@article {pmid41062341,
year = {2025},
author = {Xia, S and Jia, D and Wang, L},
title = {Microbiota: a dawn for cancer metastasis therapy.},
journal = {Trends in molecular medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molmed.2025.09.008},
pmid = {41062341},
issn = {1471-499X},
abstract = {Metastasis remains a major contributor to the poor prognosis for patients with cancer, primarily driven by dynamic interactions between cancer cells and the tumor microenvironment. Accumulating evidence highlights the pivotal involvement of both gut microbiota and intratumoral bacteria in cancer progression and metastatic spread. Here, we review the intricate links between microbiota and cancer metastasis, elucidating the multifaceted mechanisms by which microbial communities modulate metastatic processes. We particularly focus on the role of microbial metabolites in cancer dissemination and discuss innovative therapeutic strategies targeting the microbiome. Targeting the gut microbiota and intratumoral microecology presents a promising avenue for novel interventions aimed at mitigating cancer metastasis.},
}

@article {pmid41062001,
year = {2025},
author = {Ghaffar, T and Valeriani, F and Romano Spica, V},
title = {The Sex Related Differences in Health and Disease: A Systematic Review of Sex-Specific Gut Microbiota and Possible Implications for Microbial Pathogenesis.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108094},
doi = {10.1016/j.micpath.2025.108094},
pmid = {41062001},
issn = {1096-1208},
abstract = {BACKGROUND: The gut microbiota, a complex ecosystem influenced by various physiological and environmental factors, has been increasingly recognized for its role in health and disease. Emerging evidence suggests that sex differences, particularly mediated by sex hormones and physiological variations, significantly influence the composition and diversity of the gut microbiome. This systematic review aimed to evaluate and synthesize the current knowledge on sex-related variations in gut microbiota across human and animal studies.

METHODS: We conducted a systematic review of 24 eligible studies, selected from an initial 13,205 articles, focusing on healthy populations and next-generation sequencing-based microbiota profiling in both humans and animal models.

RESULTS: The results reveal sex-specific differences in microbial diversity and taxa abundance; however, the consistency and significance of these findings vary across studies, with females generally exhibiting higher levels of Akkermansia and Bifidobacterium, while males showed increased levels of Prevotella and Escherichia. These findings suggest that sex may be a contributing, but not necessarily dominant, biological variable shaping microbiome architecture across various species, including mice, pigs, deer, and humans, and highlight the influence of hormonal fluctuations, body composition, and lifestyle factors on gut microbial ecosystems.

CONCLUSION: Our findings underscore the importance of considering sex as a key biological variable in microbiome research and its potential implications for disease susceptibility, therapeutic interventions, and microbiome-targeted strategies in microbial pathogenesis. Moreover, evidence from human studies remains limited, especially those using 16S rRNA gene sequencing, which may lack the resolution to detect strain-level or functional differences. Incorporating multi-omics approaches such as metagenomics, metatranscriptomics, and metabolomics may offer deeper insights into sex-dependent microbial dynamics.However, these implications remain largely associative and require mechanistic validation in future studies.},
}

@article {pmid41061857,
year = {2025},
author = {Massey, WJ and Brown, JM},
title = {Microbe-Derived Cyclopropane Lipids Activate Host Nuclear Receptors.},
journal = {Journal of lipid research},
volume = {},
number = {},
pages = {100923},
doi = {10.1016/j.jlr.2025.100923},
pmid = {41061857},
issn = {1539-7262},
}

@article {pmid41061735,
year = {2025},
author = {Marsella, R},
title = {Theories and mechanisms of environmental factors that cause allergies in dogs: veterinarian involvement in lifestyle choices to support long-term well-being.},
journal = {American journal of veterinary research},
volume = {},
number = {},
pages = {1-10},
doi = {10.2460/ajvr.25.07.0275},
pmid = {41061735},
issn = {1943-5681},
abstract = {Over the last few decades, the occurrence of chronic inflammatory and allergic disorders has increased exponentially in people and pets. Changes in our environment impact both human and animal health, as One Health recognizes. Several theories have been proposed, and various mechanisms have been considered. The first was the "hygiene hypothesis," which focused on the observation that allergies became more common once hygienic conditions improved. Although the concept that allergies happen because living conditions are too clean has been mostly disproven, parts of it are included in the "old friends hypothesis," which emphasizes the importance of exposure to harmless bacteria through food and the environment that have evolved with us. A further refinement of this idea is incorporated in the "biodiversity hypothesis," which emphasizes the importance of diverse environmental, food, and microbial exposures in educating the immune system and promoting tolerance. The most recent hypothesis is the "epithelial barrier hypothesis," which emphasizes the role of pollutants and chemicals that chronically disrupt epithelia, whether in the skin, gut, or respiratory tract, promoting low-grade inflammation and increasing the risk of allergic sensitization. Each of these theories has focused on the role of urbanization in promoting allergies, and each theory has some supporting evidence. Numerous epidemiological studies, addressed in the companion Currents in One Health by Marsella, JAVMA, forthcoming 2025, demonstrated that urban life increases the risk for allergies in people and dogs. The purpose of this review is to present the current knowledge in dogs and raise awareness regarding these topics.},
}

@article {pmid41061417,
year = {2025},
author = {Hundam, S and Al-Zghoul, MB and Mayyas, M and Dahadha, R},
title = {In ovo isoquinoline alkaloid injection alters gut microbiota and improves tight junction gene expression in broiler chickens.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {105921},
doi = {10.1016/j.psj.2025.105921},
pmid = {41061417},
issn = {1525-3171},
abstract = {In ovo feeding (IOF) is a modern technique that involves injecting beneficial substances into bird eggs prior to hatching, aiming to enhance poultry health and productivity. This study investigated the effects of in ovo injection of isoquinoline alkaloid (IQ) on hatchability, early growth performance, jejunal tight junction gene expression (OCLN, CLDN-1, and ZO2), and cecal microbiome composition in broiler chickens. A total of 460 Indian River hatching eggs were incubated and randomly assigned to either a control group (CON) or an IQ-injected group (INOVO) at a dose of 150 µg/egg. Post-hatch growth parameters, body temperature, jejunal tight junction gene expression, and cecal microbial profiles were studied. In ovo IQ injection did not significantly affect hatchability or alpha diversity indices; however, it led to a transient increase in body weight during the early post-hatch period (days .3-7 post-hatch). Beta diversity analysis showed significant differences in microbial community composition between the groups. Notably, the relative abundance of beneficial taxa, such as Lactobacillaceae and Lactobacillus, was significantly higher in the INOVO group. Furthermore, in ovo IQ injection significantly increased jejunal expression of OCLN and ZO2. These findings suggest that in ovo IQ administration may enhance early growth, promote beneficial microbial colonization, and strengthen intestinal barrier function without compromising hatchability, offering a natural approach to improve poultry performance.},
}

@article {pmid41061376,
year = {2025},
author = {Wekking, D and Ende, TVD and Bijlsma, MF and Vidal-Itriago, A and Nieuwdorp, M and van Laarhoven, HWM},
title = {Fecal microbiota transplantation to enhance cancer treatment outcomes across different cancer types: A systematic literature review.},
journal = {Cancer treatment reviews},
volume = {140},
number = {},
pages = {103025},
doi = {10.1016/j.ctrv.2025.103025},
pmid = {41061376},
issn = {1532-1967},
abstract = {BACKGROUND: The gut microbiome is increasingly recognized as a critical modulator of cancer therapy response. This systematic review evaluates Fecal Microbiota Transplantation (FMT)'s impact on cancer treatment outcomes and treatment-related toxicity and explores its mode of action.

METHODS: A systematic search was conducted for prospective or retrospective clinical studies published until May 2025 that investigated FMT in cancer patients undergoing immunotherapy, chemotherapy, radiotherapy, targeted therapy, or a combination regimen.

RESULTS: 45 studies were included. No large-scale RCTs with published efficacy data were available, and most findings were derived from studies that lacked statistical power to assess efficacy. The majority of the articles demonstrated the safety and feasibility of FMT. Most toxicities reported were grade 1 or 2. Mechanistically, donor FMT restores gut microbiota diversity and reprograms the gut ecosystem, with increases in tumor-infiltrating lymphocytes and lower levels of regulatory T cells being observed. Furthermore, studies reported clinical improvement and endoscopic and/or histologic remission of treatment-induced colitis following FMT, alongside decreased colonic CD8+ T cell infiltration.

CONCLUSION: Donor FMT appears to be a safe and feasible adjunctive strategy during both first and later-line therapy and has potential for managing treatment-related colitis; however, its efficacy and its role in preventing immune-related adverse events remain to be elucidated in RCTs, as well as its application for graft-versus-host disease. The variability in clinical outcomes and context-dependent microbiota-host interactions that result in inconsistent findings underscores the complexity of FMT as a therapeutic modality. Furthermore, subclassifying recipient cancer patients could (based on gut microbiome ecosystem features) enhance biomarker identification for treatment responses.},
}

@article {pmid41061330,
year = {2025},
author = {Noll, J and Roosen, H and Fritzenwanker, M and Amati, AL and Braun, J and Schneider, M and Padberg, W and Hecker, A and Reichert, M},
title = {Perioperative multidrug-resistant bacteria impair clinical outcome after pancreatic surgery: Missed targets of antibiotic prophylaxis.},
journal = {Surgery},
volume = {188},
number = {},
pages = {109717},
doi = {10.1016/j.surg.2025.109717},
pmid = {41061330},
issn = {1532-7361},
abstract = {BACKGROUND: Multidrug-resistant bacteria represent major concerns in perioperative medicine. The extent to which preoperative colonization and postoperative detection of multidrug-resistant bacteria affect outcome in pancreatic surgery is largely unknown. Microbiome analyses provide insights into appropriate perioperative antibiotic prophylaxis.

METHODS: This was a retrospective, single-center cohort study of patients who underwent elective pancreatic surgery between January 2018 and December 2022 with a complete set of preoperative screening swabs.

RESULTS: Of 212 patients, n = 168 (79.25%) were classified as multidrug-resistant negative, whereas 44 (20.75%) were tested multidrug-resistant positive perioperatively. Among these, 19 had preoperative detection of multidrug-resistant bacteria and 25 had postoperative detection of multidrug-resistant bacteria. No differences in baseline characteristics were observed. Inflammatory parameters, including blood leukocytes and C-reactive protein, were elevated perioperatively in patients who were multidrug-resistant positive. Postoperative outcomes were significantly impaired in patients who were multidrug-resistant positive compared with those who were multidrug-resistant negative, including greater rates of pancreatic fistula (grade B/C), postpancreatectomy hemorrhage, and reoperation (all P < .0001). Major complication rates, length of intensive care, and in-hospital stay were increased (all P < .0001). Progression of pancreatic fistula to hemorrhage and reoperation was particularly high in patients who were multidrug-resistant positive (37.84% vs 3.92%; P < .0001). Subgroup analyses revealed no differences in postoperative outcomes between patients who were preoperatively tested multidrug-resistant positive and those who were postoperatively tested multidrug-resistant positive. High intrinsic or acquired bacterial resistance rates were observed against commonly used perioperative antibiotics in pancreatic surgery, including metronidazole/second-generation cephalosporins or piperacillin/tazobactam.

CONCLUSION: Both preoperative and postoperative colonization with multidrug-resistant bacteria have deleterious effects on postoperative outcomes. Pancreatic fistula is a crucial cause for severe morbidity in patients who are multidrug-resistant positive. Preoperative decolonization, broad-spectrum perioperative antibiotic prophylaxis, and continued postoperative antibiotics should be considered for high-risk pancreatic surgery patients.},
}

@article {pmid41061172,
year = {2025},
author = {Niu, M and Arshad, U and Islam, MZ and Barrientos-Blanco, MA and Slack, E and Giannoukos, S and Zenobi, R},
title = {Breathprints of the Barn: The Future of Livestock Research and Monitoring with Exhalomics.},
journal = {Annual review of animal biosciences},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-animal-030424-085944},
pmid = {41061172},
issn = {2165-8110},
abstract = {Livestock farming faces increasing demands for sustainability and improved animal welfare. Noninvasive approaches for monitoring animal health and physiology are of growing interest. Exhaled breath analysis, or exhalomics, has emerged as a promising tool for detecting volatile organic compounds and gases associated with metabolism, disease states, physiological processes, and microbiome in livestock. This review synthesizes current advancements in breath sampling and analytical technologies and evaluates applications in disease diagnostics, nutritional assessment, and physiological and microbial profiling across livestock species. Although progress is evident, key challenges remain, including sampling variability, incomplete metabolite annotation, and limited scalability for field use. Future efforts should prioritize standardizing protocols; expanding livestock-specific spectral libraries; and developing affordable, real-time sensors for on-farm deployment. Integrating exhalomics with multi-omics and artificial intelligence-driven analytics holds potential to enable earlier disease detection, improve production efficiency, and reduce environmental impacts, ultimately advancing precision livestock farming and animal welfare over the coming decade.},
}

@article {pmid41061126,
year = {2025},
author = {Thomazella, DPT and Pereira, LB and Teixeira, PJPL},
title = {Understanding microbiome shifts and their impacts on plant health during pathogen infections.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiaf498},
pmid = {41061126},
issn = {1532-2548},
abstract = {Pathogen infections can drastically reshape plant-associated microbiomes, yet the mechanisms underlying these shifts and their consequences for plant health remain elusive. In this review, we integrate recent advances to delineate how pathogen attack drives both local and systemic microbiome restructuring via three major processes: (i) collateral effects of the plant immune system, including alterations to the local physicochemical niche; (ii) active recruitment of beneficial microbes through pathogen-induced root exudates (primary and secondary metabolites, volatiles and organic compounds); and (iii) pathogen-mediated manipulation of the host microbiome through microbial effectors, antimicrobial production, or niche competition. By contrasting adaptive outcomes (enrichment of disease-suppressive taxa) with detrimental consequences (dysbiosis, mutualist loss or proliferation of disease-promoting microbes), we emphasize the need for time-resolved, mechanistic studies that move beyond correlative surveys. Although the enrichment of protective microbes is a recurring theme in current literature, it is important to recognize that not all microbiome shifts are adaptive or host-directed. Considering alternative explanations is critical to avoid survivorship bias and to accurately interpret microbiome dynamics in the context of plant-pathogen interactions. Building on these insights, we discuss the rational design of microbiome-based interventions to enhance crop resilience, including synthetic microbial consortia and elicitor-mediated recruitment of beneficial microbes. Notably, integrating microbiome dynamics into plant pathology offers a promising path toward sustainable disease management, transforming the microbiome from a passive background into an active, designable component of plant immunity.},
}

@article {pmid41061000,
year = {2025},
author = {Cummings, CL and Landreville, KD and Kuzma, J},
title = {Public perceptions and support for introduced microbes to combat hospital-acquired infections and antimicrobial resistance.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0332578},
doi = {10.1371/journal.pone.0332578},
pmid = {41061000},
issn = {1932-6203},
mesh = {Humans ; *Cross Infection/prevention & control/microbiology ; Female ; Adult ; Male ; Middle Aged ; *Microbiota ; *Public Opinion ; Surveys and Questionnaires ; Aged ; Young Adult ; *Drug Resistance, Microbial ; Adolescent ; United States ; },
abstract = {Hospital-acquired infections and antimicrobial resistance (AMR) remain major global health threats, prompting interest in microbiome-based interventions that introduce beneficial microbes or genetic interventions to control pathogens and reduce AMR genes in hospital environments. Microbiome engineering, which can use advanced biotechnology, genetics, and microbial ecology principles to restructure microbial communities, is a rapidly growing field with applications in infection control. As researchers explore deploying beneficial microbes and other genetic interventions in clinical settings like hospital sinks, public perception becomes critical to responsible implementation. This study addresses how U.S. adults perceive microbiome evaluation, and education. Drawing on a nationally representative survey (N = 1,000), we conducted hierarchical ordinary least squares regression modeling to assess predictors of support across three domains: implementation of introduced microbiomes (IM), rigorous testing, and education for healthcare stakeholders. Results demonstrate that support for IM in hospital sinks is shaped less by demographic traits and more by emotional responses, trust in institutional efficacy, belief in intervention benefits, and a desire to learn about microbiome science. These findings advance previous knowledge by distinguishing cognitive, affective, and contextual predictors across distinct types of support. Contrary to expectations, prior familiarity and information-seeking were negatively associated with IM support, suggesting that some engagement or exposure to risk-framing may drive skepticism. Meanwhile, emotional reactions and perceived efficacy consistently predicted support for IM, testing, and education (i.e., across all dependent variables), underscoring the need to address affective and trust-based components of public engagement. This research contributes to an emerging empirical foundation for responsible microbiome innovation by grounding the analysis in the Responsible Research and Innovation (RRI) framework. With the technology still in early development, these insights provide critical guidance for biotechnology developers, policymakers, and hospital leaders seeking to align microbiome engineering with societal values through transparent communication, rigorous oversight, and inclusive education.},
}

Humans
*Cross Infection/prevention & control/microbiology
Female
Adult
Male
Middle Aged
*Microbiota
*Public Opinion
Surveys and Questionnaires
Aged
Young Adult
*Drug Resistance, Microbial
Adolescent
United States

@article {pmid41060906,
year = {2025},
author = {Sawyer, FM and Stossi, F and Nachman, E and Britton, RA and Bolt, MJ and Mancini, MA and Estes, MK and Blutt, SE},
title = {A pipeline for rapid, high-throughput imaging and quantitative analysis of human intestinal organoids.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0332418},
doi = {10.1371/journal.pone.0332418},
pmid = {41060906},
issn = {1932-6203},
mesh = {Humans ; *Organoids/cytology/metabolism ; *Intestinal Mucosa/cytology ; *High-Throughput Screening Assays/methods ; Microscopy, Confocal/methods ; Image Processing, Computer-Assisted/methods ; *Intestines/cytology ; Cell Proliferation ; },
abstract = {Human intestinal organoids (HIOs) are a model system for studying human intestinal epithelium. Utilizing HIOs for high-throughput studies remains inefficient, as analyzing their cellular composition and responses to varying experimental conditions requires extensive time and labor. We describe a 96-well plate-based automated pipeline for rapidly imaging and quantifying fluorescent labeling in HIOs using a high-throughput confocal microscope and image analysis software. The pipeline was leveraged to quantify varying levels of cell proliferation among donor HIO lines in response to microbial products. Cytoplasmic fluorescence via antibody labeling was also quantified with the pipeline, enabling measurement of the prevalence of specific cell types in HIOs. This platform offers a novel approach to efficiently and rapidly image and quantify fluorescent staining and immunolabeling in HIOs and has many potential applications, including drug screening, toxicity testing, intestinal barrier integrity and transport studies, microbiome and host-pathogen interaction studies, and lineage tracking.},
}

Humans
*Organoids/cytology/metabolism
*Intestinal Mucosa/cytology
*High-Throughput Screening Assays/methods
Microscopy, Confocal/methods
Image Processing, Computer-Assisted/methods
*Intestines/cytology
Cell Proliferation

@article {pmid41060905,
year = {2025},
author = {Xu, L and Hu, Z and Zhang, X and Zhang, S and Li, W and Wang, M and Ning, R and Guo, W},
title = {Captivity-driven microbiota reshaping: A cross-species analysis of divergent patterns in the gut microbiota of giant pandas (Ailuropoda melanoleuca), red pandas (Ailurus fulgens), and Asiatic black bears (Ursus thibetanus).},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0332481},
doi = {10.1371/journal.pone.0332481},
pmid = {41060905},
issn = {1932-6203},
mesh = {Animals ; *Ursidae/microbiology ; *Gastrointestinal Microbiome/genetics ; *Ailuridae/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Species Specificity ; Bacteria/genetics/classification ; },
abstract = {The relative influence of diet, host phylogeny, and environment on animal gut microbiota remains unresolved, particularly for endangered ursids lacking quantitative data. Here, we systematically evaluated the drivers of gut microbial assembly in captive versus wild giant pandas (Ailuropoda melanoleuca), red pandas (Ailurus fulgens), and Asiatic black bears (Ursus thibetanus) using 16S rRNA V4 sequencing. Compared with wild cohorts, captive giant pandas exhibited significantly reduced α-diversity (P < 0.05), whereas captive red pandas and black bears showed significant increases (P < 0.05). Weighted UniFrac-based β-diversity analysis revealed that intra-species distances between captive and wild individuals exceeded those observed between species within either habitat (P < 0.001), indicating profound community restructuring under captivity. At the phylum level, captive animals were dominated by Firmicutes (68.6 ± 23.0%), in contrast to Proteobacteria dominance in wild populations (81.2 ± 17.6%). Genus-level shifts included an enrichment of Sarcina in captive bears and Streptococcus and Escherichia-Shigella in captive pandas, whereas wild bears and pandas were predominantly enriched in Burkholderia and Pseudomonas, respectively. PERMANOVA attributed 21.6% of community variance to environment (F = 23.62), compared to 12.3% for host phylogeny (F = 6.75) and 3.9% for diet (F = 4.32). These findings demonstrate that captive management is the primary determinant of gut microbiota divergence in giant pandas, red pandas, and Asiatic black bear provide microbiome-based guidance for improving captive husbandry and reintroduction success.},
}

Animals
*Ursidae/microbiology
*Gastrointestinal Microbiome/genetics
*Ailuridae/microbiology
RNA, Ribosomal, 16S/genetics
Phylogeny
Species Specificity
Bacteria/genetics/classification

@article {pmid41060894,
year = {2025},
author = {Rosas-Plaza, S and Mainou, L and Delgado, G and Morales, R and Aguilar-Romero, A and Escalante, AE and Cerritos, R},
title = {Microbiome characterization of a pre-Hispanic man from Zimapán, Mexico: Insights into ancient gut microbial communities.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0331137},
doi = {10.1371/journal.pone.0331137},
pmid = {41060894},
issn = {1932-6203},
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/genetics ; Mexico ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Phylogeny ; Mummies/microbiology ; },
abstract = {The research of microbiome derived from mummified human remains, coprolites and paleofeces has gained significant interest over several decades, aiming to elucidate the evolution of microbial interactions and shed light on the lifestyles of past populations. In this study, we analyzed the gut microbiome of a pre-Hispanic male individual referred to as the Zimapán man, dated to 936 BP, discovered on the border between Mesoamerica and Aridoamerica. Employing high-throughput 16S rRNA gene sequencing on both the paleofeces and mummified intestinal tissue, we conducted a comprehensive characterization of the Zimapán man's gut microbiome. The bacterial community was described, and a weighted UniFrac-based principal coordinates analysis (PCoA) was performed. The multivariate analysis incorporated microbiome samples from diverse environments, such as soils, compost, and both contemporary and ancient human gut microbiota. The analysis revealed bacterial groups associated with the human microbiome, including families such as Peptostreptococcaceae, Clostridiaceae, Enterobacteriaceae, and Enterococcaceae. Notably, a high abundance of the Clostridiaceae group was found, similar to those discovered in the intestinal tissue of mummies from other geographic regions. Additionally, unique groups such as Romboutsia hominis, exclusively isolated from human intestines and not previously reported in ancient human microbiomes, were identified. Furthermore, our analysis demonstrated that the bacterial composition did not resemble soil and compost environments. This initial characterization successfully achieved the goal of identifying bacterial groups of the gut microbiome in the Zimapán samples. Consequently, this study contributes to the ongoing expansion of knowledge regarding ancient microbiomes across diverse temporal, historical, geographical, and environmental contexts.},
}

Humans
Male
*Gastrointestinal Microbiome/genetics
Mexico
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
Phylogeny
Mummies/microbiology

@article {pmid41060694,
year = {2025},
author = {Herman, R and West, DT and Meaden, S and Khan, I and Cornmell, R and Hunt, J and Rudden, M and Wilkinson, HN and Hardman, MJ and Wilkinson, AJ and Murphy, B and Thomas, GH},
title = {High-resolution Staphylococcus profiling reveals intra-species diversity in a single skin niche.},
journal = {Microbial genomics},
volume = {11},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001531},
pmid = {41060694},
issn = {2057-5858},
mesh = {*Skin/microbiology ; Humans ; *Microbiota/genetics ; Staphylococcus epidermidis/genetics/isolation & purification/classification ; *Staphylococcus/genetics/classification/isolation & purification ; Whole Genome Sequencing ; Phylogeny ; Genome, Bacterial ; Staphylococcus hominis/genetics/isolation & purification/classification ; Staphylococcus capitis/genetics/isolation & purification/classification ; Genetic Variation ; },
abstract = {The skin microbiome is dominated by a few key genera, among which Staphylococcus is one of the most well characterized. Recent studies have examined the roles of various Staphylococcus species such as Staphylococcus epidermidis and Staphylococcus hominis within broader skin microbial communities. However, these investigations often rely on isolates from multiple individuals and hence limit their ability to capture intra-community interactions. In this study, we focused on the axillary microbiome of a single healthy individual to characterize the genetic and functional diversity of resident Staphylococcus isolates. Using a low-cost, high-throughput DNA extraction and long-read whole-genome sequencing pipeline, we generated complete genomes for 93 isolates spanning 7 genetically distinct lineages across 3 major skin species. These comprised one dominant and three additional lineages of S. epidermidis, two of S. hominis and one of Staphylococcus capitis. Functional and metabolic analyses revealed species- and strain-specific features, suggesting potential metabolic cross-feeding and specialization within this community, including within strains of S. epidermidis. These findings highlight the metabolic complexity and potential interdependence of staphylococci inhabiting a single skin site and the need for strain-level resolution of the community. The strains form part of the York Skin Microbiome (YSM) collection, a growing open biobank of genetically diverse skin isolates from matched individuals.},
}

*Skin/microbiology
Humans
*Microbiota/genetics
Staphylococcus epidermidis/genetics/isolation & purification/classification
*Staphylococcus/genetics/classification/isolation & purification
Whole Genome Sequencing
Phylogeny
Genome, Bacterial
Staphylococcus hominis/genetics/isolation & purification/classification
Staphylococcus capitis/genetics/isolation & purification/classification
Genetic Variation

@article {pmid41060578,
year = {2025},
author = {Zorzi, VSG and Ramos, JV and Conrad, NL and Piraine, REA and Santos, FDS and Leite, FPL},
title = {Lacticaseibacillus casei CB054 short-term supplementation effect on murine splenocyte cytokine transcription and the gut bacterial microbiota.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {41060578},
issn = {1678-4405},
abstract = {Immunomodulation by Lacticaseibacillus sp. is a subject of increasing interest; however, the time-period of administration for its immunomodulatory effect to occur is not well established. In the present study, we examined the effect of L. casei CB054 on cytokine transcription ex vivo in mouse splenocytes and the bacterial microbiota profile at 24, 48, and 72 h after oral administration of 1 × 10[6] UFC/g viable L. casei. Cytokine mRNA transcription was evaluated for IL4, IL10, IL12, IFNɣ, and TNFα at different time points by qPCR. Microbiota was analyzed using fecal samples collected at zero, 24, 48, and 72 h after L. casei administration. A significant upregulation (p < 0.05) for IL10 at 72 h and IL12 at 48 and 72 h in supplemented groups was observed. IFNɣ and TNFα showed similar significant upregulation patterns (p < 0.05) at all time points evaluated, whereas IL4 showed significant transcriptional downregulation during the supplementation period. After DNA extraction, the V3-V4 region from the 16 S rRNA gene was sequenced, and reads were processed using the Divisive Amplicon Denoising Algorithm (DADA2). Bacteroides and Lactobacillus were the most abundant genera in the supplemented groups. At the phylum level, Actinobacteria and Bacteroidetes were reduced to 24 h and 48 h compared to 0 h, whereas the phylum Firmicutes significantly increased at 72 h compared to 0 h. In conclusion, evidence suggests that L. casei CB054 has a specific, time-dependent immunomodulatory effect on splenocyte cytokine transcription, modulating the bacterial communities of the mouse gut microbiome.},
}

@article {pmid41060553,
year = {2025},
author = {Rajesh, V and Hegde, A and Ballal, M and Mutreja, A and Garg, M and Kumar, V and Kamath, A and Vasudevan, K and Mahesh, S and Shetty, V},
title = {Influence of Feeding Pattern on Infant Growth: A Longitudinal Study with Gut Microbiome Insights.},
journal = {Indian pediatrics},
volume = {},
number = {},
pages = {},
pmid = {41060553},
issn = {0974-7559},
abstract = {OBJECTIVES: To determine the proportion of exclusive breastfeeding in the study population. To determine the effect of various infant feeding patterns on anthropometric measurements, incidence of infectious diseases, antibiotic exposure and developmental milestones in infancy. The study also assessed the overall gut microbial abundance, alpha and beta diversity, by preliminary gut microbiome analysis.

METHODS: A prospective cohort study was conducted by collecting feeding pattern data from mothers of healthy newborns (n = 374) who were assessed at birth, 1.5, 3.5, 6, 9 and 12 months. The gut microbiome analysis was done using stool samples collected at birth, 1.5, 3.5 and 9 months.

RESULTS: Weight-for-height Z-scores indicated a higher prevalence of overweight in 'mixed milk feeding' and 'mixed complementary feeding' at 6 months (P = 0.907) with a significant association at 12 months (P = 0.019). A significant association was seen between 'mixed complementary feeding' and episodes of antibiotic exposure at 6 months (P = 0.007) and 12 months (P = 0.002), and episodes of fever (P = 0.009), cold (P = 0.007) and diarrhea (P = 0.024) after 9 months of age. Predominant phyla observed in the gut microbiome were Firmicutes; genera Bifidobacterium and Streptococcus were in abundance with increasing age.

CONCLUSIONS: Breastfeeding promotes beneficial bacteria in the gut microbiome with microbial diversity increasing during complementary feeding. Home-based complementary feeding contributes to improved nutritional status and reduced infectious diseases.},
}

@article {pmid41060346,
year = {2025},
author = {Yao, L and Li, L and Chen, J and Ma, Y and Alalawy, AI and Jiang, Y and Zhang, W and Gu, Y and Xi, Y},
title = {Multi-omics profiling reveals key microbial and metabolic variations in ischemic stroke: insights into gut and oral microbiota.},
journal = {Archives of microbiology},
volume = {207},
number = {11},
pages = {291},
pmid = {41060346},
issn = {1432-072X},
support = {20230060104//"Excellence Plan" of the First School of Clinical Medicine/ ; 20230060104//"Excellence Plan" of the First School of Clinical Medicine/ ; 2023-ZD-89//Lanzhou Science and Technology Program Project/ ; 2023-ZD-89//Lanzhou Science and Technology Program Project/ ; 24JRRA360//Natural Science Foundation of Gansu Province/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Male ; Female ; Middle Aged ; Aged ; *Mouth/microbiology ; *Ischemic Stroke/microbiology/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Fatty Acids, Volatile/metabolism ; Metabolomics ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Multiomics ; },
abstract = {Dysbiosis of oral and gut microbiota may influence ischemic stroke (IS) pathogenesis through immune and metabolic mechanisms. This study investigated microbial translocation between oral and gut niches and its functional metabolic impact in IS patients. A total of 57 individuals were analyzed, including 25 controls (FC/KC) and 32 IS patients (FS/KS). Samples were obtained from the gut and oral subgingival plaque. The microbiome analysis was performed using the PacBio platform 16 S rRNA full-length gene sequencing, while non-targeted metabolomics was used to assess intestinal metabolites. The oral cavity of IS patients harbored abundant periodontal pathogens, including Porphyromonas and Fusobacterium. Bacterial genera (such as Streptococcus, Neisseria, Ligilactobacillus, Leptotrichia, Blautia, Veillonella, and Capnocytophaga) significantly overlapped between the oral and gut niches in IS patients, suggesting mutual transfer. IS patients exhibited increased diversity and dysbiosis in their gut microbiota, characterized by a deficiency of short-chain fatty acids (SCFA)-producing bacteria (Bacteroides and Faecalibacterium), and an enrichment of opportunistic pathogens (Streptococcus and Ligilactobacillus). Metabolomic analysis revealed concomitant disturbances in microbial metabolism, marked by decreased SCFAs (butyrate) and increased levels of specific amino acids (L-tryptophan). These metabolic changes were correlated with the microbial shifts. IS is associated with distinct dysbiosis in both the oral and gut ecosystems, which are interconnected through bacterial translocation. The metabolic disruption may link microbial dysbiosis to stroke pathogenesis through the oral-gut axis.},
}

Humans
*Gastrointestinal Microbiome
Dysbiosis/microbiology
Male
Female
Middle Aged
Aged
*Mouth/microbiology
*Ischemic Stroke/microbiology/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
Fatty Acids, Volatile/metabolism
Metabolomics
RNA, Ribosomal, 16S/genetics
Microbiota
Multiomics

@article {pmid41060325,
year = {2025},
author = {Lopes-Júnior, LC},
title = {The Emerging Epidemic of Early-Onset Cancer: Global Patterns, Biological Complexity, and Urgent Calls for Action.},
journal = {Cancer control : journal of the Moffitt Cancer Center},
volume = {32},
number = {},
pages = {10732748251386505},
doi = {10.1177/10732748251386505},
pmid = {41060325},
issn = {1526-2359},
mesh = {Humans ; *Neoplasms/epidemiology/etiology ; Age of Onset ; Risk Factors ; Female ; Global Health ; },
abstract = {Cancer is often considered a disease of older adults, yet in recent decades an increasing number of people under the age of 50 have been diagnosed with cancer worldwide. According to global data, the most common early-onset cancers include breast, tracheal/bronchus/lung, stomach, and colorectal cancers, followed by thyroid, pancreas, and liver malignancies. These cancers often behave more aggressively than those diagnosed later in life and contribute substantially to premature mortality and disability. Researchers believe that this trend is driven less by hereditary syndromes and more by cumulative environmental and lifestyle exposures beginning early in life. Diets high in ultra-processed foods, reduced physical activity, antibiotic overuse, pollution, psychosocial stress, and disruptions of the gut microbiome have all been implicated as potential contributors. Unlike inherited cancer syndromes, most early-onset cancers are sporadic, arising from complex interactions between modifiable exposures and host biology. Younger patients face unique challenges: they are underrepresented in clinical trials, often lack access to age-appropriate multidisciplinary care, and experience disruptions to education, employment, and family planning. Addressing this growing public health concern requires earlier screening for high-risk groups, investment in adolescent and young adult (AYA)-specific biorepositories and research, and policies that prioritize prevention, equity, and tailored care for younger populations.},
}

Humans
*Neoplasms/epidemiology/etiology
Age of Onset
Risk Factors
Female
Global Health

@article {pmid41060256,
year = {2025},
author = {Schult-Hannemann, D and Gassner, C and Thur, N and Hennig, C and Fricke, L and Liotta, L and Weidlich, S and Matchado, MS and Stecher, B and Arps, L and Steiger, K and Shakhtour, J and Jesinghaus, M and List, M and Janssen, KP and Pourjam, M and Neuhaus, K and Haller, D and Schmid, RM and Quante, M and Middelhoff, M and Maurer, HC and , },
title = {Comparison of Different Sites of Microbiota Shows Increased Pseudomonas Species in the Gut Mucosa in Inflammatory Bowel Disease.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf185},
pmid = {41060256},
issn = {1536-4844},
support = {395357507//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), is associated with changes in the gut microbiome. Studies comparing fecal, gut mucosal, and salivary microbiomes are rare, and questions remain regarding the interaction of these compartments.

METHODS: In this case-control study, 16S rRNA gene amplicon sequencing was performed on samples from stool, intestinal mucosa, and saliva of 120 patients with IBD. Patients with signs of non-IBD colonic inflammation (N = 28) and healthy subjects (N = 67) served as controls. A total of 480 16S profiles were analyzed. The results were evaluated with multiple clinical and pathological parameters and potential confounders were considered. The study aimed to find microbial biomarkers specific to IBD and signatures of intestinal barrier dysfunction.

RESULTS: Fecal α-diversity of IBD patients was reduced and Pseudomonas species was significantly increased in the mucosa of IBD patients (Pseudomonas-positive mucosa [PSM positive], P value < .001, Mann-Whitney U test). Comparison of matched stool and mucosa samples showed high abundance of Pseudomonas species in gut mucosa but not in fecal samples, especially in CD patients. Interestingly, in PSM positive, Paracoccus species, Bacteroides species, and Streptococcus species were more abundant. Importantly, the results were independent of disease severity, histopathology, medication, and other metadata.

CONCLUSIONS: The opportunistic pathogenic bacterium Pseudomonas species is more prevalent in the gut mucosa of patients with IBD. This indicates a disruption of the gut barrier with increasing mucosal colonization or invasion of the bacteria. The finding is independent of clinical metadata and confounders and occurs in new-onset IBD but not in non-IBD intestinal inflammation, which suggests disease specificity.},
}

@article {pmid41059691,
year = {2025},
author = {Zhang, T and Gu, F and Li, W and Han, R and Liu, X and Dai, C and Zhang, D and Li, H},
title = {Characterization of cervical microbiota in cervical intraepithelial neoplasia and cervical cancer using low-coverage whole genome sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0320624},
doi = {10.1128/spectrum.03206-24},
pmid = {41059691},
issn = {2165-0497},
abstract = {This study characterized compositional shifts in cervical microbiota across disease stages from benign conditions through cervical intraepithelial neoplasia (CIN) to cervical cancer (CC) and investigated interactions with high-risk HPV (hr-HPV) infection using species-resolution profiling to identify severity-associated biomarkers. Cervical exfoliated epithelial cells from 50 patients (eight normal/CIN1, 15 CIN2, 19 CIN3, 5 CC) were analyzed using Low-Coverage Whole Genome Sequencing combined with the Ultrasensitive Chromosomal Aneuploidy Detector (UCAD), a technology featuring a two-step normalization framework that systematically converts raw microbial reads into statistically validated abundance deviations. This enables quantitative identification of pathologically relevant microbiota through cohort-wide Z-score benchmarking. Microbial diversity, differential biomarkers, and HPV-microbiota interactions were assessed using Kruskal-Wallis tests, LEfSe, and Random Forest modeling. Results revealed progressive Lactobacillus depletion (e.g., Lactobacillus crispatus: 32.9% in ≤CIN2 vs. 8.8% in CC) and enrichment of pathobionts like Gardnerella and Bacteroides with lesion severity. CC exhibited the highest microbial diversity (Shannon index: CC vs. CIN2, P=0.045), dominated by HPV16 (11.8%), Bacteroides (55.4%), and Porphyromonas (25.2%). LEfSe identified HPV16, HPV35, Parvimonas micra, and Anaerococcus lactolyticus as CC-specific markers, while Random Forest highlighted Mobiluncus curtisii (importance score=2.0) and HPV16 as key discriminators. CC microbiota showed significant Bacteroidetes enrichment (82% at class level) and reduced Firmicutes abundance. These findings suggest carcinogenesis-associated microbial restructuring, marked by Lactobacillus loss, anaerobic proliferation, and HPV16/35 dominance, potentially modulating disease progression. The identified signatures may inform diagnostic development and microbiome-targeted therapies.IMPORTANCEOur study pioneers an LC-WGS/UCAD approach to characterize microbial across the spectrum from benign lesions through precancerous cervical intraepithelial neoplasia to invasive cervical carcinoma. By identifying lesion-specific microbial biomarkers and HPV-associated cofactors, this work advances mechanistic understanding of microbiota-driven oncogenesis and informs future strategies for microbiota-targeted cervical cancer prevention.},
}

@article {pmid41059690,
year = {2025},
author = {Venkatachalam, S and Granskog, MA and Gonçalves-Araujo, R and Divine, DV and Vipindas, PV and Jabir, T and Shereef, A and Jain, A},
title = {Distinct bacterial community structures with abundant carbon degradation and sulfur metabolisms found in different sea-ice types from the Central Arctic Ocean.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0129125},
doi = {10.1128/spectrum.01291-25},
pmid = {41059690},
issn = {2165-0497},
abstract = {The rapid decline of sea ice in the relatively understudied Central Arctic Ocean has a significant impact on bacterial biodiversity and the ecological functions they support. We investigated the bacterial community composition and the associated metabolic functions from three geographically distinct sea-ice floes: first-year ice (FYI) at the North Pole and western Nansen Basin and second-year or multi-year ice (SYI/MYI) in the western Amundsen Basin. We resolved the sea-ice bacterial community diversity at species-level precision using a long-read amplicon (n = 18) and metagenomic (n = 3) sequencing approach. The amplicon sequencing highlighted marked differences in bacterial community structure driven by ice age, floe origin, and environmental factors, demonstrating pronounced vertical structuring among ice horizons. Bacterial taxa like Paraglaciecola psychrophila, Hydrogenophaga crassostreae, Octadecabacter arcticus, and Polaribacter irgensii mainly dominated the bottom layers of SYI/MYI, whereas species Actimicrobium antarcticum, Polaromonas cryoconiti, O. antarcticus, and Rhodoferax sp. dominated the FYI. Similarly, notable taxonomic differences were observed in bacterial taxa inhabiting the surface and interior layers of FYI and SYI/MYI (e.g., F. frigoris and Hydrogenophaga sp.). The metagenomic analysis showed the prevalence of sulfur cycling-associated (assimilatory and dissimilatory sulfur metabolism) and complex carbon degradation processes in sea ice. We also elucidated the potential ecological role of novel metagenome-assembled genomes belonging to the genus Aquiluna through phylogenomic and pangenomic analyses. Overall, our findings revealed novel insights on the distinct bacterial communities that inhabit ice horizons and their associated ecological functions correlating with sea-ice type, origin, and habitat characteristics in the Central Arctic Ocean.IMPORTANCEThe Arctic region is warming nearly four times faster than the global average, leading to the continuous replacement of its thick multi-year sea ice with thinner first-year ice. The reduction in Arctic sea-ice cover was previously shown to have cascading effects on sea-ice-associated microbial communities and their role in the functioning of the ecosystem. This study provides the first high-resolution, species-level insight into the bacterial community composition and metabolic potential across different sea-ice types in the Central Arctic Ocean-an understudied yet rapidly changing environment. By combining long-read amplicon and metagenomic sequencing, we uncover distinct bacterial assemblages and functional metabolic roles that were shaped by the ice age and other physicochemical properties. Our findings highlight the ecological importance of sea-ice associated bacterial communities and the prevalence of sulfur metabolism and carbon degradation processes in different sea-ice types found in the central Arctic Ocean through genome-resolved metagenomics.},
}

@article {pmid41059655,
year = {2025},
author = {Yimer, TM and Chan, GCK and Stjepanović, D and Sun, T and Shin, D and Lucey, M and Choi, J and Saunders, JB and Connor, JP and Leung, J},
title = {The Short-Term Health Effects of Dealcoholised Red Wine: A Systematic Review and Meta-Analysis.},
journal = {Drug and alcohol review},
volume = {},
number = {},
pages = {},
doi = {10.1111/dar.70047},
pmid = {41059655},
issn = {1465-3362},
support = {//NHMRC/ ; //Australian Government/ ; },
abstract = {ISSUES: Health benefits of red wine are claimed and attributed to its high polyphenol content, but these claims are controversial due to the array of known alcohol-related harms. We undertook a systematic review and meta-analysis to identify whether there are health benefits of dealcoholised red wine.

APPROACH: We searched PubMed, Embase, Scopus, PsycINFO and Web of Science for randomised controlled or cross-over trials. Comparisons analysed were: (i) dealcoholised red wine versus red wine; and (ii) dealcoholised red wine versus water. Health outcomes included serum/plasma antioxidant capacity, cardiovascular function, immune function, liver function, metabolism, microbiome diversity and inflammatory markers. Random effects meta-analyses were performed to estimate standardised mean differences (SMD = d).

KEY FINDINGS: From 865 identified records, we included 36 studies. Dealcoholised red wine was associated with increased serum/plasma antioxidant capacity (d = 0.72; 95% CI [0.42, 1.01]) and microbiome diversity (d = 0.63 [0.32, 0.93]) compared to water, but has less effect on microbiome diversity (d = -0.32 [-0.52, -0.11]) compared to red wine. No significant differences were observed in other health outcomes.

IMPLICATIONS: Dealcoholised red wine may have some short-term health benefits, but there is uncertainty on long-term population-level impacts; therefore, the precautionary principle should be applied.

CONCLUSIONS: Dealcoholised red wine may have some short-term health benefits in increasing serum/plasma antioxidant capacity and microbiome diversity, but the evidence is limited by small sample size, short-term follow-up, and heterogeneous studies. These data do not support a rationale for drinking red wine for purported health benefits due to the known long-term health harms of alcohol consumption.},
}

@article {pmid41059496,
year = {2025},
author = {Ciszewski, A and Jarosz, ŁS and Grądzki, Z and Marek, A and Kaczmarek, B and Hejdysz, M and Rysiak, A},
title = {Influence of a multi-strain probiotic and zinc-glycine chelate, administered in ovo, on immune response in newly hatched chicks.},
journal = {Frontiers in physiology},
volume = {16},
number = {},
pages = {1646143},
pmid = {41059496},
issn = {1664-042X},
abstract = {INTRODUCTION: The supplementation of chicken embryos with bioactive compounds may elicit a beneficial effect on the development of their gut microbiome and enhance protection against infectious agents after hatching. Therefore, this study aimed to evaluate the effect of in ovo co-supplementation with a multi-strain probiotic and zinc-glycine chelate on the levels of pro- and anti-inflammatory cytokines, acute-phase proteins, and immunoglobulins in the peripheral blood and tissues of broiler chickens on the day of hatching and 7 days post hatching. The effect of supplementation on the growth parameters of chickens was assessed as well.

METHODS: The study was conducted on 1,500 hatching eggs from a broiler breeding flock (Ross × Ross 308) at 36 weeks. ELISA kits were used to determine levels of acute-phase proteins and immunoglobulins. Expression of immunoglobulins was determined by means of qRT-PCR.

RESULTS: The results indicate enhanced synthesis of acute-phase proteins in the liver and increased levels of serum amyloid A in the small intestine tissue, as well as IgA and IgM mRNA and suppressed synthesis of pro-inflammatory cytokines IFN-γ and TNF-α. During the cumulative experimental period (days 0-42), the mean body weight gain (BWG) and feed intake (FI) in the group supplemented with a multi-strain probiotic were statistically significantly lower than the control group.

DISCUSSION: It may be concluded that the combined in ovo use of a multi-strain probiotic and Zn-Gly chelate modulates the immune response, helps maintain the balance between the synthesis of Th1 and Th2 cytokines, inhibits inflammatory processes, and stimulates immune system development.},
}

@article {pmid41059489,
year = {2025},
author = {Chen, H and Yang, H and Guo, L and Sun, Q},
title = {The Role of Immune Checkpoint Inhibitors in Cancer Therapy: Mechanism and Therapeutic Advances.},
journal = {MedComm},
volume = {6},
number = {10},
pages = {e70412},
pmid = {41059489},
issn = {2688-2663},
abstract = {The rapid development of immune checkpoint inhibitors has fundamentally changed the landscape of cancer treatment. These agents restore T cell-mediated antitumor immune responses by targeting key immune checkpoint molecules, thereby suppressing or eliminating tumors. However, their clinical application still faces multiple challenges, mainly including efficacy heterogeneity, drug resistance, immune-related adverse events. Furthermore, there is still a lack of reliable biomarkers for predicting efficacy and toxicity. More critically, there is absence of precise predictive models that can systematically integrate multiomics features, dynamic tumor microenvironment evolution, and patient individual differences to comprehensively address the above issues. This review systematically summarizes the latest advancements in this field. The main contents include emerging targets like lymphocyte activation gene 3, T cell immunoreceptor with immunoglobulin and tyrosine-based inhibitory motif domain, and mucin-domain-containing-3, combination strategies, and the current research status and limitations of various predictive biomarkers. Moreover, it focuses on the potential of microbiome regulation, metabolic reprogramming, and artificial intelligence-driven multiomics analysis technologies in achieving dynamic patient stratification and personalized treatment. By integrating the frontier research results and clinical insights, the review aims to provide a systematical theory framework and future directions for advancing precision immunotherapy.},
}

@article {pmid41059464,
year = {2025},
author = {Turk-Kubo, K and Benavides, M and Mills, MM and Smith, SR},
title = {Rhizosolenia mat diatoms associate with nitrogen-fixing microbes.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf159},
pmid = {41059464},
issn = {2730-6151},
abstract = {Some Rhizosolenia diatoms living in oligotrophic marine ecosystems are known to form large, conspicuous mats and are thought to be sources of new nitrogen to surface waters via vertical migration to the nitracline where subsurface nitrate is accessed for growth. These vertically migrating Rhizosolenia mats are chronically under sampled, and both the diatom species comprising the mats and the associated microbiome have not been characterized using modern molecular techniques. Here we present the first DNA-based analysis of Rhizosolenia mats collected in the North Pacific Subtropical Gyre. Using sequencing of 18S rRNA and nifH genes (a proxy for N2 fixation capacity), we report on the molecular diversity of mat-forming Rhizosolenia species, which include two newly sequenced clades, and an assemblage of associated N2-fixing microorganisms that is distinct from the non-mat associated water column assemblage. Our findings advance knowledge of oligotrophic diatom diversity and challenge prevailing views of their nitrogen sources, suggesting these mats may obtain nitrogen through association-based N2 fixation. Further work is needed to understand the nature of these associations, and whether Rhizosolenia mat communities are a significant unrecognized source of N2-fixation-derived new nitrogen to the oligotrophic surface waters.},
}

@article {pmid41059459,
year = {2025},
author = {Yan, Z and Yang, Y and Yu, X and Hao, Z and Du, Y and Wang, Y and Wu, Y and Zhao, Y and Niu, L and Zhou, X and Shen, L and Gan, M and Zhu, L},
title = {Characterization of the gut microbiome in Wuhuang pigs and their crossbred offspring.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1668076},
pmid = {41059459},
issn = {2297-1769},
abstract = {INTRODUCTION: As an indigenous Chinese breed, Wuhuang pigs are valued for their stress resistance, tolerance to coarse feed, and high lean meat yield, while Berkshire pigs serve as ideal sires due to superior meat quality and early maturity. To explore the microbial basis of hybrid vigor in these breeds, we compared the gut microbiota of purebred Wuhuang pigs and Wuhuang-Berkshire hybrids.

METHODS: Microbial composition was assessed via 16S rDNA sequencing, and predictive functional profiling was performed using PICRUSt2 analysis.

RESULTS: Hybrids exhibited significantly increased microbial α-diversity and altered β-diversity. Notably, hybrid ceca were enriched with probiotic genera involved in fiber degradation and short-chain fatty acid (SCFA) production-such as Prevotella, Ruminococcus, Lachnospiraceae, and Roseburia-accompanied by a higher Firmicutes-to-Bacteroidetes ratio and strengthened microbial network connectivity. Predictive functional profiling further revealed significantly elevated activity in hybrid pigs for key metabolic pathways including tryptophan synthesis, pyridoxal salvage, and galacturonic acid metabolism (FDR < 0.05).

DISCUSSION: These results imply that hybrid animals leverage enriched probiotic consortia to augment nutrient metabolism and immune function, thereby supporting improved stress resilience and feed efficiency. This study provides potential microbial targets for the future genetic improvement of indigenous pig breeds.},
}

@article {pmid41059409,
year = {2025},
author = {Somyong, S and Mhuantong, W and Phetchawang, P and Thompson, DK and Thepsilvisut, O and Pootakham, W},
title = {Influence of organic, synthetic and biofertilizers on the diversity of cassava rhizosphere microbiome in Northeastern Thailand.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20085},
pmid = {41059409},
issn = {2167-8359},
mesh = {*Manihot/microbiology/growth & development ; *Fertilizers ; *Rhizosphere ; Thailand ; *Soil Microbiology ; *Microbiota ; Animals ; Manure ; },
abstract = {Cassava, one of Thailand's main economic crops, is capable of growing in nearly all soil types. However, continuous monocropping depletes soil nutrients over time. Adopting good agricultural practices can help farmers reduce costs while improving soil fertility. The aim of this study was to compare cassava rhizosphere microbial communities resulting from cultivation under eight different fertilizer treatments, including synthetic, organic, and biological fertilizers, and to identify beneficial microbes that promote cassava growth and yield. The study was conducted at two sites in Northeastern Thailand. Results show that bacterial abundance and species richness (alpha diversity) peaked at 5 months after planting (MAP), showing a significant increase compared to 2 MAP. However, by 10 MAP, alpha diversity began to decline at both sites, Nampong and Seungsang. Among the treatments, the most notable differences in alpha diversity were observed at 5 MAP. At the Nampong site, experimental treatments with chicken manure (T3) and chicken manure combined with other fertilizers (T5, T6, and T8) exhibited significantly higher alpha diversity than did the control (without fertilizer, T1). At the Seungsang site, sole treatment with the full recommended rate of chicken manure (T3), and half of the recommended dose of synthetic fertilizer combined with half the recommended dose of chicken manure (T6) resulted in greater alpha diversity than did swine manure extract application (T4), half of the recommended dose of synthetic fertilizer combined with half of the recommended dose of swine manure extract (T7), and chicken manure application combined with stalk inoculation with plant growth-promoting rhizobacteria (PGPRs) (T8). Since T3 and T8 had the most significant impact on microbial abundance and diversity, as well as cassava growth and yield, the predominant bacteria in these treatments were identified as key targets. A total of eight target bacterial genera were identified: Pseudomonas, Tumebacillus, Lysinibacillus, Paenibacillus, Dongia, Acidibacter, Sphingomonas, and Bacillus. Among them, Tumebacillus was the most notable, as it showed a significant correlation with fresh tuber yield. These beneficial bacteria may serve as key candidates for future biofertilizer production.},
}

*Manihot/microbiology/growth & development
*Fertilizers
*Rhizosphere
Thailand
*Soil Microbiology
*Microbiota
Animals
Manure

@article {pmid41059290,
year = {2025},
author = {Fang, J and Wu, M and Shen, H and Liu, W and Zhang, T},
title = {Intratumoral microbial abundance and load influence the immune microenvironment of oral squamous cell carcinoma.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1616928},
pmid = {41059290},
issn = {2234-943X},
abstract = {OBJECTIVE: This study aimed to explore the characteristics intratumoral microbiome in oral squamous cell carcinoma, and elucidate the interplay between intratumoral microbial profiles (relative abundance/absolute load) and tumor-infiltrating lymphocytes markers (CD4[+]/CD8[+]/FOXP3) and PD-L1 in oral squamous cell carcinoma.

METHODS: We analyzed 45 OSCC tissue samples alongside paired paracancerous (n=10) and normal oral microbiota controls (n=8). Microbial composition was characterized by 16S rRNA sequencing (V3-V4 regions), with bacterial load quantified via qPCR targeting the V4-1 region. Tumor-infiltrating lymphocytes markers were assessed by immunohistochemistry.

RESULTS: Spirochaetota was concentrated in the CD4[+] as well as CD8[+] low infiltration groups, Proteobacteria in the CD8[+] high infiltration group and Actinobacteriota in the FOXP3 low infiltration group. Tumor microbial load was negatively correlated with CD4[+], CD8[+], and FOXP3, but of these, only the correlation coefficient of -0.309 for CD4[+] was statistically significant. However, no significant correlation was observed in the analysis of PD-L1 expression with the relative abundance of intratumoral microbiome, α-diversity, and intratumoral microbial load values.

CONCLUSION: Changes in the abundance of specific intratumoral microbiome affect the infiltration of TILs markers, and there is a negative relationship between intratumoral microbial load and T-cell infiltration, suggesting that intratumoral microbiome contribute to the processes of the tumor immunosuppressive microenvironment.},
}

@article {pmid41059212,
year = {2025},
author = {Lee, CT and Tribble, GD},
title = {Correction: Roles of specialized pro-resolving mediators and omega-3 polyunsaturated fatty acids in periodontal inflammation and impact on oral microbiota.},
journal = {Frontiers in oral health},
volume = {6},
number = {},
pages = {1691158},
doi = {10.3389/froh.2025.1691158},
pmid = {41059212},
issn = {2673-4842},
abstract = {[This corrects the article DOI: 10.3389/froh.2023.1217088.].},
}

@article {pmid41059063,
year = {2025},
author = {Hu, J and Cyle, KT and Yuan, W and Shi, W},
title = {Metagenomic evidence clarifies the texture-dependent cascading effects of organic degradation on soil hypoxia and N2O emission.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1670657},
pmid = {41059063},
issn = {1664-302X},
abstract = {INTRODUCTION: Soil pore-scale aeration is a crucial yet often overlooked factor influencing the effectiveness of nitrous oxide (N2O) emission mitigation strategies. Our previous work revealed a hundred-fold variation in N2O emissions among soils under apparently aerobic conditions and texture-dependent mitigation effects of biochar-manure co-compost (BM) compared to manure compost (M).

METHODS: We analyzed soils of three textures-clay loam (CL), silt loam (SL), and sand (SA)-amended with BM or M. Metagenomic sequencing was used to profile microbial community composition and functional genes, with a focus on aeration-sensitive taxa and pathways.

RESULTS: We demonstrate that these changes of N2O emissions are aligned with variations in aeration-sensitive microbes and genes. SA, with the highest N2O emissions, was most abundant in obligate and facultative anaerobes and denitrification-related genes, while CL, with the lowest emissions, had more genes related to fermentation and dissimilatory nitrate reduction. Compared to M, BM in CL favored genes for microbial processes requiring a more reducing environment, likely because biochar-induced finer pores, exacerbating oxygen diffusion limitations. This severe oxygen restriction in CL after BM addition was substantiated by greater reductions in CO2 efflux and C-cycling genes than in the other soils.

DISCUSSION: Our findings suggest that hypoxic pore abundance and the severity of pore anaerobiosis imparted by degradation of organic amendments varied with soil texture and are the overriding factors of soil greenhouse gas (GHG) emissions. Metagenomic traits provide a sensitive tool for detecting pore-scale environmental shifts, improving our mechanistic understanding of soil-dependent GHG emissions following organic amendments.},
}

@article {pmid41059060,
year = {2025},
author = {Xu, J and Wang, S and Jia, Z and Wang, Z and Bao, Y and Wei, J},
title = {Desertification gradients shape Medicago sativa rhizosphere microbiomes in inner Mongolia's agro-pastoral ecotone.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1651717},
pmid = {41059060},
issn = {1664-302X},
abstract = {This study investigated the spatial heterogeneity of rhizosphere microbial communities in alfalfa (Medicago sativa) across desertification gradients in Inner Mongolia, China. Rhizosphere soils were collected from non-, lightly-, and moderately- desertified sites. Using 16S rRNA and ITS high-throughput sequencing alongside soil physicochemical analyses, we found that desertification intensity significantly altered microbial structure and function. Actinobacteriota dominated in moderately-desertified soils, whereas Proteobacteria prevailed in non-desertified areas. Ascomycota was the dominant fungal phylum, with Basidiomycota and Mortierellomycota enriched in non- and lightly- desertified sites, respectively. Soil pH and available phosphorus were the key factors shaping bacterial and fungal communities, respectively. Co-occurrence networks indicated enhanced microbial connectivity and a shift toward cooperative interactions under desertification. Functional prediction revealed conserved bacterial metabolic pathways but increased abundance of fungal stress-response enzymes (e.g., monooxygenases). These findings underscore microbial adaptive strategies to desertification and provide insights for sustainable agriculture in arid regions.},
}

@article {pmid41059058,
year = {2025},
author = {Wang, Y and Bai, Z and Liu, Y and Wang, Y and Xu, J and Lai, Z},
title = {Influence of the gut microbiota on the pharmacokinetics of tacrolimus in liver transplant recipients: insights from microbiome analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1616985},
pmid = {41059058},
issn = {1664-302X},
abstract = {INTRODUCTION: Tacrolimus is crucial for immunosuppression after liver transplantation, but its pharmacokinetics vary markedly among individuals. Emerging evidence suggests that the gut microbiota may influence its metabolism, although the underlying mechanisms remain unclear.

METHODS: This study analyzed the fecal microbiota from 38 postliver transplant patients and 31 healthy controls via 16S rDNA amplicon and shotgun metagenomic sequencing. Patients were stratified into three groups on the basis of oral tacrolimus dosage and blood concentration: LDLBC (low dose, low blood concentration), LDHBC (low dose, high blood concentration), and SDLBC (standard dose, low blood concentration).

RESULTS: Posttransplant patients presented significantly reduced gut microbial diversity. Specific bacterial taxa, including Enterococcus raffinosus, Intestinibacter bartlettii, and Bacteroides fragilis, were enriched in patients with lower tacrolimus blood concentrations. In contrast, Phascolarctobacterium faecium and Streptococcus salivarius were associated with increased drug levels. Functional analysis revealed differences between patient subgroups in ATP-binding cassette (ABC) transporters and drug efflux pumps, suggesting a potential microbial influence on tacrolimus absorption and metabolism. Additionally, antibiotic resistance genes were more abundant in patients with lower tacrolimus blood concentrations, particularly in the Escherichia coli-enriched groups.

DISCUSSION: These findings underscore the influence of the gut microbiota on tacrolimus pharmacokinetics and support the potential of microbial composition as a biomarker for optimizing immunosuppressive therapy.},
}

@article {pmid41059057,
year = {2025},
author = {Harker, SA and Bonham, KS and McCann, SH and Volpe, AR and Zhu, Q and D'Sa, V and Koinis-Mitchell, D and Deoni, SCL and Klepac-Ceraj, V and Lewis, CR},
title = {Associations between relative abundances of Bifidobacterium species in the gut and DNA methylation of cortisol-related genes in a pediatric population.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1558809},
pmid = {41059057},
issn = {1664-302X},
abstract = {INTRODUCTION: Human epigenetics, specifically DNA methylation, and the gut microbiome are dynamic systems influenced by environmental factors, such as diet and earlylife exposures, with profound implications for health and disease. Metabolites produced by the gut microbiome interact with the host, shaping physiological processes. While prior research has linked Bifidobacterium abundance to anxiety and cortisol function, the role of DNA methylation as a potential mechanism underlying these associations remains unexplored. This study examines the relationship between the relative abundance of Bifidobacterium species in the gut and DNA methylation of hypothalamic-pituitary-adrenal (HPA) axis genes in a pediatric cohort. We hypothesized that Bifidobacterium abundance would predict DNA methylation at key HPA genes associated with stress response, including NR3C1, FKBP5, and more.

METHODS: Multiple linear regression and regularized canonical correlation analysis (rCCA) were used.

RESULTS: There were significant associations between Bifidobacterium abundance and DNA methylation at HPA gene loci, while control analyses showed no association with global methylation levels. rCCA further pinpointed specific Bifidobacterium species, such as B. angulatum and B. adolescentis, as strong contributors to the first canonical component, correlating with CpG sites influencing HPA gene methylation.

DISCUSSION: These findings suggest that microbiome-derived metabolites, such as folate, may modulate DNA methylation and stress physiology. This work provides new insights for exploring how the gut microbiome impacts mental health and stress resilience, offering potential pathways for microbiome-targeted interventions.},
}

@article {pmid41059042,
year = {2025},
author = {Shang, KM and Ma, H and Wei, YJ and Zhao, JX and Qin, Y and Li, JM and Zhao, ZY and Yu, HL and Zhao, Q and Chen, BN and Elsheikha, HM and Zhang, XX and Yang, X},
title = {Enterocytozoon bieneusi infection disrupts bile acid metabolism in the wild rodent gut microbiota: adaptive shifts in microbial metabolism and community structure.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1647377},
pmid = {41059042},
issn = {2235-2988},
mesh = {Animals ; *Enterocytozoon ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome ; Mice ; *Microsporidiosis/microbiology/veterinary/metabolism ; Humans ; Rodentia/microbiology ; Phylogeny ; Animals, Wild/microbiology ; Glycoside Hydrolases/genetics/metabolism ; Metabolic Networks and Pathways ; },
abstract = {INTRODUCTION: Bile acids (BAs) are central to host-microbiota interactions, yet their metabolism in wild rodents remains poorly characterized. This study aimed to explore the genomic potential of gut microorganisms in wild rodents for BA metabolism and its implications for host adaptation and pathogen interactions.

METHODS: We reconstructed 6,332 genomes from the gut microbiota of wild rodents and performed genome-resolved metabolic profiling. Comparative analyses were conducted across host species, including humans, pigs, laboratory mice, and chickens. Functional enrichment was further assessed in relation to glycoside hydrolase families and Enterocytozoon bieneusi infection status.

RESULTS: A total of 5,208 genomes were identified as participants in key BA metabolic pathways, including deconjugation, oxidation, and dihydroxylation, predominantly from Bacillota_A and Bacteroidota. Notably, Muribaculaceae and CAG-485 lineages within Bacteroidota encoded bile salt hydrolase (BSH). Cross-species comparisons revealed a striking absence of 7β-hydroxysteroid dehydrogenase (7β-HSDH) in laboratory mice, indicating their limited suitability for modeling intestinal BA metabolism. BSH-encoding genomes were significantly enriched in glycoside hydrolase families GH13 and GH16, suggesting a potential link between BA transformation and carbohydrate metabolism. Furthermore, Enterocytozoon bieneusi infection was associated with a marked increase in BA-related microbial taxa in wild rodents.

DISCUSSION: Our findings highlight the intricate interconnections between gut microbial functions, BA metabolism, and pathogen interactions. The absence of 7β-HSDH in laboratory mice underscores wild rodents as potentially more suitable models for BA research. These results open new avenues for understanding microbiome-driven host adaptation and health.},
}

Animals
*Enterocytozoon
*Bile Acids and Salts/metabolism
*Gastrointestinal Microbiome
Mice
*Microsporidiosis/microbiology/veterinary/metabolism
Humans
Rodentia/microbiology
Phylogeny
Animals, Wild/microbiology
Glycoside Hydrolases/genetics/metabolism
Metabolic Networks and Pathways

@article {pmid41059040,
year = {2025},
author = {Zhu, N and Gao, J and Wu, R and Jia, S and Guo, X and Sun, D and Guan, Q},
title = {Metagenomic insights into respiratory viral signatures in lower respiratory tract infections with and without respiratory failure.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1637352},
pmid = {41059040},
issn = {2235-2988},
mesh = {Humans ; *Respiratory Tract Infections/virology/microbiology/complications ; *Metagenomics ; Male ; Middle Aged ; Female ; Bacteria/classification/genetics/isolation & purification ; *Viruses/classification/genetics/isolation & purification ; *Virome ; Bronchoalveolar Lavage Fluid/virology/microbiology ; Microbiota ; Aged ; *Respiratory Insufficiency/virology/microbiology ; Adult ; },
abstract = {OBJECTIVE: Lower respiratory tract infections (LRTIs) are a significant cause of morbidity and mortality worldwide, with the respiratory microbiome playing a pivotal role in disease pathogenesis. Comprehensive profiling of the lower respiratory tract virome allows investigation of potential differences between LRTIs and non-LRTIs, helps identify virus-associated taxa linked to pulmonary disease, and provides insights into virome-host interactions involved in respiratory health.

METHODS: In this study, we compared viral and bacterial microbiome characteristics of LRTI patients with non-LRTI controls by α-diversity, β-diversity (PCoA, NMDS, ANOSIM), and differential abundance (LEfSe) analyses using metagenomic sequencing of bronchoalveolar lavage fluids, and further performed these comparisons similarly in respiratory failure (RF) patients and non-RF patients in the LRTI group. In addition, virus-bacteria co-occurrence patterns, the correlations between viral and bacterial abundance profiles, and the associations between microbial features and host clinical indicators were assessed using Spearman correlation analysis.

RESULTS: Overall, no significant differences in viral and bacterial α- or β-diversity were detected between LRTI (n=39) and non-LRTI (n=9) groups. However, among LRTI patients with RF (n=5), distinct viral taxonomic signatures were observed, including enrichment of Phixviricota, Malgrandaviricetes, Petitvirales, and Microviridae lineages. Despite taxonomic shifts, overall viral diversity remained similar between RF and non-RF subgroups. Bacterial communities showed no notable stratification across clinical categories. Correlation analyses revealed that uncultured human fecal viruses were negatively associated with lymphocyte counts, while Streptococcus-related bacteriophages correlated positively with C-reactive protein (CRP) levels.

CONCLUSION: The overall composition and diversity of the respiratory microbiome were insufficient to distinguish LRTI from non-LRTI conditions. However, within the LRTI cohort, patients with RF exhibited distinct viral taxonomic profiles compared to non-RF individuals. Additionally, several viral taxa were correlated with host clinical indicators irrespective of clinical subgroup. These findings highlight virome compositional differences associated with RF within LRTI patients, but do not imply causal effects, and warrant further investigation.},
}

Humans
*Respiratory Tract Infections/virology/microbiology/complications
*Metagenomics
Male
Middle Aged
Female
Bacteria/classification/genetics/isolation & purification
*Viruses/classification/genetics/isolation & purification
*Virome
Bronchoalveolar Lavage Fluid/virology/microbiology
Microbiota
Aged
*Respiratory Insufficiency/virology/microbiology
Adult

@article {pmid41058698,
year = {2025},
author = {Staley, S and Walkup, V and Oxendine, S and Mauya, Z and Williams, J and Busbee, PB and Wilson, K},
title = {Sex-dependent modulation of acute respiratory distress syndrome by Bacteroides acidifaciens: gut microbiome impact on lung inflammation.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1653309},
pmid = {41058698},
issn = {1664-3224},
mesh = {Animals ; *Respiratory Distress Syndrome/microbiology/immunology/pathology ; Female ; *Gastrointestinal Microbiome/immunology ; Male ; Mice ; Sex Factors ; *Pneumonia/immunology/microbiology ; Disease Models, Animal ; *Bacteroides/immunology ; Mice, Inbred C57BL ; Enterotoxins ; Lung/immunology/pathology/microbiology ; Th17 Cells/immunology ; },
abstract = {Bacteroides acidifaciens (BA), a common gut commensal, is known to modulate immune responses, but its role in acute respiratory distress syndrome (ARDS) and potential sex-specific effects remain poorly understood. To investigate this, male and female mice were colonized with BA prior to induction of ARDS using dual doses of staphylococcal enterotoxin B (SEB), a potent superantigen that triggers cytokine storm-driven lung injury. Clinical parameters, histopathology, gene expression, ELISA, flow cytometry, and gut barrier assessments were used to evaluate outcomes. BA pre-treatment significantly improved lung function, and attenuated pulmonary inflammation in male mice, correlating with increased IL-22, expansion of γδ T cells, and upregulation of colonic tight junction proteins. In contrast, BA exacerbated ARDS symptoms in females, increasing Th17 responses, neutrophil infiltration, and IgA-associated immune activation while impairing gut barrier integrity. These findings reveal that BA exerts divergent, sex-dependent effects in ARDS, highlighting the critical need to consider sex as a biological variable in microbiome-based therapies targeting inflammatory lung disease.},
}

Animals
*Respiratory Distress Syndrome/microbiology/immunology/pathology
Female
*Gastrointestinal Microbiome/immunology
Male
Mice
Sex Factors
*Pneumonia/immunology/microbiology
Disease Models, Animal
*Bacteroides/immunology
Mice, Inbred C57BL
Enterotoxins
Lung/immunology/pathology/microbiology
Th17 Cells/immunology

@article {pmid41058503,
year = {2025},
author = {Castro, M and Vida, R and Galeano, J and Cuesta, JA},
title = {Scarce data, noisy inferences and overfitting: the hidden flaws in ecological dynamics modelling.},
journal = {Journal of the Royal Society, Interface},
volume = {22},
number = {231},
pages = {20250183},
doi = {10.1098/rsif.2025.0183},
pmid = {41058503},
issn = {1742-5662},
support = {//Agencia Estatal de Investigación/ ; },
mesh = {*Models, Biological ; *Ecosystem ; Bayes Theorem ; *Microbiota ; Humans ; },
abstract = {Metagenomic data has significantly advanced microbiome research by employing ecological models, particularly in personalized medicine. The generalized Lotka-Volterra (gLV) model is commonly used to understand microbial interactions and predict ecosystem dynamics. However, gLV models often fail to capture complex interactions, especially when data are limited or noisy. This study critically assesses the effectiveness of gLV and similar models using Bayesian inference and a model reduction method based on information theory. We found that ecological data often leads to non-interpretability and overfitting due to limited information, noisy data and parameter sloppiness. Our results highlight the need for simpler models that align with the available data and propose a distribution-based approach to better capture ecosystem diversity, stability and competition. These findings challenge current bottom-up ecological modelling practices and aim to shift the focus towards a statistical mechanics view of ecology based on distributions of parameters.},
}

*Models, Biological
*Ecosystem
Bayes Theorem
*Microbiota
Humans

@article {pmid41058467,
year = {2025},
author = {Chekhun, V and Burda, T and Mushii, O and Pavlova, A and Borikun, T and Zadvornyi, T and Lukianova, N},
title = {STRESS-INDUCED MODULATION OF THE TUMOR MICROENVIRONMENT: MECHANISMS AND IMPLICATIONS FOR CANCER PROGRESSION.},
journal = {Experimental oncology},
volume = {47},
number = {2},
pages = {127-142},
doi = {10.15407/exp-oncology.2025.02.127},
pmid = {41058467},
issn = {2312-8852},
mesh = {Humans ; *Tumor Microenvironment ; *Neoplasms/pathology/etiology/metabolism ; Disease Progression ; Animals ; *Stress, Physiological ; *Stress, Psychological ; },
abstract = {Chronic stress is one of the key exogenous factors that can significantly affect tumor cell biology by disrupting the regulation of the tumor microenvironment (TME), thereby promoting the manifestation of the malignant process. Activation of the hypothalamic-pituitary-adrenal axis and the sympathetic nervous system induced by stressors leads to the secretion of glucocorticoids and catecholamines, which contribute to the deregulation of microenvironmental components that determine the aggressiveness of malignant neoplasms. This review systematizes the current views on the impact of stress-induced signals on the immune, stromal, vascular, and metabolic components of the TME and analyzes their contribution to the formation of an aggressive tumor phenotype. Particular attention is given to the interplay between neurohumoral stress, the gut, and the intratumoral microbiome, forming a complex networked environment supporting tumor progression. Advancing the understanding of molecular interactions between stress mediators and cellular elements of the TME will provide a foundation for developing innovative therapeutic strategies targeting not only the tumor itself but also minimizing the adverse effects of stress on individual components of the TME.},
}

Humans
*Tumor Microenvironment
*Neoplasms/pathology/etiology/metabolism
Disease Progression
Animals
*Stress, Physiological
*Stress, Psychological

@article {pmid41058431,
year = {2025},
author = {Jiménez-Arroyo, C and Molinero, N and Del Campo, R and Delgado, S and Moreno-Arribas, MV},
title = {Human gut microbiome study through metagenomics: Recent advances and challenges for clinical implementation.},
journal = {Enfermedades infecciosas y microbiologia clinica (English ed.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.eimce.2025.09.011},
pmid = {41058431},
issn = {2529-993X},
abstract = {Metagenomics has decisively advanced the study of the gut microbiome, enabling a better understanding of its importance for human health. Metataxonomics, based on the sequencing of the 16S rRNA gene, provides taxonomic profiles of prokaryotes, while shotgun metagenomics allows a comprehensive characterization of all DNA present in a sample. With adequate sequencing depth, the latter increases taxonomic resolution to the strain level and provides detailed information on the functional potential of the microbiota. However, the lack of standardization in sample collection and processing, sequencing technologies, and data management limits the comparability of results and their implementation in clinical laboratories. This review offers a practical and updated framework on metagenomic methodologies, data analysis, and the application of artificial intelligence tools, highlighting advances and best practices to facilitate the integration of functional microbiome analysis into clinical practice and to overcome current challenges.},
}

@article {pmid41058155,
year = {2025},
author = {Pan, R and Min, Z and Li, K and Feng, F and Zheng, B and Luo, X},
title = {Sea Cucumber Peptides Promote Testosterone Synthesis in Male Mice: Possibly via Alistipes-Bile Acid-FXR Signaling Pathway.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70286},
doi = {10.1002/mnfr.70286},
pmid = {41058155},
issn = {1613-4133},
support = {2024J08041//Natural Science Youth Fund of Fujian Province/ ; },
abstract = {In this study, the effects of sea cucumber peptides (SCP) on hormonal regulation in male mice and their underlying mechanisms were explored. SCP was administered to mice, followed by in vivo mating experiments, serum hormone profiling, gene expression analysis, and intestinal microbiome characterization. The impact of SCP on key intestinal bacteria was further validated using in vitro antibacterial assays. In vivo, SCP effectively improved mating ability, increased serum levels of testosterone, and enhanced the expression of testosterone synthesis-related genes. Furthermore, these phenomena may be related to the significant inhibition of Alistipes in the colon of mice by SCP. In vitro, SCP demonstrated antimicrobial activities against Alistipes, characterized by disruption of its cellular membrane integrity and suppression of bile salt hydrolase (BSH) activity. Consistently, there was a significant increase in serum total conjugated bile acids, accompanied by reduced fecal BSH activity and downregulation of farnesoid X receptor (FXR) expression in the testis. Correlation analysis suggested that SCP may promote testosterone synthesis through the Alistipes-bile acid-FXR signaling pathway. Conclusively, SCP can promote testosterone synthesis in male mice through the gut-testosterone axis, providing a new perspective for the study of active peptide-regulated hormones.},
}

@article {pmid41057967,
year = {2025},
author = {Jobert, L and Boulard, G and Poncelet, N and Adreit, H and Béna, G and Moulin, L},
title = {Variations in plant's cry for help evidenced by modifications of rice root microbiota induced by blast or brown spot diseases.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {128},
pmid = {41057967},
issn = {2524-6372},
support = {AF 2003-003//Agropolis Fondation/ ; AF 2003-003//Agropolis Fondation/ ; AF 2003-003//Agropolis Fondation/ ; AF 2003-003//Agropolis Fondation/ ; AF 2003-003//Agropolis Fondation/ ; AF 2003-003//Agropolis Fondation/ ; PhD//Ministère de l'Enseignement Supérieur et de la Recherche/ ; },
abstract = {BACKGROUND: Plants can recruit specific microbes to help them defend themselves against phytopathogens in a process known as "cry for help". In this study, we investigated whether a plant species modulates its root-associated microbiome differently - i.e. "cries out differently" - depending on the diversity of fungal pathogens attacking its leaves. To address this question, we monitored changes in the root microbiome of Oryza sativa cv. Nipponbare following infection with two fungal pathogens: Pyricularia oryzae (leaf blast) and Bipolaris oryzae (brown spot), under controlled conditions and using the same soil.

RESULTS: Our results support the "cry for help" hypothesis, suggesting that pathogen-induced stress drives the recruitment of beneficial microbes. While the composition of the root-associated microbiota remained globally stable after infection, subtle but significant taxonomic shifts were observed. Alpha diversity was unaffected, but changes in beta diversity occurred in micro-eukaryotic communities one week after brown spot infection and in bacterial communities two weeks after blast infection. Notably, beneficial taxa such as the bacterial genera Lentzea and Streptomyces, as well as the fungi Cladosporium halotolerans and Rhizophagus irregularis, were enriched in the below-ground microbiome of leaf-infected plants. The biocontrol potential of Rhizophagus irregularis was confirmed against blast but not brown spot infection.

CONCLUSIONS: These results advance our understanding of the "cry for help" hypothesis in rice and provide potential candidates for biocontrol. They highlight the complexity of plant-microbe interactions and suggest that rice plants specifically modulate their root microbiome in response to fungal infections, potentially shaping microbial communities to enhance defence strategies.},
}

@article {pmid41057822,
year = {2025},
author = {Parveen, S and Alhazmi, YA and Ibrahim, WI and Preethanath, RS and Khan, SS and Vempalli, S and Alam, MN and Ara, SA and Osman, HA and Homeida, HE and Elamin, NMH},
title = {Knowledge-to-practice gap in oral microbiome counseling: a mixed-methods study among dental practitioners in Saudi Arabia.},
journal = {BMC medical education},
volume = {25},
number = {1},
pages = {1363},
pmid = {41057822},
issn = {1472-6920},
mesh = {Humans ; Saudi Arabia ; Male ; Female ; *Microbiota ; *Counseling ; Adult ; *Dentists ; *Clinical Competence ; *Health Knowledge, Attitudes, Practice ; Surveys and Questionnaires ; Middle Aged ; *Mouth/microbiology ; },
abstract = {BACKGROUND: Evidence links the oral microbiome to systemic diseases, yet its integration into dental practice remains limited, particularly in Saudi Arabia, where non-communicable diseases are prevalent. Equipping dental practitioners with microbiome-related competencies is essential. This study evaluated the knowledge, confidence, and counseling practices of dental practitioners, identifying predictors and barriers to the clinical application of these practices.

METHODS: A convergent mixed-methods design involved 286 dental practitioners (general dentists, specialists, academics) across Saudi Arabia. Participants completed a 23-item validated questionnaire (13 assessing objective knowledge, 8 evaluating beliefs, confidence, and barriers, 2 open-ended). Quantitative data were analyzed using descriptive statistics, chi-square tests, and binary logistic regression. Qualitative data from 30 open-ended responses were qualitatively analyzed to explore contextual factors.

RESULTS: Practitioners exhibited moderate-to-high objective knowledge (mean score: 9.14 ± 1.87 out of 13), with 55.9% in the medium category, 28.3% high, and 15.7% low. Confidence in counseling was moderate, with 39.6% reporting high or very high confidence. Prior microbiome training (OR = 3.21, 95% CI: 1.82-5.65, p < 0.001), frequent participation in Continuing Professional Development (CPD), and journal use (OR = 2.15, 95% CI: 1.25-3.70, p = 0.006) predicted higher confidence. Barriers included lack of formal training (52.6%), time constraints (17.9%), and patient disinterest (29.5%). Social media was a key knowledge source (24.2%), while dental curricula were underutilized (14.4%). Qualitative themes reinforced barriers and highlighted conditional motivation linked to patient risk factors.

CONCLUSIONS: A notable knowledge-to-practice gap persists in oral microbiome counseling. We propose integrating microbiome science into dental curricula and utilizing mobile Continuing Professional Development (CPD) tools to enhance confidence and increase counseling frequency, thereby addressing training gaps and infrequent updates. Additionally, Electronic Health Record (EHR) prompts are recommended to overcome time constraints and patient disinterest, aligning with Saudi Vision 2030's goals for preventive care.},
}

Humans
Saudi Arabia
Male
Female
*Microbiota
*Counseling
Adult
*Dentists
*Clinical Competence
*Health Knowledge, Attitudes, Practice
Surveys and Questionnaires
Middle Aged
*Mouth/microbiology

@article {pmid41057523,
year = {2025},
author = {Liu, Z and Wu, Y and Wang, C and Hou, N and Liu, X},
title = {Changes in the vaginal microbiome in female patients with condyloma acuminatum and its impact on persistent HPV infection.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34996},
pmid = {41057523},
issn = {2045-2322},
mesh = {Humans ; Female ; *Microbiota/genetics ; *Vagina/microbiology/virology ; *Condylomata Acuminata/microbiology/virology ; Adult ; *Papillomavirus Infections/microbiology/virology ; RNA, Ribosomal, 16S/genetics ; Papillomaviridae ; Young Adult ; *Persistent Infection/microbiology/virology ; Middle Aged ; },
abstract = {Condyloma acuminatum (CA) is one of the most common sexually transmitted diseases, and is characterized by a long incubation period and a high recurrence rate. The vaginal microbiome significantly impacts female reproductive health, influencing susceptibility to human papillomavirus (HPV) infections and related conditions such as CA. However, the role of the vaginal microbiome in the development of CA, especially regarding persistent HPV infection and CA recurrence, remains unclear. We aimed to investigate changes in the vaginal microbiota among female patients with vaginal CA and to determine if disturbances in vaginal flora contribute to persistent HPV infection and CA recurrence. In this study, vaginal swabs were collected from 63 female patients with vaginal CA and 20 healthy females. Furthermore, in the patient cohort, CA patients were stratified into two groups, the HPV persistent-positivity (HPV_PP) group and the HPV turn-negative (HPV_TN) group, based on whether the HPV status converted to negative after a 2-year follow-up. 16S V3-V4 rRNA gene sequencing was performed on these collected samples, followed by a comprehensive analysis of the sequencing data. We performed clinical feature analysis, assessment of the alpha and beta diversity of the vaginal microbiota, comparative analysis of microbial taxa, and functional prediction analysis. We further analyzed the relative abundance and functional profiles between the HPV_PP and HPV_TN groups. The composition and function of the vaginal microflora differed between female patients with vaginal CA and healthy controls, with an increase in alpha diversity observed in the CA group. The relative abundances of P. bivia, Gemella asaccharolytica, Streptococcus agalactiae and Metamycoplasma hominis in the CA group were significantly higher than those in the control group. Moreover, P. bivia and Anaerococcus prevotii were more highly expressed in the HPV_PP group than in the HPV_TN group. With respect to the functional profile, the Kyoto Encyclopedia of Genes and Genomes (KEGG) categories of signal transduction, drug resistance antimicrobial, xenobiotic biodegradation and metabolism, and MAPK signaling pathway, were significantly enriched in the HPV_PP group. In conclusion, the composition and function of the vaginal flora in female patients with vaginal CA are altered, and P. bivia is expected to be a diagnostic biomarker for persistent HPV infection. An imbalance in the vaginal flora is significantly associated with the recurrence of CA and HPV persistent infection.},
}

Humans
Female
*Microbiota/genetics
*Vagina/microbiology/virology
*Condylomata Acuminata/microbiology/virology
Adult
*Papillomavirus Infections/microbiology/virology
RNA, Ribosomal, 16S/genetics
Papillomaviridae
Young Adult
*Persistent Infection/microbiology/virology
Middle Aged

@article {pmid41057449,
year = {2025},
author = {Sun, J and Dai, X and Zhao, Z and Li, H and Sun, L and Liu, Y and Xue, Z and Dong, L},
title = {Fenlong-ridging combined with composite modifier reconstructs soil microbiome to mitigate saline stress and enhance sustainable cultivation of Isatis indigotica Fortune.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34900},
pmid = {41057449},
issn = {2045-2322},
support = {2022YFD1900105//the National Key Research and Development Program of China/ ; },
mesh = {*Soil Microbiology ; *Microbiota ; *Soil/chemistry ; *Isatis/growth & development/microbiology ; *Salt Stress ; Biomass ; },
abstract = {Structural barriers and nutrient scarcity constrain medicinal plant cultivation in coastal saline soils. To address these challenges, we investigated a physical-chemical-microbial synergistic remediation strategy using Fenlong-ridging (FR) and a composite modifier (CM) by evaluating four soil treatments: conventional tillage; FR only; a CM only and FR combined with a CM (FR_CM). A comparative analysis of the four treatments revealed FR_CM to be the most influential strategy for improving coastal saline soil. The FR_CM treatment reduced soil electrical conductivity and bulk density by 78.38% and 29.31%, respectively; enhanced soil nutrient content and Isatis indigotica Fortune biomass by 68.91-114.29% and 126.52%, respectively; induced significant reorganization of microbial community structure at the phylum/OTU levels; elevated microbial network parameters, including positive/negative correlation ratios, modularity, and average path length; and enriched functional taxa such as fermentation and chitinolysis, while enhancing stress-tolerant phenotypes and suppressing potentially pathogenic phenotypes. This work establishes a theoretical foundation and technical paradigm for microbial-mediated remediation in saline-alkali ecosystems to assist crop-to-environment adaptation strategies and maintain sustainable medicinal plant production.},
}

*Soil Microbiology
*Microbiota
*Soil/chemistry
*Isatis/growth & development/microbiology
*Salt Stress
Biomass

@article {pmid41057417,
year = {2025},
author = {Manoharan-Basil, S and Gestels, Z and Abdellati, S and Vanbaelen, T and Van Den Bossche, D and van Alebeek, L and Van Herrewege, Y and Poppe, L and Vandenhove, L and Bracke, S and Smekens, B and Jacobs, B and Genbrugge, E and Kenyon, C},
title = {Concentrations of ciprofloxacin in food defined as safe alter the gut microbiome and ciprofloxacin susceptibility in humans: an interventional clinical study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34908},
pmid = {41057417},
issn = {2045-2322},
mesh = {Humans ; *Ciprofloxacin/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Escherichia coli/drug effects ; Male ; Female ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; Adult ; Microbial Sensitivity Tests ; Middle Aged ; Young Adult ; Enrofloxacin ; Drug Resistance, Bacterial ; },
abstract = {It is unknown if the low residual concentrations of ciprofloxacin/enrofloxacin allowed in food could influence the human microbiome. The European Medicines Agency reports that it is safe for an average human to ingest 372 µg of enrofloxacin/ciprofloxacin daily. We randomized 30 individuals to either 372 µg of ciprofloxacin or placebo daily for 27 days in a 2:1 fashion and measured the effect on the gut microbiome and the susceptibility of Escherichia coli to ciprofloxacin. After 27 days the E. coli of the individuals in the ciprofloxacin, but not the placebo arm, had reduced ciprofloxacin susceptibility. The receipt of ciprofloxacin was also associated with a reduction in the number of E. coli colony forming units in the gut. The low concentration of antimicrobials allowed in food may have an impact on the composition of the gut microbiome and antimicrobial susceptibility.},
}

Humans
*Ciprofloxacin/pharmacology/administration & dosage
*Gastrointestinal Microbiome/drug effects
Escherichia coli/drug effects
Male
Female
*Anti-Bacterial Agents/pharmacology/administration & dosage
Adult
Microbial Sensitivity Tests
Middle Aged
Young Adult
Enrofloxacin
Drug Resistance, Bacterial

@article {pmid41057288,
year = {2025},
author = {van Leeuwen, LM and van Beveren, GJ and Peeters, MAG and Souverein, D and Euser, S and Bogaert, D and van Houten, MA},
title = {Aberrant Growth in 5-Year-Old Children After Antibiotics in the First Week of Life.},
journal = {Acta paediatrica (Oslo, Norway : 1992)},
volume = {},
number = {},
pages = {},
doi = {10.1111/apa.70322},
pmid = {41057288},
issn = {1651-2227},
support = {SCAF/16/03/CSO_/Chief Scientist Office/United Kingdom ; //Spaarne Gasthuis stimuleringsfonds/ ; 91715359//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 205300001/ZONMW_/ZonMw/Netherlands ; },
abstract = {AIM: We examined the relationship between early-life antibiotics, different regimens, and growth until age five years.

METHODS: Data from two parallel birth cohorts were analysed: 128 healthy term-born children and 147 term-born children who received antibiotics for suspected neonatal sepsis, randomised across three regimens: Amoxicillin+Cefotaxime, Augmentin+Gentamicin, Penicillin+Gentamicin. Until age five years, growth, environmental exposures, diet, and physical activity data were collected. Primary outcomes were weight-for-age, height-for-age, and weight-for-height z-scores with early-life antibiotic exposure and the regimen as determinants of interest.

RESULTS: The median antibiotic exposure duration was 3 days (interquartile range 2.4-5.5 days). Children exposed to early-life antibiotics had on average 0.26 lower weight-for-height z-scores over the first five years compared to unexposed controls (p = 0.014). Especially children treated with Augmentin+Gentamicin showed lower weight-for-height z-scores, compared to unexposed controls (coefficient = 0.36; p = 0.013). Additionally, at age five years, higher birth weight percentiles were associated with higher weight-for-age, height-for-age and weight-for-height and weekly lemonade consumption was associated with higher weight-for-age z-scores.

CONCLUSION: Antibiotics in the first week of life are associated with lower weight-for-height up to age five years, with effects varying by treatment type. To explain these effects, further examination of antimicrobial-induced early-life microbiome perturbations and subsequent growth is needed.

TRIAL REGISTRATION: International Clinical Trial Registry Platform (https://trialsearch.who.int/): NL4882 and NL3821.},
}

@article {pmid39896668,
year = {2025},
author = {Akbary Moghaddam, V and Acharya, S and Schwaiger-Haber, M and Liao, S and Jung, WJ and Thyagarajan, B and Shriver, LP and Daw, EW and Saccone, NL and An, P and Brent, MR and Patti, GJ and Province, MA},
title = {Gene-Embedded Multi-Modal Networks for Population-Scale Multi-Omics Discovery.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.22.634403},
pmid = {39896668},
issn = {2692-8205},
support = {P30 DK056341/DK/NIDDK NIH HHS/United States ; U19 AG063893/AG/NIA NIH HHS/United States ; },
abstract = {We present Gene-Embedded Multi-modal Networks (GEM-Net), a semi-supervised framework for constructing multi-modal networks centered on genes. GEM-Net uses gene-level modules and selectively incorporates heterogeneous omics profiles using a correlated meta-analysis strategy that accounts for scale imbalance, missingness, and intra-modular correlation. Prior to network inference, we developed a harmonized data processing protocol that adjusts each omic layer independently through a shared mathematical workflow involving transformation, dimensionality reduction, and regression-based covariate adjustment. GEM-Net modules were inferred and benchmarked against unsupervised methods using transcriptomic, metabolomic, and lipidomic data from the Long Life Family Study (LLFS), a unique cohort enriched for exceptional familial longevity and health. GEM-Net modules were more diverse and biologically interpretable, with stronger support from protein- protein interactions, transcriptional regulation, and metabolic annotations. Applying GEM-Net to metabolic health in LLFS revealed an axis between the microbiome-derived metabolite N-acetylglycine and immune genes (FCER1A, HDC, CPA3, MS4A2) associated with improved insulin sensitivity and reduced inflammation in healthy older individuals. GEM-Nets offer a reusable reference from a long-lived population and a generalizable framework for multi-omics discovery. https://doi.org/10.5281/zenodo.15003731 .},
}

@article {pmid39764050,
year = {2025},
author = {Nasr, E and Pechlivanis, N and Strepis, N and Amato, P and Bernt, M and Bhardwaj, A and Blankenberg, D and Brites, D and Cumbo, F and Do, K and Ferrari, E and Griffin, TJ and Gruening, B and Hiltemann, S and Hyde, CJ and Jagtap, P and Mehta, S and Métris, KL and Momin, S and Nelson, TM and Oba, A and Pavloudi, C and Péguilhan, R and Price, GR and Psomopoulos, F and Rosic, N and Schatz, MC and Schiml, VC and Siguret, C and Soranzo, N and Stubbs, A and Van Heusden, P and Vohra, M and , and Zierep, P and Batut, B},
title = {Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.23.629682},
pmid = {39764050},
issn = {2692-8205},
support = {U24 AI183870/AI/NIAID NIH HHS/United States ; U41 HG006620/HG/NHGRI NIH HHS/United States ; },
abstract = {The explosion of microbial omics data has outpaced the ability of many researchers to analyze it, with complex tools and limited computational resources creating barriers to discovery. To address this gap, we present the Microbiology Galaxy Lab: a free, globally accessible, community-supported platform that combines state-of-the-art analytical power with user-friendly accessibility. Supported by the Galaxy and global microbiology communities, this platform integrates over 315 tool suites and 115 curated workflows, enabling comprehensive metabarcoding, (meta)genomic, (meta)transcriptomic, and (meta)proteomic data analysis within a FAIR-aligned environment. It also supports research in the health and infectious disease sectors, as well as in environmental microbiology. The platform's utility is exemplified through various use cases, including antimicrobial resistance tracking, biomarker prediction, microbiome classification, and functional annotation of key microbes. Built on reproducibility and community engagement, it supports creation, sharing, and updating of best-practice workflows. Over 35 tutorials and learning paths empower scientists, fostering an ecosystem that keeps resources at the forefront of microbial science. The Microbiology Galaxy Lab enables collective analysis, democratising research, thereby accelerating discovery across the global microbiology community (microbiology.usegalaxy.org, .eu, .org.au, .fr).},
}

@article {pmid41057270,
year = {2025},
author = {Hallett, EN and Comte, J},
title = {Identification and Global Distribution of a Core Microbiome From High-Arctic Lakes.},
journal = {Environmental microbiology},
volume = {27},
number = {10},
pages = {e70182},
doi = {10.1111/1462-2920.70182},
pmid = {41057270},
issn = {1462-2920},
support = {RGPIN-2020-06874//Natural Sciences and Engineering Research Council of Canada/ ; RGPNS-2020-06874//Natural Sciences and Engineering Research Council of Canada/ ; //Natural Resources Canada/ ; },
mesh = {*Lakes/microbiology ; Arctic Regions ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Biodiversity ; High-Throughput Nucleotide Sequencing ; },
abstract = {Arctic lakes are sentinels of climate change, yet their microbial community structure and functioning remain poorly understood. This study analysed the genetic content of clear-water Arctic lakes and their surroundings using high-throughput amplicon sequencing of the 16S rRNA gene to identify their core microbiome and its contribution to the overall taxonomy pool. To assess geographical constraints and oligotrophic conditions, these results were compared with a latitudinally diverse multi-basin oligotrophic lake in a temperate climate. Arctic and temperate lakes exhibited different assemblages, but both showed similar transitional gradients of microbial community composition from upstream soils/inlets through the lake system to the outlet, driven mainly by the dissolved organic matter (DOM) characteristics. Distinct core microbiomes were identified for temperate and Arctic lakes, with Arctic lakes appearing more diverse. A limited shared core microbiome was observed between the two regions, composed mostly of typical freshwater bacteria. While core taxa identities differed between regions, most exhibited characteristics of generalist bacteria with a strong global presence. These results provide key insights into the structure of remote high Arctic lakes, contributing to our understanding of aquatic microbial ecology in a transitioning Arctic and identifying microbial communities and individual taxa of interest for further study on oligotrophy.},
}

*Lakes/microbiology
Arctic Regions
*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Phylogeny
DNA, Bacterial/genetics
Biodiversity
High-Throughput Nucleotide Sequencing

@article {pmid41057255,
year = {2025},
author = {Maurice, K and Roy, J and Boukcim, H and Selosse, MA and Ducousso, M},
title = {Historical Land Use Drives Present Microbial Community Assembly in an Extreme Environment.},
journal = {Environmental microbiology},
volume = {27},
number = {10},
pages = {e70189},
doi = {10.1111/1462-2920.70189},
pmid = {41057255},
issn = {1462-2920},
support = {//RCU (Royal Commission for AlUla)/ ; //AFALULA (Agence Française pour le développement d'AlUla)/ ; },
mesh = {*Soil Microbiology ; Phylogeny ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; *Microbiota ; Biodiversity ; *Extreme Environments ; Ecosystem ; Agriculture ; Desert Climate ; Soil/chemistry ; },
abstract = {The extent to which past disturbances influence present-day microbial composition and assembly remains poorly understood, especially in extreme environments such as deserts. Using a phylogenetic framework of diversity partitioning, linked to soil composition, we aimed to disentangle the impacts of past disturbance on present-day bacterial and fungal communities, where we also distinguish abundant and rare taxa. Our findings demonstrate that past agricultural activity promoted strong phylogenetic clustering and turnover, accompanied by increased phylogenetic diversity and niche width, reflecting the influence of transient resource availability and niche diversification. Conversely, long-term disturbances reduced phylogenetic diversity and niche width while amplifying selection processes and phylogenetic turnover. These patterns indicate intensified abiotic constraints in this system, where historical contingencies-characterised by enduring drought-wetting cycles-differentially shaped bacterial and fungal communities. Rare taxa were more sensitive to land use and deterministic, while abundant taxa showed broader niche adaptability and stochastic influences, highlighting the need for targeted conservation strategies. This work highlights the critical role of historical disturbances in shaping microbial assembly, provides actionable insights into enhancing desert ecosystem resilience and informing sustainable restoration practices. Si content-a key driver of phylogenetic turnover-could be targeted for ecosystem recovery and conservation strategies in degraded arid regions.},
}

*Soil Microbiology
Phylogeny
*Bacteria/classification/genetics/isolation & purification
*Fungi/classification/genetics/isolation & purification
*Microbiota
Biodiversity
*Extreme Environments
Ecosystem
Agriculture
Desert Climate
Soil/chemistry

@article {pmid41057215,
year = {2025},
author = {Leitao Filho, FS and Milne, S},
title = {The MUSIC trial: harmonising our understanding of inhaled corticosteroids and the COPD airway microbiome.},
journal = {The European respiratory journal},
volume = {66},
number = {4},
pages = {},
doi = {10.1183/13993003.01605-2025},
pmid = {41057215},
issn = {1399-3003},
}

@article {pmid41056987,
year = {2025},
author = {Tsante, K and Petrou, E and Tsalas, S and Tsantes, AG and Lianou, A and Kartelias, G and Kyriakou, E and Kokoris, S and Nikolopoulos, G and Bonovas, S and Sokou, R},
title = {Do we Have the Gut to Beat Thrombosis?.},
journal = {Seminars in thrombosis and hemostasis},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-2704-8487},
pmid = {41056987},
issn = {1098-9064},
abstract = {Arterial and venous thromboembolism represent major contributors to global morbidity and mortality. Despite substantial progress in risk stratification and clinical management, a significant proportion of thromboembolic events occur in individuals not classified within traditional high-risk groups indicating the involvement of additional, non-conventional risk factors in thrombotic pathophysiology.Recent evidence has highlighted the gut microbiome as a critical determinant of human health, with increasing recognition of its role in cardiovascular and thrombotic disorders. Furthermore, the gut microbiome constitutes a modifiable risk factor, offering new horizons for therapeutic intervention and emerging evidence suggests that alterations in the microbiome may significantly impact thrombotic risk.Moreover, microbiome-derived metabolites have gathered considerable scientific attention for their potential involvement in the initiation and progression of thrombosis. These metabolites may serve as novel biomarkers, complementing conventional risk indicators in disease diagnosis, prognosis, screening, and patient monitoring. Microbiome-derived metabolites may hold dual utility, first as diagnostic and prognostic biomarkers, and, second, as potential targets for pharmacologic modulation. Collectively, these findings underscore the growing significance of the gut microbiome as an environmental factor in thromboembolic disease and justify the constantly increasing employment of the scientific community in several aspects of health and disease.},
}

@article {pmid41056719,
year = {2025},
author = {Huang, X and He, Y and Zhang, L and Chen, J and Zhang, G and Zhang, Z and Huang, W and Ma, L and Cheng, F and Wang, Y and Zhu, X and Ju, F},
title = {Deciphering structuring mechanism and increased health risk of antibiotic resistome from a coastal river basin to the downstream estuary and bay under anthropogenic disturbances.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140040},
doi = {10.1016/j.jhazmat.2025.140040},
pmid = {41056719},
issn = {1873-3336},
abstract = {Environmental microbiome harbors antibiotic resistance genes (ARGs) integrable with human and animal resistomes. Despite the prevailing concerns on the continental-scale contamination of estuaries with ARGs, the resistome structuring mechanisms and health risks in hydrodynamically-disturbed coastal ecosystems are unknown. This study showed that the resistome structure shifted from the Qiantang River Basin via its estuary to Hangzhou Bay in eastern China, driven by both biotic (e.g., microbial community and mobile genetic elements) and abiotic factors (e.g., pharmaceutical and personal care products, and tidal hydrodynamics), suggesting the combined role of vertical and horizontal transmission in shaping antibiotic resistome. The notable abundance increases (by at least 1.8 times) of extended-spectrum β-lactamases (e.g., CTX-M-65, SHV-67), carbapenemase (e.g., KPC-2), and mobile ARGs of synthetic veterinary antibiotics (e.g., florfenicol-resistant floR and sulfonamide-resistant sul1) reflected the prevalence of clinically important antibiotic resistance in the estuary and contributed to the observed elevation in resistome risks. Further discovery of macrolide resistance gene macB and extended-spectrum β-lactamase TEM-116 in uncultured indigenous Nitrospirota strains implicated the alarming invasion of clinically important antibiotic resistance into the coastal sediment resistomes. These results emphasize the prominent role of anthropogenic disturbances in shaping resistome structure and escalating health risks in coastal ecosystems.},
}

@article {pmid41056662,
year = {2025},
author = {Kolli, RD and Kasireddy, B and Bortoluzzi, C and Iuspa, MA and Olukosi, OA},
title = {Precision biotic modulates the impact of mixed Eimeria infection in broiler chickens fed wheat-corn-soybean meal diets.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {105909},
doi = {10.1016/j.psj.2025.105909},
pmid = {41056662},
issn = {1525-3171},
abstract = {Coccidiosis leads to gut damage, impairing nutrient digestibility and modifying the substrates available to the microbiome. This study assessed the supplementation of a precision biotic (PB) on growth performance, ileal amino acid digestibility, mRNA expression of nutrient transporter genes, jejunal histomorphology, and litter surface ammonia emission in broilers challenged with a mixed Eimeria inoculum (CH) and fed corn-SBM (C) or wheat-corn-SBM (W) diets. Zero-day-old male chicks (1,012) were used (6 treatments with at least seven replicates) in a randomized incomplete block design. Treatments were: C diet, no challenge (C-NCH); or with challenge (C-CH-0); W diet plus challenge, without PB (W-CH-0); W diet plus challenge, plus 300 (W-CH-300), 600 (W-CH-600), or 900 (W-CH-900) mg/kg of PB. On d 12, all birds, except C-NCH, were challenged with mixed Eimeria oocysts by feed inoculation to induce enteric stress. Jejunal tissues were collected on d 20 and 42 for gene expression and histomorphology. On d 42, ammonia emissions were recorded, and ileal digesta were collected for digestibility. The Eimeria challenge significantly (P < 0.05) reduced weight gain (WG) and feed intake (FI) during the challenge phase, and increased FCR compared to C-NCH. PB supplementation tended to reduce FCR in a quadratic fashion (P =0.053). The expression of GLUT2 and EAAT3 was significantly reduced by the challenge (P < 0.05) compared to C-NCH. Apparent ileal digestibility of DM, N, and amino acids (AA) was significantly (P < 0.001) reduced in challenged birds but improved quadratically (P < 0.01) with PB. Litter ammonia levels were significantly (P = 0.01) lower in W-CH-0 than C-CH-0. It can be concluded that PB supplementation improved the gastrointestinal tract functionality likely via modulation of microbiome metabolism, which produced increased digestible nutrient intake, especially during the compensatory growth phase, which might have contributed to partially reversing the adverse effect of the Eimeria challenge on the growth performance of the broiler chickens.},
}

@article {pmid41056661,
year = {2025},
author = {Sun, Y and Wang, T and Zhang, Y and Ma, N and Zhao, X and He, X},
title = {Daidzein-betaine cocrystal alleviates high-energy and low-protein diet induced fatty liver hemorrhagic syndrome in laying hens through gut-liver axis.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {105867},
doi = {10.1016/j.psj.2025.105867},
pmid = {41056661},
issn = {1525-3171},
abstract = {Fatty liver hemorrhagic syndrome (FLHS) severely endangers the health and productivity of laying hens, marked by hepatic steatosis and impaired lipid metabolism. Daidzein-betaine cocrystal improves lipid metabolism in the diet-induced obesity mice. We investigated the effects of daidzein-betaine cocrystal diet on production performance, egg quality, intestinal injury, cecal microbiota, the metabolites of intestinal microbiota and hepatic lipid metabolism in FLHS laying hens. A total of 108 twenty-eight-week-old laying hens were allocated to 6 treatments: the control group (normal diet), model group (high-energy and low-protein (HELP) diet), daidzein group (200 mg/kg daidzein + HELP diet), betaine group (184.62 mg/kg betaine + HELP diet), physical mixture group (384.62 mg/kg physical mixture + HELP diet) and daidzein-betaine cocrystal group (384.62 mg/kg daidzein-betaine cocrystal + HELP diet). The findings showed that intake of daidzein, betaine, physical mixture and daidzein-betaine cocrystal effectively alleviated the disordered lipid metabolism in laying hens fed a HELP diet. Moreover, daidzein-betaine cocrystal was best supplement in the improvement of the lipid metabolism. The daidzein-betaine cocrystal modulated the dysbiosis induced by HELP-diet through reducing the abundance of Desulfovibrio and increasing the abundance of Rikenellaceae_RC9_gut_group and Unclassified_f_Lachnospiraceae, whereas enhancing β-diversity of the gut microbiome, to restore equilibrium. Fecal metabolomics analysis showed that the indicators related to the 6 differentially abundant metabolites (DAMs) of lipid metabolism were improved. Transcriptome analysis identified 12 differentially expressed genes (DEGs) related to lipid metabolism. DAMs and DEGs were mainly co-enriched in peroxisome proliferators-activated receptor (PPAR) signaling pathways. To sum up, our results showed that dietary daidzein-betaine cocrystal could alleviate hepatic metabolic disorders associated with FLHS in laying hens by regulating the "gut-liver axis". This highlights the significant potential of the daidzein-betaine cocrystal as a therapeutic agent for counteracting the impacts of a HELP diet.},
}

@article {pmid41056462,
year = {2025},
author = {Mahdavi, S},
title = {Precision Nutritional Genomics, Gut Microbiota and Artificial Intelligence in Chronic Kidney Disease.},
journal = {Journal of the American Nutrition Association},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/27697061.2025.2549893},
pmid = {41056462},
issn = {2769-707X},
abstract = {Chronic kidney disease (CKD) is a prevalent global health issue, and nutritional management of CKD is an integral component through all stages of the disease. However, response to dietary interventions varies, potentially due to genetic variations influencing metabolic pathways. This review highlights key gene-diet interactions relevant to CKD management, including risk factors and comorbidities such as hypertension, diabetes, and proteinuria. Variants in the ACE gene influence salt sensitivity and blood pressure responses, while TCF7L2 polymorphisms affect the relationship between dietary glycemic load and diabetes risk, impacting kidney complications. Protein intake, a key modifier of CKD, correlates with proteinuria risk, moderated by a PPM1K polymorphism. Dietary bioactives, such as caffeine, may also alter the progression rate of proteinuria and hypertension, with effects contingent upon CYP1A2 genotype. Additional markers of cardiovascular disease, CKD-associated bone-mineral disease, and CKD anemia are also discussed as well as role of the gut microbiome in nutrition modulation and vice versa. The review concludes with the potential of artificial intelligence as a clinical tool to refine precision nutrition, enabling clinicians to adopt targeted approaches, stratified by genetic-metabolic patient profiles that match best nutritional interventions for prevention and management of CKD. Vitamin D is used as a model nutrient to illustrate a simulated framework for precision nutrition, incorporating molecular mechanisms, genetic variation, epigenetic modifications, and translational tools applicable to both population health and clinical practice.},
}

@article {pmid41056270,
year = {2025},
author = {Ahmed, S and Hexun, Z and Yano, Y and Okami, Y and Azahar, NM and Kondo, K and Arima, H and Torii, S and Moniruzzaman, M and Ganbaatar, G and Kadota, A and Andoh, A and Shiino, A and Ueshima, H and Miura, K and , },
title = {Relationship between Gut microbiome and brain volumes among Japanese Men.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0333612},
doi = {10.1371/journal.pone.0333612},
pmid = {41056270},
issn = {1932-6203},
mesh = {Humans ; Male ; Aged ; Middle Aged ; *Gastrointestinal Microbiome ; Magnetic Resonance Imaging ; *Brain/anatomy & histology/diagnostic imaging ; Aged, 80 and over ; Cross-Sectional Studies ; Japan ; Organ Size ; RNA, Ribosomal, 16S/genetics ; Gray Matter/diagnostic imaging/anatomy & histology ; Asian People ; East Asian People ; },
abstract = {Evidence of preclinical interactions between the gut microbiome and brain health is accumulating. Studies of animal models and specific patient populations have suggested a relationship between gut microbiomes and brain volumes, but this association is understudied in apparently healthy humans. We conducted a population-based cross-sectional study of 623 Japanese men from the Shiga Epidemiological Study on Subclinical Atherosclerosis (SESSA). We performed 16S ribosomal RNA gene sequencing of stool samples collected during the follow-up stage (mean [SD] age, 68.0 [8.0] years; range, 46-83 years). All participants underwent brain magnetic resonance imaging and automated voxel-based morphometry. Principal coordinate analysis, linear discriminant, and multivariable linear regression analyses were performed. In multivariable linear regression analysis, after adjusting for age and total intracranial volume, only gray matter volume showed a positive association with alpha diversity (the Shannon index richness, q-value <0.01). However, no association was found after further adjustments for body mass index, physical activity, smoking, drinking, and hypertension. The weighted UniFrac distances (beta diversity) measured using principal coordinate analysis showed that lower and higher white and gray matter volumes formed distinct clusters (q < 0.01). In linear discriminant analysis and multivariable-adjusted linear regression analysis, several genera were significantly associated with gray and white matter volumes (q < 0.01); however, Lachnospiraceae, a butyrate-producing bacterium, was consistently related to a higher white matter volume in different statistical analysis models. Egarthellaceae, Bifidobacteraceae, and Selenomonadaceae showed a positive association with greater gray matter volume. Our findings support an association between gut microbiome diversity and brain volumes in middle-aged to older Japanese men. This study provides insight into the underlying effects of the gut microbiome on human brain volume.},
}

Humans
Male
Aged
Middle Aged
*Gastrointestinal Microbiome
Magnetic Resonance Imaging
*Brain/anatomy & histology/diagnostic imaging
Aged, 80 and over
Cross-Sectional Studies
Japan
Organ Size
RNA, Ribosomal, 16S/genetics
Gray Matter/diagnostic imaging/anatomy & histology
Asian People
East Asian People

@article {pmid41056245,
year = {2025},
author = {Roongpiboonsopit, D and Wairit, S and Nithisathienchai, C and Pakdee, A and Cheibchalard, T and Sayasathid, J and Wilantho, A and Tongsima, S and Somboonna, N},
title = {Oral microbiome dysbiosis in acute ischemic stroke and transient ischemic attack patients.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0333676},
doi = {10.1371/journal.pone.0333676},
pmid = {41056245},
issn = {1932-6203},
mesh = {Humans ; Male ; Female ; *Dysbiosis/microbiology ; *Ischemic Attack, Transient/microbiology ; *Microbiota/genetics ; Middle Aged ; Case-Control Studies ; Aged ; *Ischemic Stroke/microbiology ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Saliva/microbiology ; Bacteria/genetics/classification ; *Mouth/microbiology ; },
abstract = {Oral microbiome (bacterial community) may influence systemic inflammation and vascular health, which both are critical factors in a pathogenesis of ischemic stroke. This study aimed to evaluate differences in the saliva microbiome of acute ischemic stroke (AIS) and transient ischemic attack (TIA) patients compared with matched healthy controls, hypothesizing that AIS and TIA patients are associated with oral microbiome shift. A prospective case-control study was conducted in Naresuan University Hospital, Thailand, to compare the saliva microbiome of AIS and TIA stroke patients of Thai ethnic with matched healthy controls. Microbial profiles were analyzed by metagenomics combined 16S rRNA gene sequencing to assess microbial alpha diversity, taxonomic composition, beta diversity, and microbial functional pathways.Forty-one patients (31 AIS and 10 TIA) and 20 age- and sex-matched stroke-free healthy controls were included in this study. Baseline characteristics were comparable between groups, apart from higher rates of hypertension, diabetes, and smoking in the patient group. Patients exhibited significantly higher alpha-diversity genus richness by OTUs and Chao1 index than controls (p < 0.001), highlighting an altered microbial community structure. Phylum-level analysis revealed an increased abundance of Bacillota (p = 0.0285) in the patient group, with a statistically decreasing trend for Bacteroidota, Actinomycetota and Pseudomonadota (p < 0.05). At the genus level, Streptococcus was more significantly abundant in the patients (p = 0.0171), while Prevotella was reduced. The patient and control groups were statistically separated in beta-diversity analysis (PERMANOVA, p < 0.001), with species biomarker analysis by LEfSe (Linear discriminant analysis effect size) could suggest species markers for each group. Functional pathway analysis showed the patient group the significantly higher in functional categories of, for examples, xenobiotics biodegradation and metabolism, cardiovascular diseases, signal transduction, and membrane transport (Welch's t-test, p < 0.05). In conclusion, this study demonstrated the statistical alterations in the saliva microbiome of AIS and TIA patients, characterized by increased genus richness diversity and relatively distinct microbial shifts that may be associated with stroke-related inflammation. The findings suggest the saliva microbiome analysis as potential as a non-invasive biomarker for stroke risk and its role in stroke pathophysiology.},
}

Humans
Male
Female
*Dysbiosis/microbiology
*Ischemic Attack, Transient/microbiology
*Microbiota/genetics
Middle Aged
Case-Control Studies
Aged
*Ischemic Stroke/microbiology
RNA, Ribosomal, 16S/genetics
Prospective Studies
Saliva/microbiology
Bacteria/genetics/classification
*Mouth/microbiology

@article {pmid41056240,
year = {2025},
author = {Brenner, LN and Huang, CY and Kim, M and Bringhurst, L and Richards, CJ and Sicilian, L and Neuringer, I and Putman, MS and Lai, PS},
title = {Dysglycemia and the airway microbiome in cystic fibrosis.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0331847},
doi = {10.1371/journal.pone.0331847},
pmid = {41056240},
issn = {1932-6203},
mesh = {Humans ; *Cystic Fibrosis/microbiology/complications ; *Microbiota ; Male ; Female ; Adult ; Sputum/microbiology ; *Diabetes Mellitus/microbiology/etiology ; Glucose Tolerance Test ; Young Adult ; Lung/microbiology ; Respiratory Function Tests ; Pseudomonas aeruginosa ; },
abstract = {BACKGROUND: Cystic fibrosis-related diabetes (CFRD) is one of the most common non-pulmonary complications in people living with cystic fibrosis (pwCF), seen in up to 50% of adults. Even when correcting for severity of CFTR mutations, those with CFRD have more pulmonary exacerbations, lower lung function, and increased mortality than those with normal glucose tolerance (NGT).

METHODS: Expectorated sputum samples were collected from 63 pwCF during routine outpatient visits (29 with CFRD, 12 with IGT and 22 with NGT). Oral glucose tolerance test results, A1c levels, and pulmonary function tests closest to the time of sputum collection were obtained from the medical record. Samples underwent metagenomics sequencing and raw reads were processed through the bioBakery workflow for taxonomic profiling at the species level as well as predicted functional profiling and antibiotic resistance profiling. Viral profiling was performed with Marker-MAGu. Differences in alpha diversity, beta diversity, and differential abundance were assessed. Microbiome and phage signatures of CFRD were generated using sparse partial least squares models which were subsequently used as a primary predictor of lung function using multivariate linear regression.

RESULTS: In linear models, CFRD status compared to NGT was associated with a lower alpha diversity (reciprocal Simpson -1.98 [-3.80,-0.16], p = 0.033) and differences in microbial community composition (Bray Curtis dissimilarity PERMANOVA R2 0.17, p = 0.011). Pseudomonas aeruginosa and Streptococcus gordonii had higher relative abundance in CRFD vs NGT participants (2.43 [0.027, 4.82], unadjusted p = 0.056 and 1.11 [0.58, 1.64] unadjusted p= < .001 respectively). There were global differences between CFRD vs NGT in both functional pathways and antibiotic resistance genes. In multivariate models adjusting for age, sex, antibiotic use, and modulator therapies, virome but not microbiome signatures of CFRD were associated with lower FEV1 percent predicted (-6.4 [95% CI -10.2, -2.6]%, p = 0.001 for each 10% increase in virome score).

CONCLUSION: Differences in the airway microbiome in those with dysglycemia in CF are associated with poorer lung function.},
}

Humans
*Cystic Fibrosis/microbiology/complications
*Microbiota
Male
Female
Adult
Sputum/microbiology
*Diabetes Mellitus/microbiology/etiology
Glucose Tolerance Test
Young Adult
Lung/microbiology
Respiratory Function Tests
Pseudomonas aeruginosa

@article {pmid41055976,
year = {2025},
author = {He, J and Chen, Z and Jiang, K and Yang, Y and Li, W and Wang, X and Xu, X and Zheng, S and Jiao, X and Chen, X and Huo, L and Lim, B and Liu, SJ and Gao, X},
title = {A nonenzymatic effector disrupts Bacteroides cell wall homeostasis via OmpA targeting to mediate interbacterial competition.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {41},
pages = {e2513207122},
doi = {10.1073/pnas.2513207122},
pmid = {41055976},
issn = {1091-6490},
support = {2024YFA0920100//MOST | National Key Research and Development Program of China (NKPs)/ ; },
mesh = {*Bacterial Outer Membrane Proteins/metabolism/genetics ; Homeostasis ; *Cell Wall/metabolism ; *Bacteroides fragilis/metabolism ; Humans ; *Bacteroides/metabolism ; Gastrointestinal Microbiome ; *Bacterial Proteins/metabolism/genetics ; Animals ; Type VI Secretion Systems/metabolism ; },
abstract = {The human gut microbiome is a dynamic ecosystem where bacteria engage in interspecies competition using molecular weapons such as the type VI secretion system (T6SS). Here, we characterize BteO-BtiO, a unique effector-immunity pair in Bacteroides fragilis that mediates antagonism via a nonenzymatic mechanism. Microscopy reveals that BteO exposure leads to cell elongation, membrane blebbing, and lysis in sensitive strains. Structural and biochemical analyses demonstrate that BteO disrupts cell wall homeostasis by binding to conserved C-terminal domains of OmpA-family proteins (OmpAs), which are critical for outer membrane integrity. The immunity protein BtiO neutralizes BteO by mimicking the OmpA-binding interface. We further show that bile salts enhance BteO-mediated killing in vitro and that BteO confers a competitive advantage in the mammalian gut. Remarkably, BteO exhibits broad-spectrum activity across Bacteroides species. These findings reveal a nonenzymatic strategy of bacterial antagonism and broaden our understanding of T6SS effector diversity within Bacteroides.},
}

*Bacterial Outer Membrane Proteins/metabolism/genetics
Homeostasis
*Cell Wall/metabolism
*Bacteroides fragilis/metabolism
Humans
*Bacteroides/metabolism
Gastrointestinal Microbiome
*Bacterial Proteins/metabolism/genetics
Animals
Type VI Secretion Systems/metabolism

@article {pmid41055944,
year = {2025},
author = {Saygin, H},
title = {Comparative genomics and ecological insights into Nonomuraea turcica sp. nov., an actinomycete from Black Sea island soil.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {10},
pages = {},
doi = {10.1099/ijsem.0.006938},
pmid = {41055944},
issn = {1466-5034},
mesh = {*Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; DNA, Bacterial/genetics ; Base Composition ; Bacterial Typing Techniques ; *Genome, Bacterial ; Black Sea ; Sequence Analysis, DNA ; Islands ; Fatty Acids/chemistry/analysis ; Turkey ; Nucleic Acid Hybridization ; Genomics ; *Actinomycetales/classification/genetics/isolation & purification ; },
abstract = {A polyphasic study was undertaken to characterize strain G32[T], an actinomycete isolated from soil collected on Giresun Island (Black Sea, Turkey). 16S rRNA phylogeny placed the strain within the genus Nonomuraea, but ≤99.1% similarity to its nearest type strains, Nonomuraea turkmeniaca DSM 43926[T], Nonomuraea aridisoli KC333[T], Nonomuraea candida NRRL B-24552[T], Nonomuraea polychroma DSM 43925[T] and Nonomuraea endophytica DSM 45385[T], suggested that it potentially represents a novel taxon. The total genome size is about 12.66 Mb, and the digital G+C content is 69.6 mol%. The high-quality draft genome shared ≤92.16% average nucleotide identity and ≤47.0% digital DNA-DNA hybridization with the closest related type strains, corroborating species-level distinctness. Comparative genomics against four type strains, N. turkmeniaca DSM 43926[T], N. polychrom DSM 43925[T], N. aridisoli KC333[T] and N. endophytica DSM 45385[T], revealed an open pangenome of 24,056 orthologous families, of which G32[T] contributed 2,785 singletons. Copy-number expansion of aqpZ with four paralogues and efeB with three paralogues, together with the sole genome-wide occurrence of ACC-deaminase and an additional fhuDBC siderophore transporter, highlights adaptations to periodic salinity, iron limitation and rhizosphere contact in island soil. Chemotaxonomic markers (meso-diaminopimelic, madurose, MK-9(H4), iso-C16 : 0, iso-C16 : 0 2OH and C17 : 0 10-methyl) of the strain were consistent with the genus Nonomuraea, but phenotypic traits further differentiated the isolate from its relatives. Based on the evidence presented here, strain G32[T] represents a novel species of the genus Nonomuraea, for which the name Nonomuraea turcica sp. nov. is proposed. The type strain of the species is G32[T] (=KCTC 49887[T]=CGMCC 4.7873[T]).},
}

*Phylogeny
RNA, Ribosomal, 16S/genetics
*Soil Microbiology
DNA, Bacterial/genetics
Base Composition
Bacterial Typing Techniques
*Genome, Bacterial
Black Sea
Sequence Analysis, DNA
Islands
Fatty Acids/chemistry/analysis
Turkey
Nucleic Acid Hybridization
Genomics
*Actinomycetales/classification/genetics/isolation & purification

@article {pmid41055728,
year = {2025},
author = {Mehta, SD and Thorington, R and Agingu, W and Otieno, F and Unitt, A and Rusie, LK and Le Van, A and Martin, I and Jerse, AE and Harrison, O},
title = {Genomic trends and emerging antimicrobial resistance in Neisseria gonorrhoeae over two decades in Kenya.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0158625},
doi = {10.1128/spectrum.01586-25},
pmid = {41055728},
issn = {2165-0497},
abstract = {We investigated the trends and antimicrobial resistance (AMR) of Neisseria gonorrhoeae (NG) in Kenya with whole-genome sequencing (WGS) of isolates collected in 2002-2009 (n = 108) and 2020-2022 (n = 110). Phenotypic AMR was confirmed by agar dilution. Predicted minimum inhibitory concentrations (MICs), multi-locus sequence typing (MLST), multi-antigen ST (NG-MAST), NG-STAR, and AMR genetic determinants were determined using WGS and detection of molecular markers. The WGS cgMLST typing used LIN codes. Resistance to penicillin, ciprofloxacin, and tetracycline was common throughout. In 2020-2022, azithromycin resistance (n = 2) and cephalosporin alert values (n = 5) were observed. Phylogenetic clusters were congruent with the LIN code lineage, though other typing schemes (MLST, NG-STAR, and NG-MAST) were not as consistent. There were major shifts over time in the lineages and genetic determinants. Circumcision and HIV status were associated with several AMR, housekeeping, metabolism, and iron acquisition genetic determinants. These findings highlight dynamic NG genomic trends, emerging macrolide resistance, and the value of WGS for surveillance. Behavioral and biological factors may contribute to AMR emergence and warrant further investigation. IMPORTANCE This work highlights the significant value of using whole-genome sequencing to track the evolution and epidemiology of gonorrhea over 20 years: (i) we documented the emergence of azithromycin resistance and cephalosporin reduced susceptibility and relationship to genetics of gonorrhea; (ii) by combining epidemiological and genetic data, we found that circumcision and HIV status were linked to specific genetic features of gonorrhea, including those tied to antibiotic resistance; and (iii) we used novel and traditional genetic typing methods to expand and refine the understanding of lineage shifts and genetic determinants, enhancing surveillance and intervention efforts. Some isolates had potential decreasing susceptibility for cephalosporins, highlighting the critical importance of ongoing surveillance and the opportunity for novel resistance gene identification. Studying how gonorrhea strains relate to a person's immune system, other bacteria (microbiome), and sexual networks could help us understand how certain strains spread and what the potential factors amplifying antimicrobial resistance are.},
}

@article {pmid41055637,
year = {2025},
author = {Kanteres, T and Angelakopoulou, IM and Angelakopoulou, EA and Tsolaki, F and Tagarakis, G and Manika, K and Exidari, M and Gioula, G},
title = {Lung microbiome dynamics in health and lung cancer.},
journal = {Microbial genomics},
volume = {11},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001509},
pmid = {41055637},
issn = {2057-5858},
mesh = {Humans ; *Lung Neoplasms/microbiology ; *Microbiota ; *Lung/microbiology ; Dysbiosis/microbiology ; },
abstract = {Application of culture-independent sequencing technologies has revealed the presence of a low-biomass, high-diversity microbiome within healthy human lungs. This community is highly dynamic, with microbes constantly being introduced into and cleared from healthy airways, and its multifaceted roles in lung physiology and disease are currently a matter of intensive investigation. In view of the rising lung cancer incidence and mortality rates, a large amount of research has already been conducted in the context of lung cancer, suggesting an association between lung cancer and local dysbiosis. In light of these developments, this review summarizes and discusses existing knowledge on lung microbiome dynamics and composition in health and how these differ in lung cancer patients, focusing on the latest research. Throughout this effort, frequently reported alterations and associated microbe-host interactions in lung cancer development and progression are highlighted, along with some critical methodological considerations, outstanding questions and suggestions for the future.},
}

Humans
*Lung Neoplasms/microbiology
*Microbiota
*Lung/microbiology
Dysbiosis/microbiology

@article {pmid41055404,
year = {2025},
author = {Colston, TJ},
title = {Digest: Theoretical advances in studying selection via microbiome-mediated traits.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/evolut/qpaf203},
pmid = {41055404},
issn = {1558-5646},
abstract = {How do microbes associated with multicellular hosts contribute to host evolution, and how do factors such as mode of transmission mediate these contributions? Week et al. (2025) provide a theoretical framework to address these questions and through simulation show that microbial transmission mode can have varying effects that interact with host life history. This expands our potential to understand host-microbiome dynamics and illustrates that a quantitative genetic framework provides a more accurate view of organismal evolution than correlative analyses of siloed datasets.},
}

@article {pmid41055348,
year = {2025},
author = {Robino, L and Navarro, N and Canales-Huerta, N and González, MJ and Cruz, E and Sauto, R and Morales, C and Neffa, F and Zeballos, J and Jessen, GL and Zunino, P and Scavone, P},
title = {Urogenital microbiome, intracellular bacterial communities, and their contribution to urinary tract infections.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0124725},
doi = {10.1128/spectrum.01247-25},
pmid = {41055348},
issn = {2165-0497},
abstract = {The urinary tract was long considered a sterile environment, but recent studies have revealed the presence of diverse microbial communities in healthy individuals collectively known as the urinary microbiome or urobiome. Although the urobiome has been studied primarily in populations from North America, Europe, and Asia, little is known about its characteristics in Latin America. In this work, we conducted a descriptive analysis of the urobiome of 77 adults, 40 females, and 37 males with and without symptoms of urinary tract infections (UTI) from Uruguay using a strategy that includes expanded quantitative uroculture, 16S rRNA gene sequencing from urine, and intracellular bacterial community evaluation. The microbial profiles revealed a wide diversity in the bacterial community composition, including both Lactobacillus-dominated and diverse non-Lactobacillus communities. Notably, several genera frequently associated with health or disease, such as Gardnerella, Staphylococcus, Streptococcus, and Escherichia, were detected in many samples. We also observed associations between community types and host factors, such as gender, presence of symptoms, and IBC. These findings contribute to expanding our understanding of the human urobiome and highlight the need to consider geographic and cultural diversities when characterizing microbial communities and their implications for health.IMPORTANCEThe concept of a sterile urinary tract has been challenged by the discovery of complex microbial communities in urine samples from healthy individuals. Most existing studies on the urinary microbiome focus on populations in the Global North, resulting in limited data from Latin America. Here, we present the first study characterizing the urobiome of an adult Uruguayan population using 16S rRNA gene sequencing. By analyzing associations between bacterial community types and individual metadata, we provide insights into the diversity and structure of urinary microbiota in a previously understudied population. These results broaden the current understanding of the urobiome and emphasize the importance of including diverse populations in microbiome research to achieve a more comprehensive and representative view of microbial contributions to health and disease.},
}

@article {pmid41055335,
year = {2025},
author = {An, R and Xie, E and Binns, J and Rey, FE and Kendziorski, C and Thibeault, SL},
title = {Gut-larynx axis and its contribution to laryngeal immunity.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0104425},
doi = {10.1128/msystems.01044-25},
pmid = {41055335},
issn = {2379-5077},
abstract = {UNLABELLED: The larynx is vital for swallowing, breathing, coughing, and voice production, supported by its unique microbial and immunological environment. We hypothesized the existence of a gut-larynx axis, where resident gut and laryngeal microbiota influence immune modulation in the larynx. To test this, conventionally raised, wild-type C57BL/6 J mice were treated with an oral antibiotic regimen to disrupt gut microbiota and compared with untreated controls. Antibiotic treatment significantly disrupted gut microbiota but left laryngeal microbiota largely unaffected. However, antibiotic-treated mice showed notable changes in laryngeal epithelial and immune cells, as well as fibroblasts. Differential gene expression analysis revealed alterations in pathways related to epithelial barrier integrity, immune signaling, and bacterial response. Gene regulatory network analysis identified significant changes in regulons Etv4(+), Irf3(+), Hltf(+), Mga(+), and Nfil3(+). Additionally, cell-cell communication, particularly immune-epithelial interactions, was altered, with integrin-mediated signaling emerging as a key pathway. These findings suggest that gut and laryngeal microbiota may synergistically modulate immune responses, highlighting the importance of gut-larynx interactions in respiratory immunity.

IMPORTANCE: This study investigates the gut-larynx axis, revealing how gut dysbiosis impacts immune responses in the larynx. Although laryngeal microbiota remained stable, significant immunological and cellular changes occurred following gut microbiota disruption. Transcriptomic alterations in epithelial integrity, immune signaling, and cell communication underscore the systemic impact of gut dysbiosis. The identification of integrin-mediated signaling as a key pathway in immune-epithelial interactions emphasizes the complexity of host-microbe dynamics. These findings suggest that gut health plays a critical role in shaping respiratory immunity, providing a foundation for future research into microbiota-driven immune modulation in the upper airway.},
}

@article {pmid41055333,
year = {2025},
author = {Sharma, S and Narahari, HP and Raman, K},
title = {Harnessing machine learning for metagenomic data analysis: trends and applications.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0164224},
doi = {10.1128/msystems.01642-24},
pmid = {41055333},
issn = {2379-5077},
abstract = {Metagenomic sequencing has revolutionized our understanding of microbial ecosystems by enabling high-resolution profiling of microbes across diverse environments. However, the resulting data are high-dimensional, sparse, and noisy, posing challenges for downstream data analysis. Machine learning (ML) has provided an arsenal of tools to extract meaningful insights from such large and complex data sets. This review surveys the existing state of ML applications in metagenomic data analysis, from traditional supervised and unsupervised learning to time-series modeling, transfer learning, and newer directions such as causal ML and generative models. We highlight certain key challenges and delve into important issues like model interpretability, emphasizing the importance of explainable AI (XAI). We also compare ML with mechanistic models, commenting on their relative advantages, disadvantages, and prospects for synergy. Finally, we preview future directions, such as the incorporation of multi-omics data, synthetic data generation, and Agentic AI systems, highlighting the increasingly prominent role that AI and ML will play in the future of microbiome science.},
}

@article {pmid41054760,
year = {2025},
author = {Sen, R and Jha, SS and Amarnath, SS and Jethwa, JT and Tiwari, JP and Das, C and Kambhampati, SBS and Poduval, M and Dave, BR and Chaddha, R and Vishwanathan, K and Chandrashekara, S and Panchagnula, R and Bhadada, S},
title = {Indian Orthopaedics Association Guidelines for Osteoporosis.},
journal = {Indian journal of orthopaedics},
volume = {59},
number = {9},
pages = {1279-1347},
doi = {10.1007/s43465-025-01393-7},
pmid = {41054760},
issn = {0019-5413},
abstract = {INTRODUCTION: These guidelines provide a comprehensive and practical framework for preventing osteoporosis. They are designed for use by healthcare professionals, including orthopaedic surgeons, primary care physicians, specialists, nurses, and allied health providers, as they work with patients at risk of or already diagnosed with osteoporosis.

METHODOLOGY: This iterative process involved multiple questionnaires sent to a panel of 62 osteoporosis and bone health experts. Experts, including clinicians, researchers, and academicians, were selected based on their recognised expertise and contributions to the field of osteoporosis.

OBSERVATIONS: There were 62 medical personnel with experience. The protocol was to get consensus from experts for each round. The set of questions was divided into six rounds. This structured Delphi methodology ensured that the resulting osteoporosis guidelines were evidence based and reflective of expert consensus, providing a robust clinical practice framework.

RESULTS: The guidelines were put up in sections with titles as: prevention of osteoporosis, Screening for osteoporosis, diagnosing osteoporosis, calcium and vitamin D in osteoporosis, microbiome, obesity in osteoporosis, postmenopausal osteoporosis, male osteoporosis. Chronic kidney disease and osteoporosis, glucocorticoid-induced osteoporosis (GIOP), therapeutics in osteoporosis, monitoring osteoporosis therapy and osteosarcopenia. Ultimately, all the details obtained in various meetings were analysed, and responses were sought from all the participant members. All such reactions were again grouped back sequentially.

CONCLUSIONS: osteoporosis is a significant problem, and many protocols exist in the literature. These guidelines were created by consensus among experts using the Delphi method. They have been developed until current knowledge is available and may be changed in the next 5-6 years, depending on the new research accumulated by that time.},
}

@article {pmid41054350,
year = {2025},
author = {Ahmad, N and Zhu, Z and Chu, T and Jiaxin, L and Danni, L and Yue, J and Zhang, L and Yuan, H and Song, Y},
title = {Preventive effects of sheep milk on DSS-induced colitis in mice: modulation of gut microbiota and inflammatory responses.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo02200b},
pmid = {41054350},
issn = {2042-650X},
abstract = {This study explores the potential of sheep milk (SM) as a therapeutic treatment for ulcerative colitis (UC) in mice, focusing on its dose-dependent effects. Sheep milk, known for its rich bioactive compounds, shows significant anti-inflammatory and antioxidant properties. Using a combination of ELISA, qPCR, IHC, microbiome analysis, and untargeted metabolomics, we examined how SM protects against UC. The results revealed that SM treatment reduced the expression of pro-inflammatory cytokines (IL-1β, TNF-α), inflammatory markers (COX-2, iNOS), and TLR-4 in mice with DSS-induced colitis. Additionally, SM increased the levels of MUC2, MUC3, and key tight junction proteins (ZO-1, claudin-1, occludin), helping to restore the intestinal barrier. Microbiome analysis and metabolomics showed that SM helped balance the gut microbiota and boosted beneficial short-chain fatty acids. These findings suggest that sheep milk supplementation significantly modulated beneficial gut microbiota groups, including Akkermansia and Lactobacillus, showing promise as a dietary intervention for improving gut health and managing inflammatory bowel disease.},
}

@article {pmid41054270,
year = {2025},
author = {Six, DL and Hammerbacher, A and Trowbridge, A and Bullington, L},
title = {From beginning to end: the synecology of tree-killing bark beetles, fungi, and trees.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {},
number = {},
pages = {},
doi = {10.1111/brv.70084},
pmid = {41054270},
issn = {1469-185X},
abstract = {Over a century of research has revealed an amazing complexity of behaviours and physiological adaptations that allow tiny bark beetles to overcome large trees, sometimes resulting in outbreaks that kill millions of trees. Turning a tree into a home and successfully raising offspring involves constant interactions among the beetles, the tree, its microbiome, and the beetles' associated microbes, all influenced by abiotic factors that can determine success or failure. While we have learned much about these systems, substantial knowledge gaps remain. This synthesis aims to clarify and integrate current understanding, identify gaps, challenge long-held assumptions, and address interpretative issues that impede progress toward a holistic understanding of these systems. We advocate for expanding perspectives using synecological approaches to understand these complex systems better. We encourage expanding research into how colonization by the bark beetle-fungi complex influences subsequent tree decay and forest carbon dynamics. An explicit goal is to provide a comprehensive resource for new researchers while encouraging them to question established hypotheses and to explore new avenues of enquiry.},
}

@article {pmid41054174,
year = {2025},
author = {Das S, S and Rm, V and Aneesa, PA and Joy Parappilly, S and Natinga Mulakal, J and Chakrapani Ps, B and Illathu Madhavamenon, K},
title = {Ferula asafoetida oleo-gum resin alleviates dyspepsia symptoms through modulation of microbiome-gut-brain axis: A randomized, double-blind, placebo-controlled study.},
journal = {Medicine},
volume = {104},
number = {40},
pages = {e44590},
doi = {10.1097/MD.0000000000044590},
pmid = {41054174},
issn = {1536-5964},
support = {//Akay Natural Ingredients Pvt Ltd/ ; },
mesh = {Humans ; Double-Blind Method ; *Gastrointestinal Microbiome/drug effects ; Male ; *Dyspepsia/drug therapy/microbiology ; Female ; Adult ; Middle Aged ; *Ferula/chemistry ; *Resins, Plant/therapeutic use ; *Brain-Gut Axis/drug effects ; Treatment Outcome ; Cognition/drug effects ; },
abstract = {BACKGROUND: Functional dyspepsia (FD) is a prevalent gut-brain interaction disorder that adversely affects cognitive function. Current treatment options offer limited efficacy and are often associated with undesirable side effects. Hence, in this study, we evaluated the efficacy of a food-grade, self-emulsifying hydrogel formulation of Ferula asafoetida oleo-gum resin (ASF) in improving dyspepsia symptoms, cognitive function, sleep quality, and gut microbiota in individuals with FD symptoms.

METHODS: A randomized, double-blind, placebo-controlled trial was conducted with 62 participants diagnosed with FD symptoms. Subjects received 250 mg/d of ASF or placebo for 14 days. Outcome measures included the Leuven Postprandial Distress Scale, choice reaction time test, Bergen Insomnia Scale (BIS), Bristol Stool Form Scale, and gut microbiome profiling.

RESULTS: ASF treatment showed a significant time, treatment, and treatment × time effect for early satiety, bloating, and heart burn (P < .05). Further analysis of Leuven Postprandial Distress Scale data by Mann-Whitney U test provided the influence of ASF on days 1, 3, 7, and 14 which indicated a progressive improvement in the number of positive responders, especially for bloating, early satiety, and postprandial fullness (P < .05). ASF also significantly modulated the gut microbiota by decreasing the Firmicutes-to-Bacteroidetes ratio (71.9%; P < .001), enhancing alpha diversity (P < .05), enriching beneficial genera (e.g., Bacteroides, Prevotella), and reducing harmful taxa (e.g., Escherichia, Clostridia). Further, ASF demonstrated improvements in digestion and reduced constipation as indicated by the Bristol Stool Form Scale, with type 1 stools decreasing from 65% to 18% and type 2 from 35% to 7% by day 14. Neurocognitive assessments showed improved attention and focus (44% reduction in reaction time, P < .001), while BIS results indicated better sleep quality (ΔBIS = 10.89 ± 3.23, P < .001) on day 14.

CONCLUSION: ASF demonstrated significant modulation of the microbiome-gut-brain axis, resulting in reduced dyspepsia symptom severity, enhanced cognitive performance, improved sleep quality, and better digestive outcomes. These findings support the potential of ASF as a safe and effective dietary supplement for gut and cognitive health in individuals with FD.},
}

Humans
Double-Blind Method
*Gastrointestinal Microbiome/drug effects
Male
*Dyspepsia/drug therapy/microbiology
Female
Adult
Middle Aged
*Ferula/chemistry
*Resins, Plant/therapeutic use
*Brain-Gut Axis/drug effects
Treatment Outcome
Cognition/drug effects

@article {pmid41053880,
year = {2025},
author = {Shittu, OE and Enagbonma, BJ and Babalola, OO},
title = {Deciphering the influence of fertilization systems on the Allium ampeloprasum rhizosphere microbial diversity and community structure through a shotgun metagenomics profiling approach.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {126},
pmid = {41053880},
issn = {2524-6372},
support = {CRP/ZAF22-03)//ICGEB, Italy/ ; NRF//South African National Research Foundation/ ; },
abstract = {BACKGROUND: Chemical fertilizer application in agriculture over the years has been a vital instrument to boost agricultural yields and soil fertility, but has threatened the diversity of the rhizosphere microbiomes in the soil. However, knowledge about the impacts of biofertilizers (BF) as well as chemical fertilizers (CF) on Allium ampeloprasum rhizosphere's microbiomes is still limited. Hence, this study investigated the metagenomic profiling of A. ampeloprasum rhizosphere under different fertilization systems and in bulk soils, to obtain a depiction of their associated microbial diversity and community structure, which will inform best agricultural practices.

METHOD: The entire DNA sample was mined from soil samples taken from an independent uncultivated bulk soil and the rhizosphere of A. ampeloprasum treated with chemical and biofertilizer and subjected to shotgun metagenomics sequencing.

RESULTS: The taxonomic analysis of our metagenome unveiled that while all soil samples exhibited similar core microbial phyla, Bacteroidota and Verrucomicrobiota were exclusive to the biofertilizer (G2) plot. Actinobacteria and Pseudomonadota (Proteobacteria) were predominant in the biofertilizer plot (G2), chemical fertilizer (G1), and bulk soil (G3) plots, respectively. Genera such as Dyadobacter, Verrucomicrobium, Streptomyces, and Haliangium were exclusively detected in the biofertilizer plot (G2). Alpha diversity analysis showed that G2 harboured the most diverse microbial community, followed by G3, with the lowest diversity found in the G1 plot, highlighting the importance of biofertilizer in increasing microbial diversity. The observed differences in the microbial diversity and community structure are highly linked to the nature of fertilizer applied and the distinct physicochemical parameters of the three plots. However, redundancy analysis subsequently highlighted total nitrogen and carbon as the key environmental influencers impacting the microbial community structure and composition.

CONCLUSION: This study underscores the potential of biofertilizers in boosting the rhizosphere microbial diversity, improving soil health, and offer a sustainable alternative to chemical fertilizers, thereby supporting long-term agricultural sustainability and resilience in food production systems.},
}

@article {pmid41053825,
year = {2025},
author = {Villette, R and Ortís Sunyer, J and Novikova, PV and Aho, VTE and Petrov, VA and Hickl, O and Busi, SB and De Rudder, C and Kunath, BJ and Heintz-Buschart, A and Trezzi, JP and Halder, R and Jäger, C and Lebrun, LA and Daujeumont, A and Schade, S and Janzen, A and Jehmlich, N and von Bergen, M and Laczny, CC and May, P and Trenkwalder, C and Oertel, W and Mollenhauer, B and Wilmes, P},
title = {Integrated multi-omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson's disease.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {200},
pmid = {41053825},
issn = {2049-2618},
support = {863664//HORIZON EUROPE European Research Council/ ; PRIDE/11823097//Fonds National de la Recherche Luxembourg/ ; CORE/16/BM/11333923//Fonds National de la Recherche Luxembourg/ ; CORE/15/BM/10404093//Fonds National de la Recherche Luxembourg/ ; FNR11264123//Fonds National de la Recherche Luxembourg/ ; MJFF-019228//Michael J. Fox Foundation for Parkinson's Research/ ; MCI-BIOME_2019//Institute for Advanced Studies, Université of Luxembourg/ ; 101038088//European Union's Horizon 2020 Widening Fellowships/ ; INTER/DFG/19/14429377//DFG Research Unit FOR2488/ ; },
mesh = {*Parkinson Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; *Metabolomics/methods ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Male ; Female ; Middle Aged ; Aged ; Feces/microbiology ; Metabolome ; Prodromal Symptoms ; Multiomics ; },
abstract = {BACKGROUND: Parkinson's disease (PD) is associated with gut microbiome shifts. These shifts are mainly described at taxonomic level, but the functional consequences remain unclear. To obtain insight into the functional disruptions of the gut microbiome in PD, we used an integrated multi-omics approach, comparing gut microbiomes of individuals with PD, prodromal PD, and healthy controls.

RESULTS: Meta-metabolomics, the most discriminatory and robust omics level, was selected to Guide the analysis. We identified 11 metabolites that were differentially abundant between the groups, among which β-glutamate was increased in PD and prodromal PD, and correlated with the transcriptional activities of Methanobrevibacter smithii and Clostridium spp. We identified decreases in transcripts, but not in gene abundances, related to glutamate metabolism, bile acids biosynthesis, chemotaxis, and flagellar assembly in PD, particularly in keystone genera such as Roseburia, Agathobacter, and Blautia. Our findings, integrated into the Expobiome map, reveal multifactorial microbiome alterations which converge with PD pathways.

CONCLUSION: Our study highlights the apparent disruption of microbial gene expression in PD, particularly in genes associated to mobility. Moreover, we showcase the importance of investigating the gut microbiome's functional dimensions to better resolve microbiome-host interactions in health and disease.},
}

*Parkinson Disease/microbiology
*Gastrointestinal Microbiome/genetics
Humans
*Metabolomics/methods
*Bacteria/classification/genetics/metabolism/isolation & purification
Male
Female
Middle Aged
Aged
Feces/microbiology
Metabolome
Prodromal Symptoms
Multiomics

@article {pmid41053813,
year = {2025},
author = {Lapid, R and Motro, Y and Juravel, K and King, R and Moran-Gilad, J and Kahila Bar-Gal, G},
title = {The golden jackal (Canis aureus): interaction of fur and fecal microbiota, host genetics and animal traits.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {106},
pmid = {41053813},
issn = {2524-4671},
}

@article {pmid41053692,
year = {2025},
author = {Ljung, A and Gio-Batta, M and Hesselmar, B and Imberg, H and Rabe, H and Nowrouzian, FL and Johansen, S and Wold, AE and Adlerberth, I},
title = {Major gut microbiota perturbations in firstborn infants compared to those with older siblings soon after delivery.},
journal = {BMC pediatrics},
volume = {25},
number = {1},
pages = {780},
pmid = {41053692},
issn = {1471-2431},
}

@article {pmid41053650,
year = {2025},
author = {Yadadi, SS and Sekar, P and Mohammed, MM and Acharya, A and Rahman, B and Ahmed, AS and Shetty, PJ and Vinay, V and Shetty, RM},
title = {FimA genotype variants of Porphyromonas gingivalis in periodontal health and disease: a preliminary observational study among the UAE population.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {1547},
pmid = {41053650},
issn = {1472-6831},
support = {2101100248//The Office of Vice Chancellor for Research and Graduate Studies, University of Sharjah, Sharjah, United Arab Emirates/ ; 2101100248//The Office of Vice Chancellor for Research and Graduate Studies, University of Sharjah, Sharjah, United Arab Emirates/ ; 2101100248//The Office of Vice Chancellor for Research and Graduate Studies, University of Sharjah, Sharjah, United Arab Emirates/ ; 2101100248//The Office of Vice Chancellor for Research and Graduate Studies, University of Sharjah, Sharjah, United Arab Emirates/ ; 2101100248//The Office of Vice Chancellor for Research and Graduate Studies, University of Sharjah, Sharjah, United Arab Emirates/ ; 2101100248//The Office of Vice Chancellor for Research and Graduate Studies, University of Sharjah, Sharjah, United Arab Emirates/ ; 2101100248//The Office of Vice Chancellor for Research and Graduate Studies, University of Sharjah, Sharjah, United Arab Emirates/ ; },
mesh = {Humans ; *Porphyromonas gingivalis/genetics ; United Arab Emirates/epidemiology ; Male ; Female ; Genotype ; Adult ; Middle Aged ; *Periodontitis/microbiology ; *Fimbriae Proteins/genetics ; Case-Control Studies ; Dental Plaque/microbiology ; Periodontal Index ; },
abstract = {BACKGROUND: This research explores the prevalence of fimA genotype variants of Porphyromonas gingivalis (P. gingivalis) in individuals with periodontitis and healthy controls within the United Arab Emirates (UAE). It seeks to examine the relationship between these genotypes and both periodontal health and disease. The study aims to improve our understanding of the involvement of P. gingivalis in periodontal diseases among the UAE population.

METHODS: This research involved 127 individuals diagnosed with periodontitis and 127 healthy participants matched for age and gender. Subgingival plaque samples were collected and examined for fimA genotypes (types I, II, III, IV, and V) employing polymerase chain reaction (PCR). A statistical evaluation using the chi-squared test was conducted to explore the relationship between fimA genotypes and periodontal condition, providing insights into the relationship between microbial profiles and periodontal health and disease.

RESULTS: The study found a significant link between specific fimA genotypes and periodontitis. The fimA genotype II was most common in periodontitis patients (41.7%) compared to healthy individuals (7.1%), with a strong association (p < 0.001). fimA genotype type IV was also more frequent in patients (15.0%) than in controls (2.4%), showing a significant correlation (p < 0.001). Other genotypes, such as fimA I, III, and V, were more frequently observed in patients, suggesting their involvement in disease development.

CONCLUSION: This study highlights a significant link between specific P. gingivalis fimA genotypes, particularly types II and IV fimA genotype combinations, and periodontitis in the UAE population. These findings provide insights into the prevalence of genotypes and suggest future research into their pathogenic mechanisms, potentially leading to new therapeutic interventions for periodontitis.},
}

Humans
*Porphyromonas gingivalis/genetics
United Arab Emirates/epidemiology
Male
Female
Genotype
Adult
Middle Aged
*Periodontitis/microbiology
*Fimbriae Proteins/genetics
Case-Control Studies
Dental Plaque/microbiology
Periodontal Index

@article {pmid41053568,
year = {2025},
author = {Krämer, CL and Müller, DW and Arndt, F and Rehm, A and Walkenfort, B and Ahmed, AS and Haben, A and Schiele, A and Auerhammer, A and Hasenberg, M and Boschert, AL and Kautenburger, R and Leuko, S and Janssen, S and Maurer, M and Mücklich, F and Siems, K},
title = {Touching Surfaces - Presence of microorganisms on antimicrobial metal surfaces on the International Space Station and in German schools.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {631},
pmid = {41053568},
issn = {1471-2180},
mesh = {Germany ; Humans ; *Bacteria/isolation & purification/genetics/classification/drug effects ; *Copper/pharmacology/chemistry ; RNA, Ribosomal, 16S/genetics ; Schools ; *Spacecraft ; Methicillin-Resistant Staphylococcus aureus/drug effects/isolation & purification ; Surface Properties ; *Anti-Infective Agents/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Fomites/microbiology ; *Environmental Microbiology ; },
abstract = {Microorganisms are an integral component of human health on Earth as well as for life on the International Space Station. However, inescapably, fomites in human habitats can serve as crucial niches for opportunistic pathogens. To explore potential countermeasures for the associated infection risk, the Touching Surfaces experiment evaluated antibacterial surfaces as high-touch surfaces on the International Space Station and on Earth. We used copper-based surfaces that integrate chemical antimicrobial properties with topography, thereby creating a metasurface. 16 S rRNA sequencing revealed that most bacteria found were human associated. While no significant distinction was observed between the microbial communities on the reference and antibacterial surfaces, isolation of microorganisms from the surfaces suggests that copper-based nanometer-structured surfaces exhibit enhanced antibacterial efficacy. The antibacterial efficacy of touched surfaces was reduced, as assessed by wet contact killing assays carried out using a methicillin-resistant Staphylococcus aureus (MRSA) isolate. The simplicity of implementing the surfaces allowed for straightforward testing of surfaces in both space and on Earth.},
}

Germany
Humans
*Bacteria/isolation & purification/genetics/classification/drug effects
*Copper/pharmacology/chemistry
RNA, Ribosomal, 16S/genetics
Schools
*Spacecraft
Methicillin-Resistant Staphylococcus aureus/drug effects/isolation & purification
Surface Properties
*Anti-Infective Agents/pharmacology
*Anti-Bacterial Agents/pharmacology
*Fomites/microbiology
*Environmental Microbiology

@article {pmid41053318,
year = {2025},
author = {Vitry, G and Angdisen, J and Sawant, MA and Arriaga, P and Irgen-Gioro, S and Peshette, P and Vuong, DC and Ilhardt, P and Fehr, J and Cwikla, B and Ponnaiya, B and Inman, JL and Snijders, AM and Hamid, S and Caballero-Lima, D and Garty, G and Apfeldorf, K and Laiakis, EC},
title = {Using a full thickness bioengineered human skin equivalent as a model for radiation biology research.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34702},
pmid = {41053318},
issn = {2045-2322},
support = {W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; },
mesh = {Humans ; *Skin/radiation effects/microbiology/metabolism ; Animals ; Mice ; Microbiota/radiation effects ; Bioengineering ; Cell Proliferation/radiation effects ; Dose-Response Relationship, Radiation ; },
abstract = {Radiation exposure from radiological or nuclear events, medical treatments, or spaceflight poses significant health risks, yet human-specific models to investigate radiation effects on skin remain limited. This study establishes a novel in vitro platform using a full-thickness bioengineered human skin equivalent colonized with natural mixed human microbiota (coHSEs) to assess radiation-induced biological responses. We exposed coHSEs to acute doses of up to 4 Gy with x-rays and evaluated their viability, structural integrity, and molecular responses over 25 days. The coHSE model demonstrated sustained viability without dose-dependent opportunistic microbial overgrowth when procedural optimizations were applied. Radiation-induced epidermal remodeling did not compromise tissue architecture or swabbing-based sample collection. Cell proliferation analyses revealed dose- and time-dependent dynamics, with consistent dermal cell density maintained across radiation doses. Comparative multi-omic analyses, including untargeted metabolomics, targeted lipidomics, and 16 S metagenomics, revealed conserved metabolic and microbial responses to radiation in both coHSEs and skin from irradiated mice. Enriched pathways such as arachidonic acid and fatty acid metabolism, along with shifts in microbial taxa including Lachnospiraceae, support the translational relevance of the coHSE model. This system offers a scalable, ethical, and physiologically relevant platform for radiation biology, biodosimetry, and therapeutic development, advancing terrestrial health research with promising application for space research.},
}

Humans
*Skin/radiation effects/microbiology/metabolism
Animals
Mice
Microbiota/radiation effects
Bioengineering
Cell Proliferation/radiation effects
Dose-Response Relationship, Radiation

@article {pmid41053210,
year = {2025},
author = {van Dyck, W and Täubel, M and Tuoresmäki, P and Dockx, Y and Luyten, L and Rasking, L and De Boever, P and Nawrot, TS and Casas, L},
title = {The association between preschoolers' retinal microcirculation and the indoor microbial environment: results of the ENVIRONAGE birth cohort.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34718},
pmid = {41053210},
issn = {2045-2322},
support = {296817//Research Council of Finland/ ; 296817//Research Council of Finland/ ; G073315N//Fonds Wetenschappelijk Onderzoek/ ; 151809N//Fonds Wetenschappelijk Onderzoek/ ; ERC-2012-StG310898/ERC_/European Research Council/International ; },
mesh = {Humans ; Male ; Female ; *Microcirculation ; Child, Preschool ; Child ; *Retinal Vessels/physiology ; *Microbiota ; Fungi/isolation & purification ; Cohort Studies ; *Retina ; Bacteria ; Birth Cohort ; },
abstract = {Early life environmental microbiota may influence normative development. Here, we explore the associations between the residential indoor microbial environment and the retinal microcirculation among preschoolers. We included 177 children aged 4-6 years from the Belgian ENVIRONAGE birth cohort. We measured retina microcirculation using fundus photography and quantified the retinal vessel tortuosity [tortuosity index (TI)] and diameters [central retinal vein equivalent (CRVE) and central retinal artery equivalent (CRAE)]. Residential indoor microbial characteristics (bacterial and fungal loads, richness, diversity, and taxa) were measured in settled dust using qPCR and amplicon sequencing. Adjusted associations were obtained using linear regression models and expressed as coefficients (β) with 95% confidence intervals (CI). We observed inverse associations between microbial loads and retinal microcirculation, significant for CRAE: β = -0.28; CI:-0.53;-0.04 (bacteria) and β = -0.27; CI:-0.50,-0.03 (fungi). Conversely, retinal microcirculation was directly associated with Gram-positive bacterial loads, significant for TI (β = 0.44; CI:0.06,0.81). These associations were stronger among boys. No consistent associations were observed for diversity. Conclusively, indoor microbial loads can affect the retinal microcirculation in preschool children. Retinal vascularization is a cardiovascular marker linked to immune factors and brain vascularization. Our findings support previously observed associations of the environmental microbiome with cognition, and open new hypotheses about potential cardiovascular effects.},
}

Humans
Male
Female
*Microcirculation
Child, Preschool
Child
*Retinal Vessels/physiology
*Microbiota
Fungi/isolation & purification
Cohort Studies
*Retina
Bacteria
Birth Cohort

@article {pmid41052982,
year = {2025},
author = {Cao, Y and Fan, X and Zang, T and Qiu, T and Fang, Q and Bai, J and Liu, Y},
title = {Prenatal depression-associated gut microbiota induces depressive-like behaviors and hippocampal neuroinflammation in germ-free mice.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {383},
pmid = {41052982},
issn = {2158-3188},
support = {2023AFB710//Natural Science Foundation of Hebei Province (Hebei Provincial Natural Science Foundation)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Female ; *Hippocampus/metabolism/pathology/immunology ; Mice ; Pregnancy ; Fecal Microbiota Transplantation ; *Depression/microbiology/metabolism ; *Dysbiosis/microbiology/complications ; Humans ; Lipopolysaccharides/blood ; Germ-Free Life ; *Neuroinflammatory Diseases/metabolism/microbiology ; Microglia ; *Pregnancy Complications/microbiology ; Disease Models, Animal ; Behavior, Animal ; Interleukin-6/metabolism ; Tumor Necrosis Factor-alpha/metabolism ; },
abstract = {Numerous studies have described the role of the microbiome-gut-brain axis in depression. However, the molecular mechanisms underlying the involvement of gut microbiota in the development of prenatal depression are limited. In this study, fecal microbiota from women with prenatal depression was transplanted into germ-free mice to investigate the potential causal relationships between the gut microbiota and depressive phenotypes. Shotgun metagenomic sequencing and untargeted metabolomics approaches were used to investigate the characteristics of gut microbiota and microbial metabolites. The levels of neuroinflammation in the brain were detected using immunofluorescence and real-time quantitative PCR. We found significant changes in gut microbiota composition and metabolites in mice with fecal microbiota transplantation (FMT) from women with prenatal depression, including decreased Ligilactobacillus, increased Akkermansia, and abnormal glycerophospholipid metabolism. Besides, significant increase in plasma lipopolysaccharide (LPS) levels and significant proliferation of microglia in the hippocampus were observed in mice receiving FMT from women with prenatal depression, accompanied by a significant increase in the expression of nuclear factor-κB (NF-κB) p65, tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) mRNA. The gut microbiota and its metabolites were strongly associated with depressive-like behaviors, plasma LPS and neuroinflammation. Our study collectively demonstrates that dysbiosis of the gut microbiota may play a causal relationship in the development of prenatal depression. This process potentially involves the activation of neuroinflammation through the LPS-NF-κB signaling pathway.},
}

Animals
*Gastrointestinal Microbiome/physiology
Female
*Hippocampus/metabolism/pathology/immunology
Mice
Pregnancy
Fecal Microbiota Transplantation
*Depression/microbiology/metabolism
*Dysbiosis/microbiology/complications
Humans
Lipopolysaccharides/blood
Germ-Free Life
*Neuroinflammatory Diseases/metabolism/microbiology
Microglia
*Pregnancy Complications/microbiology
Disease Models, Animal
Behavior, Animal
Interleukin-6/metabolism
Tumor Necrosis Factor-alpha/metabolism

@article {pmid41052412,
year = {2025},
author = {Dias, ME and Breyer, GM and Torres, MC and Wuaden, CR and Rebelatto, R and Kich, JD and Dorn, M and Siqueira, FM},
title = {Overview of the microbiome and resistome of swine manure in commercial piglet farms and its application in grazing soils.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/09593330.2025.2566429},
pmid = {41052412},
issn = {1479-487X},
abstract = {The environmental spread of antimicrobial resistance genes (ARGs) through the use of animal manure in agriculture has become a significant concern. This study investigated the impact of applying swine manure treated through biodigestion on the spread of ARGs in agricultural soils in the Midwest region of Brazil. Samples of untreated and treated manure, fertilized soil, and unfertilized soil were collected from three piglet production units. Bacterial communities and ARGs were characterized through metagenomic sequencing and bioinformatics. Bacterial profiles in fertilized and unfertilized soils were highly similar across all farms. In contrast, biodigestion reduced the total number of ARGs in treated manure. Of the 399 ARGs detected in fertilized soils, 67% were also found in unfertilized soils, and 12% were shared exclusively with treated manure. The presence of numerous ARGs in unfertilized soils highlights the role of environmental dissemination routes, such as runoff, dust, or wildlife, in shaping soil resistomes even in areas without manure application. These findings suggest a stable bacterial and resistome profile in soils, regardless of manure application. Although antimicrobial residues were not evaluated, the results reinforce the need for responsible antibiotic use and effective manure management to minimize environmental ARG dissemination.},
}

@article {pmid41052276,
year = {2025},
author = {Sherwani, MK and Ruuskanen, MO and Feldner-Busztin, D and Nisantzis Firbas, P and Boza, G and Móréh, Á and Borman, T and Putu Erawijantari, P and Scheuring, I and Gopalakrishnan, S and Lahti, L},
title = {Multi-omics time-series analysis in microbiome research: a systematic review.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {5},
pages = {},
doi = {10.1093/bib/bbaf502},
pmid = {41052276},
issn = {1477-4054},
support = {952914//European Union's Horizon 2020 research and innovation programme/ ; },
mesh = {*Microbiota ; Humans ; *Computational Biology/methods ; Machine Learning ; *Genomics/methods ; Multiomics ; },
abstract = {Recent developments in data generation have opened up unprecedented insights into living systems. It has been recognized that integrating and characterizing temporal variation simultaneously across multiple scales, from specific molecular interactions to entire ecosystems, is crucial for uncovering biological mechanisms and understanding the emergence of complex phenotypes. With the increasing number of studies incorporating multi-omics data sampled over time, it has become clear that integrated approaches are pivotal for these efforts. However, standard data analytical practices in longitudinal multi-omics are still shaping up and many of the available methods have not yet been widely evaluated and adopted. To address this gap, we performed the first systematic literature review that comprehensively categorizes, compares, and evaluates computational methods for longitudinal multi-omics integration, with a particular emphasis on four categories of the studies: (i) host and host-associated microbiome studies, (ii) microbiome-free host studies, (iii) host-free microbiome studies, and (iv) methodological framework studies. Our review highlights current methodological trends, identifies widely used and high-performing frameworks, and assesses each method across performance, interpretability, and ease of use. We further organize these methods into thematic groups-such as statistical modeling, machine learning, dimensionality reduction, and latent factor approaches-to provide a clear roadmap for future research and application. This work offers a critical foundation for advancing integrative longitudinal data science and supporting reproducible, scalable analysis in this rapidly evolving field.},
}

*Microbiota
Humans
*Computational Biology/methods
Machine Learning
*Genomics/methods
Multiomics

@article {pmid41051602,
year = {2025},
author = {Pereira, HS and Rashid, M and Alissa, A and Keraidi, S and Wipf, N and Sowa, AM and McDonnell, JM and Darwish, S and Butler, JS},
title = {Exploring osteomicrobiology: A narrative review of the gut-bone axis in osteoporosis.},
journal = {Irish journal of medical science},
volume = {},
number = {},
pages = {},
pmid = {41051602},
issn = {1863-4362},
abstract = {Osteoporosis is a chronic condition that presents with decreased bone mass and changes in bone microarchitecture, leading to an increased fracture risk. While the relationship between the gut microbiome and the immune system is well established, its impact on bone health remains underexplored. This narrative review aims to investigate the relationship between gut microbiota, bone health, and osteoporosis. Key findings indicate that the gut microbiome influences bone density through various mechanisms. Specific bacterial strains such as Lactobacillus and Bifidobacterium enhance the absorption of calcium, magnesium, and phosphorus, increasing bone mineral density. Additionally, the ability to produce essential vitamins like K and B makes the gut microbiota crucial for bone synthesis and integrity. Studies also revealed notable differences in the gut microbiome composition of individuals diagnosed with primary osteoporosis (PO) compared to those who were healthy controls. PO patients exhibited higher microbiota diversity and certain distinctive phylogenetic shifts. Important bacterial taxa such as Bacteroidetes, Faecalibacterium, and Dialister exist in high numbers in PO and may be useful as biomarkers. Additionally, a correlation was found between H. Pylori infections and reduced lumbar spine bone mineral density in older males. The review identifies certain gaps in the current knowledge and research such as the role of viral and fungal components within the gut microbiome. This review highlights the potential role of the gut microbiome as a target for osteoporosis diagnosis, treatment and prevention, underscoring the need for dietary and lifestyle interventions to modify the microbiome and improve bone health.},
}

@article {pmid41051464,
year = {2025},
author = {Muigano, MN and Liu, J and Liu, X and Luo, P and Li, Z and Li, J},
title = {The Impact of Dietary Patterns on the Human Gut Microbiome and Its Health Significance: A Review.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {19},
pages = {e71072},
doi = {10.1096/fj.202502040R},
pmid = {41051464},
issn = {1530-6860},
support = {//Shanghai Stomatological Hospital & School of Stomatology/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diet ; Diet, Mediterranean ; Diet, Vegetarian ; Obesity/microbiology ; },
abstract = {The gut microbiome constitutes a dynamic and complex ecosystem within the human body, playing a crucial role in maintaining metabolic homeostasis, immune regulation, and disease prevention. Among the various factors shaping this ecosystem, dietary patterns represent a major determinant of microbial composition and function. Recent studies have identified dietary patterns as one of the primary factors influencing the composition and function of the gut microbiome. This review summarizes the effects of various dietary patterns, including the Mediterranean diet, vegetarianism, low-carbohydrate high-fat diets, and high-protein diets, on gut microbiome dynamics. Furthermore, it explores the mechanisms by which the gut microbiome contributes to the pathophysiology of multiple chronic diseases, such as obesity, diabetes, inflammatory bowel disease, osteoporosis, and neurodegenerative disorders. The potential of dietary interventions to improve health by modulating the gut microbiome is also evaluated, emphasizing recent findings that unveil the intricate network of dietary microbiome-host interactions. This review aims to provide a scientific basis for the development of future dietary strategies that leverage gut microbiome modulation, ultimately contributing to personalized nutrition and precision medicine.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Diet
Diet, Mediterranean
Diet, Vegetarian
Obesity/microbiology

@article {pmid41051418,
year = {2025},
author = {Seth, M and Mondal, M and Mukhopadhyay, SK},
title = {Paracoccus sp. PS1: a novel probiotic strain for the mitigation of cardiometabolic risk factors TMA, TMAO, and methylglyoxal.},
journal = {Archives of microbiology},
volume = {207},
number = {11},
pages = {285},
pmid = {41051418},
issn = {1432-072X},
support = {DST/INSPIRE Fellowship/2018/IF180258//Department of Science and Technology Innovation in Science Pursuit for Inspired Research (DST INSPIRE), Government of India/ ; },
mesh = {*Methylamines/metabolism ; *Pyruvaldehyde/metabolism ; *Probiotics ; Humans ; *Paracoccus/genetics/metabolism/isolation & purification/growth & development/physiology ; Gastrointestinal Microbiome ; *Cardiovascular Diseases/prevention & control ; Risk Factors ; Genome, Bacterial ; },
abstract = {The gut microbiome is increasingly recognized as a critical modulator of host health, particularly in the context of non-communicable diseases like cardiovascular disease and diabetes. Central to this connection are microbially-derived metabolites such as trimethylamine N-oxide (TMAO), trimethylamine (TMA), and methylglyoxal, which have emerged as significant biomarkers and mediators of disease progression. All these toxic metabolites are generated in the body by the type of food we consume on daily basis. As the epicentre of TMA mediated ailments is human gut, a probiotic microbial strain with TMA degrading ability may be useful in mitigating those ailments. Due to its strong TMA-degrading ability and non-pathogenic nature of our isolated strain Paracoccus sp. PS1 prompted further investigation of its other physio-biochemical properties to judge its suitability as a probiotic strain. With this aim, viability of PS1 under anaerobic and microaerophilic conditions, which mimic human gut, were examined. Strain PS1 showed positive growth under both microaerophilic and anaerobic conditions and also showed other probiotic features such as tolerance to bile, lysozyme, acidic pH, gastric juices (pepsin), hydrophobicity, aggregation, coaggregation, adhesion and antioxidant properties. Furthermore, analysis of the whole genome sequence of Paracoccus sp. PS1 identified the genes and their respective proteins responsible for its probiotic properties, supporting its potential for use as a novel probiotic strain. The present study is the first to identify and characterize a potential probiotic from the genus Paracoccus with the unique capacity to degrade TMA, TMAO, and methylglyoxal.},
}

*Methylamines/metabolism
*Pyruvaldehyde/metabolism
*Probiotics
Humans
*Paracoccus/genetics/metabolism/isolation & purification/growth & development/physiology
Gastrointestinal Microbiome
*Cardiovascular Diseases/prevention & control
Risk Factors
Genome, Bacterial

@article {pmid41051380,
year = {2025},
author = {Jendraszak, M and Andrusiewicz, M},
title = {Uncovering hidden connections: the role of the male reproductive system microbiome and gut microorganisms in implantation: a critical review.},
journal = {Critical reviews in clinical laboratory sciences},
volume = {},
number = {},
pages = {1-31},
doi = {10.1080/10408363.2025.2562894},
pmid = {41051380},
issn = {1549-781X},
abstract = {Recent advancements in sequencing technologies have uncovered complex and diverse microbial communities inhabiting various niches of the human body, including the reproductive system. This review explores the significance of the male genital and gut microbiomes in maintaining reproductive health, focusing on their potential roles in embryo implantation and pregnancy outcomes. A comprehensive literature search was conducted using MEDLINE, Web of Science, and Scopus for articles published between 2004 and 2024. Search terms included "microbiome," "implantation," "inflammation," "male reproductive system," "recurrent miscarriage," "recurrent implantation failure," and "probiotics." From an initial pool of 1,091 articles, 107 were selected after applying filters for clinical, comparative, and observational studies. Ultimately, 21 articles met the quality criteria and were included in the review. While the female genital microbiome has been extensively studied and its role in implantation and embryo development well established, research on the male genital microbiome remains limited, and its influence is not yet fully understood. Nevertheless, emerging data suggest that the male reproductive tract harbors its own distinct microbial community, which may affect fertility, implantation, and pregnancy outcomes. The presence of certain bacteria and leukocytes in semen has been associated with sperm DNA damage, potentially compromising fertility and embryo development. Moreover, microbial exchange between partners during intercourse may alter the composition of the female reproductive microbiome, potentially influencing implantation success. The male and female reproductive tracts are colonized by microbial communities that play crucial roles in preventing infections and supporting reproductive health. Disruptions in these ecosystems have been linked to infertility, miscarriage, and preterm birth. Additionally, the gut microbiome is believed to interact with the reproductive system, possibly influencing implantation through immune and metabolic pathways. A deeper understanding of these connections is essential for identifying new preventive and therapeutic strategies for individuals experiencing recurrent pregnancy loss or implantation failure. Identifying specific microbial patterns associated with dysbiosis is critical for the development of targeted interventions. Potential therapeutic approaches include probiotics, prebiotics, and antibiotics, which may help restore microbial balance, enhance fertility, and reduce the risk of miscarriage. Antibiotic treatment may also prove beneficial in addressing infections that disrupt implantation. As microbial exchange, sperm DNA integrity, and immune regulation are all influenced by the microbiome, further research is necessary to understand its role in reproductive outcomes fully. Microbiome-targeted therapies represent a promising frontier in reproductive medicine. However, their clinical efficacy must be validated through rigorous research. This review underscores the importance of characterizing the composition and functional roles of the genital and gut microbiomes in order to inform the development of novel diagnostic tools and therapeutic strategies aimed at improving reproductive health and pregnancy outcomes.},
}

@article {pmid41051239,
year = {2025},
author = {Hamidi Nia, L and Alqudah, S and Markley, RL and DeLucia, B and Bobba, V and Elmallah, J and Nemet, I and Sangwan, N and Claesen, J},
title = {The antimicrobial metabolite nisin Z reduces intestinal tumorigenesis and modulates the cecal microbiome in Apc[Min/+] mice.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0155725},
doi = {10.1128/spectrum.01557-25},
pmid = {41051239},
issn = {2165-0497},
abstract = {UNLABELLED: Nisin Z, an antimicrobial metabolite produced by Lactococcus lactis, has been safely used as a food preservative for many years. Nisin Z also showed promising activity against various cancer types in vitro and significantly reduced tumor size in an ectopic head and neck cancer model. Here, we investigate the activity of nisin Z for colorectal cancer treatment and observed an in vitro reduction in cellular proliferation and a moderate enhancement in cell death. We next analyzed the effect of oral nisin Z administration in the Apc[Min/+] intestinal adenoma mouse model. We measured tumor burden along the gastrointestinal tract and observed a decrease in tumor burden in the middle region of the small intestine but not in the lower region or colon. Since tumor progression in the Apc[Min/+] model is exacerbated by an inflammatory environment, we next determined whether nisin Z impacts this in a direct or indirect manner. We show that nisin Z directly reduces NF-κB activation in a dose-dependent manner in a cell-based assay, and we observe a corresponding reduction in NF-κB protein expression in the middle region of the small intestine. In addition, nisin Z impacted the cecal microbiome composition as well as microbiota-associated plasma metabolites, leading to changes that are in part associated with beneficial outcomes. Interestingly, the Apc[Min/+] genotype differentially impacted the nisin Z-mediated differences in cecal microbiome composition and plasma metabolites compared to wild-type animals. In summary, our data suggest that the reduction in small intestinal tumor burden could be due to nisin Z's contribution to a reduced pro-inflammatory environment. Future studies will reveal whether nisin's localized effect is due to degradation of the peptidic compound in more distal regions of the gastrointestinal tract and focus on development of delivery systems to increase efficacy.

IMPORTANCE: With the increased incidence of colorectal cancer, especially among younger individuals, it is critical to study approaches that help with the prevention and treatment of this debilitating disease. Our study indicates that nisin Z, a bacterially produced peptide antibiotic, decreases the growth of colorectal cancer cells and moderately increases cell death in vitro. Oral administration of nisin Z in an intestinal adenoma mouse model revealed a reduction of tumor burden in the middle region of the small intestine. This decreased tumor burden might in part be attributed to a direct anti-inflammatory effect, as well as an indirect effect on the gut microbiota and their metabolites due to nisin Z's antibacterial activity. Overall, we demonstrate a potential activity for nisin Z in the prevention or amelioration of inflammation-associated colorectal cancer, underscoring the significance of investigating the properties of bacterial natural products in human health.},
}

@article {pmid41051180,
year = {2025},
author = {Ganesan, SM and Yadav, M and Ghimire, S and Lehman, PC and Patel, AJ and Woods, S and Olalde, H and Hoang, J and Paullus, M and Cherwin, C and Gill, C and Cho, T and Mangalam, AK},
title = {Relapsing-Remitting Multiple Sclerosis Is Associated With a Dysbiotic Oral Microbiome.},
journal = {Annals of clinical and translational neurology},
volume = {},
number = {},
pages = {},
doi = {10.1002/acn3.70212},
pmid = {41051180},
issn = {2328-9503},
support = {1RO1AI137075//National Institute of Allergy and Infectious Diseases, USA/ ; 1P20NR018081-01/NR/NINR NIH HHS/United States ; 5T90DE023520/GF/NIH HHS/United States ; T32AI007260/GF/NIH HHS/United States ; //Department of Pathology, University of Iowa/ ; 10.13039/100000002//National Institute of Health, USA/ ; //University of Iowa Environmental Health Sciences Research Center/ ; //Carver Trust/ ; 1I01CX002212//US department of Veterans Affairs/ ; },
abstract = {OBJECTIVE: Multiple sclerosis (MS) is a chronic autoimmune disorder characterized by inflammation, demyelination, and neurological impairment. While the gut microbiota's role in MS is extensively studied, the association between the oral microbiota and MS remains underexplored, particularly in North American cohorts. This study aimed to investigate the microbiota (bacterial) composition as well as functional pathways and immune profiles of the oral cavity in 60 patients with relapsing-remitting MS (RRMS), stratified by treatment status, compared to 44 healthy controls (HC).

METHODS: Unstimulated saliva was collected for genomic DNA extraction and salivary cytokine quantification. Oral bacterial composition and diversity were analyzed using 16S rRNA sequencing, with functional pathways inferred using PICRUSt2. Salivary cytokine levels were measured via multiplex immunoassays. LEfSe and random forest models identified key discriminatory taxa, and correlations between microbiota and cytokines were assessed using Spearman's rank analysis.

RESULTS: RRMS patients exhibited distinct microbial communities compared to HC and a higher Bacteroidota to Firmicutes ratio. Key taxa such as Campylobacter, Lachnoanaerobaculum, and Porphyromonas were enriched in RRMS. Functional profiling revealed 49 differentially abundant pathways, including the enrichment of lipopolysaccharide biosynthesis in MS. Elevated levels of IFN-γ, IL-6, and other cytokines correlated with the altered microbiome. IL-21, elevated in HC, correlated with anti-inflammatory pathways, suggesting a protective role in immune homeostasis.

INTERPRETATION: This study provides, for the first time, insights into oral microbiome-host interactions in North American RRMS patients, underscoring the interplay between microbial dysbiosis, functional pathways, and immune dysregulation. The oral microbiome shows potential as a biomarker for MS-related immune alterations.},
}

@article {pmid41051094,
year = {2025},
author = {Cheng, Z and Xia, W and McKelvey, S and He, Q and Chen, Y and Yuan, H},
title = {Building Predictive Understanding of the Activated Sludge Microbiome by Bridging Microbial Growth Kinetics and Microbial Population Dynamics.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c05925},
pmid = {41051094},
issn = {1520-5851},
abstract = {Modeling microbiomes can provide predictive insights into microbial ecology, but current modeling approaches suffer from inherent limitations. In this study, a novel modeling approach was developed based on the intrinsic connection between the growth kinetics of guilds and the dynamics of microbial populations. To implement this approach, 466 samples from four full-scale activated sludge systems were retrieved. The raw samples were processed using a data transformation method that tripled the data set size and enabled quantification of population dynamics. Of the 42 family level core populations, 36 showed overall dynamics statistically close to zero (within ± 0.05 d[-1]). Bayesian networks were built to classify the core populations into heterotrophic and autotrophic guilds. Topological data analysis was applied to identify keystone populations and time-dependent microbial interactions. The data-driven inferences were validated directly using the Microbial Database for Activated Sludge (MiDAS) and indirectly by predicting community structure using artificial neural networks. The Bray-Curtis similarity between predicted and observed communities was higher with microbial kinetic parameters than without these parameters (0.70 vs 0.66, t test, p < 0.05). Owing to the flexibility of the modeling framework, this proposed hybrid approach might potentially be adapted to time-dependent data from natural systems for predictive understanding of the involved microbiomes.},
}

@article {pmid41050887,
year = {2025},
author = {Lyu, WN and Shen, CY and Lee, YH and Chen, SK and Chuang, EY and Lou, PJ and Tsai, MH},
title = {Novel biomarker identification for oral squamous cell carcinoma development in nonsmoker, nondrinker, and nonchewer patients using third-generation sequencing of oral microbiome.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2565452},
pmid = {41050887},
issn = {2000-2297},
abstract = {BACKGROUND/OBJECTIVE: Oral squamous cell carcinoma (OSCC) in patients without tobacco, alcohol, or betel-quid habits is poorly understood and difficult to detect early. This study aimed to identify microbial biomarkers specific to this habit-free population using third-generation sequencing (TGS).

Twenty-seven habit-free OSCC patients were recruited at National Taiwan University Hospital (NTUH). Paired tumor and adjacent normal tissues were collected with informed consent and NTUH Research Ethics Committee approval (IRB 201902080RINC, 201304078RIND). Full-length 16S rRNA sequencing (PacBio Sequel IIe) was processed with DADA2 and SILVA. Biomarkers were identified using sparse partial least squares discriminant analysis (sPLS-DA) and random forest with cross-validation, and validated against three public OSCC cohorts.

RESULTS: A three-species panel-Eikenella corrodens, Slackia exigua, and Eggerthia catenaformis-discriminated tumor from normal tissues (AUC = 0.905 training; 0.733 testing). Functional and network analyses showed tumor-enriched taxa forming pro-inflammatory clusters linked to lipid and glutamine metabolism, while commensals correlated with homeostatic pathways. Cross-cohort comparison confirmed this panel's specificity to habit-free OSCC.

CONCLUSIONS: Using TGS, we revealed distinct microbial signatures in habit-free OSCC that may aid early diagnosis and underscore the role of microbiome-host interactions in carcinogenesis.},
}

@article {pmid41050878,
year = {2025},
author = {Chetty, C and Mafunda, N and Happel, AU and Khan, A and Cooley Demidkina, B and Yende-Zuma, N and Saidi, Y and Mahabeer Polliah, A and Lewis, L and Osman, F and Radebe, P and Passmore, JS and Kwon, D and Ravel, J and Ngcapu, S and Liebenberg, L and Symul, L and Holmes, S and Mitchell, CM and Potloane, D},
title = {Randomized trial of multi-strain Lactobacillus crispatus vaginal live biotherapeutic products after antibiotic therapy for bacterial vaginosis: study protocol for VIBRANT (vaginal lIve biotherapeutic RANdomized trial).},
journal = {Contemporary clinical trials communications},
volume = {48},
number = {},
pages = {101554},
pmid = {41050878},
issn = {2451-8654},
abstract = {BACKGROUND: Globally, approximately 30 % of women have bacterial vaginosis (BV). Antibiotic treatment is frequently followed by recurrence, likely due to lack of colonization with beneficial lactobacilli.

METHODS: This is a Phase 1, randomized, placebo-controlled trial of vaginal live biotherapeutic products (LBP) after antibiotic treatment for BV to establish Lactobacillus colonization. The LBP are vaginal tablets containing 6 L. crispatus strains (LC106) or 15 L. crispatus strains (LC115), at 2 x 10[9] colony forming units (CFU) per dose. Participants with BV in the United States and South Africa will receive seven days of oral metronidazole twice daily and will be randomized 1:1:1:1:1 to: seven days placebo; seven days LC106; three days LC106/four days placebo; seven days LC106 starting day 3 of the metronidazole course; or seven days LC115. Safety will be assessed by the number and percentage of ≥ Grade 2 related adverse events during or after product use. The primary outcome is LBP colonization defined as relative abundance ≥5 % of any LBP strain or ≥10 % of a combination of LBP strains by metagenomic sequencing any time in the 5 weeks after randomization. A generalized linear model will measure the association between treatment group and colonization, adjusting for site.

CONCLUSIONS: This study seeks to establish proof of concept for a multi-strain LBP to promote vaginal L. crispatus colonization in two geographically distinct populations.

TRIAL REGISTRATION: South African National Clinical Trials Registry (SANCTR DOH-27-102023-8342; October 27, 2023) and ClinicalTrials.gov (NCT06135974; November 11, 2023).

PROTOCOL VERSION: 2.0 dated October 03, 2023.},
}

@article {pmid41050755,
year = {2025},
author = {Wang, L and Zhang, J and Zhang, M and Xu, Z and Zheng, Y and Lv, B and Pan, M},
title = {Insights into the alteration of vaginal microbiota and metabolites in pregnant woman with preterm delivery: prospective cohort study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1580801},
pmid = {41050755},
issn = {2235-2988},
mesh = {Female ; Humans ; Pregnancy ; *Vagina/microbiology/metabolism ; *Premature Birth/microbiology ; Prospective Studies ; Adult ; *Microbiota ; *Bacteria/classification/isolation & purification/metabolism/genetics ; Metabolomics ; Young Adult ; },
abstract = {Disruptions in vaginal microbiota and metabolites during pregnancy may be the most important risk factor for preterm delivery, thus the difference in vaginal microbiota and metabolites between women who subsequently delivered at term and who eventually experienced preterm birth. In this study, 63 participants were enrolled before the cervical cerclage surgery (namely pre-cerclage), comprising women who subsequently delivered at term and who eventually experienced preterm birth. The cervical-vaginal fluid (CVF) was collected two days prior to the cervical cerclage surgery. Compared with the term birth groups (PrTG), the proportion of beneficial bacteria (Lactobacillus, Prevotella, Trichococcus, Neisseria and Gemella) in the preterm birth group (PrPG) were significantly reduced (p < 0.05), while the proportion of harmful bacteria (Thauera, Ochrobactrum, Gardnerella, Massilia, Phyllobacteriaceae and Atopobium) were significantly increased (p < 0.05). In addition, vaginal metabolomics-based LC-Orbitrap-MS/MS revealed that the contents of 2-Piperidone, Melphalan, N-acetylputrescine, Obatoclax, Eurostoside, Pregnanediol 3-O-glucuronide, O-Phospho-L-serine, 1-Kestose and N-arachidonylglycine were significantly decreased in the PrPG group compared with the PrTG group, while Acenocoumarol, Isopyrazam, Pentosidine, hexose, 7-Hydroxymitragynine, PE, Tamoxifen and 1-Deoxynojirimycin contents were significantly increased. These results suggest that specific bacterial species and metabolites may serve as potential biomarkers for preterm birth prediction, and approve the theoretical basis for the intervention of preterm birth.},
}

Female
Humans
Pregnancy
*Vagina/microbiology/metabolism
*Premature Birth/microbiology
Prospective Studies
Adult
*Microbiota
*Bacteria/classification/isolation & purification/metabolism/genetics
Metabolomics
Young Adult

@article {pmid41050748,
year = {2025},
author = {Castellano, P and Ceccarani, C and Djusse, ME and Mazzetti, M and Morselli, S and Camboni, T and Conti, S and Prinelli, F and Severgnini, M and Foschi, C and Dall'Asta, M and Consolandi, C and Marangoni, A},
title = {Linking antibiotic resistance genes in the vaginal microbiota to health-related behaviors and antibiotic awareness in reproductive-age women: a cross-sectional study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1640992},
pmid = {41050748},
issn = {2235-2988},
mesh = {Humans ; Female ; Cross-Sectional Studies ; *Vagina/microbiology ; *Microbiota/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; Adult ; RNA, Ribosomal, 16S/genetics ; Young Adult ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Drug Resistance, Bacterial/genetics ; Adolescent ; DNA, Bacterial/genetics ; },
abstract = {INTRODUCTION: The vaginal microbiota (VMB), predominantly shaped by Lactobacillus species, plays a crucial role in maintaining vaginal health and preventing infections. However, its delicate balance is increasingly challenged by the widespread use of antibiotics and the consequent rise in antibiotic resistance genes (ARGs). While the VMB has been recognized as a potential reservoir for ARGs, limited research has explored how microbial composition, antibiotic exposure, and individual behavioral factors converge to shape the vaginal resistome.

MATERIALS AND METHODS: In this cross-sectional study, vaginal swabs were collected from 105 reproductive-age Caucasian women. The VMB composition was characterized and classified into Community State Types (CSTs), by sequencing the hypervariable V3-V4 regions of the bacterial 16S rRNA gene. In order to highlight common patterns of abundance among taxa, a co-abundance groups (CAGs) analysis was performed. We assessed the distribution of 14 ARGs conferring resistance to macrolides, tetracyclines, beta-lactams, and quinolones along with two associated transposons by means of PCR. An overall composite ARGs score was also calculated. Participants completed detailed questionnaires assessing demographics and behavioral factors, with a particular focus on both health- and antibiotic-related behaviors. Statistical analyses examined associations between ARG prevalence, vaginal microbiome composition and relevant exposures.

RESULTS: CSTs I and III were the most prevalent, with the most frequently detected ARGs being erm(F), tet(M), erm(B), erm(A), and tet(W), each present in over 65% of participants. ARG presence was positively correlated with a higher vaginal microbiome alpha-diversity. Moreover, BV-associated bacterial taxa showed strong associations with ARGs, while Lactobacillus species generally exhibited negative correlations. Smoking, a higher body mass index (BMI), presence of Candida spp. and a history of antibiotic use were significantly associated with increased ARG prevalence, whereas oral contraceptive use and higher diet quality scores were negatively associated. Correlating together the relative abundances of the microbial CAGs and the presence/absence of specific ARGs, we found a positive association between several genes related to macrolide and tetracycline resistance and the Gardnerella-Prevotella CAG. Additionally, the Gardnerella-Prevotella, and the Streptococcus CAGs were positively correlated to the total ARG score, whereas the L. crispatus/jenesenii/gasseri CAG was negatively correlated.

CONCLUSIONS: These findings underscore the role of the VMB as a dynamic reservoir of ARGs and highlight the influence of individual lifestyle and antibiotic-related behaviors on ARG dissemination in the vaginal niche. This supports the need for integrated public health strategies that combine antibiotic stewardship with targeted lifestyle and behavioral interventions, as well as the development of individualized therapeutic approaches.},
}

Humans
Female
Cross-Sectional Studies
*Vagina/microbiology
*Microbiota/genetics/drug effects
*Anti-Bacterial Agents/pharmacology
Adult
RNA, Ribosomal, 16S/genetics
Young Adult
*Bacteria/genetics/drug effects/classification/isolation & purification
*Drug Resistance, Bacterial/genetics
Adolescent
DNA, Bacterial/genetics

@article {pmid41050727,
year = {2025},
author = {Humphreys, LR and Lucas, JM and Spicer, ME},
title = {Canopy Height and Epiphytic Bryophytes Shape Fungal Communities in a Temperate Rainforest.},
journal = {Ecology and evolution},
volume = {15},
number = {10},
pages = {e72241},
pmid = {41050727},
issn = {2045-7758},
abstract = {Fungal communities contribute to plant ecology and evolution in forested ecosystems. Their diverse interactions with associated host plants can vary along abiotic and biotic gradients, but these gradients are poorly understood in complex natural ecosystems. Given the high diversity of epiphytic plants in many ecosystems, forest canopies offer a unique and underexplored system for studying plant-associated microbial diversity and distribution. We explored both abiotic and biotic factors structuring arboreal fungal communities. Specifically, we hypothesized that bryophyte-associated fungal communities are structured by the vertical height gradient within host trees (from the ground to high in the canopy), vary across host plant species, and that living bryophytes host distinct fungal communities compared to dead bryophyte matter. To test these hypotheses, we sampled living and dead bryophytes (mosses and liverworts) across three different bryophyte host species and four heights, ranging from the forest floor to 18 m above the ground. We characterized the fungal community composition in each sample using metabarcoding. Fungal communities showed significant variation across substrates: bryophytes collected from the ground exhibited 17% greater Shannon diversity and 34% higher taxonomic richness than epiphytic bryophytes, while living bryophytes had 15% higher diversity and 30% greater richness than dead tissues. This pattern suggests that the diverse microhabitats within living bryophytes may drive microbial diversity. Community analysis identified a core fungal community across living bryophyte samples, but rare taxa accounted for a majority of reads, driving differences in community composition between different heights and bryophyte species. Synthesis: Epiphytic bryophyte-associated fungal communities show high heterogeneity across different substrates and heights, which provides insight into the structuring of the forest microbiome and epiphyte ecology. These results demonstrate the importance of exploring canopy-associated microbes to better understand microbial diversity and function in forest ecosystems.},
}

@article {pmid41050722,
year = {2025},
author = {Pfau, MJ and Weber, S and Kennedy, S and Krehenwinkel, H and Roderick, G and Gillespie, R},
title = {Invasive Spiders and Their Microbiomes: Patterns of Microbial Variation in Native and Invasive Species in Hawai'i.},
journal = {Ecology and evolution},
volume = {15},
number = {10},
pages = {e72175},
pmid = {41050722},
issn = {2045-7758},
abstract = {Invasive species can have detrimental impacts on the community structure and native species persistence, causing cascading impacts on ecosystem function. These effects are amplified in remote island ecosystems that are characterized by non-representative and often diverse biota. The mechanisms behind successful invasions, particularly of arthropods, are varied, but growing evidence suggests that invasive species escape from their native predators and competitors. Recent research has suggested that gut microbiota can play an important role in arthropod fitness, with vertically transmitted endosymbionts and horizontally acquired microbes performing different functions. Here, we explored the extent to which the microbiome may facilitate the ability of spiders to exploit and ultimately adapt to novel environments. We examined co-occurring pairs of native and invasive spiders across three locations in the Hawaiian Islands and compared them with mainland counterparts to test two core predictions: (1) gut microbiota would be shaped primarily by local environmental filters rather than invasion status, and (2) vertically transmitted endosymbionts would show stronger host-specificity and reduced diversity in invasives. Using 16S rRNA amplicon sequencing, we found that the site explained 11.7% of gut-microbial compositional variance compared to 6.5% for host species. These results suggest that each spider maintains a species-specific level of α-diversity but reassembles taxonomic composition according to local microbial pools, thus indicating high context dependence in environmental filtering. Invasive species were found to have a lower relative abundance of gut endosymbiont taxa, with one species, Badumna longinqua, showing little to no endosymbiont presence across sites, and the other, Steatoda grossa, exhibiting low but site-specific abundance. We observed a strong localization effect, suggesting that these endosymbionts are also being acquired from local environments, not carried from ancestral ranges. These results suggest host-symbiont interactions have differential impacts on native and invasive species and that microbiota may facilitate the success of spiders in novel environments.},
}

@article {pmid41050671,
year = {2025},
author = {Duan, H and Xu, B and Luo, P and Chen, T and Zou, J},
title = {Microbial metabolites and their influence on the tumor microenvironment.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1675677},
pmid = {41050671},
issn = {1664-3224},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Neoplasms/immunology/metabolism/therapy/microbiology ; Animals ; Immunotherapy ; *Microbiota/immunology ; Fatty Acids, Volatile/metabolism ; },
abstract = {While tumor immunotherapy has achieved remarkable progress in many hematological malignancies, its efficacy remains limited by key challenges, including the immunosuppressive microenvironment of solid tumors, metabolic abnormalities, and drug resistance. As a central mechanism underlying impaired immune function, metabolic reprogramming of immune cells has emerged as a pivotal focus for unraveling tumor immune evasion and therapeutic resistance. Advances in metagenomics have highlighted the significance of the human commensal microbiome as a 'second genome.' Microbial metabolites, whether circulating systemically or accumulating locally, serve as key messengers linking the microbiota to tumor immunometabolism. This review comprehensively examines the regulatory roles and metabolic mechanisms through which microbial metabolites-including short-chain fatty acids (SCFAs), bile acids, tryptophan metabolites, and lipopolysaccharides (LPS)-modulate tumor immunity and immunotherapeutic responses via immune cell metabolism. These metabolites shape the tumor immune microenvironment and influence immunotherapeutic efficacy by reprogramming immune cell metabolic and biosynthetic pathways. This review underscores the central regulatory role of microbial metabolites as the 'second genome' in tumor immunometabolism, offering a theoretical foundation and potential targets to elucidate mechanisms of immunotherapeutic resistance and advance microbiota metabolism-based precision interventions.},
}

Humans
*Tumor Microenvironment/immunology
*Neoplasms/immunology/metabolism/therapy/microbiology
Animals
Immunotherapy
*Microbiota/immunology
Fatty Acids, Volatile/metabolism

@article {pmid41050662,
year = {2025},
author = {Wierzbińska, W and Kuźmycz, O and Kowalczyk, A and Stączek, P},
title = {The role of dysbiosis in shaping host immunity in endometrial cancer development.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1627285},
pmid = {41050662},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/immunology/microbiology ; *Endometrial Neoplasms/immunology/microbiology/pathology/etiology ; Female ; Tumor Microenvironment/immunology ; Animals ; Microbiota/immunology ; Carcinogenesis/immunology ; },
abstract = {In recent years, research into the background of carcinogenic processes has increasingly focused on the role of the tumor microenvironment (TME) in tumorigenesis. In addition to the presence of tumor cells and non-malignant components, which include immune cells, extracellular matrix elements, stroma, and endothelial cells, the microbiome is now increasingly being classified as an integral part of the TME. The establishment of the Human Microbiome Project (HMP) in 2007 along with the development of next-generation sequencing (NGS) techniques proved to be a breakthrough in terms of human microbiota research, shedding new light on the existing knowledge of microorganisms inhabiting various niches of the human body and their functions. Emerging scientific evidence from preclinical and clinical studies indicates significant differences in the microbiome composition between tumor tissues and benign controls. The presence of specific pathogenic strains within a tissue may play a key role in the initiation and progression of inflammation, which not only may be directly responsible for the stimulation of tumorigenic processes but may also affect the destabilization of the host genome, causing significant disruption of its metabolism. The role of microorganisms in the induction and promotion of pathological processes, including cancer, has been confirmed in many studies to date. Recent years of research on the microbiota of the female reproductive tract (FRT) have not only indicated that the endometrium has its unique microbial composition but have also made it possible to point out differences in composition between the microbiome of healthy and tumor-lesioned tissue, suggesting a potential role for dysbiotic disorders in the pathogenesis of endometrial cancer (EC). In this review, we aim to highlight the complex interplay between bacterial interactions and host immunity, and how this phenomenon contributes to the development and progression of endometrial cancer.},
}

Humans
*Dysbiosis/immunology/microbiology
*Endometrial Neoplasms/immunology/microbiology/pathology/etiology
Female
Tumor Microenvironment/immunology
Animals
Microbiota/immunology
Carcinogenesis/immunology

@article {pmid41050659,
year = {2025},
author = {Almansour, N and Al-Rashed, F and Choudhry, K and Alqaderi, H and Sindhu, S and Al-Mulla, F and Ahmad, R},
title = {Gut microbiota: a promising new target in immune tolerance.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1607388},
pmid = {41050659},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Immune Tolerance ; Animals ; Dysbiosis/immunology ; },
abstract = {Gut microbiota research has highlighted its pivotal role in human health and disease. Its composition is shaped by diet, genetics, age, and environmental factors. When the balance of these microbes is disrupted (dysbiosis), it can contribute to health problems like metabolic, inflammatory, and mental disorders. The microbiota supports digestion, fermentation, and vitamin production, which are essential for overall health. The gut microbiota has emerged as a critical modulator of immune function, with increasing evidence highlighting its role in establishing and maintaining immune tolerance. Despite significant advances in understanding the interactions between the gut microbiome and immune system, gaps remain in the literature regarding the specific mechanisms through which microbiota influences immune tolerance. This review aims to address these knowledge gaps by synthesizing current research on the microbiota impact on immune tolerance, emphasizing key factors such as microbial diversity, metabolic byproducts, and the microbiota interaction with immune cells, specifically focusing on the role of microbial tryptophan metabolites in PD-1/PD-L1 tolerance. We also highlight critical areas for future research, including the identification of microbial species or strains that can modulate immune tolerance, the influence of diet and environmental factors on microbiota composition, and the development of microbiota-based therapies. By bridging these gaps, this review seeks to provide a comprehensive understanding of the mechanistic role of microbiota immune tolerance and its potential as a novel therapeutic target for autoimmune and inflammatory diseases.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Immune Tolerance
Animals
Dysbiosis/immunology

@article {pmid41050155,
year = {2025},
author = {Widjaja, N and Agustina, C and Felicia, F and Wijaya, F and Limanjaya, J and Yulandi, A and Waturangi, DE and Simatupang, ST and Tan, S and Tjandrawinata, RR},
title = {Gut microbiome in adult Asians with obesity, type 2 diabetes mellitus, and a combination of obesity and type 2 diabetes mellitus.},
journal = {Bioscience of microbiota, food and health},
volume = {44},
number = {4},
pages = {251-260},
pmid = {41050155},
issn = {2186-6953},
abstract = {Obesity and type 2 diabetes (T2D) are two of the most common health problems in the world, particularly in adult Asians, with a significant impact on morbidity and mortality. Numerous studies have revealed that the gut microbiome of people with obesity and T2D differs significantly from those of healthy people. Those who suffer from certain illnesses often encounter disruption in their gut microbiome, leading to a decrease in richness diversity and diminished microbial activity. This disruption can also result in the loss of the gut mucosal barrier, increased gut permeability, and most likely, the development of a leaky gut. Recent studies have also emphasized the essential role of the gut microbiome in these conditions. However, conflicting findings were found between one study and another investigation. Therefore, this paper aims to provide an overview of gut microbiome characteristics in adult Asians with obesity, T2D, and the combination of both. In addition, this paper elaborates on the current understanding regarding the association of the gut microbiome with health status, thereby serving as a foundation for developing probiotics or prebiotics to modulate the gut microbiome and improve metabolic health.},
}

@article {pmid41049923,
year = {2025},
author = {Pedraza, A and Bonnice, S and Won, MN and Kesselman, MM and Demory Beckler, M},
title = {Impact of COVID-19 on the Gut Microbiome: A Review.},
journal = {Cureus},
volume = {17},
number = {9},
pages = {e91470},
pmid = {41049923},
issn = {2168-8184},
abstract = {Coronavirus Disease 2019 (COVID-19) has resulted in over 6 million deaths worldwide in fewer than four years and is a result of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The protein that mediates SARS-CoV-2 host cell entry is the angiotensin-converting enzyme 2 (ACE2), which is highly expressed on the membrane of gastrointestinal (GI) cells. Consequently, infection can lead to direct damage to the GI tract and gut dysbiosis, which is associated with an imbalance of microbiota, inflammation, and other systemic infections and diseases. In this review, we will focus on the impact of COVID-19 on the GI system. We will examine the pathophysiology of gut dysbiosis in COVID-19 patients, as well as emphasize the significance of probiotics in addressing this condition. Additionally, we will identify key areas of interest that warrant further investigation.},
}