact with stress-related proteins and potentially influence autophagy-associated pathways, suggesting stress responses that could contribute to fungal growth inhibition or cell death. Although autophagy was not directly demonstrated, these findings highlight VOCs as important mediators of plant defense signaling and may support the development of eco-friendly VOC-based antifungal strategies.},
}

@article {pmid41518802,
year = {2026},
author = {Yang, X and Ji, XH and Li, C and Lai, JL and Luo, XG},
title = {Multi-omics assessment of synthetic microbiome-mediated remediation of cyclotetramethylene tetranitroamine (HMX) contaminated water.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141026},
doi = {10.1016/j.jhazmat.2026.141026},
pmid = {41518802},
issn = {1873-3336},
abstract = {Cyclotetramethylene tetranitroamine (HMX) is a typical high-energy nitramine pollutant with an environmental persistence and toxic effects that pose serious ecological risks. In this study, a synthetic microbiome with complementary functions is built that enables the integration of multigroup technology to conduct a systematic analysis of the mechanism of remediation of HMX-contaminated water bodies. Four core bacterial strains (Bacillus altitudinis, B. cereus, B. subtilis, and Pseudomonas stutzeri) were directionally domesticated and screened from HMX-contaminated water. Through functional verification, they were confirmed to express key enzymes NfsA, YdhA, FdhA, and NirS, respectively, to form a complete HMX deep degradation-level connection path. The synthetic microbiome achieved 100 % removal of HMX and its intermediates within 60 days, and isotope tracing (δ[15]N enrichment +2.7 ‰) confirmed its complete mineralization ability. Multiomic analysis showed that the restoration process is accompanied by a systematic reshaping of the water microecology and chemical environment, so that the microbial community structure is optimized and the synthetic microbiome is successfully colonized and becomes the core node. Meanwhile, the energy metabolic network (glycolysis, TCA cycle, oxidative phosphorylation) is significantly enhanced; metagenomic data also revealed reduced viral abundance. Ionomics revealed that key nutrient elements, such as P and S, are efficiently assimilated and utilized. These findings identify an efficient HMX bioremediation strategy that utilizes the multiple dimensions of "community structure-metabolic function-environmental effects" through a multigroup integration framework. More importantly, this study provides a theoretical basis and practical paradigm for the rational design of functional microbial communities.},
}

@article {pmid41518158,
year = {2026},
author = {Barberá, A and Ortolá, R and Sotos-Prieto, M and Rodríguez-Artalejo, F and Moya, A and Ruiz-Ruiz, S},
title = {The Role of the Gut Microbiome in the Complex Network of Frailty Syndrome and Associated Comorbidities in Aging.},
journal = {Aging cell},
volume = {25},
number = {2},
pages = {e70365},
pmid = {41518158},
issn = {1474-9726},
support = {PID2019-105969GB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PMPTA22/00107//Carlos III Health Institute (ISCIII)/ ; PMPTA22/00037//Carlos III Health Institute (ISCIII)/ ; PMPTA23/00001//Carlos III Health Institute (ISCIII)/ ; INVEST/2022/309//Next Generation-EU/ ; 22/1111//ISCIII/ ; //The Secretary of R + D + I/ ; //ERDF/ESF/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Frailty/microbiology ; Male ; Female ; Aged ; *Aging ; Comorbidity ; Aged, 80 and over ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; },
abstract = {The gut microbiota changes throughout life, potentially influencing health and triggering physiological disorders. Frailty syndrome (FS) is an age-related condition that reduces quality of life and increases hospitalization and mortality risks, making early detection and prevention essential in older populations. This study analyzed 16S rRNA gene and metagenomics sequencing of fecal samples from 203 older adults (FS: n = 64, non-FS (NFS): n = 139) to assess the role of gut microbiota in FS and related comorbidities, such as sarcopenia and impaired lower extremity function (ILEF) or anthropometric variables. Consistent taxonomic patterns were observed: Eggerthella, Parabacteroides, and Erysipelatoclostridium were significantly abundant in FS, while Christensenellaceae R-7 group, Erysipelotrichaceae UCG-003, and Hungatella were enriched in NFS. Christensenellaceae R-7 group was also associated with better mobility. Metagenomics analysis identified 680 KEGG functions differing between groups, categorized into 28 metabolic pathways. FS individuals had overrepresented biotin metabolism, antimicrobial resistance, and energy production, but underrepresented ribosomal and protein synthesis and sporulation pathways. Resistome analysis found the tetM/tetO (K18220) gene most abundant, alongside tetracycline, β-lactam, and macrolide resistance, primarily mediated by antibiotic efflux and transporters. These findings highlight distinct microbial and functional signatures associated with FS, underscoring the complex interplay between the gut microbiota and host physiology in aging. Adjusting for covariates, age and diabetes acted as confounding factors in FS for both 16S gene and metagenomics sequencing. This study offers new insights into fundamental questions in the biology of aging and opens avenues for microbiota-targeted strategies to improve the quality of life in older adults.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Frailty/microbiology
Male
Female
Aged
*Aging
Comorbidity
Aged, 80 and over
RNA, Ribosomal, 16S/genetics
Metagenomics

@article {pmid41517910,
year = {2026},
author = {Gewirtzman, J},
title = {The Global Woody Surface: A Planetary Interface for Biodiversity, Ecosystem Function, and Climate.},
journal = {Global change biology},
volume = {32},
number = {1},
pages = {e70699},
doi = {10.1111/gcb.70699},
pmid = {41517910},
issn = {1365-2486},
support = {DGE-2139841//National Science Foundation/ ; //Institute for Biospheric Studies, Yale University/ ; 80NSSC25M7127//NASA CT Space Grant/ ; },
}

@article {pmid41517814,
year = {2026},
author = {Jacob, SM and Son, B and Bagheri, S and Lee, S and Leckie, J and Chohan, B and Belway, C and Mascarenhas, J and Mobach, T and Korngut, LW and Sharkey, KA and Park, J and Nguyen, MD and Kim, SH and Pfeffer, G},
title = {The Oral Microbiome in Amyotrophic Lateral Sclerosis Shows Differentially Abundant Organisms in Limb Versus Bulbar Onset Disease: A Binational Study.},
journal = {Journal of clinical neurology (Seoul, Korea)},
volume = {22},
number = {1},
pages = {66-75},
doi = {10.3988/jcn.2025.0219},
pmid = {41517814},
issn = {1738-6586},
support = {//ALS Canada Discovery Grant/Canada ; //Barry Barrett Foundation/Canada ; /CAPMC/CIHR/Canada ; //International Development Research Council/Canada ; //Rose Family Foundation/Canada ; //Fondation Brain Canada/Canada ; /MOHW/Ministry of Health and Welfare/Korea ; RS-2024-00348451/MSIT/Ministry of Science and ICT, South Korea/Korea ; },
abstract = {BACKGROUND AND PURPOSE: Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease of upper and lower motor neurons leading to progressive disability and death. Approximately 10% of cases are caused by single-gene disorders with the remaining 90% of cases presumed to be caused by a combination of environmental and genetic factors. The microbiome (the ensemble of microorganisms that colonize body surfaces and organs) was recently identified for its importance in the pathogenesis of ALS.

METHODS: In this study, we recruited 100 participants from two ethnically and geographically distinct sites (71 from Calgary, Canada, and 29 from Seoul, Republic of Korea) which included 59 ALS participants and 41 controls. All participants provided saliva samples for oral microbial analysis using 16S rRNA sequencing. Basic demographic information was collected from all participants, and ALS participants provided additional clinical information including site of disease onset, disease duration, and ALS Functional Rating Scale - Revised score.

RESULTS: Significant differences in beta diversity of the oral microbiomes were seen between limb- and bulbar-onset ALS participants. Two bacterial genera were differentially abundant between these groups, Bifidobacteriaceae Bifidobacterium was enriched in bulbar-onset cases, while Pasteurellaceae Haemophilus was enriched in limb-onset cases. No significant differences were found between ALS participants and controls, but there were significant differences when comparing participants from different sites of recruitment. Amongst household pairs (n=35 pairs), ALS participants differed from control participants at the Seoul site.

CONCLUSIONS: Despite the cohort and household effects, our study identified differentially abundant organisms that may be important to the phenotypic variability of ALS and should be considered for future study. Our study provides novel insights into design for future multi-site microbiome research in ALS.},
}

@article {pmid41517622,
year = {2026},
author = {Bicknell, B and Liebert, A and McLachlan, C and Kiat, H},
title = {Five-Year Follow-Up of Photobiomodulation in Parkinson's Disease: A Case Series Exploring Clinical Stability and Microbiome Modulation.},
journal = {Journal of clinical medicine},
volume = {15},
number = {1},
pages = {},
pmid = {41517622},
issn = {2077-0383},
support = {NA//private donor/ ; },
abstract = {Background: Parkinson's disease (PD) involves progressive neurodegeneration with clinical or subclinical disturbance of the gut-brain axis, including altered gastrointestinal motility and enteric nervous system involvement. Clinical studies have reported gut microbiome alterations in PD, with shifts in taxa associated with inflammatory signalling and short-chain fatty acid (SCFA) metabolism. Photobiomodulation (PBM), a non-invasive light therapy, has been investigated as a potential adjunctive treatment for PD, with proposed effects on neural, metabolic, and immune pathways. We previously reported the five-year clinical outcomes in a PBM-treated Parkinson's disease case series. Here we report the five-year gut microbiome outcomes based on longitudinal samples collected from the same participants. This was an exploratory, open-label longitudinal study without a control group. Objective: Our objective was to assess whether long-term PBM was associated with changes in gut microbiome diversity and composition in the same Parkinson's disease cohort as previously assessed for changes in Parkinson's symptoms. Methods: Six participants from the earlier PBM proof-of-concept study who had been diagnosed with idiopathic PD and who had continued treatment (transcranial light emitting diode [LED] plus abdominal and neck laser) for five years had their faecal samples analysed by 16S rDNA sequencing to assess microbiome diversity and taxonomic composition. Results: Microbiome analysis revealed significantly reduced evenness (α-diversity) and significant shifts in β-diversity over five years, as assessed by Permutational Multivariate Analysis of Variance (PERMANOVA). At the phylum level, Pseudomonadota and Methanobacteriota decreased in four of the six participants. Both of these phyla are often increased in the Parkinson's microbiome compared with the microbiomes of healthy controls. Family-level changes included increased acetate-producing Bifidobacteriaceae (five of the six participants); decreased pro-inflammatory, lipopolysaccharide (LPS)-producing Enterobacteriaceae (two of the three participants who have this bacterial family present); and decreased LPS- and H2S-producing Desulfovibrionaceae (five of six). At the genus level, Faecalibacterium, a key butyrate producer, increased in four of the six participants, potentially leading to more SCFA availability, although other SCFA-producing bacteria were decreased. This was accompanied by reductions in pro-inflammatory LPS and H2S-producing genera that are often increased in the Parkinson's microbiome. Conclusions: This five-year case series represents the longest follow-up of microbiome changes in Parkinson's disease, although the interpretation of results is limited by very small numbers, the lack of a control group, and the inability to control for lifestyle influences such as dietary changes. While causal relationships cannot be inferred, the parallel changes in improvements in mobility and non-motor Parkinson's symptoms observed in this cohort, raises the hypothesis that PBM may interact with the gut-brain axis via the microbiome. Controlled studies incorporating functional multi-omics are needed to clarify potential mechanistic links between microbial function, host metabolism, and clinical outcomes.},
}

@article {pmid41517479,
year = {2025},
author = {Wu, B and He, Z and Xu, T},
title = {A Vanished Association Between Proton Pump Inhibitors and Clostridioides Difficile Infection After Minimizing Bias.},
journal = {Journal of clinical medicine},
volume = {15},
number = {1},
pages = {},
pmid = {41517479},
issn = {2077-0383},
abstract = {Background: The gut microbiome might be affected by proton-pump inhibitors (PPIs), increasing the risk of Clostridioides difficile infection (CDI); however, the association between PPIs and Clostridioides difficile infection (CDI) remains controversial. Aim: The aim of this study is to reevaluate the association between PPIs and CDI based on pharmacovigilance data, taking competition bias into account. Methods: PPI-related CDI adverse event reports, based on the Food and Drug Administration adverse event reporting system database from 2004 to 2023, were analyzed. Included PPI cases were stratified into CDI and non-CDI groups. Disproportionality analysis was performed using the reporting odds ratio (ROR) and information component (IC). The effect of competition bias on signal detection was quantitatively investigated. Age-stratified analyses were conducted to assess residual confounding. Results: A total of 238,470 PPI reports were included, with 1268 cases in the CDI group and 237,202 cases in the non-CDI group. Initial analysis revealed a significant PPI-CDI association (ROR = 2.36, 95% confidence interval (95%CI) 2.19 to 2.53; IC = 1.21, 95%CI 0.97 to 1.45), with CDI signals detected for five PPI agents, including pantoprazole, omeprazole, lansoprazole, rabeprazole, and dexlansoprazole. After excluding competition from antibacterial drugs, CDI signal strength decreased substantially (ROR = 1.47, 95%CI 1.34 to 1.62; IC = 0.55, 95%CI 0.23 to 0.87), retaining a significant CDI signal only for rabeprazole and pantoprazole. Upon further exclusion of antibacterial or immunosuppressive drug users and renal injury event cases, CDI signal strength decreased (ROR = 1.48, 95%CI 1.32 to 1.66; IC = 0.56, 95%CI 0.18 to 0.94), with pantoprazole as the sole CDI signal drug. Age-stratified analyses demonstrated complete signal loss after antibacterial drug adjustment across all age groups. Conclusions: The current large-scale pharmacovigilance study indicated that the observed PPI-CDI association may be mediated predominantly by antibacterial drug co-exposure rather than PPI direct causation.},
}

@article {pmid41517247,
year = {2026},
author = {Shah, SMH and Volpe, S and Colonna, F and Valentino, V and De Filippis, F and Torrieri, E and Cavella, S},
title = {Combined Effect of Plasma-Activated Water, Edible Coating, and Active Packaging on Cherry Tomato Shelf-Life: Kinetics and Microbiome Approach.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
pmid = {41517247},
issn = {2304-8158},
support = {817936//European Commission/ ; },
abstract = {Cherry tomatoes are highly appreciated for their nutritional value but remain highly perishable due to rapid respiration and senescence. This study evaluated a multi-hurdle strategy combining plasma-activated water (PAW), sodium caseinate-based edible coating, and antioxidant active packaging to preserve minimally processed (MP) cherry tomatoes stored at 1 °C, 4 °C, and 8 °C for 15 days. Quality evolution was monitored through physical, chemical, nutritional, and microbiological parameters and described using pseudo-zero- and first-order kinetic models, with temperature dependence expressed by the Arrhenius equation. The combined treatment (prototype) slowed the degradation rates of pH, titratable acidity, total polyphenols, and antioxidant capacity, as reflected by consistently lower kinetic rate constants across all temperatures. Prototype samples showed better retention of polyphenols and antioxidant capacity, particularly at 1 °C and 4 °C, without detrimental effects on visual appearance. Metagenomic analysis revealed that the multi-hurdle treatment reshaped the microbial community, reducing the relative abundance of potentially problematic taxa such as Acinetobacter johnsonii and limiting the occurrence of antimicrobial resistance (AMR) genes at the end of storage. This study provides the first integrated assessment of PAW, edible coating, and antioxidant active packaging as a synergistic multi-hurdle strategy, demonstrating their combined ability to extend shelf life while modulating the microbiome and resistome of minimally processed cherry tomatoes.},
}

@article {pmid41517237,
year = {2026},
author = {Yao, Y and Wu, X and Wu, H and Su, W and Li, P},
title = {Multi-Omics Analyses Unveil the Effects of a Long-Term High-Salt, High-Fat, and High-Fructose Diet on Rats.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
pmid = {41517237},
issn = {2304-8158},
abstract = {BACKGROUND: Unhealthy diets characterized by high salt, fat, and fructose content are established risk factors for metabolic and cardiovascular disorders and may have indirect effects on cognitive function. However, the combined impact of a high-salt, high-fat, and high-fructose diet (HSHFHFD) on systemic physiology and brain health remains to be fully elucidated.

METHODS: Sprague-Dawley (SD) rats received a customized high-salt, high-fat diet supplemented with 30% fructose water for 18 weeks. Physiological and brain parameters were assessed, in combination with multi-omics analyses including brain proteomics and metabolomics, serum metabolomics, and gut microbiota profiling.

RESULTS: HSHFHFD significantly elevated blood glucose, blood pressure, and serum levels of TG, TC, and LDL in rats. Serum metabolomic profiling identified over 100 differentially abundant metabolites in the Model group. Proteomics, metabolomics, and gut microbiome integration revealed pronounced alterations in both brain proteomic and metabolomic profiles, with 155 differentially expressed proteins associated with glial cell proliferation and 65 differential metabolites linked to fatty acid and amino acid metabolism, among others. Experimental validation confirmed marked upregulation of GFAP and Bax protein, concomitant with downregulation of ZO-1 and occludin. Furthermore, HSHFHFD perturbed the CREB signaling pathway, leading to diminished BDNF expression. The levels of inflammatory factors, including IL-6, IL-10, IL-1β and TNFα, were significantly elevated in the brain. Oxidative stress was evident, as indicated by elevated malondialdehyde (MDA) levels, increased superoxide dismutase (SOD) activity, and altered NAD[+]/NADH ratio. Additionally, HSHFHFD significantly reduced the abundance of beneficial gut bacteria, including Lactobacillus, Romboutsia, and Monoglobus.

CONCLUSIONS: HSHFHFD-induced depletion of gut Lactobacillus spp. may disrupt the linoleic acid metabolic pathway and gut-brain axis homeostasis, leading to the impairment of neuroprotective function, blood-brain barrier dysfunction, and exacerbated neuroinflammation and oxidative stress in the brain. These effects potentially increase the susceptibility of rats to neurodegenerative disorders.},
}

@article {pmid41517189,
year = {2026},
author = {Grigore-Gurgu, L and Leuștean-Bucur, FI and Bahrim, GE},
title = {Genetic Engineering and Encapsulation Strategies for Lacticaseibacillus rhamnosus Enhanced Functionalities and Delivery: Recent Advances and Future Approaches.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
pmid = {41517189},
issn = {2304-8158},
support = {GI 7960/2025//"Dunarea de Jos" University of Galati/ ; },
abstract = {This review addresses the recent advances made through various genetic engineering techniques to improve the properties of Lacticaseibacillus rhamnosus, not only for industrial applications, but also for the health-related benefits. However, due to the strict regulations on microorganisms intended for human consumption, concerning the insufficient characterization degree of the newly isolated strains and the lack of data regarding the safety of the genetically modified (GM) variants, the feasibility of bringing such L. rhamnosus strains to the market and their safety prospects were evaluated. Given their multiple in vivo functions in the contexts of synbiotic and symbiotic functionality, L. rhamnosus strains are more than classic probiotics and need furthermore attention. In the functional food context, this review highlights the impact of L. rhamnosus derived bioactives on the human gut-organ axis, pointing out recently demonstrated molecular mechanisms of action with the host's gut microbiome to reduce the negative effects of obesity and its related metabolic disorders, as well as depression and Parkinson's disease, as the major challenges confronting humans today. Beyond that, considering L. rhamnosus delivery and its postbiotics accessibility to consumers via functional foods, notable progress was made to enhance their stability by developing various encapsulation systems, which are also emphasized.},
}

@article {pmid41517135,
year = {2025},
author = {Liao, L and Yu, Z and Lu, Y and Hu, Y and Zhu, Y and Zhang, Y and Yu, D},
title = {Integrative Analysis of Nutritional Components, Differential Metabolites, and Endophytic Microbiota Reveals Flavor Determinants of Lushan Russet Potato.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
pmid = {41517135},
issn = {2304-8158},
support = {32160075//National Natural Science Foundation of China/ ; jjsbsq2020026//"Double Hundred and Double Thousand" Talent Project of Jiujiang City/ ; JXXTCiX202205//Jiangxi Modern Agriculture Research Collaborative Innovation Special Project/ ; S2024ZDYFN0025//the Key R&D Program Project of Jiujiang City/ ; S2024ZDYFN00151//the Key R&D Program Project of Jiujiang City/ ; 2020ZWZX03//Scientific Planning Project of Lushan Botanical Garden/ ; 2020ZWZX05//Scientific Planning Project of Lushan Botanical Garden/ ; jxsq2020104003//Double Thousand Plan of Jiangxi Province (PR China)/ ; },
abstract = {The Lushan Russet potato, cultivated in Lushan Mountain (China), is renowned for its unique flavor, which deteriorates when cultivated at low altitudes. To unravel its flavor determinants, we compared high/low-altitude-cultivated Lushan Russet potato (LsM/LS) and reference Zhongshu5 (Zs) via nutritional, metabolomic, and endophytic microbiota analyses. LsM/LS had higher dry matter, potassium, and other flavor-related components than Zs. Non-targeted LC-MS metabolomics identified 461 metabolites. Pairwise comparisons revealed 263 significant differential metabolites (SDMs) between LsM and Zs (205 more abundant in LsM), 240 between LS and Zs, and 237 between LsM and LS. KEGG enrichment showed that SDMs were mainly involved in metabolic pathways. High-throughput sequencing of endophytic microbiota showed clear beta diversity separation, which correlated with metabolomic changes. These results indicate that Lushan Russet potato's unique flavor is jointly determined by nutrient/metabolite accumulation and endophytic microbiome diversity, providing a basis for optimizing its quality and mitigating flavor deterioration in low-altitude cultivation.},
}

@article {pmid41517088,
year = {2025},
author = {Xue, R and Zong, X and Jiang, X and You, G and Wei, Y and Guo, B},
title = {Artificial Intelligence-Driven Food Safety: Decoding Gut Microbiota-Mediated Health Effects of Non-Microbial Contaminants.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
pmid = {41517088},
issn = {2304-8158},
support = {7244451//Beijing Natural Science Foundation/ ; },
abstract = {A wide range of non-microbial contaminants-such as heavy metals, pesticide residues, antibiotics, as well emerging foodborne contaminants like micro- and nanoplastics and persistent organic pollutants-can enter the human body through daily diet and exert subtle yet chronic effects that are increasingly recognized to be gut microbiota-dependent. However, the relationships among multi-contaminant exposure profiles, dynamic microbial community structures, microbial metabolites, and diverse clinical or subclinical phenotypes are highly non-linear and multidimensional, posing major challenges to traditional analytical approaches. Artificial intelligence (AI) is emerging as a powerful tool to untangle the complex interactions between foodborne non-microbial contaminants, the gut microbiota, and host health. This review synthesizes current knowledge on how key classes of non-microbial food contaminants modulate gut microbial composition and function, and how these alterations, in turn, influence intestinal barrier integrity, immune homeostasis, metabolic regulation, and systemic disease risk. We then highlight recent advances in the application of AI techniques, including machine learning (ML), deep learning (DL), and network-based methods, to integrate multi-omics and exposure data, identify microbiota and metabolite signatures of specific contaminants, and infer potential causal pathways within "contaminant-microbiota-host" axes. Finally, we discuss current limitations, such as data heterogeneity, small-sample bias, and interpretability gaps, and propose future directions for building standardized datasets, explainable AI frameworks, and human-relevant experimental validation pipelines. Overall, AI-enabled analysis offers a promising avenue to refine food safety risk assessment, support precision nutrition strategies, and develop microbiota-targeted interventions against non-microbial food contaminants.},
}

@article {pmid41516959,
year = {2025},
author = {Huang, CH and Lu, MC and Koo, M},
title = {Global Research on Hemodialysis Nutrition and Patient-Centered Priorities: A Bibliometric Analysis (2006-2025).},
journal = {Healthcare (Basel, Switzerland)},
volume = {14},
number = {1},
pages = {},
pmid = {41516959},
issn = {2227-9032},
abstract = {Background: Optimal nutritional care is essential to improving outcomes in hemodialysis, yet translation of evidence into routine practice remains uneven across settings. To inform health system planning and implementation priorities, we mapped global research on hemodialysis-related nutrition. Methods: We searched the Web of Science Core Collection for English-language original articles on nutrition and hemodialysis from 1 January 2006 to 13 October 2025. Publication trends, productivity by country and institution, influential journals and authors, citation impact, and conceptual structure via Keyword Plus co-occurrence, trend, and thematic evolution analyses were assessed using the bibliometrix package (version 5.0) in R. Results: A total of 332 articles from 115 journals were identified, with substantial growth and multidisciplinary authorship, though international collaboration remains limited. The United States contributed 21.4% of publications and achieved the highest citation impact, while China, Japan, Iran, and Brazil formed the next tier of contributors. The Journal of Renal Nutrition accounted for 16.6% of papers. Highly cited studies established links between dietary intake, mineral and electrolyte management, and survival, while supporting the use of intradialytic oral nutritional supplements. Thematic evolution showed a shift from biochemical markers toward patient-centered priorities, including diet quality, adherence, body composition, mental health, and quality of life. Emerging directions point to whole-diet approaches and microbiome-modulating strategies. Conclusions: Global research on diet and hemodialysis has progressed from foundational nutrient studies to multidimensional, patient-focused approaches. Our findings suggest opportunities for health systems to strengthen dietitian-led models of care, integrate patient-reported outcomes, and prioritize scalable nutrition interventions within routine dialysis services.},
}

@article {pmid41516317,
year = {2025},
author = {Dubiński, P and Odzimek-Rajska, M and Podlewski, S and Brola, W},
title = {Emerging Insights into the Role of the Microbiome in Brain Gliomas: A Systematic Review of Recent Evidence.},
journal = {International journal of molecular sciences},
volume = {27},
number = {1},
pages = {},
pmid = {41516317},
issn = {1422-0067},
support = {SUPB.RN.25.016//The Jan Kochanowski University in Kielce, Poland/ ; },
mesh = {Humans ; *Glioma/microbiology/pathology ; *Gastrointestinal Microbiome ; *Brain Neoplasms/microbiology/pathology ; Animals ; Dysbiosis/microbiology ; },
abstract = {Gliomas, particularly glioblastoma multiforme, remain among the most lethal brain tumours despite multimodal therapy. Increasing evidence indicates that systemic factors, including the gut microbiota, may influence glioma progression through immune, metabolic, and neurochemical pathways. We conducted a comprehensive systematic review in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines to synthesize recent evidence on the role of gut and intratumoral microbiota in glioma biology. Peer-reviewed studies published within the last five years were identified through structured searches of major biomedical databases, and original studies using human cohorts, animal models, or Mendelian randomization approaches were included. The 17 studies met the eligibility criteria. Glioma was consistently associated with gut dysbiosis characterized by a reduced Firmicutes:Bacteroidetes ratio and enrichment of Verrucomicrobia, particularly Akkermansia, alongside decreased short-chain fatty acids and altered neurotransmitter profiles, contributing to neuroinflammation, immune suppression, and blood-brain barrier dysfunction. Antigenic mimicry by Bacteroidetes-derived peptides may impair antitumour T-cell responses, while intratumoral Fusobacteriota and Proteobacteria appear to promote angiogenesis and pro-inflammatory chemokine expression. In contrast, SCFA-producing taxa such as Ruminococcaceae and probiotic genera including Lactobacillus and Bifidobacterium show protective associations. Evidence is limited by small cohorts and methodological heterogeneity. Standardized humanized models and integrated multi-omics approaches are required to clarify causal mechanisms and support microbiome-targeted therapies in glioma.},
}

Humans
*Glioma/microbiology/pathology
*Gastrointestinal Microbiome
*Brain Neoplasms/microbiology/pathology
Animals
Dysbiosis/microbiology

@article {pmid41516296,
year = {2025},
author = {Nikolova, R and Donchev, D and Vaseva, K and Ivanov, IN},
title = {Gut Microbiome and Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS): Insights into Disease Mechanisms.},
journal = {International journal of molecular sciences},
volume = {27},
number = {1},
pages = {},
pmid = {41516296},
issn = {1422-0067},
support = {project № BG-RRP-2.004-0007-С03//European Union-NextGenerationEU, through the National Recovery and Resilience Plan of the Republic of Bulgaria/ ; },
mesh = {Humans ; *Fatigue Syndrome, Chronic/microbiology/etiology/immunology ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Animals ; },
abstract = {Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a disabling clinical condition, whose hallmark characteristic is post-exertional malaise (PEM). It can affect many organs and systems, leading to severe impairment of patients' quality of life. Although numerous post-infectious, immunological, neurological, metabolic, and endocrine alterations have been documented, neither a definitive diagnostic marker nor approved treatments are available. The etiology and pathophysiology remain incompletely understood; however, emerging evidence suggests that the gut microbiome plays a role in immune responses and the development of ME/CFS. It is hypothesized that specific disturbances in gut microbiome composition, known as dysbiosis, may compromise the integrity of the intestinal barrier. This consequently leads to translocation of microbial components, which further triggers an immune response and systemic inflammation complicating the clinical presentation of ME/CFS. Furthermore, in terms of the so-called gut-brain axis, microbiome changes may lead to distinct neurocognitive impairments observed in ME/CFS patients. This review offers the readers a broad perspective on the topic on ME/CFS, with a particular emphasis on the interplay between the gut microbiome and disease mechanisms. Last but not least, recent data on potential treatment strategies for intestinal dysbiosis in ME/CFS patients have been included.},
}

Humans
*Fatigue Syndrome, Chronic/microbiology/etiology/immunology
*Gastrointestinal Microbiome
Dysbiosis/microbiology
Animals

@article {pmid41516244,
year = {2025},
author = {Tassibekova, G and Zholdassova, M and Novosolova, N and Malm, T and Giniatullin, R and Kustubayeva, A},
title = {More than Dysbiosis: Imbalance in Humoral and Neuronal Bidirectional Crosstalk Between Gut and Brain in Alzheimer's Disease.},
journal = {International journal of molecular sciences},
volume = {27},
number = {1},
pages = {},
pmid = {41516244},
issn = {1422-0067},
support = {BR27198099//This research has been funded by the Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
mesh = {Humans ; *Alzheimer Disease/metabolism/microbiology/pathology/etiology ; *Dysbiosis/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Brain/metabolism ; Animals ; Neurons/metabolism ; Brain-Gut Axis ; },
abstract = {The intestinal microbiota, a diverse community of microorganisms residing in the human gut, recently attracted considerable attention as a contributing factor to various neurological disorders, including Alzheimer's Disease (AD). Within the established framework of the gut-brain axis (GBA) concept, it is commonly suggested that dysbiosis, through microbial metabolites entering the brain, affect the cognitive functions in patients with AD. However, evidence for such a role of dysbiosis remains largely associative, and the complexity of the communication channels between the gut and the brain is not fully understood. Moreover, the new players of the GBA are emerging and the AD concept is constantly evolving. The objective of this narrative review is to synthesize the current evidence on the humoral, endocrine, immune, and neural communication mechanisms linking the gut and brain in AD and highlight newly discovered GBA messengers such as microRNAs, extracellular vesicles, T-cells, and the intestinal hormones, including emerging neuroprotective role for glucagon-like peptide-1 (GLP-1). Based on this knowledge, we aimed to develop a conceptual understanding of the GBA function in health and AD. We specify that, in AD, the GBA goes beyond a disrupted microbiome, but operates in conjunction with impaired intestinal secretion, motility, barrier permeability, and neuroinflammatory signaling. These factors are associated with the dysfunction of the hypothalamic-pituitary axis, altered somatic and autonomic neuronal gut regulation, and abnormal, due to memory problems, behavioral aspects of food intake. Identifying the individual profile of key molecular and cellular players contributing to an unbalanced GBA should optimize existing approaches or propose new approaches for the complex therapy of AD.},
}

Humans
*Alzheimer Disease/metabolism/microbiology/pathology/etiology
*Dysbiosis/metabolism/microbiology
*Gastrointestinal Microbiome
*Brain/metabolism
Animals
Neurons/metabolism
Brain-Gut Axis

@article {pmid41516240,
year = {2025},
author = {Micu, AE and Popescu, IA and Halip, IA and Mocanu, M and Vâță, D and Hulubencu, AL and Gheucă-Solovăstru, DF and Gheucă-Solovăstru, L},
title = {From Gut Dysbiosis to Skin Inflammation in Atopic Dermatitis: Probiotics and the Gut-Skin Axis-Clinical Outcomes and Microbiome Implications.},
journal = {International journal of molecular sciences},
volume = {27},
number = {1},
pages = {},
pmid = {41516240},
issn = {1422-0067},
mesh = {Humans ; *Dermatitis, Atopic/microbiology/therapy ; *Probiotics/therapeutic use ; *Dysbiosis/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Skin/microbiology/pathology/immunology ; Inflammation/microbiology ; },
abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disease in which barrier impairment, immune dysregulation, and gut-skin dysbiosis intersect, prompting growing interest in probiotics as microbiota-modulating adjuncts. We conducted a narrative review of peer-reviewed articles indexed in PubMed, Scopus, and Google Scholar, restricted to publications from 1 January 2018 to 31 October 2025 (searches last run in December 2025). Eligible evidence included randomized controlled trials (RCTs), observational studies, and mechanistic or conceptual reviews addressing microbiome alterations and microbiota-modulating interventions in AD. Most pediatric RCTs using multistrain, Lactobacillus-dominant formulations (often combined with Bifidobacterium) reported modest improvements in AD severity and pruritus and in selected barrier- and inflammation-related biomarkers. However, direct cutaneous microbiome "restoration" outcomes were reported in a minority of studies, and most clinical evidence relies on clinical endpoints and gut-skin axis plausibility rather than longitudinal skin microbiome readouts. Single-strain regimens showed inconsistent effects, and evidence in adolescents and adults remained heterogeneous. Mechanistically, probiotics may enhance short-chain fatty acid (SCFA) signaling, dampen toll-like receptor 2/4 (TLR2/4)-nuclear factor kappa B (NF-κB) activation, and promote interleukin-10 (IL-10)- and transforming growth factor-β (TGF-β)-driven tolerance. Probiotics are a biologically plausible adjunct targeting the gut-skin axis in AD and are generally well tolerated; however, heterogeneity across trials, limited follow-up, inconsistent adverse-event reporting, and scarce skin microbiome endpoints preclude firm clinical recommendations.},
}

Humans
*Dermatitis, Atopic/microbiology/therapy
*Probiotics/therapeutic use
*Dysbiosis/microbiology
*Gastrointestinal Microbiome/drug effects
*Skin/microbiology/pathology/immunology
Inflammation/microbiology

@article {pmid41516219,
year = {2025},
author = {Duman, H and Avcı, İ and Salih, B and Kayılı, HM and Bechelany, M and Karav, S},
title = {Exploring the Activity of a Novel N-Glycosidase (EndoBI-2): Recombinant Production to Release Bioactive Glycans.},
journal = {International journal of molecular sciences},
volume = {27},
number = {1},
pages = {},
pmid = {41516219},
issn = {1422-0067},
mesh = {*Polysaccharides/metabolism/chemistry ; Recombinant Proteins/metabolism/genetics ; *Glycoside Hydrolases/metabolism/genetics ; Ribonucleases/metabolism ; Tandem Mass Spectrometry ; *Bifidobacterium/enzymology ; Glycoproteins/metabolism ; *Bacterial Proteins/metabolism/genetics ; *Mannosyl-Glycoprotein Endo-beta-N-Acetylglucosaminidase/metabolism/genetics ; },
abstract = {The gut microbiome evolves in response to host development, health state, lifestyle, nutrition, and microbial interactions. The survival of gut microbiota depends on its ability to utilize its host-indigestible complex oligosaccharides. Certain gut microbes produce glycosidases that cleave N-glycoproteins to release N-glycans that are then used as a carbon source. However, commercial glycosidases are inefficient and, thus, require improved deglycosylation strategies to study their functions and scale up their production. Therefore, the main objective of this study was to recombinantly produce and characterize the novel endo-β-N-acetylglucosaminidase 2 (EndoBI-2) from Bifidobacterium longum subsp. infantis (B. infantis) and to evaluate its enzymatic performance for controlled N-glycan release. Furthermore, the optimum reaction conditions for EndoBI-2 were investigated on model glycoprotein RNAse B using model glycoprotein. The released N-glycans were profiled by hydrophilic interaction liquid chromatography-fluorescence detection-quadrupole time-of-flight tandem mass spectrometry (HILIC-FLD-QTOF-MS/MS). We demonstrated that EndoBI-2 possesses a strong temperature tolerance and efficiently cleaves N-glycans under mild reaction conditions, exhibiting high activity at pH 5. These findings highlight EndoBI-2 as a robust and efficient biocatalyst for the production of bioactive N-glycans from diverse N-glycoproteins, with potential applications in glycobiotechnology.},
}

*Polysaccharides/metabolism/chemistry
Recombinant Proteins/metabolism/genetics
*Glycoside Hydrolases/metabolism/genetics
Ribonucleases/metabolism
Tandem Mass Spectrometry
*Bifidobacterium/enzymology
Glycoproteins/metabolism
*Bacterial Proteins/metabolism/genetics
*Mannosyl-Glycoprotein Endo-beta-N-Acetylglucosaminidase/metabolism/genetics

@article {pmid41516169,
year = {2025},
author = {Uvarova, YE and Khlebodarova, TM and Vasilieva, AR and Shipova, AA and Babenko, VN and Zadorozhny, AV and Slynko, NM and Bogacheva, NV and Bukatich, EY and Shlyakhtun, VN and Korzhuk, AV and Pavlova, EY and Chesnokov, DO and Peltek, SE},
title = {Genetic Characterisation of Closely Related Lactococcus lactis Strains Used in Dairy Starter Cultures.},
journal = {International journal of molecular sciences},
volume = {27},
number = {1},
pages = {},
pmid = {41516169},
issn = {1422-0067},
support = {075-15-2025-516//Ministry of Science and Higher Education of the Russian Federation (the Federal Scientific-technical program for genetic technologies development for 2019-2030)/ ; FWNR- 2022-0022//Ministry of Science and Higher Education project "Study of metabolic control networks in living systems under environmental interaction, including in genetically modified organisms."/ ; },
mesh = {*Lactococcus lactis/genetics/classification/isolation & purification/metabolism ; *Cheese/microbiology ; Food Microbiology ; Phylogeny ; Genome, Bacterial ; Fermentation ; Microbiota/genetics ; },
abstract = {The complex microbiota of cheese starters plays a key role in determining the structure and flavour of the final product, primarily through their acid-forming capacity, protease activity, and exopolysaccharide synthesis. However, the specific microbial communities underlying the unique qualities of artisanal cheeses remain poorly understood. This study presents the microbiological and molecular genetic characterisation of the microbiome isolated from an artisanal cheese starter in Kosh-Agach, Altai, Russia. Metagenomic analysis of this starter revealed the presence of three bacterial genomes corresponding to those of Lactococcus lactis. Pure cultures from this starter were obtained by sequential subculture, and seventeen colonies displaying distinct characteristics on differential media were selected. Genome sequencing was performed for each colony. Bioinformatic analysis based on the rpoB gene grouped the isolates into three clusters, each corresponding to a distinct strain of Lactococcus lactis subsp. diacetilactis. This classification was further confirmed by microbiological and microscopic analyses. A notable finding was that none of the strains produced the characteristic aroma compounds of L. l. subsp. diacetilactis, namely, diacetyl and CO2. The functional properties and metabolic characteristics of this starter consortium are discussed.},
}

*Lactococcus lactis/genetics/classification/isolation & purification/metabolism
*Cheese/microbiology
Food Microbiology
Phylogeny
Genome, Bacterial
Fermentation
Microbiota/genetics

@article {pmid41522201,
year = {2023},
author = {Kim, E},
title = {Effects of natural mono- and di-saccharide as alternative sweeteners on inflammatory bowel disease: a narrative review.},
journal = {Korean journal of community nutrition},
volume = {28},
number = {3},
pages = {181-191},
pmid = {41522201},
issn = {2951-3146},
abstract = {OBJECTIVES: The incidence of inflammatory bowel disease (IBD) is increasing globally, and excessive added sugar consumption has been identified as one of the contributing factors. In the context of IBD, it is essential to explore functional sweeteners that can improve metabolic health and minimize the risk of IBD-related symptoms. This review article aims to shed light on the effects of natural mono- and di-saccharides as alternative sweeteners, specifically focusing on potential benefits for IBD.

METHODS: A comprehensive literature review was performed using PubMed and Google Scholar databases with articles published after the year 2000. The search terms 'IBD', 'added sugar', 'sweeteners', 'mono-saccharide', and 'di-saccharide' were combined to retrieve relevant articles. A total of 21 manuscripts, aligning with the objectives of the study, were selected. Papers focusing on artificial or high-intensity sweeteners were excluded to ensure relevant literature selection.

RESULTS: Multiple studies have emphasized the association between the high consumption of added sugars such as simple sugars and the increased risk of developing IBD. This is suggested to be attributed to the induction of pro-inflammatory cytokine productions and dysbiosis of the gut microbiota. Consequently, there is a growing demand for safe and functional sweeteners, in particular mono- and di-saccharides, that can serve as alternatives for IBD patients. Those functional sweeteners regulate inflammation, oxidative stress, and Intestinal barrier protection, and restore microbiome profiles in various IBD models including cells, animals, and humans.

CONCLUSIONS: Understanding these mechanisms resolves the link between how sugar consumption and IBD, and highlights the beneficial effects of natural alternative sweeteners on IBD when they were administered by itself or as a replacement for simple sugar. Further, exploration of this relationship leads us to recognize the necessity of natural alternative sweeteners in dietary planning. This knowledge could potentially lead to more effective dietary strategies for individuals with IBD.},
}

@article {pmid41516078,
year = {2025},
author = {Lupusoru, R and Moleriu, LC and Mare, R and Sporea, I and Popescu, A and Sirli, R and Goldis, A and Nica, C and Moga, TV and Miutescu, B and Ratiu, I and Belei, O and Olariu, L and Dumitrascu, V and Dragomir, RD},
title = {AI-Guided Multi-Omic Microbiome Modulation Improves Clinical and Inflammatory Outcomes in Refractory IBD: A Real-World Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {1},
pages = {},
pmid = {41516078},
issn = {1422-0067},
support = {without a Grant Number.//"Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Adult ; Female ; Male ; *Inflammatory Bowel Diseases/microbiology/therapy ; Middle Aged ; Biomarkers/blood ; *Artificial Intelligence ; Feces/microbiology ; Inflammation/microbiology ; Metagenomics/methods ; Treatment Outcome ; Young Adult ; Multiomics ; },
abstract = {Inflammatory bowel disease (IBD) remains difficult to manage in patients who fail multiple therapeutic lines, and growing evidence suggests that alterations in the gut microbiome contribute to persistent symptoms and inflammatory activity. This study evaluated a three-month, AI-guided, multi-omic personalized microbiome modulation program in adults with treatment-refractory IBD. Baseline stool metagenomic sequencing, blood biomarkers, micronutrient panels, and clinical data were integrated through an artificial intelligence platform to generate individualized plans combining dietary adjustments, targeted synbiotics, selective antimicrobials, and micronutrient correction. Clinical outcomes, inflammatory markers, and microbial signatures were reassessed after three months. Across 358 participants, stool frequency decreased substantially, urgency and rectal bleeding resolved in most patients, and over 70% reported a "much improved" overall condition. Inflammatory biomarkers showed marked normalization, with reductions in hs-CRP and fecal calprotectin observed in over 85% of cases. Micronutrient deficiencies, particularly iron and zinc, also improved, and beneficial microbial taxa such as Faecalibacterium prausnitzii, Bifidobacterium longum, and Akkermansia muciniphila increased significantly. These findings suggest that personalized, multi-omic microbiome modulation may support clinically meaningful improvements by targeting microbial, metabolic, and immune imbalances rather than symptoms alone. While encouraging, these results require confirmation in randomized controlled studies.},
}

Humans
*Gastrointestinal Microbiome
Adult
Female
Male
*Inflammatory Bowel Diseases/microbiology/therapy
Middle Aged
Biomarkers/blood
*Artificial Intelligence
Feces/microbiology
Inflammation/microbiology
Metagenomics/methods
Treatment Outcome
Young Adult
Multiomics

@article {pmid41515997,
year = {2025},
author = {Ahmed, I and Nijs, J and Vanroose, M and Vandeputte, D and Kindt, S and Elma, Ö and Hendrix, J and Huysmans, E and Lahousse, A},
title = {Oral and Gut Health, (Neuro) Inflammation, and Central Sensitization in Chronic Pain: A Narrative Review of Mechanisms, Treatment Opportunities, and Research Agenda.},
journal = {International journal of molecular sciences},
volume = {27},
number = {1},
pages = {},
pmid = {41515997},
issn = {1422-0067},
mesh = {Humans ; *Chronic Pain/therapy/microbiology/etiology/metabolism ; Animals ; *Gastrointestinal Microbiome ; *Central Nervous System Sensitization ; *Oral Health ; *Neuroinflammatory Diseases ; Dysbiosis ; },
abstract = {Given the limited efficacy of current interventions and the complexity of chronic pain, identifying perpetuating factors is crucial for uncovering new mechanistic pathways and treatment targets. The oral and gut microbiome has emerged as a potential modulator of pain through immune, metabolic, and neural mechanisms. Contemporary evidence indicates that chronic pain populations exhibit altered oral and gut microbiota, characterized by reduced short-chain fatty acid (SCFA)-producing taxa and an overrepresentation of pro-inflammatory species. These compositional changes affect metabolites such as SCFAs, bile acids, and microbial cell wall components, which interact with host receptors to promote peripheral and central sensitization. Microbiota-derived metabolites modulate peripheral sensitization by altering nociceptive neuron excitability and stimulating immune cells to release pro-inflammatory cytokines that increase blood-brain barrier permeability, activate microglia, and amplify neuroinflammation. Activated microglia further disrupt the balance between excitatory and inhibitory neurotransmission by enhancing glutamatergic activity and weakening GABAergic signaling, thereby contributing to the induction and maintenance of central sensitization. While observational studies establish associations between dysbiosis and chronic pain, animal models and early human fecal microbiota transplantation studies suggest a potential causal role of dysbiosis in pain, although human evidence remains preliminary and influenced by diet, lifestyle, and comorbidities. Overall, microbiota appears to regulate pain via peripheral and central mechanisms, and targeting it through specific interventions, such as dietary modulation to enhance SCFA production, alongside broader lifestyle measures like sleep, physical activity, stress management, and oral hygiene, may represent a new therapeutic strategy for the management of chronic pain.},
}

Humans
*Chronic Pain/therapy/microbiology/etiology/metabolism
Animals
*Gastrointestinal Microbiome
*Central Nervous System Sensitization
*Oral Health
*Neuroinflammatory Diseases
Dysbiosis

@article {pmid41515464,
year = {2026},
author = {Mendóza, R and Santos, JM and Liu, X and Elmassry, MM and Ji, G and Kiritoshi, T and Neugebauer, V and Shen, CL},
title = {Gingerol-Enriched Ginger Extract Effects on Anxiety-like Behavior in a Neuropathic Pain Model via Colonic Microbiome-Neuroimmune Modulation.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {1},
pages = {},
pmid = {41515464},
issn = {1420-3049},
support = {GRANT2020-04545//United States Department of Agriculture-NIFA/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Zingiber officinale/chemistry ; Male ; *Neuralgia/drug therapy/microbiology ; *Anxiety/drug therapy ; Disease Models, Animal ; *Plant Extracts/pharmacology/chemistry ; Rats, Sprague-Dawley ; Behavior, Animal/drug effects ; Colon/microbiology ; Catechols ; Fatty Alcohols ; },
abstract = {Growing evidence has revealed that gut dysbiosis is associated with the development of anxio-depressive disorders through mechanisms that involve neuroimmune signaling, neurotransmitter changes, and neuroplasticity in the brain. This study investigated the effects of gingerol-enriched ginger (GEG) on specifically anxiety-related neuroinflammation-, neuroimmunity-, neuroplasticity-, neurotransmission-, and neurotoxicity-associated genes in different brain regions, as well as on alterations linked to colonic microflora-driven dysbiosis, in the spinal nerve ligation (SNL) rat model of neuropathic pain (NP). Twenty-seven male rats were assigned to 3 groups: sham, SNL, and SNL-treated with GEG at 200 mg/kg body weight (SNL+200GEG) via oral gavage for 5 weeks. Anxiety-like behavior was assessed on the elevated plus maze (EPM). mRNA expression was assessed by qRT-PCR using respective primers. Correlation between behavioral parameters and colonic microbiome composition was analyzed using the Spearman rank correlation. The SNL+200GEG group demonstrated decreased anxiety-like behavior in the SNL model. Compared to the SNL group, the SNL+200GEG group had increased mRNA expression of NRF2 (amygdala: left), LXRα (amygdala: both sides), and CX3CR1 (amygdala: both sides, hippocampus: right). GEG modulated neuroplasticity as shown by increased gene expression of PGK1 (amygdala: right, hippocampus: both sides), MEK1 (frontal cortex: both sides), LDHA (frontal cortex: both sides), GPM6A (frontal cortex: both sides, amygdala: right, hippocampus: right, and hypothalamus), and GLUT1 (amygdala: right) as well by decreased gene expression of HIF1α (in all brain regions except for the hypothalamus). GEG modulated neurotransmission via clearance of excessive glutamate release as suggested by increased gene expression of SLC1A3 (frontal cortex: both sides, hippocampus: right) and via augmenting mGluR5 signaling as shown by increased gene expression of GRM5 (hippocampus: both sides, hypothalamus) as well as downregulation of KMO, HAAO, GRIN2B, and GRIN2C influencing downstream serotonergic neurotransmission and NMDA receptor-mediated glutamatergic pathways in different brain regions. GEG further alleviated neurotoxicity through downregulated gene expression of SIRT1, KMO, IDO1, and HAAO in different brain regions. Moreover, the increased relative abundance of Bilophila spp., accompanied by decreased time spent in the EPM open arms, suggests that increased Bilophila abundance increases anxiety-like behavior. GEG supplementation mitigated anxiety-like behavior in male rats with NP, at least in part, by reducing SNL-induced inflammatory sequelae-related mRNA gene expression in different brain regions. In addition, there is a positive correlation between the abundance of Bilophila wadsworthia and the degree of anxiety-like behavior.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Rats
*Zingiber officinale/chemistry
Male
*Neuralgia/drug therapy/microbiology
*Anxiety/drug therapy
Disease Models, Animal
*Plant Extracts/pharmacology/chemistry
Rats, Sprague-Dawley
Behavior, Animal/drug effects
Colon/microbiology
Catechols
Fatty Alcohols

@article {pmid41515410,
year = {2025},
author = {Zykova, MV and Trofimova, ES and Azarkina, LA and Lasukova, TV and Mihalyov, DA and Drygunova, LA and Danilets, MG and Ligacheva, AA and Tsupko, AV and Bashirov, SR and Belousov, MV},
title = {Pharmacological Effects of Humic Substances and Their Signaling Mechanisms.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {1},
pages = {},
pmid = {41515410},
issn = {1420-3049},
support = {056-00065-24-02//The research was supported by the State Task of the Ministry of Health of the Russian Federation/ ; },
mesh = {*Humic Substances/analysis ; Humans ; *Signal Transduction/drug effects ; Animals ; Gastrointestinal Microbiome/drug effects ; Antioxidants/pharmacology/chemistry ; },
abstract = {This comprehensive review presents the results of an in-depth analytical literature search on the biological activity of humic substances and their possible pharmacological mechanisms of action. The unique chemical structure of humic substances has determined their widespread use in many economic sectors, including medicine. Thanks to modern advances in pharmaceuticals, pharmacology, and toxicology, it has been possible to demonstrate the multifaceted biological activity of humic substances and, consequently, the possibility of using them to treat and prevent many infectious and non-infectious pathologies, including diseases considered incurable. The article presents data on their immunotropic, antibacterial, antiviral (including HIV), antitumor, antioxidant and antiradical, cardiotropic, hepatoprotective, regenerative, detoxifying, and adaptogenic effects; their influence on the intestinal microbiome; studies of the toxic properties of humic substances and the safety of their use in medicine; and the current trend of using humic substances as unique matrices for creating next-generation bionanomaterials. An analysis of data on the intracellular mechanisms that play a key role in the implementation of the effects of humic substances is conducted. Thus, the natural genesis of humic substances, their multifaceted biological activity, and the absence of toxic and allergenic properties explain the growing interest of scientists from all over the world in their study.},
}

*Humic Substances/analysis
Humans
*Signal Transduction/drug effects
Animals
Gastrointestinal Microbiome/drug effects
Antioxidants/pharmacology/chemistry

@article {pmid41515284,
year = {2026},
author = {Curca, FR and Luchian, I and Bida, FC and Virvescu, DI and Rotundu, G and Butnaru, OM and Balan, G and Surlari, Z and Georgescu, A and Pasarin, L and Budala, DG},
title = {From Diet to Oral and Periodontal Health: Exploring the Crucial Role of Nutrition-A Narrative Review.},
journal = {Nutrients},
volume = {18},
number = {1},
pages = {},
pmid = {41515284},
issn = {2072-6643},
mesh = {Humans ; *Oral Health ; *Periodontal Diseases/prevention & control/etiology ; *Diet/adverse effects ; *Nutritional Status ; Microbiota ; Dental Caries/etiology ; Feeding Behavior ; Dysbiosis ; Inflammation ; },
abstract = {Background: The growing body of evidence linking dietary factors to oral and periodontal health is characterized by substantial heterogeneity in study design, dietary assessment methods, and reported outcomes, warranting a comprehensive narrative synthesis. Diet is a key determinant of oral and periodontal health, influencing inflammation, oxidative stress, salivary composition, and the oral microbiome. Objectives: This narrative review aims to synthesize current clinical, epidemiological, and mechanistic evidence on how dietary patterns and specific nutrients affect oral and periodontal health, focusing on inflammatory pathways, microbiome modulation, nutrient-dependent tissue mechanisms, and clinical outcomes. Methods: A structured narrative search was conducted in PubMed, Scopus, Web of Science, and Google Scholar (2000-2025). Studies examining diet, nutrients, the oral microbiome, caries, gingival inflammation, or periodontal disease were screened through a multistep process, resulting in 98 included articles. Results: High-sugar and ultra-processed diets trigger inflammation and oral dysbiosis, increasing caries and periodontal susceptibility. In contrast, nutrient-rich and anti-inflammatory diets improve immune regulation, support microbial balance, and are associated with better periodontal parameters. Conclusions: Dietary habits significantly shape oral and periodontal outcomes through interconnected metabolic, microbial, and immunological pathways. Integrating targeted nutritional counseling into dental care may strengthen prevention strategies and improve long-term oral health.},
}

Humans
*Oral Health
*Periodontal Diseases/prevention & control/etiology
*Diet/adverse effects
*Nutritional Status
Microbiota
Dental Caries/etiology
Feeding Behavior
Dysbiosis
Inflammation

@article {pmid41515276,
year = {2026},
author = {Kowalczewski, PŁ and Gumienna, M and Jeżowski, P and Świątek, M and Górna-Szweda, B and Rybicka, I and Ruszkowska, M and Kluz, MI and Bordiga, M},
title = {Potato Protein-Based Vegan Burgers: Discovering the Health-Promoting Benefits and Impact on the Intestinal Microbiome.},
journal = {Nutrients},
volume = {18},
number = {1},
pages = {},
pmid = {41515276},
issn = {2072-6643},
support = {LIDER/27/0105/L-11/19/NCBR/2020//National Centre for Research and Development/ ; },
mesh = {Humans ; *Solanum tuberosum/chemistry ; *Gastrointestinal Microbiome/drug effects ; Caco-2 Cells ; HT29 Cells ; *Plant Proteins/pharmacology ; *Diet, Vegan ; Dietary Fiber/analysis ; Nutritive Value ; Glucuronidase/metabolism ; Digestion ; },
abstract = {INTRODUCTION: The increasing global interest in plant-based diets has led to the development of innovative meat analogs that not only mimic the sensory properties of traditional products but may also offer potential health benefits. In this study, we investigated the nutritional characteristics and biological activity of potato protein-based vegan burgers (PBBs) enriched with plant-derived iron and fiber sources.

METHODS: The burgers were subjected to in vitro gastrointestinal digestion, followed by evaluation of their cytotoxic potential against human intestinal cancer cell lines (Caco-2 and HT-29) and normal colon epithelial cells (CCD 841 CoN). Additionally, their influence on the intestinal microbiota composition and enzymatic activity of β-glucosidase and β-glucuronidase was assessed.

RESULTS: PBBs demonstrated favorable nutritional profiles, high protein and fiber contents, and a balanced fatty acid ratio (n-6/n-3). After digestion, bioaccessible fractions showed selective cytotoxicity toward cancer cells, while maintaining safety for normal intestinal cells. Furthermore, PBBs modulated the gut microbiota by promoting the growth of beneficial genera (Lactobacillus, Bifidobacterium) and reducing potentially harmful Enterobacteriaceae, accompanied by decreased β-glucuronidase activity.

CONCLUSIONS: These findings suggest that potato protein-based burgers could represent a functional plant-based alternative to conventional meat products, contributing to intestinal health and potentially reducing colorectal cancer risk.},
}

Humans
*Solanum tuberosum/chemistry
*Gastrointestinal Microbiome/drug effects
Caco-2 Cells
HT29 Cells
*Plant Proteins/pharmacology
*Diet, Vegan
Dietary Fiber/analysis
Nutritive Value
Glucuronidase/metabolism
Digestion

@article {pmid41515254,
year = {2026},
author = {Sujani, S and Czerwinski, KJ and Savaiano, DA},
title = {A Narrative Review: A1 and A2 Milk Beta Caseins Effect on Gut Microbiota.},
journal = {Nutrients},
volume = {18},
number = {1},
pages = {},
pmid = {41515254},
issn = {2072-6643},
support = {F.90029218.06.002//a2 milk company/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Milk/chemistry ; Animals ; *Caseins/pharmacology ; Dysbiosis ; },
abstract = {Background/Objectives: The composition and function of gut microbiome is significantly influenced by dietary factors. Growing evidence suggests that A1-type and A2-type beta casein (β-CN) may exert distinct effects on the gut environment, with implications for digestive discomfort and broader health outcomes. This review summarizes current evidence on how milk-derived A1 and A2 β-CN affect the gut microbiota. Methods: We conducted a literature search using PubMed, Web of Science, and Scopus to identify studies examining effects of milk β-CN on gut microbiota. Results: A total of eight studies were included. Results show inconsistencies within the limited number of studies. However, compared to A2, A1 β-CN was more frequently associated with dysbiosis and an increased abundance of potentially pathogenic species. Conversely, A2 β-CN promoted microbial diversity, which is linked to improved gut integrity and metabolic health. Conclusions: These findings suggest that β-CN variants distinctly influence the gut microbiota composition, and results were more significant in immunosuppressed subjects or those with other underlying health conditions, indicating that dairy products rich in A2 β-CN may offer advantages in personalized dietary management. However, well-designed human studies are essential to translate findings from rodent models to clinically relevant outcomes and future research should focus on mechanistic exploration and population-specific responses.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Milk/chemistry
Animals
*Caseins/pharmacology
Dysbiosis

@article {pmid41515240,
year = {2025},
author = {Dong, X and Lin, L and Miao, W and Zhai, Z and Hao, Y and Zhang, M and Wang, R and Ge, S and Zhang, H and Ai, L and Zhao, L},
title = {Subcellular Localization Dictates Therapeutic Function: Spatially Targeted Delivery of Amuc_1100 by Engineered Lacticaseibacillus paracasei L9 Enhances Intestinal Barrier in Colitis.},
journal = {Nutrients},
volume = {18},
number = {1},
pages = {},
pmid = {41515240},
issn = {2072-6643},
mesh = {Animals ; *Colitis/chemically induced/therapy/microbiology/drug therapy ; Mice ; *Probiotics/administration & dosage ; *Intestinal Mucosa/metabolism/microbiology ; *Lacticaseibacillus paracasei/genetics/metabolism ; Disease Models, Animal ; Macrophages/metabolism ; Mice, Inbred C57BL ; Cytokines/metabolism ; Dextran Sulfate ; Akkermansia ; },
abstract = {Background/Objectives: Impaired intestinal barrier function is a hallmark of inflammatory bowel disease (IBD). Akkermansia muciniphila and its outer membrane protein Amuc_1100 can enhance this barrier, but the clinical application of Amuc_1100 is limited by the fastidious growth of its native host. This study aimed to overcome this by utilizing the robust probiotic Lacticaseibacillus paracasei L9 for targeted Amuc_1100 delivery. Methods: We engineered Lc. paracasei L9 to express Amuc_1100 via intracellular (pA-L9), secretory (pUA-L9), and surface-display (pUPA-L9) strategies. Their efficacy was assessed in Lipopolysaccharide (LPS)-induced macrophages and a dextran sulfate sodium (DSS)-induced colitis mouse model, evaluating inflammation, barrier integrity, and mucosal repair. Results: The secretory (pUA-L9) and surface-display (pUPA-L9) strains most effectively suppressed pro-inflammatory cytokines (IL-6, IL-1β, and TNF-α) in macrophages. In mice, both strains alleviated colitis and outperformed native A. muciniphila in improving disease activity. Crucially, they exhibited distinct, specialized functions: pUA-L9 acted as a systemic immunomodulator, reducing pro-inflammatory cytokines (IL-6, IL-1β, and TNF-α), elevating anti-inflammatory mediators (IL-4 and IL-10), and promoting goblet cell differentiation; notably, the inhibitory effect of pUA-L9 on IL-6 expression was approximately 2-fold greater than that of pUPA-L9. In contrast, pUPA-L9 excelled in local barrier repair, uniquely restoring mucus layer integrity (Muc1, Muc2, and Tff3) and reinforcing tight junctions (ZO-1, Occludin, Claudin1, Claudin3, and Claudin4). In particular, pUPA-L9 increased Muc2 expression by approximately 3.6-fold compared with pUA-L9. Conclusions: We demonstrate that the subcellular localization of Amuc_1100 within an engineered probiotic dictates its therapeutic mode of action. The complementary effects of secretory and surface-displayed Amuc_1100 offer a novel, spatially targeted strategy for precision microbiome therapy in IBD.},
}

Animals
*Colitis/chemically induced/therapy/microbiology/drug therapy
Mice
*Probiotics/administration & dosage
*Intestinal Mucosa/metabolism/microbiology
*Lacticaseibacillus paracasei/genetics/metabolism
Disease Models, Animal
Macrophages/metabolism
Mice, Inbred C57BL
Cytokines/metabolism
Dextran Sulfate
Akkermansia

@article {pmid41515223,
year = {2025},
author = {Liu, Q and Gu, W and Ma, J and Wang, J and Yu, M and Xu, M and Wang, S},
title = {A Pilot Randomized Controlled Trial and Multi-Omics Analysis of Electrolysed Alkaline Water: Impacts on Gut Microbiota and Metabolic Signatures in Hyperuricemia.},
journal = {Nutrients},
volume = {18},
number = {1},
pages = {},
pmid = {41515223},
issn = {2072-6643},
support = {NA//Shanghai Kangshi Food Technology Co., Ltd., Shanghai 201103, China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Adult ; Female ; Middle Aged ; *Hyperuricemia/therapy/microbiology/metabolism/blood ; Pilot Projects ; Aged ; Quality of Life ; Young Adult ; Uric Acid/blood ; *Drinking Water/chemistry ; Adolescent ; Metabolomics ; China ; *Metabolome ; Multiomics ; },
abstract = {Background/Objectives: Hyperuricemia (HUA) is the second most common metabolic disease in China (24.5% in males, 3.6% in females), which can induce multiple complications such as gout and diabetes. Existing urate-lowering drugs have significant hepatorenal toxicity, necessitating safe lifestyle interventions. Electrolyzed alkaline water (EAW) as daily drinking water has shown preliminary effectiveness, but it lacks randomized controlled evidence and mechanistic studies at the microbiome-metabolome interface. Methods: We conducted a 12-week randomized controlled trial in 40 adults aged 18-65 years with elevated serum uric acid (SUA). Participants consumed either 1.5 L/day of EAW (pH 8.5-9.5) or purified water (pH 7.0). Clinical indicators, quality of life (SF-36), gut microbiota, and gut metabolomics were comprehensively assessed to evaluate intervention efficacy and explore potential mechanisms. Results: After 12 weeks, the EAW group exhibited a larger reduction in serum uric acid than the control group, along with improvements in selected physical health-related quality-of-life measures. Modest differences in gut microbial composition were observed between groups. Metabolomic analyses identified group-level differences in metabolites enriched in pathways related to purine metabolism and other urate-associated metabolic processes. Conclusions: This pilot randomized controlled trial suggests that consumption of EAW is associated with a modest reduction in serum uric acid. Exploratory multi-omics analyses indicate concurrent changes in gut microbiota and metabolic profiles. These findings support further investigation of electrolyzed alkaline water as a potential adjunctive, non-pharmacological option for hyperuricemia in larger and longer-term studies. Ethics: This trial was registered with the Chinese Clinical Trial Registry under the identifier ChiCTR2500100190. Ethical approval for the present study was granted by the Nankai University Institutional Review Board (NKUIRB2025001, 23 January 2025).},
}

Humans
*Gastrointestinal Microbiome/drug effects
Male
Adult
Female
Middle Aged
*Hyperuricemia/therapy/microbiology/metabolism/blood
Pilot Projects
Aged
Quality of Life
Young Adult
Uric Acid/blood
*Drinking Water/chemistry
Adolescent
Metabolomics
China
*Metabolome
Multiomics

@article {pmid41515213,
year = {2025},
author = {Marano, G and Traversi, G and Mazza, O and Caroppo, E and Capristo, E and Gaetani, E and Mazza, M},
title = {The Immune Mind: Linking Dietary Patterns, Microbiota, and Psychological Health.},
journal = {Nutrients},
volume = {18},
number = {1},
pages = {},
pmid = {41515213},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Diet, Mediterranean/psychology ; *Depression/immunology ; *Mental Health ; Probiotics/administration & dosage ; Anxiety/immunology ; Prebiotics/administration & dosage ; Adult ; *Diet ; },
abstract = {Background/Objectives: Nutritional patterns influence the gut-brain axis and immune signaling with potential consequences for depression and anxiety. We conducted a review focused on clinically meaningful psychiatric outcomes (symptom severity/diagnosis) to synthesize recent evidence (2020-2025) on Mediterranean-style dietary interventions; ultra-processed food (UPF) exposure; and psychobiotic/prebiotic strategies, integrating mechanistic insights relevant to practice. Methods: Searches in PubMed/MEDLINE, Scopus, and Web of Science (January 2020-October 2025) combined terms for diet, Mediterranean diet (MD), UPF, microbiota, probiotics, psychobiotics, depression, and anxiety. Eligible designs were randomized/controlled trials (RCTs), prospective cohorts, and systematic reviews/meta-analyses reporting clinical psychiatric outcomes in adults. We prioritized high-quality quantitative syntheses and recent RCTs; data were extracted into a prespecified matrix and synthesized narratively. Results: Recent systematic reviews/meta-analyses support that MD interventions reduce depressive symptoms in adults with major or subthreshold depression, although large, long-term, multicenter RCTs remain a gap. Exposure to UPF is consistently associated with higher risk of common mental disorders and depressive outcomes in large prospective cohorts. Psychobiotics (specific probiotic strains and prebiotics) show small-to-moderate benefits on depressive symptoms across clinical and nonclinical samples, with heterogeneity in strains, dosing, and duration. Mechanistic reviews implicate microbiota-derived metabolites (short-chain fatty acids) and immune-inflammatory signaling (including tryptophan-kynurenine pathways) as plausible mediators. Conclusions: Clinically, emphasizing Mediterranean-style dietary patterns, reducing UPF intake, and considering targeted psychobiotics may complement standard psychiatric care for depression. Future work should prioritize adequately powered, longer RCTs with standardized dietary protocols and microbiome-informed stratification to clarify responders and mechanisms.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Diet, Mediterranean/psychology
*Depression/immunology
*Mental Health
Probiotics/administration & dosage
Anxiety/immunology
Prebiotics/administration & dosage
Adult
*Diet

@article {pmid41515205,
year = {2025},
author = {Nikolaidis, CG and Gyriki, D and Stavropoulou, E and Karlafti, E and Didangelos, T and Tsigalou, C and Thanopoulou, A},
title = {Modulating the Gut Microbiome in Type 2 Diabetes: Nutritional and Therapeutic Strategies.},
journal = {Nutrients},
volume = {18},
number = {1},
pages = {},
pmid = {41515205},
issn = {2072-6643},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/therapy/diet therapy ; *Gastrointestinal Microbiome/physiology ; Probiotics/administration & dosage/therapeutic use ; Prebiotics/administration & dosage ; Dysbiosis/therapy/microbiology ; Animals ; Synbiotics/administration & dosage ; Blood Glucose/metabolism ; },
abstract = {Type 2 diabetes mellitus (T2DM) is a complex metabolic disorder influenced not only by genetics, diet, and lifestyle but also by the gut microbiota. Dysbiosis (imbalances in microbial composition) can disrupt gut barrier integrity, alter microbial metabolites, and trigger low-grade inflammation, contributing to insulin resistance and β-cell dysfunction. Nutritional interventions, such as probiotics, prebiotics, synbiotics, postbiotics, and bioactive food components, represent potential therapeutic approaches for ameliorating gut eubiosis and advancing glycemic regulation. This narrative review incorporates evidence from selected studies identified by searches in PubMed, Scopus, and Google Scholar for studies published up to November 2025. The methodology included a structured literature search of in vitro, animal, and human studies, with a focus on intervention trials and mechanistic research. There are many positive signals from randomized controlled trials (RCTs), but heterogeneity and short follow-up limit definitive recommendations. Evidence from clinical and experimental studies indicates a beneficial effect on fasting glucose, hemoglobin A1c, and inflammatory markers, though heterogeneity of the individual and the variability in study designs limit generalization. There is insufficient evidence to recommend microbiota modulation as standard therapy in any disease. Key knowledge gaps include standardized interventions, stratified analyses by medication use (e.g., metformin), clinically meaningful endpoints, and long-term safety data. This review summarizes current knowledge on gut microbiota-driven mechanisms in T2DM and evaluates emerging microbiota-targeted therapies as adjunctive strategies for metabolic improvement.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology/therapy/diet therapy
*Gastrointestinal Microbiome/physiology
Probiotics/administration & dosage/therapeutic use
Prebiotics/administration & dosage
Dysbiosis/therapy/microbiology
Animals
Synbiotics/administration & dosage
Blood Glucose/metabolism

@article {pmid41515177,
year = {2025},
author = {Odriozola, A and González, A and Odriozola, I and Corbi, F and Álvarez-Herms, J},
title = {Thyroid-Microbiome Allostasis and Mitochondrial Performance: An Integrative Perspective in Exercise Physiology.},
journal = {Nutrients},
volume = {18},
number = {1},
pages = {},
pmid = {41515177},
issn = {2072-6643},
mesh = {Humans ; *Exercise/physiology ; *Thyroid Gland/physiology/metabolism ; *Mitochondria/physiology/metabolism ; *Allostasis/physiology ; *Microbiota/physiology ; Thyroid Hormones/metabolism ; },
abstract = {Exercise acts as a physiological stimulus, requiring precise coordination among endocrine, microbial, and mitochondrial systems to maintain metabolic stability through allostatic regulation. The goal of the article is to integrate multidisciplinary evidence to characterize the thyroid-microbiome-mitochondrial axis as a key regulator of the allostatic state in athletic physiological response. During acute, chronic, and overload training phases, the thyroid-microbiome-mitochondrial axis operates bidirectionally, coupling microbial signaling with endocrine and mitochondrial networks to mediate metabolic response to exercise. This response shows interindividual variability driven by sex, age, genetics, and nutritional status, shaping the boundaries between adaptive efficiency and allostatic overload. Microbial metabolites, such as short-chain fatty acids (SCFA) and secondary bile acids, modulate deiodinase activity, bile acid recycling, and mitochondrial biogenesis through AMPK-SIRT1-PGC1α signaling, optimizing substrate use and thermogenic capacity. Thyroid hormones reciprocally regulate gut motility, luminal pH, and bile secretion, maintaining microbial diversity and mineral absorption. Under excessive training load, caloric restriction, or inadequate recovery, this network becomes transiently unbalanced: SCFA synthesis decreases, D3 activity increases, and a reversible low-T3/high-rT3 pattern emerges, resembling early Hashimoto- or Graves-like responses. Selenium-, zinc-, and iron-dependent enzymes form the redox link between microbial metabolism, thyroid control, and mitochondrial defense. In conclusion, the thyroid-microbiome-mitochondrial axis provides the physiological basis for the allostatic state, a reversible phase of dynamic recalibration that integrates training, nutrition, environmental stress, and circadian cues to sustain thyroid activity, mitochondrial efficiency, and microbial balance. This integrative perspective supports precision interventions to optimize recovery and performance in athletes.},
}

Humans
*Exercise/physiology
*Thyroid Gland/physiology/metabolism
*Mitochondria/physiology/metabolism
*Allostasis/physiology
*Microbiota/physiology
Thyroid Hormones/metabolism

@article {pmid41515166,
year = {2025},
author = {Stavrou, G and Menni, AE and Kotzampassi, K},
title = {Probiotics at the Frontline: Redefining Therapeutic Possibilities.},
journal = {Nutrients},
volume = {18},
number = {1},
pages = {},
pmid = {41515166},
issn = {2072-6643},
mesh = {*Probiotics/therapeutic use ; Humans ; *Gastrointestinal Microbiome ; },
abstract = {Recently, advances in microbiome research have emphasized the fundamental role of probiotics-in addition to their inanimate form, postbiotics, and psychobiotics, a rapidly expanding group of probiotics with psychotropic potential [...].},
}

*Probiotics/therapeutic use
Humans
*Gastrointestinal Microbiome

@article {pmid41515159,
year = {2025},
author = {Robert, M and Saha, S and Dizman, N and Rohlfs, M and Sirmans, E and Simon, J and Amaria, RN and Glitza Oliva, IC and Tawbi, HA and Davies, MA and Ikeguchi, A and Basen-Engquist, K and Schadler, K and Roth, ME and Song, W and Zhang, X and Ajami, NJ and Cohen, L and Wargo, JA and Peterson, CB and McQuade, JL and Daniel, CR},
title = {Investigating Chronic Toxicity, Diet, Patient-Reported Outcomes and the Microbiome in Immunotherapy-Treated Metastatic Melanoma Survivors: A New Frontier.},
journal = {Nutrients},
volume = {18},
number = {1},
pages = {},
pmid = {41515159},
issn = {2072-6643},
support = {na/MRA/Melanoma Research Alliance/United States ; na//Andrew Sabin Family Fellowship/ ; na//MD Anderson Melanoma Moon Shot/ ; 1P30CA016672/NH/NIH HHS/United States ; 1R01CA291965/NH/NIH HHS/United States ; 1P50CA221703/NH/NIH HHS/United States ; 1R01HL158796/NH/NIH HHS/United States ; },
mesh = {Humans ; *Melanoma/therapy/drug therapy/psychology ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; *Patient Reported Outcome Measures ; *Cancer Survivors/psychology ; *Diet ; Aged ; Adult ; *Immunotherapy/adverse effects ; Quality of Life ; *Immune Checkpoint Inhibitors/adverse effects/therapeutic use ; Depression ; Anxiety ; Prospective Studies ; Exercise ; },
abstract = {Background/Objectives: Immune checkpoint blockade (ICB) therapies have significantly improved outcomes in metastatic melanoma. However, immune-related adverse events (irAEs) and persistent chronic toxicities (CTs) among this emerging survivor population likely influence different facets of quality of life. This study characterized CT, patient-reported outcomes (PROs), diet, physical activity and gut microbiome features in a cohort of long-term survivors with a history of ICB-treated metastatic melanoma. Methods: Forty-eight patients with a history of metastatic melanoma who initiated ICB treatment at least 3 years earlier and were not currently on treatment were prospectively enrolled from a melanoma survivorship clinic. Participants completed screening questionnaires for depression, anxiety, diet and physical activity. The gut microbiome was characterized via metagenomic sequencing in a subsample (n = 39). Patients' clinicopathological characteristics and experience of irAEs (during treatment) and CT (persisting >6 months after completion of therapy) were extracted retrospectively from the medical record. Results: In the overall cohort, 60% were experiencing CT, while 16% and 20% reported clinically relevant levels of depression and anxiety symptoms, respectively. We observed significant differences in overall gut microbiome composition between survivors with and without CT (p = 0.02). Consumption of fruit and vegetables was inversely associated with anxiety (ρ = 0.3, p = 0.038). Added sugar consumption was correlated with the severity of experienced symptoms (ρ = 0.4, p = 0.003), with pronounced associations across the spectrum of symptoms, including pain, fatigue and shortness of breath (p < 0.05). Conclusions: These results suggest that CT is experienced by a substantial proportion of ICB-treated metastatic melanoma survivors. Patients experiencing CT also showed distinct microbiome features. However, additional research in prospective settings is needed to confirm these hypotheses.},
}

Humans
*Melanoma/therapy/drug therapy/psychology
Male
Female
Middle Aged
*Gastrointestinal Microbiome
*Patient Reported Outcome Measures
*Cancer Survivors/psychology
*Diet
Aged
Adult
*Immunotherapy/adverse effects
Quality of Life
*Immune Checkpoint Inhibitors/adverse effects/therapeutic use
Depression
Anxiety
Prospective Studies
Exercise

@article {pmid41515150,
year = {2025},
author = {Tonacci, A and Gorini, F},
title = {Sensory Characteristics of Probiotic-Containing Foods: A Multidisciplinary Perspective on Enhancing Acceptability and Consumer Adherence.},
journal = {Nutrients},
volume = {18},
number = {1},
pages = {},
pmid = {41515150},
issn = {2072-6643},
mesh = {*Probiotics ; Humans ; *Consumer Behavior ; *Taste ; Gastrointestinal Microbiome ; *Food Preferences ; },
abstract = {Globally, the consumption of foods containing probiotics has increased significantly due to their well-recognized health benefits, including the modulation of gut microbiota and immune function. However, despite strong scientific support, daily massive adherence to probiotic food remains limited, mainly because of their suboptimal sensory appeal and the huge variability in consumer expectations. Sensory attributes-flavor, aroma, texture, and appearance-strongly influence liking, purchase, and the habitual consumption necessary for probiotics to exert the physiological effects for which they are consumed. The present narrative review explores the complex, multidimensional interplay between sensory features, consumer perception, and probiotic efficacy. By integrating evidence from nutritional science, microbiology, sensory science, and behavioral psychology, we outline how technological innovation and sensory optimization can improve both product acceptability and adherence. We also discuss how cross-modal perception, the cultural framework, and labeling influence hedonic responses. Finally, we highlight emerging directions, such as sensory-driven strain selection, omics-based flavor profiling, and personalized sensory nutrition, as tools to bridge the gap between scientific efficacy and consumer satisfaction. Improving the sensory design of probiotic foods is pivotal to translate microbiome science into meaningful, sustainable dietary behaviors that support the nutrition-gut-immunity axis.},
}

*Probiotics
Humans
*Consumer Behavior
*Taste
Gastrointestinal Microbiome
*Food Preferences

@article {pmid41515148,
year = {2025},
author = {Kowalcze, K and Dyńka, D and Klus, W and Dudzińska, M and Paziewska, A},
title = {Modulation of Gut Microbiome and Metabolome as One of the Potential Mechanisms of Ketogenic Diet Effect in the Treatment of Epilepsy.},
journal = {Nutrients},
volume = {18},
number = {1},
pages = {},
pmid = {41515148},
issn = {2072-6643},
support = {xxx//University of Siedlce/ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; *Diet, Ketogenic ; Humans ; *Epilepsy/diet therapy/microbiology/metabolism ; *Metabolome ; Animals ; Fatty Acids, Volatile/metabolism ; Dysbiosis ; },
abstract = {BACKGROUND/OBJECTIVES: The over 100-year-old practice of using ketogenic diet (KD) in the treatment of epilepsy has consolidated its position as an effective therapeutic tool. The available publications suggest a significant influence of KD on gut microbiome and metabolome and, on the other hand, a correlation between microbiome and metabolome changes and the course of epilepsy. The conclusion is therefore justified that KD can exert a therapeutic effect in epilepsy through the mechanism of gut microbiome and metabolome modulation.

METHODS: This article is a narrative review aimed at a comprehensive analysis of the literature to gather existing evidence on the relationship between ketogenic diet, its antiepileptic effects and modulation of gut microbiome and metabolome.

RESULTS: It has been demonstrated that a ketogenic diet exerts a significant effect on intestinal bacteria and their metabolites, among other actions, increasing the Bacteroides to Firmicutes (B/F) ratio, alleviating dysbiosis, reducing the inflammatory condition in the gut and whole body, increasing the number of specific strains associated with antiepileptic effect, mediating the production of neurotransmitters (GABA, serotonin), exerting influence on the dopaminergic system, on a number of metabolic pathways, on inhibition of genotoxicity and production of short-chain fatty acids (SCFA) in the intestine.

CONCLUSIONS: Further studies are needed, since the effect of KD on gut microbiome and metabolome modulation in the treatment of epilepsy is an extremely promising and trendsetting direction of research.},
}

*Gastrointestinal Microbiome/physiology
*Diet, Ketogenic
Humans
*Epilepsy/diet therapy/microbiology/metabolism
*Metabolome
Animals
Fatty Acids, Volatile/metabolism
Dysbiosis

@article {pmid41515128,
year = {2025},
author = {Juhl, AE and Westfall, M and Hebbelstrup Jensen, B and Mirsepasi-Lauridsen, HC},
title = {Gut Microbiota in IBD: The Beneficial and Adverse Effects of Diet and Medication.},
journal = {Nutrients},
volume = {18},
number = {1},
pages = {},
pmid = {41515128},
issn = {2072-6643},
support = {4289-00312B//Innovation fonden/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Inflammatory Bowel Diseases/microbiology/drug therapy/diet therapy/therapy ; *Diet/adverse effects ; Probiotics/therapeutic use ; *Anti-Bacterial Agents/adverse effects/therapeutic use ; Crohn Disease/microbiology/drug therapy ; Diet, Western/adverse effects ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a global disease with a considerable increase in prevalence and the impact on the health and well-being of patients suffering from this condition is vast. Diet has been suspected of being a contributor to IBD severity as well as intake of antibiotics.

METHODS: A literary search was conducted on the most recent studies on the subject of IBD, diet, and medical treatment to identify high-quality research findings within this area of research. Research published within the last decade was prioritized. Studies in English language were included in the search, and the knowledge gained was synthesized in the review.

RESULTS: Dietary patterns, specifically intake of Westernized diets, were associated with increased inflammation and increased disease severity in patients suffering from IBD, specifically patients suffering from Crohn's disease (CD). A co-administration of pre- and probiotics was found to contribute to disease remission in ulcerative colitis patients, however, to a lesser extent in patients with CD. A bidirectional effect on the intestinal microbiome was seen as a result of intake of the medicines used for the treatment of IBD patients, which affects both bioavailability of the drug and efficacy of the treatment. The baseline composition of the intestinal microbiome in IBD patients dictates their response to the different treatments.

CONCLUSIONS: Diet and medical treatment both have a large impact on the architecture of the intestinal Microbiome in IBD patients and are, as such, both essential to understand to enable individualized and optimized treatment.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Inflammatory Bowel Diseases/microbiology/drug therapy/diet therapy/therapy
*Diet/adverse effects
Probiotics/therapeutic use
*Anti-Bacterial Agents/adverse effects/therapeutic use
Crohn Disease/microbiology/drug therapy
Diet, Western/adverse effects

@article {pmid41515107,
year = {2026},
author = {Thomaidis, G and Boutzikas, G and Alexopoulos, A and Zamioudis, C},
title = {Phylogenetic Divergence and Domestication Jointly Shape the Tomato Root Microbiome.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
pmid = {41515107},
issn = {2223-7747},
support = {3082//Hellenic Foundation for Research and Innovation (H.F.R.I.) under the "2nd Call for H.F.R.I. Research Projects to support Faculty Members & Researchers"/ ; },
abstract = {Domestication reduced the genetic diversity in modern crops, often resulting in reduced resilience to biotic and abiotic stress. Evidence is now accumulating that domestication also altered the structure and function of root-associated microbiomes, creating new opportunities to harness beneficial microbes for breeding and crop improvement. Using multi-region 16S rRNA sequencing, we compared the rhizosphere and endosphere bacterial communities of cultivated tomato (Solanum lycopersicum cv. Moneymaker) with six wild relatives (S. pimpinellifolium, S. huaylasense, S. peruvianum, S. chilense, S. habrochaites, and S. pennellii) spanning the main wild lineages within Solanum sect. Lycopersicon. Bacterial community structure in the rhizosphere was broadly conserved across all seven hosts, and diversity remained comparable among genotypes. Despite this overall stability, the rhizosphere microbiomes were ordered along a gradient consistent with host phylogeny, with Moneymaker clustering near S. pimpinellifolium, the four green-fruited Eriopersicon species forming a cohesive block, and S. pennellii occupying the most distinct position. Within this hierarchy, individual hosts showed specific recruitment preferences, including enrichment of Streptomycetaceae in S. pimpinellifolium, Bacillaceae in S. chilense, and contrasting patterns of nitrifiers among Eriopersicon species and S. pennellii. Differential abundance testing in the endosphere revealed consistent reductions in several bacterial families in wild accessions, alongside the enrichment of Streptomycetaceae and Rhodobiaceae in multiple wild species. Overall, our study suggests that domestication exerted a modest effect on tomato root microbiomes, while wild relatives retained microbial association traits that could be harnessed in microbiome-informed breeding to improve resilience in cultivated tomato.},
}

@article {pmid41515088,
year = {2026},
author = {Durán-Sequeda, DE and Soto-Valera, ZE and Pizarro Castañeda, R and Torres, MJ and Tobias, LS and Vergel, C and Quintero Linero, AP and Bolívar-Anillo, HJ and Amils, R and Iglesias-Navas, MA},
title = {Increased Drought Stress Tolerance in Maize Seeds by Bacillus paralicheniformis Halotolerant Endophytes Isolated from Avicennia germinans.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
pmid = {41515088},
issn = {2223-7747},
support = {BPIN 2022000100074//Sistema General de Regalias (SGR) de Colombia/ ; },
abstract = {Avicennia germinans, a representative of the marine coastal mangrove ecosystem, vital in the Colombian Caribbean, harbors a unique microbial diversity that could contain microorganisms with the potential to promote plant growth of agricultural species such as maize. The objective of this research was to evaluate A. germinans endophytes at different sampling sites and in diverse plant organs in order to identify the growth-promoting role of the most sodium chloride-tolerant endophyte found. These were then inoculated in maize seeds under drought stress conditions simulated by polyethylene glycol (PEG) in vitro. To this end, samples of adult A. germinans plants were collected from four mangrove ecosystems in the Colombian Caribbean. Several isolates were able to tolerate up to 15% NaCl (w/v), produce indole-3-acetic acid (IAA), show proteolytic activity, and inhibit phytopathogenic fungi. The best-performing strain, C1T-KM1901-B, was genomically identified as Bacillus paralicheniformis and evaluated as a bioinoculant in maize seeds under PEG-induced drought stress. Inoculation with B. paralicheniformis significantly increased germination potential and germination index of drought-resistant seeds compared to non-inoculated controls under severe drought stress conditions (40% PEG). In addition, inoculated seedlings exhibited significantly higher roots and shoot fresh and dry biomass at moderate to severe drought stress levels (15% and 20% PEG). These results are position B. paralicheniformis C1T-KM1901-B, isolated from Avicennia germinans, as a promising bioinoculant to enhance maize establishment under drought conditions.},
}

@article {pmid41515076,
year = {2026},
author = {Cano-Serrano, S and Castelán-Sánchez, HG and Oyaregui-Cabrera, H and Hernández, LG and Pérez-Pérez, MC and Santoyo, G and Orozco-Mosqueda, MDC},
title = {Assessment of Bacterial Diversity and Rhizospheric Community Shifts in Maize (Zea mays L.) Grown in Soils with Contrasting Productivity Levels.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/plants15010130},
pmid = {41515076},
issn = {2223-7747},
support = {2024-2025//CIC-UMSNH/ ; },
abstract = {The resident microbiota in agricultural soils strongly influences crop health and productivity. In this study, we evaluated the prokaryotic diversity of two clay soils with similar physicochemical characteristics but contrasting levels of maize (Zea mays L.) and wheat (Triticum aestivum L.) production using 16S rRNA gene sequencing. Yield records showed significant differences in grain production over five consecutive years. When comparing prokaryotic alpha diversity between the "non-productive" and "productive" soils, no major differences were found, and the abundance of ammonia-oxidizing archaea (AOA) and bacterial genera such as Arthrobacter, Neobacillus, and Microvirga remained consistent across soils. Analysis of the top 20 genera showing the greatest abundance shifts by compartment (bulk soil vs. rhizosphere) revealed that genera such as Priestia, Neobacillus, Sporosarcina, and Pontibacter decreased in the rhizosphere of the non-productive soil, while in the productive soil, these genera remained unchanged. In the non-productive soil, genera such as Flavisobacter decreased in abundance in the rhizosphere, whereas Arthrobacter increased. Principal coordinates analysis (PCoA) showed no clear clustering by compartment (bulk vs. rhizosphere), but two distinct clusters emerged when grouping by soil type (productive vs. non-productive). Interaction networks varied by soil type: non-productive soils showed positive Candidatus-Bacillus and negative Massilia links, while productive soils were dominated by Flavisolibacter and negative Pontibacter. Across soils, Rhizobium-Bradyrhizobium associations were positive, whereas Neobacillus and Priestia were negative. These findings highlight that a few potential beneficial microbiota and their interactions may be key drivers of soil productivity, representing targets for microbiome-based agricultural management.},
}

@article {pmid41515075,
year = {2026},
author = {Seemakram, W and Suebrasri, T and Chankaew, S and Boonlue, S},
title = {Influence of Arbuscular Mycorrhizal Fungi on Soybean Growth and Yield: A Metabarcoding Approach.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/plants15010131},
pmid = {41515075},
issn = {2223-7747},
support = {grant number B13F680065//the NSRF via the Program Management Unit for Human Resources & Institutional Development, Research and Innovation/ ; },
abstract = {This study evaluated the efficiency of arbuscular mycorrhizal fungi (AMF) in promoting the growth, yield, protein, and phytochemical contents of Glycine max cv. Morkhor 60. A completely randomized pot experiment was conducted for 90 days in non-sterile soil with nine replications. Three AMF species were tested and compared with two non-mycorrhizal controls, with and without NPK fertilizer. All AMF treatments enhanced plant growth, photosynthetic rate, and water-use efficiency compared with the unfertilized control. Inoculation with Acaulospora dilatata KKU-SK202 produced the highest pod number and increased 100-seed weight by 27.00% and 4.13% over the non-inoculated and NPK treatments, respectively. Gigaspora margarita KKU-SK210 yielded the highest total protein and phenolic contents, while A. dilatata KKU-SK401 showed the highest antioxidant activity (72.09%). Metabarcoding analysis revealed that AMF inoculation reduced root colonization by pathogenic fungi, with G. margarita KKU-SK210 and A. dilatata KKU-SK202 being the most effective. These results suggest that AMF inoculation can enhance soybean productivity and seed quality while reducing chemical fertilizer dependency and pathogenic fungal incidence.},
}

@article {pmid41515021,
year = {2025},
author = {Teng, Y and Yin, C and Xu, F and Chen, J and Wu, Q and Ye, M and Liu, Y and Zhu, K},
title = {Citrus Genotype Modulates Rhizosphere Microbiome Structure and Function Under Drought Stress.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/plants15010077},
pmid = {41515021},
issn = {2223-7747},
support = {KJQN202303518//Science and Technology Research of Chongqing Municipal Education Commission/ ; sxzybs-202201//Research Initiation Project for Doctor Recruitment of Chongqing Three Gorges Vocational College/ ; 32201766//National Natural Science Foundation of China/ ; },
abstract = {Drought stress substantially impairs citrus growth and alters the rhizosphere microbial composition; however, the role of these microbial communities in plant drought tolerance remains poorly understood. This study investigated the rhizosphere microbial structure, soil enzymatic activities, and physicochemical properties of drought-tolerant (DR) and drought-sensitive (DS) citrus varieties under drought stress conditions. High-throughput sequencing revealed that drought significantly altered microbial community composition, reducing the bacterial Shannon diversity by about 15% and enriching Gram-negative, stress-tolerant, and potentially pathogenic bacteria, as well as plant pathogenic fungi (upregulated 25.4% in DS), while reducing undefined saprotrophs (downregulated from 76.2 to 54.0% in DS). Notably, the DR variety exhibited a more stable and complex bacterial network, with 23.5% more edges and a higher proportion of positive correlations (54.3%), higher enrichment of beneficial fungi like Penicillium and Trichoderma, and unique recruitment of mycorrhizal fungi (up to 10.2%), which were nearly absent in DS. Furthermore, soil catalase and urease activities decreased under drought stress conditions. In contrast, acid phosphatase activity increased by up to 40% in DR. Correlation analyses indicated that these microbial shifts were closely associated with changes in soil nutrient availability. Our findings demonstrated that the drought-tolerant citrus variety modulates its rhizosphere microbiome towards a more cooperative and resilient state, highlighting the critical role of host-specific microbial recruitment in enhancing plant adaptation to drought stress for sustainable agriculture.},
}

@article {pmid41514971,
year = {2025},
author = {Wang, Q and Huang, J and Zhang, Y and Li, Z and Wei, L and Yin, X and Zhang, X and Zhou, Y},
title = {Long-Term Excess Nitrogen Fertilizer Reduces Sorghum Yield by Affecting Soil Bacterial Community.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/plants15010025},
pmid = {41514971},
issn = {2223-7747},
support = {the Natural Science Foundation of Chongqing (CSTB2024NSCQ-MSX0836) the Chongqing Research Institute Performance Incentive Guide Project (cstc2022jxjl80016, cqaas2020jxjl03) the Chongqing Technology Innovation and Application Development Project (cstc2019j//The research was supported by the Natural Science Foundation of Chongqing (CSTB2024NSCQ-MSX0836), the Chongqing Research Institute Performance Incentive Guide Project (cstc2022jxjl80016, cqaas2020jxjl03), and the Chongqing Technology Innovation and Ap-pli/ ; },
abstract = {The application of nitrogen (N) fertilizer is one of the most important measures to affect crop yield and soil bacterial communities. In this study, the four rates of N (namely N0F 0 kg N ha[-1], N1F 90 kg N ha[-1], N2F 180 kg N ha[-1], and N3F 270 kg N ha[-1]) along with a control (no fertilization, CK) were evaluated for their influence on sorghum yield, soil chemical properties, bacterial community, and diversity. The results showed that the yield-increasing effect was reduced by the higher dose of N input. Compared with N0F, sorghum yield increased by 58.8% in N1F and 68.2% in N2F but decreased by 8.1% in N3F relative to N2F. The soil pH decreased significantly with increasing N application. Compared with CK or N0F, N3F treatment increased the available P content by up to 18.6% or 32.2% but decreased the alkaline hydrolysis N, available K, organic matter, and total N contents by 8.4% or 23.8%, 5.5% or 10.6%, 8.4% or 28.8%, and 11.1% or 39.6%, respectively. In addition, different fertilization treatments altered the soil bacterial communities. Excess N fertilizer led to a decrease in bacterial abundance, and compared with N0F, the absolute abundance of bacteria increased by 18.7% in N1F, while it decreased by 31.8% in N3F. The predominant phyla, including Acidobacteria, Proteobacteria, and Chloroflexi, in the microbiome shift under different N application levels. The redundancy analysis (RDA) and Pearson's correlation analyses indicated that the soil properties, especially soil pH, available P, total P, total N, and organic matter, were the key environmental factors that defined the bacterial community in the ecosystem. Within the scope of the present experiment, N application at 90 kg N ha[-1] (N1F) optimized soil bacterial community abundance in sorghum-cultivated soil, while N2F (180 kg N ha[-1]) achieved the highest sorghum yield, suggesting a trade-off between optimizing the soil microbiome and maximizing crop yield under long-term fertilization.},
}

@article {pmid41514963,
year = {2025},
author = {Yoshioka, H and Morota, G and Iwata, H},
title = {Reciprocal BLUP: A Predictability-Guided Multi-Omics Framework for Plant Phenotype Prediction.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/plants15010017},
pmid = {41514963},
issn = {2223-7747},
support = {JP23KJ0506//Japan Society for the Promotion of Science/ ; JP22K21352//Japan Society for the Promotion of Science/ ; JPMJCR16O2//Japan Science and Technology Agency/ ; JPMJAN23D1//Japan Science and Technology Agency/ ; },
abstract = {Sustainable improvement of crop performance requires integrative approaches that link genomic variation to phenotypic expression through intermediate molecular pathways. Here, we present Reciprocal Best Linear Unbiased Prediction (Reciprocal BLUP), a predictability-guided multi-omics framework that quantifies the cross-layer relationships among the genome, metabolome, and microbiome to enhance phenotype prediction. Using a panel of 198 soybean accessions grown under well-watered and drought conditions, we first evaluated four direction-specific prediction models (genome → microbiome, genome → metabolome, metabolome → microbiome, and microbiome → metabolome) to estimate the predictability of individual omics features. We evaluated whether subsets of features with high cross-omics predictability improved phenotype prediction. These cross-layer models identify features that play physiologically meaningful roles within multi-omics systems, enabling the prioritization of variables that capture coherent biological signals enriched with phenotype-relevant information. Consequently, metabolome features were highly predictable from microbiome data, whereas microbiome predictability from metabolomic data was weaker and more environmentally dependent, revealing an asymmetric relationship between these layers. In the subsequent phenotype prediction analysis, the model incorporating predictability-based feature selection substantially outperformed models using randomly selected features and achieved prediction accuracies comparable to those of the full-feature model. Under drought conditions, the phenotype prediction models based on metabolomic or microbiomic kernels (MetBLUP or MicroBLUP) outperformed the genomic baseline (GBLUP) for several biomass-related traits, indicating that the environment-responsive omics layers captured phenotypic variations that were not explained by additive genetic effects. Our results highlight the hierarchical interactions among genomic, metabolic, and microbial systems, with the metabolome functioning as an integrative mediator linking the genotype, environment, and microbiome composition. The Reciprocal BLUP framework provides a biologically interpretable and practical approach for integrating multi-omics data, improving phenotype prediction, and guiding omics-based feature selection in plant breeding.},
}

@article {pmid41514871,
year = {2025},
author = {Brajdic, L and Reed, EK and Pearson, HB and Brown, HL},
title = {Cutibacterium acnes: An Emerging Prostate Cancer Pathogen.},
journal = {Biology},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/biology15010030},
pmid = {41514871},
issn = {2079-7737},
support = {A27894/CRUK_/Cancer Research UK/United Kingdom ; 02-456679//Applied Microbiology International/ ; },
abstract = {Cutibacterium acnes (C. acnes) has emerged as a potential contributor to prostate cancer (PCa) pathogenesis, yet the mechanistic basis remains unclear. This review explores the prevalence, persistence and mechanistic impact of C. acnes within the prostate to help decipher the functional consequence and diagnostic value of a C. acnes infection in this setting. We examine the evidence supporting C. acnes colonisation of both premalignant and malignant tissue, and critically evaluate how prostate tumour physiology, particularly hypoxia and low pH, may facilitate microbial persistence. Emerging data suggest that C. acnes modulates inflammatory and immune pathways, influencing macrophage activation, cytokine production, and the regulation of immune checkpoints. Additionally, we discuss studies demonstrating its involvement in DNA damage, host cell metabolism, and extracellular matrix remodelling. The identification of C. acnes in urinary and gut microbiomes, alongside the presence of its genomic DNA in extracellular vesicles in circulation indicate broad diagnostic potential. While discrepancies in methodology have hampered a consensus, recent genomic and functional studies provide new avenues to distinguish contamination from true pathogenicity. Ultimately, future research exploring whether C. acnes is a biomarker, bystander, or bona fide driver of PCa, and its potential role in personalised diagnostics are crucial to advance the field and unravel the predictive and therapeutic value of C. acnes. Clarifying this relationship will advance our understanding of microbiome-cancer dynamics and could help inform innovative early detection and screening strategies that improve patient care.},
}

@article {pmid41514803,
year = {2025},
author = {Zhu, Y and Chai, Y and Chen, S and Qian, W and Si, H and Li, Z},
title = {Distinct Rumen Microbial Features and Host Metabolic Responses in Three Cervid Species.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/ani16010116},
pmid = {41514803},
issn = {2076-2615},
support = {2023YFD1302000//National Key Research and Development Program of China/ ; U24A20434//National Natural Science Foundation of China/ ; 20240101012JJ//Natural Science Foundation of Jilin Province/ ; },
abstract = {Rumen microbiota is pivotal for nutrient metabolism and physiological adaptation in ruminants. This study investigated the rumen microbial community, fermentation parameters, and serum biochemistry of three Cervid species-Sika deer (Cervus nippon), Reindeer (Rangifer tarandus), and Milu deer (Elaphurus davidianus) (n = 5/group)-fed an identical diet. Using 16S rRNA sequencing and biochemical analyses, we found that while Bacteroidota, Firmicutes, and Proteobacteria were dominant phyla across species. Sika deer and Milu deer exhibited significantly higher microbial diversity and abundance of carbohydrate-digesting genera (e.g., Butyrivibrio, Saccharofermentans), and pathways of carbohydrate digestion and absorption, starch and sucrose metabolism compared to Reindeer. Conversely, Reindeer showed increased abundances of Lachnospiraceae ND3007 and butyrate metabolism pathway, and significantly elevated rumen volatile fatty acid concentrations, particularly acetate and butyrate. Serum profiling revealed that Milu deer had significantly higher lipid levels (CHO, TG, LDL-C) but lower total protein and AST levels compared to other species. Notably, WGCNA linked these blood lipid traits to host genes enriched in PI3K-Akt, MAPK, and bile secretion pathways. These findings demonstrate distinct species-specific rumen fermentation patterns and host metabolic adaptations, suggesting a coordinated regulation between the rumen microbiome and host genetics in Cervid.},
}

@article {pmid41514762,
year = {2025},
author = {Wei, M and Wang, S and Lin, F and Han, S and Zhang, T and Kuang, Y and Tong, G},
title = {A Hypothesis of Gut-Liver Mediated Heterosis: Multi-Omics Insights into Hybrid Taimen Immunometabolism (Hucho taimen ♀ × Brachymystax lenok ♂).},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/ani16010074},
pmid = {41514762},
issn = {2076-2615},
support = {2023YFD2400405//the National Key Research and Development Program of China/ ; NO.HSY2024Q09//the Central Public-interest Scientific Institution Basal Research Fund (HIRFRI)/ ; NO. 2023TD59//the Central Public-interest Scientific Institution Basal Research Fund (HIRFRI)/ ; },
abstract = {This study investigated the molecular and microbial factors behind the higher disease resistance of hybrid taimen by combining gut microbiome profiling with host transcriptomic analysis of intestinal and liver tissues. Both hybrid taimen and H. taimen were raised under the same recirculating aquaculture system (RAS) conditions. After recording survival rates following three enteritis outbreaks, samples of intestinal contents and tissues were collected from both groups. The gut microbiota was analyzed using full-length 16S rRNA sequencing in PacBio, and host gene expression was assessed with Illumina RNA-seq. Functional predictions were made using PICRUSt2 and Gene Set Enrichment Analysis (GSEA). Results showed that hybrids had significantly higher survival rates after enteritis (p < 0.05). Although microbial alpha diversity was similar, beta diversity revealed slight compositional differences. Hybrids showed higher levels of Hapalosiphon and Tepidimicrobium, microbes associated with antimicrobial compounds and the metabolism of short-chain fatty acids (SCFAs). Functional predictions indicated enrichment in selenocompound metabolism and ansamycin biosynthesis in hybrids. Transcriptomic analysis identified 4233 differentially expressed genes (DEGs) in the intestine and 3980 in the liver. In hybrids, intestinal tissues exhibited increased expression of immune pathways, including complement activation, lysosomal activity, and the transforming growth factor-beta (TGF-β) signaling pathway. Liver tissues demonstrated higher expression of genes related to cholesterol synthesis, fatty acid degradation, and the peroxisome proliferator-activated receptor (PPAR) signaling pathway. qRT-PCR validated the expression patterns of 20 selected DEGs. These findings tentatively suggest that the elevated disease resistance of hybrid taimen may be linked, at least in part, to a combination of microbial taxa inferred to produce antimicrobial metabolites and short-chain fatty acids, as well as an apparent intensification of intestinal immune and barrier-related gene expression, and hepatic pathways that possibly support energy supply and steroid-based immunity. However, this multi-omics data set is only correlational. We still do not know whether a single strain or a few host genes are enough to produce the resistant phenotype. Gnotobiotic trials, microbiota transplants, and targeted metabolomics will be necessary to turn these interesting associations into solid evidence.},
}

@article {pmid41514732,
year = {2025},
author = {Zhou, Y and Wu, Y and Ma, C and Ruan, X and Cha, M and Zhou, Y and Li, T and Sun, W and Liu, H},
title = {Comparative Profiling of the Fecal Bacteriome, Mycobiome, and Protist Community in Wild Versus Captive (Cervus canadensis).},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/ani16010044},
pmid = {41514732},
issn = {2076-2615},
support = {2022YFDZ0072//The 2022 Inner Mongolia Autonomous Region Key R&D and Achievement Transformation Project (Science and Technology Support for Northeast Revitalization), titled "Innovation and Promotion of Application of Deer Source Probiotic Preparation"/ ; 2023RC-Industry-Research-Institute-7//The Hohhot Science and Technology Innovation Project/ ; },
abstract = {Diet and living environments exert a profound influence on gut microbiota composition. This study presents the first comprehensive characterization of fecal bacteria, fungi, and protozoa in wild (WA) (n = 10) and captive (DA) (n = 11) wapiti (Cervus canadensis) in China. Results reveal distinct microbial profiles between the two groups. In wild wapiti, Escherichia-Shigella and UCG-005 were the dominant bacterial genera, while Succinivibrio and Treponema predominated in captive individuals. Among fungi, Agaricus and Preussia were most abundant in wild wapiti, whereas Xeromyces was identified in captive ones. For protozoa, Heteromita was the primary genus in wild wapiti, while Heteromita, Entamoeba, and Eimeria were the main genera in captive wapiti. Functional predictions further underscored these differences. In wild wapiti, bacterial and fungal functions were primarily associated with carbon metabolism and the pyruvate cycle, with mutualistic interactions prevailing among bacteria, fungi, and protozoa. Conversely, captive wapiti exhibited functional profiles centered on lipopolysaccharide and amino acid metabolism, also characterized by mutualistic coexistence among microbial communities. These findings highlight the significant impact of dietary composition on the gut microbiome. In summary, wild wapiti appear to possess a superior capacity for plant fiber utilization. These findings provide valuable data for the health management of farmed wapiti and their adaptability in natural habitats.},
}

@article {pmid41514731,
year = {2025},
author = {Fu, D and Mao, K and Zang, Y and Qu, M and Qiu, Q and Zhao, X and Ouyang, K and Li, Y},
title = {Effects of Rumen-Protected β-Alanine on Growth Performance, Rumen Microbiome, and Serum Metabolome of Beef Cattle.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/ani16010043},
pmid = {41514731},
issn = {2076-2615},
support = {No. 3230810//National Natural Science Foundation of China/ ; 20232BCJ23016//the Young Talents Training Program for Academic and Technical Leaders of Major Disciplines in Jiangxi Province/ ; CARS-37//the China Agriculture Research System of MOF and MARA/ ; },
abstract = {β-alanine has been shown to significantly improve nitrogen utilization efficiency in beef cattle, but its impact on growth performance remains unclear. This study involved 36 healthy 18-month-old Simmental crossbred bulls with similar weights (627 ± 41 kg). The cattle were divided into two groups, with each group comprising six replicates of three animals. While the control group received the basal diet, the treatment group was administered an additional 96 g/d/cattle rumen-protected β-alanine (RP-β-Ala). The study was conducted over a 35-day period, which included an initial 7 days for adaptation. At the end of the trial, body weight was recorded, and samples were collected. Results show that RP-β-Ala enhanced average daily gain (p = 0.065) and crude protein (CP) digestibility (p = 0.065) and reduced gain-to-feed ratio (p = 0.078). Analysis of rumen microbiota revealed that RP-β-Ala positively modulated the rumen microbiota by enriching beneficial genera such as Prevotella, Treponema, and Selenomonas. This enrichment increased volatile fatty acid production and nitrogen utilization efficiency, as evidenced by elevated ruminal ammonia-N and microbial CP levels, along with decreased serum urea nitrogen. Metabolomics identified key alterations in arachidonic acid metabolism, specifically the upregulation of metabolites 14,15-DiHETrE and prostaglandin D2, and enhanced antioxidative capability indicated by increased serum total antioxidant capacity (T-AOC). Concurrently, RP-β-Ala reduced serum TNF-α levels. This reduction was achieved by suppressing harmful bacteria like Thermoactinomyces and Saccharopolyspora, along with inhibiting their polyamine synthesis, specifically spermine and spermidine. Collectively, these effects alleviated oxidative stress and inflammation. These findings demonstrate that RP-β-Ala enhances beef cattle growth through improved energy supply and antioxidant capacity.},
}

@article {pmid41514654,
year = {2025},
author = {Liu, KYP and Huang, A and Pepin, C and Shen, Y and Tsang, P and Poh, CF},
title = {Oral Microbiome in Oral Cancer Research from Sampling to Analysis: Strategies, Challenges, and Recommendations.},
journal = {Cancers},
volume = {18},
number = {1},
pages = {},
doi = {10.3390/cancers18010145},
pmid = {41514654},
issn = {2072-6694},
abstract = {The oral microbiome has become an emerging focus of oral cancer research, with growing evidence linking microbial communities to disease development, progression, and prognosis. However, there is limited consensus on optimal sampling strategies, storage methods, and analytical approaches. This narrative review critically evaluates current strategies for sampling, preservation, DNA extraction, sequencing, and data analysis in oral microbiome research related to oral cancer. We compared commonly used sampling methods, including saliva, oral rinse, swab, brush, and tissue biopsy, and reviewed preservation conditions, extraction kits, sequencing platforms, and analytical pipelines reported in recent oral microbiome studies. Sampling approaches affect microbial yield and site specificity. Saliva and oral rinse samples are convenient and noninvasive but may dilute lesion-specific microbial signals, whereas lesion-directed swabbing or brushing yields greater microbial biomass and biological relevance. Preservation media and storage temperature significantly influence microbial stability, and DNA extraction methods vary in their ability to remove host DNA. Although 16S rRNA gene sequencing remains the most common approach, shotgun metagenomics offers higher resolution and function insights but is still limited by clinical applicability. Differences in data pre- and post-processing models and normalization strategies further contribute to inconsistent microbial profiles. Given that oral mucosal sites differ markedly in structure and microenvironment, careful consideration is required to ensure that collected samples accurately represent the biological question being addressed. Methodological consistency across all workflow stages-from collection to analysis-is essential to generate reproducible, high-quality data and to enable reliable translation of oral microbiome research into clinical applications for cancer detection and risk assessment. Together, these insights provide a framework to guide future study design and support the development of clinically applicable microbiome-based biomarkers.},
}

@article {pmid41514614,
year = {2025},
author = {Peddireddi, RSS and Kuchana, SK and Kode, R and Khammammettu, S and Koppanatham, A and Mattigiri, S and Gobburi, H and Alahari, SK},
title = {Role of Gut Microbiome in Oncogenesis and Oncotherapies.},
journal = {Cancers},
volume = {18},
number = {1},
pages = {},
doi = {10.3390/cancers18010099},
pmid = {41514614},
issn = {2072-6694},
abstract = {The gut microbiome has emerged as a key regulator of human health, influencing not only metabolism and immunity but also the development and treatment of cancer. Mounting evidence suggests that microbial dysbiosis contributes to oncogenesis by driving chronic inflammation, producing genotoxic metabolites, altering bile acid metabolism, and disrupting epithelial barrier integrity. At the same time, the gut microbiome significantly modulates the host response to oncotherapies including chemotherapy, radiotherapy, and especially immunotherapy, where microbial diversity and specific taxa determine treatment efficacy and toxicity. This review synthesizes current evidence on the role of the gut microbiome in both oncogenesis and oncotherapies, focusing on thirteen cancers with the strongest and most clinically relevant microbiome associations, colorectal cancer, gastric cancer, hepatocellular carcinoma, gallbladder cancer, esophageal cancer, pancreatic cancer, oral squamous cell carcinoma, cervical cancer, prostate cancer, breast cancer, lung cancer, brain cancer, and melanoma. These cancers were selected based on robust mechanistic data linking microbial alterations to tumor initiation, progression, and therapy modulation, as well as their global health burden and translational potential. In addition, we have provided mechanistic insights or clinical correlations between the microbiome and cancer outcomes. Across cancers, common microbial mechanisms included pro-inflammatory signaling (e.g., NF-κB and STAT3 pathways), DNA damage from bacterial toxins (e.g., colibactin, nitrosating species), and metabolite-driven tumor promotion (e.g., secondary bile acids, trimethylamine N-oxide). Conversely, beneficial commensals such as Faecalibacterium prausnitzii and Akkermansia muciniphila supported antitumor immunity and improved responses to immune checkpoint inhibitors. In conclusion, the gut microbiome functions as both a driver of malignancy and a modifiable determinant of therapeutic success. Integrating microbiome profiling and modulation strategies such as dietary interventions, probiotics, and fecal microbiota transplantation into oncology practice may pave the way for personalized and more effective cancer care.},
}

@article {pmid41514613,
year = {2025},
author = {Leonov, G and Starodubova, A and Makhnach, O and Goldshtein, D and Salikhova, D},
title = {Intratumoral Microbiome: Impact on Cancer Progression and Cellular Immunotherapy.},
journal = {Cancers},
volume = {18},
number = {1},
pages = {},
doi = {10.3390/cancers18010100},
pmid = {41514613},
issn = {2072-6694},
support = {КBК: 075 0110 47 2 U8 70440 621. Scientific topic code: FSSF-2025-0004.//This research was funded by Ministry of Education and Science, grant number КBК: 075 0110 47 2 U8 70440 621. Scientific topic code: FSSF-2025-0004./ ; },
abstract = {The intratumoral microbiota, comprising bacteria, fungi, and viruses within the tumor microenvironment, actively influences carcinogenesis. Key mechanisms include the induction of host DNA damage, modulation of critical oncogenic signaling pathways such as WNT-β-catenin, NF-κB, and PI3K, and the orchestration of inflammatory processes. The microbiome's interaction with the host immune system is complex and bidirectional. On one hand, specific microbes can foster a pro-tumorigenic niche by suppressing the activity of cytotoxic T cells and natural killer (NK) cells or by promoting the accumulation of immunosuppressive cell types like tumor-associated macrophages (TAMs). On the other hand, microbial components can serve as neoantigens for T cell recognition or produce metabolites that reprogram the immune landscape to enhance anti-tumor responses. The composition of this microbiome is emerging as a crucial factor influencing the outcomes of immunotherapies. Prospective investigations in cancer immunotherapy ought to prioritize mechanistic inquiry employing integrative multi-omics methodologies. The execution of meticulously designed clinical trials for the validation of microbial biomarkers, and the systematic, evidence-based development of microbiome-targeted therapeutic interventions aimed at enhancing antitumor immune responses.},
}

@article {pmid41514460,
year = {2026},
author = {Vander Elst, N},
title = {Clinical implementation of endolysins targeting gram-positive bacteria points toward a combination strategy with standard-of-care antibiotics: a selective review.},
journal = {European journal of medical research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40001-025-03655-4},
pmid = {41514460},
issn = {2047-783X},
abstract = {Endolysins, which are peptidoglycan hydrolases derived from bacteriophages, are expected to innovate antimicrobial treatment. More specifically, several endolysins that target gram-positive bacteria are currently being evaluated in clinical trials, reflecting increasing interest in their therapeutic application. Research involving endolysins has expanded exponentially over the last 20 years, which has resulted in a substantial diversification. With most of the field having focused on endolysin discovery, biochemical characterization and applying protein engineering strategies, it remains unclear whether endolysins should eventually be implemented as stand-alone antimicrobials or alongside standard-of-care antibiotics, an ambiguity that is also reflected in the endolysins that are currently being evaluated in clinical trials. This selective review, inspired by a selection of preclinical studies in which endolysin monotherapy had inconsistent outcomes, concludes that endolysins hold their greatest therapeutic potential when used in combination with standard-of-care antibiotics, except in cases, where therapy is limited to a local or topical application only. In the latter, antibiotic supplementation can negatively impact the microbiome that is essential to maintain, for example, skin, ear, eye, nasopharyngeal, gut and vaginal homeostasis. By combining endolysins with antibiotics that preferably target the bacterial cell wall or membrane, such as β-lactams, as well as lipo- and glycopeptides, synergistic or additive effects can be exploited that substantially reduce minimal inhibitory concentrations, restoring antibiotic susceptibility in otherwise resistant bacteria. Overall, this selective review asserts that endolysins may be best implemented alongside standard-of-care antibiotics, as this may lead to more consistent and reliable clinical outcomes, particularly in systemic infections.},
}

@article {pmid41514445,
year = {2026},
author = {Li, M and Zhu, S and Sun, H and Huo, Y and Cao, Q and Deng, Z and Li, K and He, Y and Lu, X and Gao, J and Xu, C},
title = {Rumen microbiota modulates metabolic stress in high-yield dairy cows: insights from early to peak lactation.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02318-0},
pmid = {41514445},
issn = {2049-2618},
support = {32402957//National Natural Science Foundation of China/ ; 32125038//National Natural Science Foundation of China/ ; BX20240417//China National Postdoctoral Program for Innovative Talents/ ; 2024M753563//China Postdoctoral Science Foundation funded project/ ; 2023YFD1801100//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Early lactation (EL) in high-yield dairy cows represents a critical lactation phase marked by significant metabolic stress, which often provokes health disorders and production losses. The rumen microbiome is instrumental in regulating host health and metabolism. However, its contribution to metabolic stress experienced by EL cows has been largely unexplored.

RESULTS: Metabolic stress was prominently observed during EL in the form of elevated oxidative stress (OS), inflammation, and lipolysis. This stress gradually decreased with the progression of lactation from day in milk (DIM) 21 to 90. To identify the underlying mechanisms, this study analyzed EL cows (DIM 32) and peak lactation (PL, DIM 72) using an integrative approach including rumen metagenomics, rumen metabolomics, host metabolomics, and their interactions. Metagenomic analysis revealed a higher abundance of methanogenic archaea (Methanobrevibacter and Methanosphaera) in EL cows, driving increased methane production and subsequent energy loss. This energy waste likely worsened the negative energy balance and caused excessive lipolysis in EL cows. In contrast, the rumen microbiota of PL cows was enriched with Prevotella species and anti-inflammatory bacterial genera (Bacteroides, Parabacteroides, and Alistipes), which are associated with the alleviation of host metabolic stress. Functional analysis of the rumen microbiota uncovered increased tryptophan biosynthesis in EL cows, driving kynurenine production. Conversely, PL cows exhibited a greater abundance of enzymes involved in tryptophan metabolism, thus facilitating the production of indole-3-acetic acid (IAA). Metabolomics analysis also identified the tryptophan metabolism pathway as a shared link between the rumen and serum. Specifically, the kynurenine pathway, associated with OS and inflammation, was upregulated in EL cows, while the indole pathway, particularly the production of IAA, was markedly elevated in PL cows, which attenuated OS and inflammation.

CONCLUSIONS: The study results indicate that the rumen microbiota is pivotal in mitigating metabolic stress in EL cows by modulating tryptophan metabolism. Specifically, the transition from EL to PL was characterized by an enhanced tryptophan-indole pathway and a suppressed tryptophan-kynurenine pathway. The results offer meaningful insights into the microbial mechanisms underlying metabolic stress and identify potential strategies for improving cow health and productivity during lactation. Video Abstract.},
}

@article {pmid41514433,
year = {2026},
author = {Yang, J and Feng, Y and Guo, T and Guo, S and Yang, M and Zhou, D and Lin, P and Wang, A and Jin, Y},
title = {The impact of rumen and hindgut microbiomes on the persistent productivity of long-lived dairy cows.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02309-1},
pmid = {41514433},
issn = {2049-2618},
support = {2023YFD1801100//National Key R&D Program of China/ ; 2022GD-TSLD-46//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2018BBF33001//The Key R&D Program of Ningxia Hui Autonomous Region/ ; },
abstract = {BACKGROUND: In high-producing dairy systems, the average productive lifespan of cows is around 2.5-4 years. Persistent productivity and longevity are key determinants of dairy cow production performance and herd profitability. Although gastrointestinal microbiota influences dairy cow productivity, the mechanisms by which host-microbiome interactions support sustained productivity in long-lived dairy cows remain unclear. Therefore, this study integrated the metagenomics and metabolomics of the rumen and rectum, along with serum and milk metabolomics, to elucidate the potential impact of the rumen and rectum microbiota on the productivity of long-lived dairy cows.

RESULTS: Serum alanine aminotransferase (ALT), alkaline phosphatase (ALP), total cholesterol (TC), and high-density and low-density lipoprotein cholesterol (HDL-C and LDL-C) levels in long-lived dairy cows were positively correlated with milk yield (MY) and elevated in long-lived high-yielding (LH) dairy cows, whereas insulin (INS) and glucagon (GCG) were negatively correlated with MY and higher in long-lived low-yielding (LL) dairy cows. Rumen propionate level was elevated in LH group and positively correlated with MY. The rumen microbiome, in LH cows upregulated pathways involved in amino acid, cofactor, and vitamin metabolism. LH cows' rumen and rectum microbial networks had cohesion and vulnerability levels similar to those of LL cows and exhibited dependence on key nodes. The rumen and rectum MY-associated purine metabolites, guanosine and D-ribose-1-phosphate, mediated 65.56% and 67.55% of the significant positive effects of Acidaminococcaceae bacterium and Parabacteroides sp. on MY, respectively. Furthermore, the specific lipid metabolism-associated rumen microbiota module enhanced serum eicosapentaenoic acid (EPA) levels by modulating rumen α-linolenic acid metabolism, thereby promoting the synthesis of Pe(20:5/0:0) in milk, which positively contributed to MY.

CONCLUSIONS: This study revealed the potential contributions of the rumen and rectum microbiota to the productivity of long-lived dairy cows via purine metabolites, as well as the potential role of the rumen microbial network module in influencing productivity through α-linolenic acid metabolism, providing new insights for nutritional management strategies aimed at improving the persistent production capacity of dairy cows. Video Abstract.},
}

@article {pmid41514203,
year = {2026},
author = {You, S and Zou, Y and Xiao, Y and He, L and Liu, L and Sun, Y and Jia, Y and Ge, G and Du, S},
title = {Animal performance and gut microbiota of cattle as affected by the unfermented or fermented total mixed ration.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04678-x},
pmid = {41514203},
issn = {1471-2180},
abstract = {Diet regulates the gut microbiota, which in turn affects animal performance, but how diet shapes the animal performance and gut microbiota remains largely unknown. To fill this gap, the author conducted a comprehensive study of the influence of total mixed ration (TMR) or fermented TMR (FTMR) on the animal performance and gut microbiome. Sixteen Simmental male cattle were randomly allocated to two treatments (one cattle per pen). The animals were fed with the TMR and FTMR diets respectively. The results showed that the contents of ADF, NDF, cellulose and total cellulose in the FTMR were significantly decreased (p < 0.05), the average daily weight gain of the Simmental male cattle shows an increasing trend (TMR: 0.31 vs. FTMR: 0.62), while no significant (p = 0.2382) difference was found between the two treatments. The metagenomics analysis showed significant (p < 0.05) difference in the α-diversity and β-diversity, and the dominant bacterial genera were Weissella, Lactiplantibacillus, Levilactobacillus and Companilactobacillus. The 16S rRNA sequencing indicated that a significant (p = 0.018) difference in the bacterial communities between the cattle fed with TMR or FTMR diet, while no significant (p < 0.05) differences were detected on the primary genus. It can be found that the FTMR diet increased the average daily gain of cattle by improving the chemical composition and microbial functional profile of the FTMR diet, and affected the growth performance of cattle.},
}

@article {pmid41514163,
year = {2026},
author = {Cullen, JT and Lawlor, PG and Cormican, P and Gardiner, GE},
title = {Profiling the bacteriome of a diet fed in meal or pelleted form, delivered as dry, wet/dry or liquid feed and its impact on the fecal and intestinal bacteriome of grow-finisher pigs.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf461},
pmid = {41514163},
issn = {1525-3163},
abstract = {Research is limited on how feed-associated microbes impact the intestinal bacteriome, growth and feed efficiency of pigs. The aims of this study were to; (1) profile the bacteriome of a meal or pelleted diet, delivered as dry, wet/dry or liquid feed using 16S rRNA gene sequencing; (2) determine its impact on the fecal and intestinal bacteriome of grow-finisher pigs; (3) investigate if differentially abundant bacterial taxa are correlated with growth parameters of these pigs. The experiment was a 2 x 3 factorial arrangement, with two factors for feed form (meal, pellets) and three factors for feed delivery (dry, liquid, wet/dry). It involved 216 Danavil Duroc x (Large White x Landrace) pigs penned in same sex pen groups of 6 pigs of similar weight (average ∼33.3 kg). Pen groups were blocked by sex and weight before being randomly assigned to 1 of 6 wheat-barley-soya-based dietary treatments in a completely randomised block design: (1) Dry meal; (2) Dry pellets; (3) Liquid meal; (4) Liquid pellets; (5) Wet/dry meal; (6) Wet/dry pellets. Diets were fed on an ad-libitum basis for 64 days. Liquid feed was prepared at a water: feed ratio of 2.5:1 (fresh matter basis). Dry feed was sampled from silos and bags and liquid feed from mixing tanks and troughs. Bacterial richness was lower in the dry pellets compared to meal (P ≤ 0.05). The liquid feed bacteriome was more diverse than that of dry feed (P ≤ 0.001). Weissella and Leuconostoc had higher relative abundance (RA) in residual-trough sampled liquid feed compared to mixing tank and fresh trough-sampled feed. The ileal bacteriome was more diverse (P ≤ 0.01) in meal-fed than pellet-fed pigs, with higher RA of Megasphaera and Mitsuokella, while Streptococcus and Escherichia-Shigella had greater RA in pellet-fed pigs (P ≤ 0.01). Lactobacillus was enriched in the intestinal digesta of liquid meal-fed pigs (P ≤ 0.05), corresponding with its predominance in this diet. Liquid meal-, liquid pellet- and wet/dry pellet-fed pigs had the highest average daily gain (P < 0.001). Feed conversion efficiency (FCE) was better in dry pellet-fed compared to liquid-fed pigs (P < 0.001). Leuconostoc (associated with feed fermentation) was most abundant in the feces and ileal digesta of liquid-fed pigs and correlated with poorer FCE (P ≤ 0.05). The same Leuconostoc found in liquid feed were also detected in the digesta and feces of liquid-fed pigs, implicating feed bacteria as a potential cause of the poorer FCE of liquid-fed pigs.},
}

@article {pmid41514147,
year = {2026},
author = {Guo, X and Dai, H and Jia, Z and Peng, Y and Lu, L and Su, Y and Li, J and Li, Q and Huang, Z and Wang, Y and Qi, F and Li, D and Lv, X and Liang, Y and Ma, B},
title = {Reactive oxygen species in the rhizosphere orchestrate the recruitment of beneficial bacteria.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {41514147},
issn = {1460-2075},
support = {42090060,42277283//the National Natural Science Foundation of China/ ; 2024SSYS0104,2021C02064-7 and 2024ZD1000603//Key Research and Development Program of Zhejiang Province (Key R&D plan of Zhejiang Province)/ ; 2024M762854//| Postdoctoral Research Foundation of China (China Postdoctoral Research Foundation)/ ; },
abstract = {Respiratory burst oxidase homolog D (RBOHD)-dependent reactive oxygen species (ROS) in Arabidopsis are well known to suppress pathogen colonization, but their influence on beneficial microbes remains unclear. Here, we found that the beneficial rhizobacterium Pseudomonas anguilliseptica was significantly less enriched in the rhizosphere of rbohD mutants than in that of wild-type plants. Conversely, elevated rhizosphere ROS levels, either triggered by pretreatment with pathogenic Dickeya solani bacteria or caused by mutations in ROS scavenging genes (e.g., in apx1 and cat2 mutants), promoted the rhizosphere recruitment of P. anguilliseptica. This promoting effect was abolished by catalase treatment. In situ microfluidic chemotaxis assays further revealed that P. anguilliseptica exhibits a chemotactic response to low concentrations of hydrogen peroxide (≤ 500 nM), accompanied by upregulated expression of chemotaxis- and motility-related genes. Notably, inoculation of P. anguilliseptica effectively suppressed D. solani-induced disease symptoms, and this protective effect was attenuated by catalase treatment. Collectively, these findings reveal a previously unrecognized role of ROS in recruitment beneficial microbiota to enhance plant growth and suppress disease symptoms.},
}

@article {pmid41513966,
year = {2026},
author = {Grübbel, H and Ly-Sauerbrey, Y and Arndt, F and Pavletić, B and Leuko, S and Rinderknecht, F},
title = {Short-time thermal inactivation of surrogates of the public transport microbiome with a low-cost thermoresistometer.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-35087-3},
pmid = {41513966},
issn = {2045-2322},
abstract = {In this study, the thermal inactivation of the bacterial genera Staphylococcus, Enterococcus and Burkholderia, which can be found in public transportation environments, as well as the bacteriophage MS2 as a surrogate for potential viral pathogens are investigated. To quantify the thermal inactivation characteristic, an automated and inexpensive thermoresistometer is constructed and set up, which enables the microorganisms to be exposed to short-term thermal shocks. The time dependent temperature curves were measured to account for heat-up and cooling times. Afterwards, the microorganisms were exposed to temperatures in the range of [Formula: see text] to [Formula: see text] for durations of 2 s up to 10 s and the thermal inactivation of the respective microorganisms was measured by counting colony forming units (CFU) and plague forming units (PFU). The data was visualized and fitted to an analytical thermodynamic model based on a first-order reaction and the Arrhenius equation to predict thermal inactivation times. This study reports the first measured thermal inactivation values for E. viikkiensis and B. lata, which have not been studied before. The results for MS2 and S. capitis show significantly shorter inactivation times than previous experiments. After exposure to [Formula: see text] for 2 s there was no measurable survival of all tested microorganisms. The semi-automated test setup used allows for consistent measurements and can be adapted by other research groups.},
}

@article {pmid41513795,
year = {2026},
author = {Wadia, R},
title = {Microbiome signatures in cancer.},
journal = {British dental journal},
volume = {240},
number = {1},
pages = {42},
doi = {10.1038/s41415-025-9491-8},
pmid = {41513795},
issn = {1476-5373},
}

@article {pmid41513699,
year = {2026},
author = {Veerus, L and Subrahmanian, A and Blaser, MJ},
title = {The testobolome in microbial testosterone metabolism and human health.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {9},
pmid = {41513699},
issn = {2055-5008},
support = {NIH U01AI22245/NH/NIH HHS/United States ; },
mesh = {*Testosterone/metabolism ; Humans ; *Gastrointestinal Microbiome/physiology ; *Bacteria/metabolism/classification/genetics ; },
abstract = {We propose the term testobolome, analogous to the estrobolome, to describe gut bacteria that metabolize testosterone. Testosterone undergoes microbial transformations similar to estrogens, potentially influencing host hormone homeostasis and health. This review defines the testobolome, identifies its known members, and explores mechanisms that are shared or distinct from the estrobolome. We outline a framework for future research into microbiome-mediated steroid metabolism, including its role in aging and hormone-driven diseases.},
}

*Testosterone/metabolism
Humans
*Gastrointestinal Microbiome/physiology
*Bacteria/metabolism/classification/genetics