@article {pmid41086989,
year = {2025},
author = {Zheng, L and Yao, L and Zhu, B and Chen, S and JinQian, and Liu, S and JinZhao, and Chen, Z and ShuaiXiang, and Xie, Z and Zhu, J and Wang, S and KaiWu, and Chen, J and Zhang, S and Lu, X},
title = {Cross-kingdom gut microbiota signatures and their associations with clinical phenotypes in adolescents with bipolar depression.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {120399},
doi = {10.1016/j.jad.2025.120399},
pmid = {41086989},
issn = {1573-2517},
abstract = {Emerging evidence highlights the pivotal role of the gut microbiota (GM) in mental health; however, investigations into its cross-kingdom composition in adolescent bipolar disorder remain critically limited. Most studies have focused solely on bacteria, overlooking the complex interactions involving archaea, viruses, and fungi. This study aimed to comprehensively characterize the taxonomic and functional alterations in the cross-kingdom gut microbiota of adolescents with bipolar depression and examine their associations with clinical parameters. We enrolled 60 adolescents aged 12-18 years, including 30 diagnosed with bipolar depression and 30 age- and sex-matched healthy controls. Fecal samples were collected alongside detailed clinical data, including psychiatric symptomatology, cognitive assessments, and dietary habits. Metagenomic sequencing was conducted to profile microbial taxa and functional gene pathways across domains. Statistical analyses assessed differences in alpha and beta diversity, differential abundance, and correlations with clinical phenotypes. Alpha diversity was significantly reduced in the viral and fungal domains among patients, while archaeal and bacterial diversity showed no significant differences. Beta diversity analysis did not reveal global community structural shifts across domains. Taxonomic profiling identified Methanohalobium evestigatum as significantly enriched in archaea, alongside increased abundance of several Firmicutes and Actinobacteria species in the bacterial domain. Viral analysis revealed elevated levels of Brussowvirus AlQ132, Orpheovirus IHUMI LCC2, Afonbuvirus coli, Carjivirus hominis, and Carjivirus communis in the patient group. LEfSe analysis uncovered 15 significantly altered metabolic pathways, including those involved in DNA repair, energy metabolism, and immune signaling. Notably, several taxa and pathways were significantly associated with clinical parameters such as symptom severity, cognitive flexibility, sleep quality, and dietary intake. Adolescents with bipolar depression exhibit distinct alterations in cross-kingdom gut microbiota composition and function, with specific microbial taxa and metabolic pathways correlating with key clinical phenotypes. These findings underscore the potential of gut microbiome signatures as biomarkers and therapeutic targets in early-onset mood disorders and highlight the importance of including archaea, fungi, and viruses in future microbiome-based mental health research.},
}

@article {pmid41086284,
year = {2025},
author = {Kime, K and Sedaghat, AR and Phillips, KM},
title = {Defining and managing acute exacerbations of chronic rhinosinusitis.},
journal = {Current opinion in otolaryngology & head and neck surgery},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOO.0000000000001096},
pmid = {41086284},
issn = {1531-6998},
abstract = {PURPOSE OF REVIEW: Currently, no universally accepted definition or management strategy for chronic rhinosinusitis (CRS) and its acute exacerbations (AECRS) exists. This review aims to provide an overview of the current research in this field and to present recent advances in diagnosis and management.

RECENT FINDINGS: A variant in the CDHR3 gene has been identified as a risk factor for AECRS, associated with increased viral replication, type-2 cytokine upregulation, and downregulation of Toll-like receptor mediated responses. Microbiome studies show that patients with AECRS are more likely to harbor rare microbial taxa, and most strains isolated during exacerbations form biofilms. Biologic therapies targeting type-2 inflammation have reduced exacerbation rates and decreased the need for antibiotics and systemic corticosteroids. Culture-directed antibiotics may improve longer-term endoscopic outcomes, though short-term symptom and quality-of-life benefits remain unclear. Cost-effectiveness modeling suggests observation is usually the most efficient initial strategy, unless the probability of bacterial etiology exceeds ~49%. In addition, a new patient-informed definition of AECRS has been proposed, although further validation is needed.

SUMMARY: Advances in genetics, microbiome analysis, and biologic therapy offer promising avenues, yet definitions and outcome measures remain inconsistent. Robust, long-term studies are still needed to harmonize definitions and standardize management.},
}

@article {pmid41086142,
year = {2025},
author = {Gao, F and Wang, D and Zuo, L and Sun, J and Dong, B and Sun, R and Shi, Y and Sun, Y and Zou, Y and Jia, Q and Han, N and Wang, H and Liu, L and Zhang, G and Yu, Z and Sun, Z and Ren, Z},
title = {Alterations in the serum metabolome in patients with the COVID-19 Omicron variant and in recovered cases.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0327297},
doi = {10.1371/journal.pone.0327297},
pmid = {41086142},
issn = {1932-6203},
mesh = {Humans ; *COVID-19/blood/virology/metabolism/diagnosis ; Male ; Female ; *SARS-CoV-2 ; *Metabolome ; Middle Aged ; Adult ; Metabolomics/methods ; Case-Control Studies ; Aged ; Tandem Mass Spectrometry ; Chromatography, Liquid ; },
abstract = {Corona Virus Disease (COVID-19) has become a global public health crisis, and the Omicron variant has rapidly taken over as soon as it was detected Serum circulating metabolites can provide extensive insights into the pathogenesis and diagnosis of many diseases. We included 336 omicron variant cases (OC), 216 recovered cases (RC), and 380 healthy controls (HC) for untargeted metabolomics analysis and analyzed their serum metabolic profiles by liquid chromatography-tandem mass spectrometry. Principal component analysis, orthogonal partial least squares discriminant analysis, t-test analysis and false discovery rate were used to characterize the serum metabolites of OC and RC. In addition, a noninvasive diagnostic model for OC was developed using Receiver operating characteristic analysis. Finally, a correlation analysis was performed using data from our published articles. The results showed that compared with HC, five metabolites, including DL-stachydrine, D-(+)-pipecolinic acid, furazolidone, L-arginine and 5α-dihydrotestosterone glucuronide were significantly elevated and one metabolite, prenylcysteine, was significantly decreased in the serum of OC, and that the increase in L-arginine and the decrease in prenylcysteine led to impaired urea cycling and a high risk of developing atherosclerosis, respectively. These metabolites were not fully restored to healthy human levels in recovered cases. In addition, we constructed a noninvasive diagnostic model for distinguishing Omicron variant patients from healthy individuals based on the six differential metabolites, and achieved high diagnostic efficacy in both the discovery and validation cohorts. Finally, the results of the correlation analysis showed a strong correlation between the alterations in the oropharyngeal microbiome and serum metabolome and the clinical indicators in the omicron variant cases. This study was the first to characterize serum metabolites in OC and RC based on a large clinical cohort, and successfully constructed and validated a noninvasive diagnostic model for Omicron variant patients.},
}

Humans
*COVID-19/blood/virology/metabolism/diagnosis
Male
Female
*SARS-CoV-2
*Metabolome
Middle Aged
Adult
Metabolomics/methods
Case-Control Studies
Aged
Tandem Mass Spectrometry
Chromatography, Liquid

@article {pmid41085867,
year = {2025},
author = {Zhang, H and Wu, Y and Li, Y and Xue, Y and Jiao, Y and Sun, R and Ma, Y and Kulyar, MF and Li, M and Xu, H and Li, Z and Wang, Y},
title = {Maternal Gut Microbiota and Metabolomic Signatures Are Potential Indicators of Neonatal Calf Birth Weight: A Preliminary Pilot Study.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {20},
pages = {e71089},
doi = {10.1096/fj.202501290RR},
pmid = {41085867},
issn = {1530-6860},
support = {252102111007//The Key Research and Development Program of Henan province (Science and Technology Foundation)/ ; 32503122//The Young Scientists Fund of the National Natural Science Foundation of China/ ; HARS-22-13-G1//Special Fund for Henan Agriculture Research System/ ; 2025T180829//The fellowship from the China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome/physiology ; Female ; Pilot Projects ; *Birth Weight/physiology ; Animals, Newborn ; Pregnancy ; *Metabolome ; Metabolomics/methods ; },
abstract = {The gut microbiota plays a crucial role in host homeostasis, influencing digestion, metabolism, and immune regulation. Neonatal birth weight is pivotal for early development and long-term productivity. The study identified distinct maternal gut microbiota and metabolomic profiles associated with neonatal calf birth weight, providing preliminary biomarkers for future microbiota-driven reproductive strategies. A cohort of periparturient Holstein dairy cows was strategically selected to establish two distinct experimental groups based on neonatal birth weight stratification: a high birth weight cohort (WU) and a low birth weight cohort (WF). WU cows exhibited enrichment of Burkholderiaceae_A, Turicibacter, Romboutsia_B, Blautia_A, Barnesiella, Clostridium_T, and Paraclostridium, while WF cows had higher levels of Elusimicrobiota, Ruminiclostridium_E, Campylobacter_B, and Odoribacter. Metabolomic profiling identified 85 differentially abundant metabolites. WU cows showed higher levels of 4-imidazoleacrylic acid, 1,2,3,4-tetrahydroacridin-9-ol, 8S-hydroxy-4Z,6E,10Z-hexadecatrienoic acid, 7-hydroxy methotrexate, sorbitol 6-phosphate, and captopril. WF cows exhibited elevated d-proline, l-hydroxy arginine, alanine betaine, sn-glycerol 3-phosphoethanolamine, and anthranilic acid. Correlation analysis further revealed strong associations between microbial taxa and key metabolic pathways. In the WU group, the genera Romboutsia_B, Paraclostridium, Clostridium_T, Turicibacter, and Blautia_A were positively correlated with metabolites such as neoabietic acid, 4-imidazoleacrylic acid, 8 s-hydroxy-4Z,6E,10Z-hexadecatrienoic acid, n-acetylcytidine, 7-hydroxymethotrexate, and O-succinyl-l-homoserine. Conversely, these genera were negatively correlated with alanine betaine, l-hydroxy arginine, d-proline, anthranilic acid (Vitamin L1), sn-glycerol 3-phosphoethanolamine, and 1-deoxy-1-(methylamino)-d-galactitol. In the WF group, Campylobacter_B was positively correlated with 1-myristoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine, sn-glycerol 3-phosphoethanolamine, and anthranilic acid (Vitamin L1), and negatively correlated with 4-imidazole acrylic acid and 7-hydroxy methotrexate. Additionally, Ruminiclostridium_E and Odoribacter negatively correlated with 7-hydroxy methotrexate and captopril. These findings suggest a coordinated microbiota-metabolite interplay influencing fetal development. Identifying maternal specific microbial taxa and metabolic pathways associated with higher-birth-weight calves offers potential biomarkers and intervention targets for optimizing neonatal growth and perinatal health management in dairy cattle.},
}

Animals
Cattle
*Gastrointestinal Microbiome/physiology
Female
Pilot Projects
*Birth Weight/physiology
Animals, Newborn
Pregnancy
*Metabolome
Metabolomics/methods

@article {pmid41085833,
year = {2025},
author = {Liu, H and Cheng, Y and Tan, S and Qu, Y and Zhang, Z and Yan, M and Wu, G},
title = {Multi-omics integration reveals gut Microbiome and Short-chain fatty acid profiles in gastric cancer cachexia patients and their clinical significance.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {10},
pages = {385},
pmid = {41085833},
issn = {1573-0972},
support = {QDFYQN2024213//he Youth Fund of the Affiliated Hospital of Qingdao University/ ; 25-1-1-138-zyyd-jch//the Qingdao Municipal Natural Science Foundation/ ; 19ZR1409100//the Municipal Natural Science Foundation of Shanghai/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Cachexia/microbiology/etiology/metabolism ; *Stomach Neoplasms/complications/microbiology ; *Fatty Acids, Volatile/metabolism/analysis ; Male ; Female ; Middle Aged ; Feces/microbiology ; Aged ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification/metabolism ; Biomarkers ; Gas Chromatography-Mass Spectrometry ; Clinical Relevance ; Multiomics ; },
abstract = {Cachexia is a common complication in gastric cancer patients, yet its microbiome-based mechanisms remain poorly understood. This study investigated gut microbiota and short-chain fatty acids (SCFAs) profiles in gastric cancer cachexia patients to evaluate their potential as diagnostic biomarkers and therapeutic targets. Fecal samples and clinical data were collected from 24 cachectic and 24 non-cachectic gastric cancer patients. Gut microbiota composition was analyzed via 16 S rRNA sequencing, and SCFAs levels were measured by gas chromatography-mass spectrometry. Bioinformatic approaches identified potential biomarkers and evaluated correlations with clinical features. Cachectic patients exhibited significantly lower BMI, higher weight loss, and elevated inflammatory markers (CRP, IL1, IL6, TNF-α; p < 0.05). Microbial α-diversity was significantly reduced (Shannon and Chao1 indices, p < 0.05), while β-diversity analyses revealed distinct community structures between groups. Ten genus-level microbial taxa were identified as potential biomarkers, including Faecalibacterium, Prevotella, and Streptococcus (p < 0.05). Functional prediction indicated significant alterations in carbohydrate and fatty acid metabolism pathways. SCFAs levels, including acetate, heptanoate, and butyrate, were significantly lower in cachectic patients (p < 0.05), demonstrating promising diagnostic value (AUC: butyrate 0.792, heptanoate 0.797, acetate 0.760). Strong correlations were observed between microbial composition changes, SCFAs levels, and clinical parameters. This study reveals distinct gut microbiota and SCFAs profiles in gastric cancer cachexia patients, elucidating disease mechanisms and providing insights for early diagnosis and targeted interventions. These findings advance our understanding of cachexia pathophysiology and support developing microbiome-based diagnostic and therapeutic strategies.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Cachexia/microbiology/etiology/metabolism
*Stomach Neoplasms/complications/microbiology
*Fatty Acids, Volatile/metabolism/analysis
Male
Female
Middle Aged
Feces/microbiology
Aged
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics/isolation & purification/metabolism
Biomarkers
Gas Chromatography-Mass Spectrometry
Clinical Relevance
Multiomics

@article {pmid41085592,
year = {2025},
author = {Lee, CH and Han, Y and Ryu, JY and Jung, M and Park, CR and Jang, MR and Kwak, YG and Cha, H and Lee, JH},
title = {A Novel Strain Bifidobacterium longum subsp. longum HN001 Ameliorates High-Fat Diet-Induced Obesity in Mice Through Microbiome-Associated Short-Chain Fatty Acids.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41085592},
issn = {1867-1314},
abstract = {Obesity, characterized by excessive fat accumulation, poses global health risks due to its association with metabolic diseases. Beyond conventional treatments, the gut microbiome has emerged as a promising therapeutic target. Given the critical role of microbiome alterations in obesity, modifying its composition through probiotics, prebiotics, or synbiotics offers a novel strategy for mitigating obesity and related conditions. In this study, we demonstrate the dose-dependent anti-obesity effects of a novel strain, Bifidobacterium longum subsp. longum HN001 (HN001), in a high-fat diet (HFD)-induced mouse model. Among the doses tested (100, 200, and 400 mg/kg), the 200 mg/kg dose showed the most pronounced effect, significantly reducing body weight gain, serum triglyceride (TG), and total cholesterol (TC) levels. These effects were associated with reductions in fat mass and adipocyte hypertrophy in white adipose tissue (WAT), suppression of lipogenesis, and enhanced energy expenditure through WAT browning and thermogenesis in brown adipose tissue (BAT). Microbiome analysis revealed that HN001 increased the abundance of beneficial, SCFA-producing microbes while reducing taxa linked to metabolic dysfunction. Importantly, HN001 restored serum short-chain fatty acid (SCFA) levels, and its lipid-lowering effect in adipocytes was attenuated by a GPR43 antagonist, supporting an SCFA-GPR43-mediated pathway that links microbiome modulation with reduced adipogenesis and enhanced thermogenesis. These findings suggest that HN001 may represent a promising therapeutic strategy for obesity via SCFA-driven modulation of host metabolism and gut microbiome composition.},
}

@article {pmid41085526,
year = {2025},
author = {Kazemi, M},
title = {Biochar in Animal Agriculture: Enhancing Health, Efficiency and Environmental Sustainability.},
journal = {Veterinary medicine and science},
volume = {11},
number = {6},
pages = {e70629},
doi = {10.1002/vms3.70629},
pmid = {41085526},
issn = {2053-1095},
mesh = {*Charcoal ; Animals ; *Animal Husbandry/methods ; Animal Feed/analysis ; *Livestock ; *Agriculture/methods ; Conservation of Natural Resources ; },
abstract = {Biochar, a carbon-rich material produced through the pyrolysis of organic biomass (e.g., wood, crop residues, manure and other organic wastes), has emerged -as an effective solution for enhancing sustainability in animal agriculture. This article reviews and integrates current research on biochar's multifaceted roles, including its use as a feed additive to improve gut health, nutrient absorption and growth performance. Notably, innovative applications of biochar in enhancing feed formulations and promoting animal resilience against diseases are discussed. Recent studies have shown that biochar can also enhance animal resilience against diseases and promote a healthier gut microbiome, which is essential for overall livestock productivity and well-being. Moreover, its unique properties allow for the development of biochar-based products that can significantly reduce feed costs while improving overall animal health. Additionally, biochar has been linked to improved feed efficiency, leading to better weight gain and reduced feed costs. Its ability to mitigate environmental impacts by reducing methane emissions and ammonia volatilization in manure management, and its long-term carbon sequestration potential are significant. Furthermore, the integration of biochar into circular agricultural systems is explored, highlighting its role in transforming waste into valuable resources. Moreover, biochar contributes to soil health by improving nutrient retention and water-holding capacity, which is crucial for sustainable farming practices. This enhancement leads to increased crop yields and a reduction in the reliance on synthetic fertilizers, thereby promoting a more circular agricultural economy. Despite these benefits, challenges such as variability in biochar quality, economic feasibility and the -need for standardized guidelines remain. Addressing these challenges is essential for widespread adoption and effective use in various agricultural systems, ensuring that biochar can be safely integrated into existing farming practices. Furthermore, this article underscores biochar's potential to bridge productivity and ecological sustainability, while calling for further research to optimize its applications and ensure safe, large-scale implementation in diverse livestock production systems.},
}

*Charcoal
Animals
*Animal Husbandry/methods
Animal Feed/analysis
*Livestock
*Agriculture/methods
Conservation of Natural Resources

@article {pmid41085348,
year = {2025},
author = {Zhang, S and Wu, Z and Zhang, S and Ru, Y and Wang, Q and Tong, H and Qin, Q and Yan, Q and Li, Z and Wu, G},
title = {The intricate microbial-gut-brain axis in Alzheimer's disease: a review of microbiota-targeted strategies.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo03139g},
pmid = {41085348},
issn = {2042-650X},
abstract = {The microbiome-gut-brain axis (MGBA) has emerged as a potential focus for the enhancement of cognitive abilities and the improvement of Alzheimer's disease (AD). Probiotics and prebiotics can improve the imbalance of gut microbiota to alleviate AD symptoms. Current research on probiotics/prebiotics and brain function mainly focuses on metabolic pathways such as those involving microbial metabolites like lipopolysaccharides and short-chain fatty acids, as well as immune pathways that regulate inflammation in the gut and brain. However, the roles played by endocrine and neural pathways remain less explored and warrant further attention. This review explores the intricate mechanisms of gut-brain communication within the MGBA, and especially systematically elaborates on the specific mechanisms of the endocrine pathway (impact of gut-derived and exogenous hormones on brain function) and the neural pathway (regulation of brain function by the sympathetic and parasympathetic systems). It also emphasizes the specific changes in gut microbiota noted in individuals with AD. Additionally, it examines the beneficial effects of probiotics, prebiotics, synbiotics, and postbiotics for cognitive function, reviewing their advancements in preclinical research, clinical trials, and commercial applications. Furthermore, this review delves into novel gut microbiota-related strategies to promote brain health, including antibiotics, certain gut-targeted inhibitors or agonists, fecal microbiota transplantation, whole microbiome transplantation, viral microbiota transplantation, genetically engineered bacteria, and bacteriophage-based in situ intestinal microbiome engineering. Ultimately, this review aims to advance the therapeutic application of gut microbiota-targeted strategies in AD.},
}

@article {pmid41085331,
year = {2025},
author = {Beckett, R and Archer, L and Barrable, A and Bogdan-Margineanu, M and Bradley, S and Hawes, S and Herr, C and Housen, M and Lacatusu, A and Laitinen, O and Roslund, M and Rumble, H and Scott, W and Sinkkonen, A and Sun, X and Robinson, JM},
title = {Priority research questions in microbiome-integrated urban design.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0061925},
doi = {10.1128/msphere.00619-25},
pmid = {41085331},
issn = {2379-5042},
abstract = {Urbanization is accelerating at an unprecedented pace, with 70% of the global population projected to live in cities by 2050. This shift presents significant challenges and opportunities for fostering sustainable urban ecosystems aligned with the United Nations Sustainable Development Goals. Microbiomes-the diverse communities of microorganisms that underpin ecosystem function-are increasingly recognized for their vital role in nutrient cycling, climate regulation, biodiversity support, and human well-being. However, their consideration and integration in urban design remain underexplored, often limited to disease mitigation. The emerging field of microbiome-integrated urban design seeks to leverage microbial activity to enhance urban health and resilience through a multispecies framework. To address critical gaps, the Probiotic Cities Working Group convened a global interdisciplinary workshop, engaging experts from ecology, architecture, urban planning, immunology, and social sciences. Using reverse brainstorming and thematic analysis, participants identified eight core themes and 40 priority research questions (via a modified Delphi technique). These themes span communication and policy, pollution prevention, interdisciplinary collaboration, experimental design, ethics, and public perception of microbiomes. A binomial concordance analysis revealed strong consensus on the top-ranked questions, which address urgent needs such as improving science communication, defining success metrics, and promoting evidence-based microbiome interventions. This paper discusses the top-ranked priority research questions and their broader implications for microbiome science, urban health, and sustainable development. By focusing on these priorities, researchers, policymakers, and practitioners can foster a transformative agenda to integrate microbiomes into urban design, advancing resilient and equitable cities for the future.},
}

@article {pmid41085286,
year = {2025},
author = {Bandopadhyay, S and Bagchi, O and Shade, A},
title = {Activation dynamics and assembly of root zone soil bacterial communities in response to stress-associated phytohormones.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0178925},
doi = {10.1128/spectrum.01789-25},
pmid = {41085286},
issn = {2165-0497},
abstract = {UNLABELLED: Plants can "cry for help" to recruit supportive microbiome members during stress, but the precise signals a plant uses to activate and assemble these microorganisms remain unclear. We evaluated the activation dynamics of root zone soil bacteria in response to phytohormones produced when plants are stressed, hypothesizing that responsive taxa could support plant resilience. We conducted a mesocosm experiment using root zone soil collected from the planted fields of two crops: the annual legume common bean (Phaseolus vulgaris L.) and the perennial grass switchgrass (Panicum virgatum). In the absence of any plant, we inactivated the root zone microbiome by drying the soil and then added abscisic acid, salicylic acid, a carrier control, or water to test their capacities to reactivate microbiome members and assessed responses for 2 weeks. Using amplicon sequencing of the 16S rRNA and rRNA genes to determine active populations, we found several actinobacteria that became active after exposure to abscisic acid and salicylic acid, with Microbispora lineages being especially responsive. While some taxa activated only in one crop's root soil, others were activated in both crops' soils in response to the same phytohormone. By comparing microbes that immediately activated 24 h after phytohormone addition with those that activated and also persisted over several days, we distinguished taxa that responded to phytohormones as signals from those that potentially also used them as resources. This work suggests that different root zone bacteria exhibit distinct specificities to phytohormones, providing insights into the signals by which plants may "cry for help" to recruit bacteria.

IMPORTANCE: Global food security is a pressing societal challenge that has been exacerbated by climate change and other anthropogenic stressors on the environment. Microbial bioinoculants are a promising solution for improving crop health and resilience, but ensuring their persistence and activation in the field remains a significant challenge. This study examined how dormant root-zone-associated bacteria reactivate after exposure to the plant stress hormones abscisic acid and salicylic acid. The experiment revealed that certain bacterial taxa could reactivate in response to these plant stress signals and persist for at least 2 weeks. This work advances our understanding of the potential cues for reactivating beneficial plant-associated microbes and supports the goal of developing microbial solutions for sustainable agriculture.},
}

@article {pmid41085282,
year = {2025},
author = {Mortensen, AS and Nielsen, DS and Røder, HL and Sølbeck Rasmussen, T},
title = {Mucofilm: a nexus for phage-microbiome interactions in gut ecology.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0126925},
doi = {10.1128/aem.01269-25},
pmid = {41085282},
issn = {1098-5336},
abstract = {The human gut is a dynamic ecosystem where bacteriophages (phages) and bacteria interact within a complex mucosal environment. Here, we introduce the concept of mucofilm, a hybrid matrix composed of mucus produced by host cells and bacterial biofilm, as a unified ecological niche in the gut while also recognizing its relevance to other mucus-covered surfaces. Traditionally treated as separate entities, mucus and biofilm are in fact deeply interwoven, forming a complex environment that shapes microbial interactions, phage dynamics, and host responses. We question whether traditional knowledge about phage-biofilm interactions is transferable to mucofilm, and we therefore believe that recognizing mucofilm as a distinct structure is essential for understanding how phages interact with the gut microbiome, influencing microbial resilience, diversity, and immune modulation. This commentary challenges conventional compartmentalization and highlights the need to consider mucofilm as a single, integrated system when designing microbiome and phage-related studies. By doing so, we can better predict microbial behavior and improve therapeutic strategies targeting gut-associated diseases.},
}

@article {pmid41084996,
year = {2025},
author = {Huang, S and Wang, T and Sheng, N and Zhang, Q and Xu, X and Ma, X},
title = {Enzyme-Activated Core-Shell Drug Co-Crystal Nanoparticles for Targeted Salmonella Clearance and Gut Microbiome Restoration.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e04914},
doi = {10.1002/smll.202504914},
pmid = {41084996},
issn = {1613-6829},
support = {2021YFD1801000//National Key Research and Development Program of China/ ; 32171389//National Natural Science Foundation of China/ ; 2020B0301030007//Guangdong Major Project of Basic and Applied Basic Research/ ; HSPHDSRF-2024-05-015//PhD Scientific Research and Innovation Foundation of The Education Department of Hainan Province, Joint Project of the Sanya Yazhou Bay Science and Technology City/ ; CARS36//earmarked fund/ ; },
abstract = {Salmonella Typhimurium-a gut-colonizing pathogen that invades mucosa and triggers colitis-remains clinically challenging due to host barriers limiting oral antibiotic efficacy. To address this issue, an innovative co-crystal nanoparticle platform is developed for targeted therapy. This platform consists of PC@Kana@TA nanoparticles (PC@Kana@TA NPs), synthesized through a simple, cost-effective, and scalable process involving two key steps: 1) self-assembly of tannic acid (TA) with kanamycin (Kana) to form the antimicrobial core Kana@TA nanoparticles (Kana@TA NPs), enhancing drug stability and bactericidal efficacy; and 2) subsequent coating of Kana@TA NPs with mixed pectin-chitosan (PC) to generate the final PC@Kana@TA NPs. This dual-layer coating strategy not only provides gastric acid resistance but also enables pectinase-responsive release in the intestinal tract, thereby significantly improving oral bioavailability compared to conventional formulations. In vitro, Kana@TA NPs exhibit above 70% intracellular Salmonella clearance rate in both the RAW264.7 and Caco-2 cells. Animal experiments revealed that PC@Kana@TA NPs achieved a 5-log reduction in luminal Salmonella, with inflammatory cytokine levels nearly returned to baseline. Notably, the relatively beneficial gut bacteria abundance is 30.53% higher than the Kana group. This strategy presents a versatile strategy for nano-enabled intracellular infection therapies, unlocking new opportunities for drug repurposing and optimization.},
}

@article {pmid41084918,
year = {2025},
author = {Afkhami, ME and Classen, AT and Dice, CG and Hernandez, DJ and Li, VW and Rawstern, AH and Rudgers, JA and Stinchcombe, JR and Crawford, KM},
title = {Unraveling complexity in climate change effects on beneficial plant-microbe interactions: mechanisms, resilience, and future directions.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70644},
pmid = {41084918},
issn = {1469-8137},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; 1754287//Division of Environmental Biology/ ; 1911451//Division of Environmental Biology/ ; 1922521//Division of Environmental Biology/ ; 2030060//Division of Environmental Biology/ ; 2105402//Division of Environmental Biology/ ; 2225029//Division of Environmental Biology/ ; 2413159//Division of Environmental Biology/ ; 2425290//Division of Environmental Biology/ ; 2440261//Division of Environmental Biology/ ; 2505581//Division of Environmental Biology/ ; 2305481//Division of Biological Infrastructure/ ; DE-FOA-0002392//Biological and Environmental Research/ ; },
abstract = {Plant microbiomes have the potential to mitigate the impacts of climate change, yet both the complexity of climate change and the complexity of plant-microbe interactions make applications and future predictions challenging. Here, we embrace this complexity, reviewing how different aspects of climate change influence beneficial plant-microbe interactions and how advances in theory, tools, and applications may improve understanding and predictability of climate change effects on plants, microbiomes, and their roles within ecosystems. New advances include consideration of (1) interactions among climate stressors, such as more variable precipitation regimes combined with warmer mean temperature; (2) mechanisms that promote the stability of microbiome functions; (3) legacies of stress affecting the functionality of microbial communities under future stress; and (4) temporally repeated plant-microbe interactions or feedbacks. We also identify key gaps in each of these areas and spotlight the need for more research bridging molecular biology and ecology to develop a more mechanistic understanding of how climate change shapes beneficial microbe-plant interactions.},
}

@article {pmid41084450,
year = {2025},
author = {Zhang, T and Chen, N and Jia, QY and Lei, XX and Wang, J and Zhao, JQ and Wei, Y and Wen, J},
title = {[Effect and mechanism of Liujunzi Pills on gut microbiota of rats with spleen Qi deficiency syndrome].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {50},
number = {15},
pages = {4333-4341},
doi = {10.19540/j.cnki.cjcmm.20250421.402},
pmid = {41084450},
issn = {1001-5302},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/administration & dosage/pharmacology ; Male ; Rats, Sprague-Dawley ; Rats ; *Qi ; *Spleen/drug effects/metabolism ; *Splenic Diseases/microbiology/drug therapy/metabolism ; Humans ; Interleukin-1beta/metabolism/genetics ; Bacteria/classification/isolation & purification/genetics/drug effects ; Feces/microbiology ; Adenosine Triphosphate/metabolism ; },
abstract = {This article aims to explore the effect and mechanism of Liujunzi Pills on the intestinal microbiota of rats with spleen Qi deficiency syndrome. The raw Rhei Radix et Rhizoma water extract(1 g·mL~(-1)) was used to prepare spleen Qi deficiency rat models. A total of 44 SD male rats were randomly divided into a control group, a model group, Liujunzi Pills groups at high(3.24 g·kg~(-1)), medium(1.62 g·kg~(-1)), low(0.81 g·kg~(-1)) doses, and Shenling Baizhu San(2.50 g·kg~(-1)) group. The drug effect was evaluated by observing the following aspects: spleen index, fecal water content, body weight, and intestinal propulsion index. Gut microbiota analysis and 16S rRNA gene sequencing were conducted on feces. Enzyme-linked immunosorbent assay(ELISA) and UV spectrophotometry were used to detect interleukin-1β(IL-1β) and adenosine triphosphate(ATP) levels in small intestine tissues. Hematoxylin-eosin staining and transmission electron microscopy were employed to observe changes in intestinal pathology and microstructure. The results show that, compared with the control group, fecal moisture content is significantly increased while spleen index, body weight, and intestinal propulsion index are significantly reduced in rats of the model group, indicating the successful establishment of the model. The above symptoms can be improved by both Shenling Baizhu San and Liujunzi Pills. Compared with the control group, in the model group, the gut microbiota abundance is changed with an unbalanced development: the abundance of beneficial bacteria within the Bacteroidetes phylum is reduced, accompanied by a significantly decreased Shannon index, and reduced signal levels of nicotinamide adenine dinucleotide phosphate(NADPH)-related enzymes relevant to mitochondria. However, Liujunzi Pills and Shenling Baizhu San can significantly improve the Bacteroidetes phylum abundance in gut microbiota, microbial diversity, and NADPH activity in the model group. Additionally, compared with the control group, the ATP level is decreased and the IL-1β level is increased in small intestinal tissues of the model group, with shorter small intestinal epithelial villi and decreased mitochondrial number. The above symptoms can be improved by Liujunzi Pills and Shenling Baizhu San. In conclusion, Liujunzi Pills can treat spleen Qi deficiency syndrome by enhancing mitochondrial function to regulate gut microbiota balance and diversity.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Drugs, Chinese Herbal/administration & dosage/pharmacology
Male
Rats, Sprague-Dawley
Rats
*Qi
*Spleen/drug effects/metabolism
*Splenic Diseases/microbiology/drug therapy/metabolism
Humans
Interleukin-1beta/metabolism/genetics
Bacteria/classification/isolation & purification/genetics/drug effects
Feces/microbiology
Adenosine Triphosphate/metabolism

@article {pmid41084236,
year = {2025},
author = {Vergoz, V and Jeong, D and Hamilton-Williams, EE},
title = {Are Bifidobacterium Species Key Players in the Progression of Type 1 Diabetes? A Systematic Review.},
journal = {Endocrinology, diabetes & metabolism},
volume = {8},
number = {6},
pages = {e70120},
doi = {10.1002/edm2.70120},
pmid = {41084236},
issn = {2398-9238},
support = {//Juvenile Diabetes Research Foundation Australia/ ; //Leona M. and Harry B. Helmsley Charitable Trust/ ; //National Health and Medical Research Council/ ; },
mesh = {Humans ; *Diabetes Mellitus, Type 1/microbiology/pathology ; *Bifidobacterium/physiology ; Disease Progression ; *Gastrointestinal Microbiome ; Probiotics ; },
abstract = {BACKGROUND: Type 1 diabetes (T1D) frequently develops in childhood and is preceded by a non-symptomatic period of autoimmunity. Alterations in the gut microbiome are implicated in T1D pathogenesis. Bifidobacterium is a significant focus due to its positive health impacts, association with breastfeeding and presence in probiotics and infant milk-formulas. This systematic review aims to investigate Bifidobacterium's association with T1D across disease stages.

METHODS: A comprehensive electronic search was conducted in MEDLINE, EMBASE and Web of Science, from 2011 to 2024. The search used a combination of medical subject headings and keywords related to Bifidobacterium. Studies included individuals at risk of T1D (pre-stage, stage 1 or 2 asymptomatic T1D) and with stage 3 symptomatic T1D while excluding T2D, clinical trials and animal studies.

RESULTS: The search initially retrieved 1120 articles. Of these, 25 papers met the inclusion criteria, covering 4533 individuals (842 cases with or at-risk of T1D and 3691 healthy controls). The studies highlighted variability in Bifidobacterium abundance in T1D, with higher abundance found more often in at-risk asymptomatic individuals and lower abundance frequently found in those with established T1D.

CONCLUSION: These findings do not support loss of Bifidobacterium as a key factor in the early development of T1D. Further studies are needed to explore Bifidobacterium's role in T1D progression and management.},
}

Humans
*Diabetes Mellitus, Type 1/microbiology/pathology
*Bifidobacterium/physiology
Disease Progression
*Gastrointestinal Microbiome
Probiotics

@article {pmid41084144,
year = {2025},
author = {Miller, CS and Yan, Q and Kirakodu, SS and Ebersole, JL and Zhang, XD},
title = {Salivary Biomarker Panel That Identifies Periodontitis in Persons With Type 2 Diabetes: A Secondary Analysis of a Cross-Sectional Study.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.70049},
pmid = {41084144},
issn = {1600-051X},
support = {//Delta Dental of Michigan Research Foundation/ ; UL1TR001998/NH/NIH HHS/United States ; P30DK020579/NH/NIH HHS/United States ; },
abstract = {AIM: This secondary analysis of a cross-sectional study tested the hypothesis that a salivary biomarker panel (i.e., consisting of 2-6 features) could accurately identify periodontitis in persons with Type 2 diabetes (T2DM) compared with non-periodontitis in systemically healthy persons.

MATERIALS AND METHODS: Salivary concentrations of 12 protein biomarkers and 14 oral microbiome species were evaluated by immunoassays and 16S rRNA sequencing, respectively, from 28 systemically healthy non-periodontitis adults and 28 T2DM patients with periodontitis. Data were analysed for the identification of periodontitis from non-periodontitis using 5-fold cross-validation logistic regression, receiver operating characteristics (ROC) and odds ratios.

RESULTS: Bacteria showed better predictive value than individual salivary proteins. Two bacteria (Porphyromonas gingivalis and Mycoplasma faucium) yielded specificities > 90%, Prevotella species yielded high sensitivity (86%) and Treponema socranskii demonstrated the top area under the curve (AUC) (0.81). A salivary panel consisting of bacteria (Selenomonas sputigena, P. gingivalis, Prevotella nigrescens, Pr. dentalis) and protein ratios (prostaglandin E2/tissue inhibitor of metalloproteinase-1 or macrophage inflammatory protein-1α/tissue inhibitor of metalloproteinase-1) produced robust diagnostic accuracy (95%) and precision (96.6%) for the detection of periodontitis in T2DM.

CONCLUSIONS: A salivary panel using bacteria and ratios of host-response biomarkers accurately identified periodontitis in T2DM compared with systemically healthy persons without periodontitis.},
}

@article {pmid41084047,
year = {2025},
author = {Mukherjee, K and Guest, PC and Nussbaumer, M and Dudeck, L and Shokati Asl, L and Meyer-Lotz, G and Dobrowolny, H and Borucki, K and Bernstein, HG and Link, A and Relja, B and Schiltz, K and Nickl-Jockschat, T and Steiner, J},
title = {Assessment of intestinal barrier integrity and associations with innate immune activation and metabolic syndrome in acutely ill, antipsychotic-free schizophrenia patients.},
journal = {Journal of neuroinflammation},
volume = {22},
number = {1},
pages = {232},
pmid = {41084047},
issn = {1742-2094},
mesh = {Humans ; Male ; Female ; Adult ; *Schizophrenia/immunology/blood/complications ; Fatty Acid-Binding Proteins/blood ; *Immunity, Innate/physiology ; Middle Aged ; Acute-Phase Proteins/metabolism ; *Metabolic Syndrome/immunology/blood ; Carrier Proteins/blood ; Membrane Glycoproteins/blood ; Young Adult ; *Intestinal Mucosa/metabolism/pathology ; Antipsychotic Agents/therapeutic use ; Biomarkers/blood ; },
abstract = {BACKGROUND: Schizophrenia (Sz), once seen solely as a brain disorder, is now recognised as a systemic illness involving immune and metabolic dysregulation. The intestinal barrier has emerged as a key player in gut-brain-immune interactions. However, studies in early, antipsychotic free stages remain scarce and often neglect confounding factors such as smoking and metabolic syndrome.

METHODS: We measured two complementary markers: lipopolysaccharide-binding protein (LBP), reflecting endotoxin exposure and systemic immune activation, and intestinal fatty acid-binding protein (I-FABP), indicating gut epithelial damage and permeability changes, in blood from 96 acutely ill, antipsychotic-free Sz patients (61 first-episode, 35 relapsed) and 96 matched controls. Associations with innate immunity, metabolic parameters, smoking, and clinical features were assessed using nonparametric statistics and random forest regression. Group differences were tested using covariate adjustment, as well as in a separate analysis of non-smokers (Sz: n = 42; controls: n = 84).

RESULTS: Median LBP was higher in Sz (21.96 µg/mL) vs. controls (18.10 µg/mL; FDR-adjusted p = 0.021, δ = 0.209) but became non-significant after adjusting for smoking (FDR-adjusted p = 0.199). In contrast, I-FABP was lower in Sz (218.2 pg/mL) than controls (315.0 pg/mL; FDR-adjusted p = 0.021, δ = -0.195) and remained robust across smoking-adjusted analyses. No differences were found between first-episode and relapsed patients for either marker. LBP correlated strongly with CRP (r = 0.557, p < 0.001) and neutrophils (r = 0.468, p < 0.001) and was moderately predicted by immune models (pseudo-R[2] = 0.354 overall; 0.273 Sz; 0.449 controls). Links to waist circumference and blood pressure were weaker (pseudo-R[2]: 0.048-0.104). I-FABP showed fewer immune associations and was not correlated with LBP (r = -0.017, FDR-adjusted p = 0.819), suggesting distinct mechanisms.

CONCLUSIONS: Our findings suggest separable gut‑related processes in antipsychotic-free Sz. The apparent LBP elevation was not schizophrenia‑specific; its strong correlations with CRP and neutrophils point to smoking related inflammation rather than a schizophrenia specific effect. Accordingly, prior findings of LBP elevations in Sz likely reflect unaccounted smoking. In contrast, reduced I-FABP, independent of smoking, may indicate epithelial injury. The absent correlation between LBP and I-FABP highlights distinct pathophysiological dimensions of gut dysfunction. Longitudinal studies, ideally spanning prodromal phases and integrating microbiome, dietary, smoking, and permeability assessments, are needed to clarify temporal dynamics and guide stratified treatments.},
}

Humans
Male
Female
Adult
*Schizophrenia/immunology/blood/complications
Fatty Acid-Binding Proteins/blood
*Immunity, Innate/physiology
Middle Aged
Acute-Phase Proteins/metabolism
*Metabolic Syndrome/immunology/blood
Carrier Proteins/blood
Membrane Glycoproteins/blood
Young Adult
*Intestinal Mucosa/metabolism/pathology
Antipsychotic Agents/therapeutic use
Biomarkers/blood

@article {pmid41083888,
year = {2025},
author = {Ye, ZW and Yang, QY and Xu, WT and Li, FQ and Luo, P and Qin, S and Wang, F},
title = {Multiomics strategy-based obesity biomarkers discovery for precision medicine.},
journal = {International journal of obesity (2005)},
volume = {},
number = {},
pages = {},
pmid = {41083888},
issn = {1476-5497},
abstract = {Obesity is a multifaceted metabolic disorder characterized by dysregulated glucose and lipid metabolism, often comorbid with conditions such as diabetes, hypertension, hyperlipidemia, cardiovascular diseases, and cancers. Due to its diverse etiological factors and inherent heterogeneity, obesity poses significant challenges for management. The advent of multiomics technologies has opened new avenues for a deeper exploration of the molecular underpinnings and clinical biomarkers of obesity, improving our ability to predict and monitor associated metabolic syndromes. However, a holistic understanding of obesity that incorporates physical fitness, living conditions, and other contributing factors remains elusive. In this review, we summarize various factors that affect the occurrence of obesity, emphasizing the diversity and complexity of obesity and its complications. We provided a detailed overview of the expression of biomarkers identified through epigenetics, transcriptomics, proteomics, metabolomics, and gut microbiome, shedding light on the latent etiological mechanisms of obesity. Additionally, we discuss the methodological landscape for data integration in multiomics research and highlight the current progress in identifying obesity biomarkers through integrative multiomics strategies. We also critically evaluate the pitfalls and limitations of current multiomics studies on obesity, emphasizing the challenges of integrating data across different omics layers and the necessity for longitudinal and population-specific studies. Furthermore, we assess the clinical applicability of obesity biomarkers, noting that although many promising biomarkers have been identified, their validation and implementation in clinical settings remain limited. These biotargets offer new directions for precision treatment of obesity, such as targeted epigenetic modifications or modulation of specific microbiome populations, which have the potential to change clinical approaches to dynamic weight management and metabolic health.},
}

@article {pmid41083526,
year = {2025},
author = {Ren, L and Li, Y and Tian, X and Guo, Y and Xian, Y and Pang, M and Zhang, Z},
title = {Shaping of the core microbiome by ginsenosides in American ginseng across diverse habitats.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35702},
pmid = {41083526},
issn = {2045-2322},
support = {CEPFQS202169-19//China Environmental Protection Foundation/ ; CEPFQS202169-19//China Environmental Protection Foundation/ ; CEPFQS202169-19//China Environmental Protection Foundation/ ; CEPFQS202169-19//China Environmental Protection Foundation/ ; CEPFQS202169-19//China Environmental Protection Foundation/ ; CEPFQS202169-19//China Environmental Protection Foundation/ ; CEPFQS202169-19//China Environmental Protection Foundation/ ; },
mesh = {*Ginsenosides/metabolism ; *Panax/microbiology/chemistry/metabolism ; Soil Microbiology ; *Microbiota ; Rhizosphere ; Bacteria/classification/genetics/metabolism ; Fungi/classification/genetics/metabolism ; Ecosystem ; },
abstract = {Geographical environmental factors affect the secondary metabolism of plants and regulate rhizosphere microorganisms. However, the metabolite characteristics and rhizosphere microbial composition of American ginseng (Panax quinquefolius L., AG) from different sources remain unclear. In this study, high-throughput sequencing technology and metabolomics technology were used to analyze the microbial community structure and metabolite content in the rhizosphere soil of AG from different habitats, and the relationships between soil microorganisms and metabolites were analyzed. The results revealed that the diversity of rhizospheric soil bacterial and fungal communities in different habitats was unusual and affected the metabolite content. The bacterial genera strongly correlated with the triterpenoid saponins of AG included Bradyrhizobium and Pseudoxanthomonas. Among these, Bradyrhizobium was strongly negatively correlated with ginsenoside Rg1 (P < 0.001, r = - 0.8204), and Pseudoxanthomonas was strongly positively correlated with (PPD -2 H)-Glc-Glc-malonyl (P < 0.01, r = 0.6305). The fungal genera included Alternaria and Colletotrichum. Alternaria was strongly negatively correlated with ginsenoside F1 (P < 0.001, r = - 0.7434), and Colletotrichum was also strongly negatively correlated with ginsenoside F1 (P < 0.001, r = - 0.7106). The results revealed a complex correlation between rhizosphere-dominant microorganisms and the saponin content of AG, providing a theoretical basis for guiding rational cultivation planning and designing microbial fertilizers to enhance AG quality.},
}

*Ginsenosides/metabolism
*Panax/microbiology/chemistry/metabolism
Soil Microbiology
*Microbiota
Rhizosphere
Bacteria/classification/genetics/metabolism
Fungi/classification/genetics/metabolism
Ecosystem

@article {pmid41083215,
year = {2025},
author = {Sree Kumar, H and Zubcevic, J},
title = {Host-microbiota interactions regulate gut serotonergic signaling and implications for hypertension.},
journal = {American journal of physiology. Cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpcell.00608.2025},
pmid = {41083215},
issn = {1522-1563},
support = {152162//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; },
abstract = {Serotonin (5-hydroxytryptamine) is a highly conserved signaling molecule present across diverse taxa, including plants, invertebrates, and vertebrates. In mammals, the majority of peripheral serotonin is synthesized in the gastrointestinal tract by enteric neurons and enterochromaffin cells via tryptophan hydroxylases. Its biosynthesis and release are influenced by dietary components and microbial metabolites, particularly short-chain fatty acids produced by the gut microbiota. Once released into the periphery, serotonin exerts pleiotropic effects, regulating intestinal motility and secretion, modulating vascular tone, and influencing blood pressure through both direct actions and vagal sensory pathways engaging central and autonomic circuits. Dysregulation of colonic serotonin production or signaling has been implicated in metabolic, neuropsychiatric, and cardiovascular disorders, including postprandial blood pressure abnormalities and hypertension. Emerging evidence highlights a bidirectional relationship between gut microbes and host serotonergic pathways, suggesting that microbiota-targeted interventions may hold therapeutic potential for cardiometabolic regulation. Advancing our understanding of gut serotonergic signaling, particularly the interplay between host and microbial factors, could inform the development of innovative strategies to treat hypertension and related conditions.},
}

@article {pmid41083214,
year = {2025},
author = {Chen, B and Gautron, L},
title = {Gut-Derived Lipopolysaccharides and Metabolic Endotoxemia: A Critical Review.},
journal = {American journal of physiology. Endocrinology and metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpendo.00355.2025},
pmid = {41083214},
issn = {1522-1555},
abstract = {The metabolic endotoxemia hypothesis proposes that low levels of gut-derived lipopolysaccharides (LPS) act in a hormone-like manner to influence metabolism, contributing to obesity and dysregulation of glucose homeostasis. However, due to methodological limitations, it remains unclear whether a significant amount of bioactive gut-derived LPS reaches the bloodstream and, if so, whether it has a meaningful impact on metabolic processes. Additionally, there are several theoretical challenges regarding the coherence of the metabolic endotoxemia hypothesis, raising questions about its validity. Here, in the light of recent literature, we critically review arguments for and against the metabolic endotoxemia hypothesis.},
}

@article {pmid41082980,
year = {2025},
author = {Sjælland, MA and Philipsen, MT and Henriksen, TB and Skipper, J and Rubak, SLM},
title = {Probiotics in Term Infants: Clinical Impact of Infant-Type Bifidobacteria - A Systematic Review and Meta-Analyses.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.10.006},
pmid = {41082980},
issn = {1541-6100},
abstract = {Probiotics labeled "infant-type bifidobacteria" (ITB), such as the B. longum subsp. infantis strains, have gained significant attention in recent years for their potential to positively influence the gut microbiome, early immune system development, and consequently future health. However, significant knowledge gaps remain regarding the actual clinical impact, the optimal strains, dosing regimens, and treatment duration-both in general and for ITB probiotics specifically. This systematic review evaluates the clinical effects of administering ITB probiotics to healthy, term infants within the first year of life. The aim was to address all categories of clinical outcomes. However, the included studies focused primarily on antibiotic use, atopic conditions, gastrointestinal health, and growth. We systematically and comprehensively searched PubMed, Embase, CENTRAL, and Scopus, followed by a meta-analysis where applicable. 25 studies were included and assessed for risk of bias using the revised Cochrane tool (RoB 2). We found that early administration of ITB probiotics was associated with a significant reduction in eczema (RR = 0.78 [0.68, 0.90]) and a borderline significant reduction in respiratory tract infections (RR = 0.74 [0.54, 1.00]). Other commonly reported outcomes, including antibiotic use, diarrhea, asthmatic bronchitis, and food allergy, also showed trends toward a preventive effect, though these findings did not reach statistical significance. This review underscores the potential clinical relevance of ITB probiotics, particularly in the prevention of eczema and respiratory tract infections. However, the evidence is limited by study heterogeneity and a lack of long-term follow-up data. Further high-quality randomized controlled trials with larger sample sizes and standardized outcome measures are needed to clarify both short- and long-term effects of ITB probiotic administration in neonates and infants. PROSPERO - REGISTRATION NUMBER: CRD42024507608.},
}

@article {pmid41082667,
year = {2025},
author = {Heinze, BM and Schwab, VF and Küsel, K and Schloemer, S and Roskam, A and Xu, X and Trumbore, S},
title = {Microbial oxidation significantly reduces methane export from global groundwaters.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {42},
pages = {e2508773122},
doi = {10.1073/pnas.2508773122},
pmid = {41082667},
issn = {1091-6490},
support = {CRC 1076 AquaDiva Project-ID 218627073//Deutsche Forschungsgemeinschaft (DFG)/ ; Cluster of Excellence: Balance of the Microverse -EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {*Methane/metabolism/analysis ; *Groundwater/microbiology/chemistry ; Oxidation-Reduction ; Germany ; Archaea/metabolism ; },
abstract = {Methane is ubiquitous in groundwater, and its release to surface environments through pumping, discharge, or diffusion is an emerging environmental concern. Microbial oxidation consumes methane and mitigates its release, but quantitative constraints in groundwater remain unknown. Using ultra-low-level [14]C-labeling, we estimate in situ microbial methane oxidation rates in shallow carbonate and sandy aquifers from central and northern Germany with methane concentrations spanning 5 orders of magnitude, from 0.15 ± 0.04 to 36,250 ± 1,390 µg L[-1]. Oxidation rates ranged from 0.001 ± 0.0003 to 74.28 ± 46.94 µgC L[-1] d[-1] and were highly correlated with groundwater methane concentrations. Oxidation-based methane turnover was rapid at low methane concentrations, with complete consumption requiring days to weeks. In contrast, microbial oxidation at high methane sites required months to decades for complete methane turnover, indicating the potential for unconsumed methane to leak into local streams or wetlands. High oxidation rates were associated with gammaproteobacterial methanotrophs that typically thrive in suboxic conditions and anaerobic methane-oxidizing archaea, while uncultivated methanotrophs of the Methylomirabilota and Verrucomicrobiota dominated low-rate sites. Based on globally distributed groundwater methane concentration data, we extrapolated the strong observed correlation between methane concentrations and oxidation rates to global groundwater volumes, estimating that microbial oxidation removes ~66% of groundwater methane globally, equivalent to 167 to 778 Tg CH4 y[-1]. This highlights the groundwater microbiome as a crucial subsurface methane filter that reduces methane release to surface waters, soils, and the atmosphere.},
}

*Methane/metabolism/analysis
*Groundwater/microbiology/chemistry
Oxidation-Reduction
Germany
Archaea/metabolism

@article {pmid41082647,
year = {2025},
author = {Yang, C and Jama, HA and Dona, MSI and Farrugia, GE and Krstevski, C and Cohen, CD and Pinto, AR and Marques, FZ},
title = {Maternal dietary fibre intake results in sex-specific single-cell molecular changes in the heart of the offspring.},
journal = {Clinical science (London, England : 1979)},
volume = {},
number = {},
pages = {},
doi = {10.1042/CS20257187},
pmid = {41082647},
issn = {1470-8736},
support = {DP230102725//Australian Research Council/ ; GNT2017382//National Health and Medical Research Council/ ; Not applicable//Sylvia and Charles Viertel Charitable Foundation/ ; 105663/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Some types of dietary fibre undergo fermentation by the gut microbiome, producing microbial metabolites called short-chain fatty acids (SCFAs) - these are protective against cardiovascular disease (CVD). Emerging evidence suggests that maternal fibre intake also protects the offspring. Here, we aimed to determine whether delivery of SCFAs during pregnancy results in sex- and cell-specific molecular changes to the offspring's heart. Female mice were subjected to high or low-fibre diets during pregnancy and lactation, while all offspring received a standard-fibre diet. We then studied the single-cell transcriptome (scRNA-seq, n=16) and immune composition (fluorescence-activated cell sorting, n=28) of the hearts and gut microbiome profiles (16S rRNA, n=28) of 6-week-old male and female offspring. Maternal fibre intake induced significant changes in the cardiac cellular and immunological landscapes, revealing sex-specific signatures at the single-cell level. High fibre intake reduced the number of monocytes in the hearts of male offspring and the number of B cells in both female and male offspring. Cardiac fibroblasts in both male and female offspring of high-fibre intake dams showed an anti-fibrotic transcriptome. In contrast, only male offspring showed an anti-inflammatory transcriptome in macrophages and endothelial cells. Our findings suggest that high-fibre intake during pregnancy may induce a CVD-protective transcriptome (i.e., anti-fibrotic and anti-inflammatory), especially in male offspring. These findings underscore the relevance of maternal dietary choices during pregnancy influencing cardiovascular health outcomes in the offspring.},
}

@article {pmid41082646,
year = {2025},
author = {Green, C and Bempong, J and Ong, ML and Shah, A and Mallia, P and Johnston, SL and Singanayagam, A and Reynolds, JC and Heaney, LM},
title = {Evaluating short-chain fatty acids in breath condensate as surrogate measurements for systemic levels and investigation into alternative respiratory sample matrices.},
journal = {Clinical science (London, England : 1979)},
volume = {},
number = {},
pages = {},
doi = {10.1042/CS20257925},
pmid = {41082646},
issn = {1470-8736},
abstract = {Short-chain fatty acids (SCFAs) are metabolic by-products from microbial fermentation of complex carbohydrates and protein. They have gained clinical interest for their protective effects, including within the lung microenvironment. SCFAs are detectable in circulation and exhaled breath condensate (EBC), posing questions as to whether exhaled SCFAs originate from the gut and/or lung microbiota. Mapping SCFAs from the lung could improve our understanding on microbial activity in respiratory conditions. SCFA measurements in EBC were evaluated using a validated gas chromatography-mass spectrometry assay. Six healthy participants ingested sodium acetate, calcium propionate, and sodium butyrate to acutely increase circulating SCFAs. EBC samples were collected alongside venous draws, with circulating and exhaled levels compared. A series of additional respiratory sample matrices from patient samples were investigated to gain novel insights into SCFAs within different respiratory biofluids. SerumSCFAs were increased in-line with known responses. However, these increases were not observed in EBC, indicating a lack of correlation between circulating and exhaled SCFAs. SCFAs were detected in all additional respiratory biosamples, with EBC and sputum reporting the highest concentrations. Interestingly, branched-chain moieties were notably abundant in sputum, indicating the potential for their local production by bacterial fermentation of lung mucus proteins. SCFAs in EBC do not reflect circulatory levels and, therefore, are not a suitable surrogate measurement to inform on systemic load. These data suggest that exhaled SCFAs are potentially derived from lung microbial metabolism, supporting the need for further investigation into SCFA production, function, and diagnostic utility in respiratory health.},
}

@article {pmid41082335,
year = {2025},
author = {Zhen, Q and Xu, Y and Xu, Y and Liu, X and Zhang, Y and Ye, D and Han, S and Liu, S and Zhang, Y},
title = {Erucic Acid, Derived by Lactobacillus Crispatus, Induces Ferroptosis in Cervical Cancer Organoids Through the PPAR-δ Signaling Pathway.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e12599},
doi = {10.1002/advs.202512599},
pmid = {41082335},
issn = {2198-3844},
support = {ZR2021QH044//Natural and Science Foundation Youth Project of Shandong Province/ ; 2021YFC2701203//National Key Research and Development Program of China/ ; Y-HR2022QN-0562//Beijing Xisike Clinical Oncology Research Foundation/ ; },
abstract = {The microbiome present throughout the human body serves a variety of functions. In this study, 16S rRNA sequencing is employed to uncover differences in the abundance of Lactobacillus within the vaginal microbiota between individuals with cervical cancer and those with healthy cervixes. The research further identifies that the metabolite of Lactobacillus crispatus can induce ferroptosis in cervical cancer cells. This conclusion is reached through targeted bacterial culture, patient-derived organoids (PDO) and single-cell RNA sequencing. Erucic acid, identified as a primary metabolite via untargeted metabolomics, acts as a ligand for PPARδ receptor. It has the capacity to activate PPARδ pathway and subsequently trigger downstream fatty acid oxidation (FAO). Excessive enhancement of FAO can generate large amounts of H2O2 and O2-, known as ROS. Utilizing PDO, cell lines and cervical cancer xenograft (CDX) models, the study demonstrate both in vitro and in vivo that the metabolite of L. crispatus, erucic acid, can modulate the proliferation, migration and invasion of cervical cancer by activating the PPAR-δ pathway. This activation leads to fatty acid oxidation, release ROS, and ultimately induces ferroptosis. Therefore, L. crispatus and erucic acid show potential as novel adjuvant therapeutic agents in the treatment of cervical cancer.},
}

@article {pmid41082307,
year = {2025},
author = {Gu, W and Wang, J and Yuan, X},
title = {The role of psychosomatic interventions on the immune system and gut microbiome diversity of pregnant women with gestational hypertension.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2025.02688},
pmid = {41082307},
issn = {1588-2640},
abstract = {This study evaluates the impact of psychosomatic interventions on the immune system and microbiome composition of pregnant women diagnosed with gestational hypertension. A case-control study on 200 pregnant women diagnosed with gestational hypertension was conducted between June 2021 and December 2024. The control group (n = 100) included pregnant women diagnosed with gestational hypertension and under only pharmacological treatment with antihypertensive drugs such as labetalol. The case group (n = 100) received standard care for hypertensive disorders in pregnancy like control group, but in addition to it, we incorporated evidence based psychosomatic medicine to this group. Psychosomatic medicine included stress management, relaxation techniques, and counseling for the study group. Primary outcomes included blood pressure levels, psychological state (SAS and SDS scores), mode of delivery, incidence of complications, neonatal outcomes, patient satisfaction, reductions in inflammatory cytokines (e.g., IL-6, TNF-alpha), and improvements in microbiome diversity. Psychosomatic intervention led to a significant increase in microbiome diversity (Shannon Index, P < 0.05). Beta-diversity analysis revealed a distinct separation in microbial community composition between the study and control groups (P = 0.02). The case group also showed a reduction in pro-inflammatory cytokines, IL-6 decreased from 40.0 to 28.0 pg mL-1 (P = 0.008) and TNF-alpha from 25.0 to 18.0 pg mL-1 (P = 0.004). The case group demonstrated significant improvements in systolic (P = 0.020) and diastolic (P = 0.003) blood pressures, psychological well-being (SAS, P = 0.006; SDS: P = 0.026), and delivery outcomes (P = 0.032). Complications were significantly lower in the case group (P = 0.013), with better neonatal outcomes, including lower rates of intrauterine distress (P = 0.011), premature birth (P = 0.003), and asphyxia (P = 0.013). Emotional resilience, coping confidence, and patient satisfaction were significantly higher in the case group (P < 0.05). These findings suggest that psychosomatic medicine may offer a novel approach for managing gestational hypertension through microbiome modulation.},
}

@article {pmid41082164,
year = {2025},
author = {Harrass, S and Quansah, M and Kumar, S and Radzieta, M and Jayawardena, B and Jones, C and David, M and Heng, B and Elbourne, LDH and Amanquah, S and Adjei, P and Capunzo, M and Aliberti, SM and Jensen, SO and Tayebi, M},
title = {Lactobacilli Probiotics Prevent Amyloid-Beta Fibril Formation In Vitro.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41082164},
issn = {1867-1314},
abstract = {Alzheimer's disease (AD) is characterized by the buildup of extracellular aggregated amyloid-β (Aβ) peptides, following sequential enzymatic cleavage of amyloid precursor protein, along with intraneuronal accumulation of hyperphosphorylated Tau proteins and subsequent neuronal loss. Despite extensive research, the precise mechanisms underlying Aβ and Tau-mediated neurodegeneration remain elusive. Inhibiting protein aggregation has been a primary focus for mitigating neuronal toxicity. Probiotics have emerged as a promising preventative measure against cognitive decline in AD, with several in vivo and clinical trials demonstrating the efficacy of select bacterial strains in slowing AD progression. However, these studies lack direct molecular evidence on the effects of probiotics on Aβ aggregation kinetic. Inhibiting protein aggregation is key to reducing neuronal toxicity. While probiotics have shown promise in preventing cognitive decline in Alzheimer's disease, supported by in vivo and clinical studies, direct molecular evidence of their impact on Aβ aggregation kinetics remains lacking. In this study, we conducted bioinformatic and physicochemical assessments, including molecular docking of proteins derived from 13 probiotic strains against Aβ and Tau, identifying four strains predicted to efficiently inhibit Aβ aggregation. Kinetic studies confirmed that both the probiotic formulation and its derived supernatant significantly inhibited the conversion of monomeric Aβ and Tau into aggregated forms. To explore bioavailability, we administered the probiotic formulation to healthy individuals and detected its presence in stool samples, demonstrating survival through the gastrointestinal tract. These findings suggest that specific probiotic strains may serve as therapeutic candidates for targeting Aβ and/or Tau aggregation, with further studies warranted to assess their potential clinical utility in AD.},
}

@article {pmid41082090,
year = {2025},
author = {Sanabani, SS},
title = {The Role of the Microbiome in Endometriosis.},
journal = {Reproductive sciences (Thousand Oaks, Calif.)},
volume = {},
number = {},
pages = {},
pmid = {41082090},
issn = {1933-7205},
support = {2022/09354-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
abstract = {Endometriosis is a chronic gynecological disease characterized by the presence of endometrial-like tissue outside the uterus, leading to pain and infertility. Recent research has highlighted the important role of the microbiome in various health conditions, including endometriosis. The aim of this review is to examine the central role of the microbiome in the development and treatment of endometriosis. Key findings include the influence of the gut microbiota on estrogen metabolism, whereby certain bacteria can increase estrogen levels and systemic inflammation and exacerbate endometriosis. Changes in the vaginal and endometrial microbiota are also associated with the disease, as they influence inflammatory and estrogen-dependent metabolic pathways. Dysbiosis in various microbiomes can affect inflammatory pathways, with a shift in the vaginal microbiota to the upper reproductive tract affecting endometriosis without symptoms. Probiotic interventions show promise in restoring a healthy microbiota and improving outcomes, with clinical trials demonstrating the efficacy of lactobacilli-based medications for pain relief. In addition, diet and lifestyle changes can directly impact the gastrointestinal microbiome, reducing inflammation and potentially influencing endometriosis. Future research should focus on establishing comprehensive microbiome profiles, mechanistic studies and longitudinal studies to discover new therapeutic targets and improve clinical outcomes for women with endometriosis.},
}

@article {pmid41082055,
year = {2025},
author = {Aderolu, AZ and Salam, LB and Lawal, MO and Kabiawu-Mutiu, LF and Bassey, ME and Shobande, MA},
title = {Microbial ecology and functional landscape of black soldier fly larval bioconversion of orange waste: A metataxonomic perspective.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {10},
pages = {377},
pmid = {41082055},
issn = {1573-0972},
mesh = {Animals ; Larva/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Gastrointestinal Microbiome/genetics ; *Simuliidae/microbiology ; *Citrus sinensis/metabolism ; *Diptera/microbiology ; Nigeria ; Metagenome ; Metagenomics ; Phylogeny ; },
abstract = {The accumulation of citrus waste, particularly orange waste (OW), presents significant environmental and economic challenges in Nigeria and worldwide. This study presents the first high-resolution, species-level metataxonomic analysis of OW bioconversion mediated by black soldier fly larvae (BSFL) in a West African context, addressing a critical gap in region-specific microbial ecology. Using long-read PacBio 16S rRNA sequencing and PICRUSt2-based functional prediction, microbial communities were profiled across three ecologically distinct substrates: untreated OW, BSFL gut microbiota (OW-BSFL), and post-digestion frass (OWF). Results revealed a dramatic microbial shift driven by host filtering: the OW-BSFL metagenome was overwhelmingly dominated (> 96%) by Lysinibacillus and Cytobacillus, while OWF exhibited markedly higher diversity (263 species), including Mycolatisynbacter and Sphingobacterium. Functional analysis revealed a significant enrichment of genes associated with carbohydrate (e.g., COG2814, COG0726) and amino acid metabolism (e.g., COG1173, COG0444) in the BSFL gut, indicating an elevated enzymatic processing capacity during waste digestion. In contrast, OWF displayed unique enrichment in genes associated with residual carbohydrate turnover and environmental colonization. This microbial succession highlights the selective enrichment and functional specialization that occur across the substrate-gut-frass continuum. By elucidating keystone taxa and metabolic signatures, the study not only advances understanding of insect-microbiome symbiosis but also provides a microbial blueprint for optimizing waste-to-value strategies. The findings support the deployment of BSFL bioconversion as a scalable, sustainable solution for organic waste valorization and biofertilizer production in sub-Saharan Africa's circular bioeconomy.},
}

Animals
Larva/microbiology/metabolism
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/metabolism/isolation & purification
Gastrointestinal Microbiome/genetics
*Simuliidae/microbiology
*Citrus sinensis/metabolism
*Diptera/microbiology
Nigeria
Metagenome
Metagenomics
Phylogeny

@article {pmid41081862,
year = {2025},
author = {Bandyopadhyay, A and Sarkar, D and Das, A and Das, A},
title = {Intersections of ABO blood group, secretor status, and the gut microbiome: implications for disease susceptibility and therapeutics.},
journal = {Archives of microbiology},
volume = {207},
number = {11},
pages = {296},
pmid = {41081862},
issn = {1432-072X},
mesh = {Humans ; *ABO Blood-Group System/genetics/metabolism ; *Gastrointestinal Microbiome ; Disease Susceptibility ; Galactoside 2-alpha-L-fucosyltransferase ; Bacteria/classification/genetics/isolation & purification ; Probiotics ; },
abstract = {The human gut microbiome is a dynamic ecosystem. It is shaped by host factors, including genetic traits such as ABO blood type and associated secretor status (FUT2 gene). In secretor individuals (~ 80% of the population), ABO antigens are expressed on the gut mucosal surfaces. These antigens serve as adhesion sites and nutrient substrates for select microorganisms. Evidence links blood groups to gut microbial ecology, with taxa such as Bacteroidessp., Eubacteriumsp., and Faecalibacterium sp. exhibiting preferential colonization patterns influenced by mechanisms including mucin glycan foraging, pathogen adhesion, and competitive exclusion. ABO blood type further modulates susceptibility to infectious, metabolic, and autoimmune diseases by affecting microbiome composition. Secretor status impacts microbiota diversity and probiotic colonization Non-secretors exhibit altered Bifidobacterium sp. profiles and reduced norovirus adhesion. These insights suggest possible avenues for tailoring microbiome-based interventions; however, current evidence remains preliminary and requires validation through controlled clinical studies. We outline a conceptual model linking host genetics, microbial ecology, and health outcomes, recognizing that these associations are still being mapped. The idea of incorporating blood type and secretor status into precision microbiome approaches remains exploratory and requires rigorous validation.},
}

Humans
*ABO Blood-Group System/genetics/metabolism
*Gastrointestinal Microbiome
Disease Susceptibility
Galactoside 2-alpha-L-fucosyltransferase
Bacteria/classification/genetics/isolation & purification
Probiotics

@article {pmid41081834,
year = {2025},
author = {Olaleye, AC and Oyewusi, HA and Akinyede, KA and Oladipo, OO and Oyeyemi, BF},
title = {Bacterial community structure and secondary metabolite insights from halophiles at Oniru Beach, Lagos.},
journal = {Archives of microbiology},
volume = {207},
number = {11},
pages = {299},
pmid = {41081834},
issn = {1432-072X},
support = {TETFund 2020_2024//Institutional Based Research, TETFunD/ ; },
mesh = {Nigeria ; *Bacteria/classification/metabolism/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Secondary Metabolism ; *Microbiota ; Phylogeny ; High-Throughput Nucleotide Sequencing ; *Seawater/microbiology ; },
abstract = {This study examines the bacterial diversity and potential for secondary metabolite production of halophilic bacteria isolated from Oniru Beach, Lagos, Nigeria, a moderately saline marine environment. Using high-throughput next-generation sequencing, we profiled the bacterial community structure and complemented this with culture-dependent techniques to identify metabolite-producing strains. Physicochemical analysis revealed a slightly alkaline, oligotrophic, and low-oxygen environment enriched with bioactive metals, such as potassium, calcium, and iron, which may influence microbial adaptation and metabolic activity. Taxonomic profiling showed Proteobacteria (53.72%) as the dominant phylum, followed by Bacteroidetes (29.43%), Actinobacteria (3.88%), Deinococci (1.59%), and Firmicutes (1.37%), with Gammaproteobacteria (47.72%) being the most abundant class. Genus-level analysis highlighted Acinetobacter, Chryseobacterium, Stenotrophomonas, Enterobacter, and Pseudomonas as key constituents of this microbial community. Salt-tolerance assays and 16 S rRNA sequencing identified highly halophilic isolates, including Serratia marcescens, Staphylococcus edaphicus and Kurthia gibsonii, which displayed diverse physiological and biochemical adaptations. Gas chromatography-mass spectrometry (GC-MS) revealed a wide range of secondary metabolites, including osmolytes, fatty acids, and sugar alcohols, underscoring the metabolic versatility of these isolates. Overall, this work demonstrates that Oniru Beach hosts a complex halophilic microbiome with specialized ecological adaptations and biotechnological potential, particularly for novel bioactive compound discovery and bioremediation strategies.},
}

Nigeria
*Bacteria/classification/metabolism/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Secondary Metabolism
*Microbiota
Phylogeny
High-Throughput Nucleotide Sequencing
*Seawater/microbiology

@article {pmid41081763,
year = {2025},
author = {Wang, X and Feng, S and Chen, H and Zhou, B and Fan, T and Qin, Y and Zhao, L and Jiang, Y and Chen, Y},
title = {Development of an Aptamer/CRISPR-Cas12a-Based Dual-Modal Biosensor for Fusobacterium nucleatum Detection in Non-Invasive Colorectal Cancer Screening.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c04132},
pmid = {41081763},
issn = {1520-6882},
abstract = {Colorectal cancer (CRC) is the third most common cancer and leading cause of cancer-related deaths worldwide. However, current CRC screening methods are complex, invasive, and tend to exhibit low sensitivity. Recent evidence has highlighted gut microbiota dysbiosis, especially elevated Fusobacterium nucleatum levels, as a promising biomarker for CRC. In this study, a sensitive and specific detection platform was developed for F. nucleatum by combining a highly specific aptamer with rolling circle amplification (RCA) and the CRISPR/Cas12a technology. The aptamer enables specific target recognition, while RCA amplifies the target signal, and the Cas12a-mediated cleavage of a fluorescence-quenching substrate generates a quantifiable fluorescence or grayscale signal. Using a microplate reader, this assay achieved a limit of detection (LOD) of 3.68 CFU/mL; furthermore, by incorporating smartphone-assisted ImageJ grayscale analysis, it elevated the LOD to 4.30 CFU/mL, thereby enabling a dual-mode output along with on-site applicability. Additionally, the strong correlation between the two signals allowed for mutual validation. Upon application to clinical fecal samples, the developed method sensitively distinguished CRC patients from healthy controls, and its results correlated with the quantitative polymerase chain reaction results. This triple-synergistic platform, integrating aptamer specificity, RCA amplification, and CRISPR/Cas12a sensitivity, enables the noninvasive, ultrasensitive detection of F. nucleatum, supporting early CRC screening, prognosis monitoring, and microbiome-targeted therapy. Moreover, this approach overcomes the challenges of detecting low-abundance bacteria in early stage CRC and advances the precision of microbiome-based diagnostics for CRC.},
}

@article {pmid41081742,
year = {2025},
author = {Baer, JL and Kajihara, KT and Vilonen, LL and Hall, AJ and Young, CM and Yogi, DK and Medeiros, MCI and Amend, AS and Hynson, NA},
title = {Microbiome spatial scaling varies among members, hosts, and environments across model island ecosystems.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf228},
pmid = {41081742},
issn = {1751-7370},
abstract = {The species area relationship is a classic ecological law describing the relationship between habitat increase and the number of species. Species area relationships are resoundingly positive across macrobes such as plants and animals, and emerge through non-exclusive stochastic and deterministic processes including changes in immigration and extinction, drift, and environmental heterogeneity. Due to unique attributes of the microbial lifestyle, they may not abide by similar rules as macrobes, especially when it comes to spatial scaling. We predict that host-associated microbiomes will exhibit shallower species area relationships than free-living microbiomes due to strong host filtering, and that the species area relationships of bacteria will be shallower than fungi due primarily to differences in dispersal ability. We test these predictions in a relatively simple field system where bromeliad phytotelmata comprise aquatic ecosystems that support invertebrates and environmental substrates such as detritus. Larger phytotelmata generate larger habitat islands for microbiomes allowing us to explicitly examine their species area relationships. We find that the species area relationships of free-living and host-associated microbiomes differ, as do those of microbiome members. By assessing the relationship between environmental conditions and richness, and measuring diversity across scales, we posit that these observed differences in species area relationships are owed to differences in realized niches and dispersal abilities among microbes. These findings highlight that the classic laws of biological spatial scaling do not necessarily accurately represent microbiomes, and that the influence of area on diversity appears to be more important for some microbiomes and microbes than others.},
}

@article {pmid41081627,
year = {2025},
author = {Yuan, Q and Yang, Y and Shen, Y and Sun, B and Chen, S and Zheng, C and Lou, Y and Zheng, M},
title = {Exploring the ocular microecology and its role in pterygium based on metagenomics.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0173025},
doi = {10.1128/spectrum.01730-25},
pmid = {41081627},
issn = {2165-0497},
abstract = {Pterygium is a chronic ocular surface condition marked by fibrovascular growth extending from the conjunctiva to the cornea. Emerging evidence suggests that microbial dysbiosis may play a role in its pathogenesis. To elucidate the microbial landscape associated with pterygium, we conducted metagenomic shotgun sequencing on conjunctival sac secretions from 24 patients with pterygium and 23 healthy controls, along with 19 pterygium tissue samples. We observed significantly higher microbial richness in the disease group, with distinct taxonomic profiles compared with healthy and tissue groups. Key species enriched in the disease group included Microbacterium proteolyticum and Bacillus cereus. Functional analyses revealed elevated bacterial motility, chemotaxis, and virulence genes, alongside a notable increase in antibiotic resistance genes such as tetB and AcrAB-TolC. In contrast, pterygium tissue samples showed limited microbial diversity and no detectable virulence or resistance genes. Importantly, the predominance of Vibrio phages in tissue samples, together with the frequent detection of their bacterial host Vibrio diabolicus, suggests a potential region-specific microbial risk factor, particularly relevant in coastal populations. These findings highlight distinct microbiome and functional profiles associated with pterygium, providing new insights into its pathogenesis and possible microbiome-based therapeutic targets.IMPORTANCEUnderstanding how microbial communities contribute to ocular diseases is crucial for advancing both diagnostics and therapy. This study provides the first integrated comparison of healthy ocular surfaces, diseased ocular surfaces, and pterygium tissues, revealing distinct microbial signatures and functional disruptions. The enrichment of specific bacterial taxa, virulence factors, and antibiotic resistance genes in diseased eyes underscores their potential role in shaping local immunity and driving disease progression. Meanwhile, the discovery of distinct viral elements in pterygium tissue expands current understanding of its microecological complexity. These findings lay a theoretical foundation for the development of microbiome-informed diagnostic tools and novel therapeutic interventions for pterygium.},
}

@article {pmid41081530,
year = {2025},
author = {Ayele, H and Jo, J and Begum, K and Hu, C and Le, TM and Alam, MJ and Eubank, TA and Haidacher, SJ and Horvath, T and Hanson, BM and Garey, KW},
title = {A randomized phase 1 study investigating gut microbiome changes with moxifloxacin vs. oral vancomycin: Implications for Clostridioides difficile risk.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf512},
pmid = {41081530},
issn = {1537-6613},
abstract = {BACKGROUND: The epidemic, hypervirulent Clostridioides difficile ribotype (RT) 027 strain is associated with bacterial virulence traits, including faster germination time and resistance to moxifloxacin, a second-generation fluoroquinolone. Although linked to the RT 027 epidemic, studies to understand moxifloxacin as a high-risk antibiotic for C. difficile infection (CDI) are limited. This study assessed the microbial taxonomic profile and metabolomic changes in healthy volunteers given moxifloxacin or oral vancomycin, an antibiotic known to increase CDI risk via gut perturbation.

METHODS: This was a phase 1, nonblinded, randomized clinical trial of healthy volunteers aged 18-40 who received moxifloxacin or vancomycin for 10 days (clinicaltrials.gov NCT06030219). Stool samples were collected at baseline and 12 follow-up visits. Metataxonomics was completed by 16S V1-V3 rRNA sequencing and bile acid metabolites by LC-MS/MS.

RESULTS: Moxifloxacin therapy caused minimal microbial disruption, although changes in bacterial species from the Clostridiales order during-therapy were observed. Secondary bile acid concentrations decreased from Day 0 to Day 7 with moxifloxacin therapy. Vancomycin caused more significant changes in the microbiome, including increased Proteobacteria, decreased Clostridiales abundance, and a longer duration of decreased secondary bile acids.

CONCLUSIONS: Moxifloxacin use was associated with specific microbiome and metabolomic changes increasing CDI risk albeit for a shorter period than vancomycin. This window of vulnerability may help to explain the risk of fluoroquinolones with the faster germination time for RT 027 strains.},
}

@article {pmid41081484,
year = {2025},
author = {Grafanaki, K and Bakoli Sgourou, D and Maniatis, A and Pasmatzi, E},
title = {The exposomal imprint on rosacea: More than skin deep.},
journal = {Journal of the European Academy of Dermatology and Venereology : JEADV},
volume = {},
number = {},
pages = {},
doi = {10.1111/jdv.70112},
pmid = {41081484},
issn = {1468-3083},
abstract = {Rosacea is a chronic, inflammatory dermatosis driven by a complex interplay of genetic, environmental and lifestyle factors, collectively known as the exposome. This review explores how intrinsic contributors such as genetic susceptibility, immune dysregulation, microbiome alterations, hormonal influences and psychosocial stress intersect with extrinsic triggers like ultraviolet radiation (UVR), air pollution, dietary factors, and climate variability to shape rosacea pathogenesis. Recent advances in single-cell transcriptomics have identified fibroblasts as key components of inflammatory and vascular pathways in rosacea. Concurrently, discoveries in non-coding RNAs and RNA modifications reveal subtype-specific molecular signatures and novel biomarkers. Mendelian randomization (MR) studies further reveal causal links between rosacea and autoimmune, metabolic and gastrointestinal comorbidities-that rosacea is more than skin deep. The role of the gut-skin axis, particularly involving small intestinal bacterial overgrowth (SIBO) and Helicobacter pylori infection, reflects the importance of microbial and neuroimmune crosstalk. Disparities in diagnosis and management persist, particularly among individuals with skin of colour (SOC) and those with limited healthcare access. By integrating an exposomal framework, this review advocates for a paradigm shift in rosacea management: from reactive treatment to proactive, exposome-informed intervention. Personalized skincare, microbiome-targeted strategies, dietary modulation and psychosocial support represent emerging pillars in a holistic, precision medicine framework. Future research should prioritize exposome-informed prevention, inclusive care models, and the development of personalized interventiouns that address both cutaneous and systemic facets of rosacea.},
}

@article {pmid41081315,
year = {2025},
author = {Yang, Y and Wang, Z and Wu, R},
title = {Comparison of Three Sympatric Desert Lizards: Digestive Tract Structure, Digestive Enzyme Activities, Gut Microbiota, and Metabolites.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70007},
pmid = {41081315},
issn = {1749-4877},
support = {32260118//National Natural Science Foundation of China/ ; 2023TSYCQNTJ0034//the second group of Tianshan Talent Training Program: Youth Support Talent Project/ ; 2022D01B100//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; },
abstract = {The flexibility of digestive tract morphology and the composition of gut microbiota play crucial roles in the environmental adaptation of reptiles. To evaluate the contributions of the dietary niches to the gut microbiota, we performed 16S rDNA sequencing and metabolite profiling for three sympatric lizard species-Teratoscincus roborowskii, Phrynocephalus axillaris, and Eremias roborowskii-and compared their goblet cell and enzyme activities of the digestive tract. The results revealed that goblet cell densities in the stomach body and pylorus were significantly higher in both T. roborowskii and E. roborowskii, which occasionally include fruit in their diets. Lipase activity was significantly higher in the insectivorous P. axillaris, while the α-amylase and cellulase activities were elevated in the omnivorous T. roborowskii and E. roborowskii. All three lizard species shared the same dominant microbiota at the phylum level. However, dietary niche differences led to P. axillaris having a higher abundance of Desulfovibrionaceae, while E. roborowskii had a significantly higher abundance of Bacteroidetes. Metabolomic profiling revealed that the metabolites involved in carbohydrate metabolism were highly upregulated in E. roborowskii, corresponding to the host's diet and metabolic pathways. Notably, a strong correlation was observed between digestive enzymes, gut microbiota, and fecal metabolites. Overall, our study suggests that the dietary niche may promote divergence or convergence of microbiota across host species, facilitating the establishment of host-specific intestinal adaptation strategies. Our findings provide insights into lizard adaptation to extreme deserts from the perspectives of the gut microbiome and digestive physiology.},
}

@article {pmid41081109,
year = {2025},
author = {Liu, Y and Wu, E and Cheng, F and Zhang, M and Rou, Q and Nuertai, Z and Xu, M and Xu, S and Li, M and Zhang, L and Nasiroula, A},
title = {Oropharyngeal microbiome dysbiosis in esophageal squamous cell carcinoma: taxonomic shifts, metabolic reprogramming, and geographic disparities in a high-incidence cohort.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20009},
pmid = {41081109},
issn = {2167-8359},
mesh = {Humans ; *Esophageal Squamous Cell Carcinoma/microbiology/epidemiology ; Male ; China/epidemiology ; Female ; Middle Aged ; *Esophageal Neoplasms/microbiology/epidemiology ; *Microbiota ; *Dysbiosis/microbiology/epidemiology ; Incidence ; Aged ; RNA, Ribosomal, 16S/genetics ; *Oropharynx/microbiology ; Cohort Studies ; Metabolic Reprogramming ; },
abstract = {BACKGROUND: Esophageal squamous cell carcinoma (ESCC) is a leading cause of cancer mortality globally, with pronounced geographic disparities in incidence. Emerging evidence links oral microbiome dysbiosis to ESCC pathogenesis, yet comprehensive insights into microbial diversity, taxonomic shifts, and functional alterations in high-risk populations remain limited.

METHODS: Using 16S rRNA amplicon sequencing, we compared the oral microbiome of ESCC patients and healthy controls from a high-incidence region in Northwest China. Alpha and beta diversity metrics, taxonomic composition, and predicted functional pathways were analyzed to identify microbial signatures associated with ESCC.

RESULTS: ESCC patients exhibited significantly elevated microbial richness (observed amplicon sequence variants (ASVs), Chao1, ACE; p < 0.05) but comparable Shannon/Simpson diversity to controls. Unique amplicon sequence variants (ASVs) were more prevalent in ESCC samples, and principal component analysis confirmed distinct community structures (p < 0.05). Taxonomically, Streptococcus and Neisseria dominated both groups, but ESCC patients showed enrichment of Gemella (p = 0.0003) and Corynebacterium (p < 0.00001), alongside depletion of Prevotella_7 (p = 0.0002) and Moraxella (p < 0.001). Functional profiling revealed upregulated amino acid metabolism (e.g., beta-alanine and valine degradation) and downregulated carbohydrate metabolism in ESCC-associated microbiota.

CONCLUSION: This study uncovers unique oral microbial signatures in ESCC patients from a high-incidence region, characterized by increased richness, taxon-specific shifts, and metabolic reprogramming favoring amino acid catabolism. These findings highlight the potential of microbial biomarkers for ESCC detection and provide mechanistic insights into microbiome-driven carcinogenesis. The geographic specificity of the cohort underscores the urgency of tailored interventions in high-risk populations and advances our understanding of microbial contributions to esophageal cancer.},
}

Humans
*Esophageal Squamous Cell Carcinoma/microbiology/epidemiology
Male
China/epidemiology
Female
Middle Aged
*Esophageal Neoplasms/microbiology/epidemiology
*Microbiota
*Dysbiosis/microbiology/epidemiology
Incidence
Aged
RNA, Ribosomal, 16S/genetics
*Oropharynx/microbiology
Cohort Studies
Metabolic Reprogramming

@article {pmid41081102,
year = {2025},
author = {Oiler, IM and Linscott, TM and Parent, CE},
title = {Geology correlates with gut microbial community composition in the Mountainsnails (Oreohelicidae: Oreohelix).},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20080},
pmid = {41081102},
issn = {2167-8359},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Snails/microbiology ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Idaho ; Soil/chemistry ; Geology ; Calcium Carbonate/metabolism ; },
abstract = {BACKGROUND: Species that require soil mineral macronutrients for survival may depend on specific microbiome communities to aid in nutrient processing. Land snails, which utilize environmental minerals to synthesize a shell of calcium carbonate (CaCO3), may rely on or possess distinct gut microbiome communities depending on soil mineral characteristics. Here, we investigate whether the occurrence of calcareous vs. non-calcareous soils is associated with shifts the composition of the gut microbiome of the calciphilous and highly diverse land snail genus Oreohelix from the Western United States.

METHODS: We collected snail and soil samples from nine sites in central Idaho: five near, and four away from calcium-rich geology. We sequenced the V4 region of the 16S rRNA gene of these samples to assess the gut microbiome compositions of Oreohelix land snails on and off calcium-rich substrates. After data clean-up and filtering we had 68 snail and 25 soil microbiome samples.

RESULTS: We found that snail gut microbiomes differed significantly from the surface soil microbiome, with many amplicon sequence variants being unique and ubiquitous in the snails. We also found small, but significant, differences between snails on and off calcium-rich rocks. Our findings indicate that the gut microbial community assembly process of land snails is complex and does not reflect a simple relationship with the underlying soil microbiome. While we find a pattern of differences associated with the proximity of calcium-rich geology, the snail microbiome communities are likely forming based on a variety of other factors, including diet and host filtering. Furthermore, we found multiple microbial taxa that were ubiquitous in the snails and rare in the nearby substrate microbiomes. Future work should focus on disentangling the role of habitat and the functional importance (or lack thereof) of the microbial taxa that are common to almost every sampled snail.},
}

Animals
*Gastrointestinal Microbiome/genetics
*Snails/microbiology
RNA, Ribosomal, 16S/genetics
*Soil Microbiology
Idaho
Soil/chemistry
Geology
Calcium Carbonate/metabolism

@article {pmid41081074,
year = {2025},
author = {Kotfis, K and Szredzki, P and Maciejewska-Markiewicz, D and Sołek-Pastuszka, J and Wiśniewska, H and Lara, LF and Marlicz, M and Kaczmarczyk, M and Kukla, M and Belina, A and Koulaouzidis, G and Syczewska, M and Jakubczyk, K and Ekstedt, N and Stachowska, E and Kaniewska, M and Rydzewska, G and Łoniewski, I and Koulaouzidis, A and Marlicz, W and Skonieczna-Żydecka, K},
title = {The effect of SARS-CoV-2 infection on the liver function tests: a systematic review and meta-analysis of observational studies.},
journal = {Przeglad gastroenterologiczny},
volume = {20},
number = {3},
pages = {261-271},
pmid = {41081074},
issn = {1895-5770},
abstract = {INTRODUCTION: SARS-CoV-2 infection has been associated with respiratory distress syndrome and hepatic injury. The mechanism of liver injury is not fully understood and may be a combined effect of viral hepatitis, systemic inflammation, gut barrier disruption, microbiome alterations or drug toxicity.

AIM: We carried out a systematic review and meta-analysis to determine whether SARS-CoV-2 infection affects the level of liver-produced molecules: alanine aminotransferase (ALT), aspartate aminotransferase (AST), γ-glutamyl transferase (GGTP), bilirubin, total protein, albumin, and prothrombin (with INR).

METHODS: Ten authors independently searched PubMed and Embase from their inception until 04/03/2021 for observational studies to evaluate whether SARS CoV-2 infection influences the level of liver-produced molecules. This early search aimed to capture changes associated with the initial variants of SARS-CoV-2 before widespread vaccination efforts. Full-text studies in adult humans in which the aim was liver damage were included. Eligible studies included adult populations with more than 30 subjects, and the analysis adhered to PRISMA guidelines. Data extraction involved a thorough process to ensure accuracy, with inconsistencies resolved by senior clinicians. Statistical analysis was conducted using random effects meta-analysis of outcomes for which ≥ 2 studies contributed data, and the risk of bias was assessed using the New Ottawa Scale. The study protocol was registered in the PROSPERO database (CRD42021242958).

RESULTS: The initial search yielded 3180 hits. 2644 studies were excluded as duplicates and/or after evaluation on the title/abstract level. No additional articles were identified via hand search. There were 536 full-text articles reviewed. Overall, the search strategy yielded 252 studies that were included in the meta-analysis.

CONCLUSIONS: The overall mean liver parameter values were not altered compared to physiological values, except for GGTP, lactate dehydrogenase activity, and INR values. In the case of AST, ALT and albumin levels, mean point estimates were close to limit values of standards. SARS-CoV-2 infection triggers gut barrier defects, which results in transient elevation of liver enzymes and clotting times.},
}

@article {pmid41080808,
year = {2025},
author = {Zhang, Z and Huang, W},
title = {Exoskeleton Robot Gait Training and Its Impact on the Gut Microbiota-Brain Axis in Incomplete Spinal Cord Injury Patients: A Narrative Review of Rehabilitation Mechanisms.},
journal = {Journal of multidisciplinary healthcare},
volume = {18},
number = {},
pages = {6411-6430},
pmid = {41080808},
issn = {1178-2390},
abstract = {Exoskeleton robot-assisted gait training represents a significant advancement in neurorehabilitation for patients with incomplete spinal cord injury (iSCI). While its efficacy in improving motor function is increasingly documented, emerging evidence suggests these interventions may exert therapeutic effects through previously unrecognized physiological pathways involving the gut microbiota-brain axis. This review synthesizes current evidence regarding the bidirectional relationship between exoskeleton-based locomotor training and alterations in gut microbiome composition and function in the context of iSCI. Following spinal cord injury, significant dysbiosis occurs, characterized by reduced microbial diversity and altered taxonomic representation, which correlates with neuroinflammation, autonomic dysfunction, and impaired recovery. Exoskeleton-mediated gait rehabilitation appears to partially restore microbial homeostasis through multiple mechanisms, including autonomic nervous system regulation, altered intestinal transit time, modified intestinal barrier integrity, and immunomodulation. These microbiome modifications potentially facilitate neuroplasticity and functional recovery through microbiota-derived metabolites that traverse the blood-brain barrier or communicate via vagal afferents. The integration of metagenomic analysis with functional neuroimaging and detailed autonomic assessment in prospective studies represents a critical research direction. This emerging perspective extends beyond biomechanical rehabilitation, suggesting a comprehensive neurobiological effect that includes modulation of the microbiota-gut-brain axis, with significant implications for optimizing therapeutic strategies for individuals with incomplete spinal cord injury.},
}

@article {pmid41080582,
year = {2025},
author = {Kou, R and Guo, Y and Qin, Z and Xu, X and Liu, Y and Wei, W and Chen, Y and Jian, Z and Lan, B},
title = {Systemic dysregulation of the gut microenvironment plays a pivotal role in the onset and progression of inflammatory bowel disease.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1661386},
pmid = {41080582},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Inflammatory Bowel Diseases/microbiology/immunology/etiology/metabolism/pathology/therapy ; Dysbiosis/immunology ; Animals ; Disease Progression ; Intestinal Mucosa/immunology/microbiology/metabolism/pathology ; Disease Susceptibility ; Cellular Microenvironment ; },
abstract = {Inflammatory bowel disease (IBD) represents a multifaceted, chronic inflammatory condition affecting the gastrointestinal tract, with its underlying pathophysiological mechanisms not yet fully elucidated. Recent research has underscored the pivotal role of the gut microenvironment, a complex ecological system, in the pathogenesis of IBD. This review systematically examines the interactions between gut microenvironment components and their roles in the pathogenesis of IBD. It is now understood that gut dysbiosis results in a decrease in beneficial microbiota, such as Faecalibacterium and Roseburia, along with an increase in pathogenic bacteria, including Adherent-invasive Escherichia coli (AIEC). This microbial imbalance results in a reduction in the production of beneficial metabolites, such as short-chain fatty acids, and the accumulation of detrimental metabolites, thereby directly disrupting the gut microbiome. The resultant gut dysbiosis leads to dysfunction in intestinal stem cells (ISCs) and a reduction in the expression of tight junction (TJ) proteins, thereby further compromising the integrity of the intestinal epithelial barrier. This dysfunction allows microorganisms and harmful metabolites to penetrate the barrier, reaching the submucosal layer, where they activate both innate and adaptive immune responses, thereby initiating a complex immune cascade. Over time, this process leads to a self-sustaining inflammatory cycle that culminates in chronic IBD and potentially contributes to the development of metabolic disorders. This paper examines this cycle, elucidating the interactions among gut microbiota dysbiosis, metabolite alterations, barrier dysfunction, and immune activation that drive the pathogenesis of IBD, while also critically assessing the limitations of current therapeutic strategies. Based on our understanding of the overarching dysregulation of the gut microenvironment, we propose a paradigm shift in IBD from "controlling inflammation" to "restoring intestinal homeostasis", and from "single therapy" to "comprehensive intervention". This integrated approach encompasses microbiome remodeling, metabolite intervention, reconstruction of the immune microenvironment, and repair of barrier function. Such a multidimensional and integrated therapeutic strategy promises to effectively disrupt the pathological feedback loop, restore gut homeostasis, and offer novel theoretical and clinical insights for the precise treatment of IBD and its progression.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Inflammatory Bowel Diseases/microbiology/immunology/etiology/metabolism/pathology/therapy
Dysbiosis/immunology
Animals
Disease Progression
Intestinal Mucosa/immunology/microbiology/metabolism/pathology
Disease Susceptibility
Cellular Microenvironment

@article {pmid41080580,
year = {2025},
author = {Ding, SQ and Lyu, XY and Zhou, SY and Fang, YW and Ji, HX and Li, JY and Lü, HZ},
title = {Metformin-associated gut microbiota remodeling correlates with reinvigorated splenic immunity in aged mice: microbiome-immune crosstalk via the gut-spleen axis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1633486},
pmid = {41080580},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/immunology ; *Metformin/pharmacology ; *Spleen/immunology/drug effects ; Mice ; Mice, Inbred C57BL ; *Aging/immunology/drug effects ; Cytokines/metabolism ; *Immunosenescence/drug effects ; Male ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND AND AIM: Immunosenescence involves age-related immune decline and chronic inflammation, with the spleen serving as a critical hub for immune dysregulation. While gut microbiota influences systemic immunity, its specific role and the potential existence of a gut-spleen axis in mediating splenic aging remains unclear. Therefore, we investigated whether metformin, a microbiota-modulating geroprotective drug, alleviates splenic immunosenescence in aged mice, specifically exploring the link between gut microbiota remodeling and splenic immune rejuvenation.

METHODS: Aged C57BL/6 mice (15-month-old) received oral metformin (300 mg/kg/day) or vehicle for 5 months. Systemic toxicity and metabolism were monitored. Splenic immune subsets were analyzed using flow cytometry and immunohistochemistry. Gut microbiota composition (16S rRNA sequencing), cytokine levels (RT-qPCR), and functional pathways were assessed.

RESULTS: Metformin caused no hepatorenal toxicity or weight changes. Treated mice exhibited increased cytotoxic T cells (Tc) and macrophages in the spleen, with reduced Th/Tc ratios and M1/M2 polarization. Pro-inflammatory cytokines (Ifng, Il17a, Il1b, Il6) decreased, while anti-inflammatory markers (Arg1, Tgfb1) rose. Gut microbiota showed enriched Akkermansia, Muribaculum, and Duncaniella, but reduced Lactobacillus. Akkermansia/Muribaculum negatively correlated with pro-inflammatory cytokines, whereas Lactobacillus and Lachnospiraceae linked to pro-inflammatory responses. Functional prediction analysis based on 16S rRNA sequencing data indicated upregulation of bile acid metabolism and oxidative phosphorylation pathways.

CONCLUSION: Metformin reshapes the gut microbiota, which is associated with mitigation of age-associated splenic immune dysregulation, favoring anti-inflammatory macrophage polarization and cytotoxic T cell expansion. Critically, our findings establish the gut-spleen axis as a key mediator of splenic immunosenescence and a novel therapeutic target, which positions metformin as a promising microbiota-directed geroprotective agent. Future research should prioritize mechanistic dissection of gut-spleen communication and clinical validation of metformin's geroprotective efficacy in human populations.},
}

Animals
*Gastrointestinal Microbiome/drug effects/immunology
*Metformin/pharmacology
*Spleen/immunology/drug effects
Mice
Mice, Inbred C57BL
*Aging/immunology/drug effects
Cytokines/metabolism
*Immunosenescence/drug effects
Male
RNA, Ribosomal, 16S/genetics

@article {pmid41080576,
year = {2025},
author = {Terrigno, K and Flamholz, ZN and Mahant Mahant, A and Agalliu, I and De Los Santos, J and Ireland, K and Keenan, J and Kazmi, JS and Correa, A and Frenette, PS and Kelly, L and Herold, BC and Manwani, D},
title = {Higher aged neutrophils and differential inflammatory profiles in sickle cell disease patients on chronic transfusion therapy versus those on hydroxyurea.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1671061},
pmid = {41080576},
issn = {1664-3224},
mesh = {Humans ; *Anemia, Sickle Cell/therapy/immunology/blood ; *Hydroxyurea/therapeutic use ; *Neutrophils/immunology/metabolism/drug effects ; Female ; Male ; Cytokines/blood ; Adolescent ; Child ; Inflammation/immunology ; *Antisickling Agents/therapeutic use ; Chemokines/blood ; Gastrointestinal Microbiome ; Child, Preschool ; *Cellular Senescence ; },
abstract = {BACKGROUND: Sickle cell disease (SCD) is characterized by a point mutation in the β globin molecule, causing the sickling of red blood cells, and leading to hemolytic anemia, pain, and end-organ damage. Hydroxyurea (HU) is a cornerstone of SCD patient treatment, while chronic transfusions (CT) are used as part of treatment for more severe SCD. Increases in aged neutrophils and inflammation have been linked to more severe SCD and contribute to vaso-occlusive crises. The current study was designed to test the hypothesis that HU reduces inflammation and aged neutrophils.

STUDY DESIGN: We compared clinical characteristics, aged neutrophils, levels of select cytokines, chemokines, and cell adhesion molecules in the blood and the Shannon diversity index (SDI) and ratio of Firmicutes/Bacteroides (F:B) in stool samples from pediatric SCD patients treated with HU (n=40) versus CT (n=14).

RESULTS: Patients in the HU group had significantly lower total and aged neutrophils (p<0.0001) compared to the CT group and also had lower levels of several chemokines including CXCL10 (IP-10), CCL2 (MCP-1) and CCL4 (MIP-1β) as well as IFN-γ and IL10. Conversely, HU was associated with higher levels of IL-1α, IL-6 and IL-8. There were no significant differences in cell adhesion markers or in markers of gut microbial dysbiosis between treatment groups. In a multivariable linear regression model, only being on CT was associated with increased number of aged neutrophils (p<0.001) whereas being on CT and having a lower SDI were associated with higher total neutrophil count.

DISCUSSION: Lower numbers of total and aged neutrophils and lower levels of several cytokines and chemokines in the HU group highlight the drug's potential to modulate leukocyte activation and recruitment. These findings suggest that adding or maintaining HU therapy in SCD patients undergoing CT could potentially enhance immunologic regulation and warrants further study.},
}

Humans
*Anemia, Sickle Cell/therapy/immunology/blood
*Hydroxyurea/therapeutic use
*Neutrophils/immunology/metabolism/drug effects
Female
Male
Cytokines/blood
Adolescent
Child
Inflammation/immunology
*Antisickling Agents/therapeutic use
Chemokines/blood
Gastrointestinal Microbiome
Child, Preschool
*Cellular Senescence

@article {pmid41080562,
year = {2025},
author = {Zhu, Z and Cheng, Y and Liu, X and Xu, X and Ding, W and Ling, Z and Liu, J and Cai, G},
title = {The microbiota-gut-brain axis in depression: unraveling the relationships and therapeutic opportunities.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1644160},
pmid = {41080562},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Depression/therapy/microbiology/metabolism/etiology ; *Brain/metabolism ; Animals ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; *Brain-Gut Axis ; },
abstract = {Depression, a highly prevalent and relapsing mental disorder, exacts profound personal and socioeconomic tolls globally, warranting urgent scientific and clinical attention. Emerging evidence from both preclinical models and human clinical investigations has established the microbiota-gut-brain axis (MGBA) as a critical determinant in depression pathogenesis. This intricate bidirectional network integrates gut microbiota with central nervous system function, influencing mental health through mechanisms previously underrecognized. This review systematically synthesizes gut microbiota alterations associated with depression and their impacts on neuroendocrine, neuroimmune, and metabolic pathways. Advanced therapeutic strategies targeting the MGBA are discussed, including probiotics, fecal microbiota transplantation, and artificial intelligence-enabled microbiome interventions for depression management. While challenges in standardization, mechanistic understanding, efficacy and safety remain, MGBA-centered approaches offer a promising shift toward microbiota-based diagnostics and personalized treatments for depression.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Depression/therapy/microbiology/metabolism/etiology
*Brain/metabolism
Animals
Fecal Microbiota Transplantation
Probiotics/therapeutic use
*Brain-Gut Axis

@article {pmid41080527,
year = {2025},
author = {Ghosh, S and Li, Y and Yang, X and Wu, G and Zhang, C and Zhao, L},
title = {Bacterial guilds, not genus-level taxa, mediate the protective effects of time-restricted feeding against high-fat diet-induced obesity in mice.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf127},
pmid = {41080527},
issn = {2730-6151},
abstract = {The gut microbiota functions as a complex adaptive system where microbes form structural modules known as "guilds." Each guild comprises taxonomically distinct microbes that work together as cohesive functional units, contributing to overall system function. Traditional taxon-based microbiome analyses often yield inconsistent associations with disease, limiting mechanistic insights. To address this, we compared guild-based and taxon-based approaches using datasets from a time-restricted feeding (TRF) study in mice. C57BL/6 J male mice were assigned to ad libitum feeding or TRF groups, with metabolic parameters and gut microbiota composition assessed over 12 weeks. Isocaloric TRF improved glucose tolerance and reduced weight gain in high-fat diet (HFD)-fed mice while maintaining metabolic stability in normal-fat diet-fed mice. To examine microbial contributions, 293 prevalent amplicon sequence variants (ASVs) from the 16S rRNA gene's V3-V4 regions were clustered into 34 co-abundance groups (CAGs), representing potential microbial guilds and accounting for 96% of the total sequence abundance. By contrast, the taxon-based approach classified 660 ASVs into 126 genera, capturing only 78% of the total sequence abundance while omitting 22% of sequences representing novel microbes. The 34 CAGs preserved community-level information more effectively than the 66 prevalent genera, as demonstrated by Procrustes analysis. Five CAGs correlated with improved metabolic phenotype under TRF, including unclassifiable ASVs. Notably, two key CAGs exhibited conserved diurnal rhythmicity under TRF. In contrast, ASVs within putative health-relevant genera displayed opposing TRF responses. This study underscores microbial guilds as key mediators of TRF's metabolic benefits and emphasizes the need to recalibrate taxon-based microbiome analysis biomarker discovery.},
}

@article {pmid41080526,
year = {2025},
author = {Fernández-Alonso, MJ and de Celis, M and Belda, I and Palomino, J and García, C and Gaitán, J and Wang, JT and Abdala-Roberts, L and Alfaro, FD and Angulo-Pérez, DF and Arthikala, MK and Chalasani, D and Corwin, J and Gui-Lan, D and Hernandez-Lopez, A and Nanjareddy, K and Nayaka, SC and Pasari, B and Patro, TSSK and Podile, AR and Quijano-Medina, T and Rivera, DS and Sarma, PVSRN and Shaaf, S and Trivedi, P and Yang, Q and Yin, Y and Zaady, E and Zhu, YG and Singh, BK and Delgado-Baquerizo, M and García-Palacios, P and Milla, R},
title = {Native edaphoclimatic regions shape soil communities of crop wild progenitors.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf143},
pmid = {41080526},
issn = {2730-6151},
abstract = {Unveiling the soil biological communities ecologically associated with crop wild progenitors (CWPs) in their habitats of origin is essential for advancing productive and sustainable agriculture. A field survey was conducted to investigate the edaphoclimatic conditions and soil bacterial, fungal, protist, and invertebrate communities of 125 populations of direct progenitors of major crops for world agriculture. The wild populations clustered into four ecoregions shaped by two edaphoclimatic dimensions: one summarizing variations in soil sand contents and nutrients concentrations, and the other featuring changes in aridity, soil pH, and carbon storage potential. We identified a common soil core community across CWPs that varied significantly along deserts to tropical seasonal forests and savannas. The assembly of the soil core community was driven by varying environmental preferences amongst soil biodiversity kingdoms, reflecting potential shifts in their functional profiles. The tropical ecoregion exhibited higher proportion of acidophilic bacteria, fungal, and protist parasites, whilst desert ecosystems harboured greater abundances of saprophytic fungi and heterotrophic protists. Moreover, CWPs displayed unique microhabitats that incorporate variability into the soil community assembly. Our work reveals the biogeography of soil communities associated with CWPs, the first step towards the development of microbial rewilding initiatives.},
}

@article {pmid41080487,
year = {2025},
author = {Boyle, JA and Murphy, B and Teng, F and Babaei Zadeh, P and Ensminger, I and Stinchcombe, JR and Frederickson, ME},
title = {Mutualism Mediates Legume Response to Microbial Climate Legacies.},
journal = {Ecology and evolution},
volume = {15},
number = {10},
pages = {e72271},
pmid = {41080487},
issn = {2045-7758},
abstract = {Climate change is altering both soil microbial communities and the ecological context of plant-microbe interactions. Heat, drought, and their legacies can alter soil microbiomes and potential plant symbionts, but the direct consequences of these microbial changes on plant performance and plant investment in symbiosis remain underexplored. Predicting how soil microbes modulate plant resilience to heat and drought is critical to mitigating the negative effects of climate change on ecosystems and agriculture. In this proof of concept study, we conducted growth chamber experiments to isolate the microbially mediated indirect effects of heat and drought on plant performance and symbiosis. In the first experiment, focused on drought, we found that drought and drought-treated microbes, along with their interaction, significantly decreased the biomass of Medicago lupulina plants compared to well-watered microbiomes and conditions. In a second experiment, we then tested how the addition of a well-known microbial mutualist, Sinorhizobium meliloti, affected heat- and drought-treated microbiomes' impact on M. lupulina. We found that drought-adapted microbiomes negatively impacted legume performance by increasing mortality and reducing branch number, but that adding rhizobia erased differences in plant responses to climate-treated soils. In contrast, heat-adapted microbiomes did not differ significantly from control microbiomes in their effects on a legume. Our results suggest microbial legacy effects, mutualist partners, and their interactions are important in mediating plant responses to drought, with some mutualists equalizing plant responses across microbial legacies.},
}

@article {pmid41080463,
year = {2025},
author = {Sengupta, S and , },
title = {Study research protocol for Phenome India-CSIR Health Cohort Knowledgebase: A prospective multi-modal follow-up study on a nationwide employee cohort.},
journal = {Biology methods & protocols},
volume = {10},
number = {1},
pages = {bpaf061},
pmid = {41080463},
issn = {2396-8923},
abstract = {Predicting individual health trajectories based on risk scores can help formulate effective preventive strategies for diseases and their complications. Currently, most risk prediction algorithms rely on epidemiological data from the Caucasian population, which often do not translate well to the Indian population due to ethnic diversity, differing dietary and lifestyle habits, and unique risk profiles. In this multi-center prospective longitudinal study conducted across India, we aim to address these challenges by developing clinically relevant risk prediction scores for cardio-metabolic diseases specifically tailored to the Indian population. India, which accounts for nearly 18% of the global population, also has a significant diaspora worldwide. This program targets longitudinal collection and bio-banking of samples from over 10 000 employees both working and retirees of the Council of Scientific and Industrial Research and their spouses, with baseline sample collection already completed. During the baseline collection, we gathered multi-parametric data including clinical questionnaires, lifestyle and dietary habits, anthropometric parameters, lung function assessments, liver elastography by Fibroscan, electrocardiogram readings, biochemical data, and molecular assays, including but not limited to genomics, plasma proteomics, metabolomics, and fecal microbiome analysis. In addition to exploring associations between these parameters and their cardio-metabolic outcomes, we plan to employ artificial intelligence algorithms to develop predictive models for phenotypic conditions. This study could pave the way for precision medicine tailored to the Indian population, particularly for the middle-income strata, and help refine the normative values for health and disease indicators in India.},
}

@article {pmid41080302,
year = {2025},
author = {Baloch, MB and Alphonse, C and Baldev, N and Nin-Arroyo, GM and Keezhath, R and Behara, A and Khurana, S and Nwokeji, S and Imam, B and Abarca-Pineda, YA},
title = {Cardiovascular Risk in Autoimmune Diseases: Mechanisms, Management, and Emerging Evidence.},
journal = {Cureus},
volume = {17},
number = {9},
pages = {e91897},
pmid = {41080302},
issn = {2168-8184},
abstract = {Cardiovascular disease is a leading cause of morbidity and mortality among patients with autoimmune disorders. Chronic inflammatory conditions such as rheumatoid arthritis, systemic lupus erythematosus, psoriasis, and inflammatory bowel disease are associated with accelerated atherosclerosis and other vascular complications. Persistent inflammation, dysregulated cytokine networks, and autoantibody-mediated pathways contribute to endothelial dysfunction, pro-thrombotic states, and metabolic disturbances. In addition to traditional risk factors, disease-specific elements such as chronic glucocorticoid exposure and altered lipid profiles influence overall risk. Management strategies emphasize the control of systemic inflammation alongside standard cardiovascular prevention measures. Biologic therapies targeting tumor necrosis factor, interleukin-6, and other inflammatory mediators may attenuate cardiovascular risk by slowing plaque progression. Lifestyle interventions and pharmacologic measures (e.g., statins and antihypertensives) are crucial to mitigate coexisting risks. Emerging evidence from recent cohort studies and clinical trials suggests that these targeted treatments can improve cardiovascular outcomes in autoimmune populations. Advanced vascular imaging and novel biomarkers now allow the earlier detection of subclinical atherosclerosis. Ongoing research into genetic predisposition, the gut microbiome, and new immune pathways offers deeper insight into risk mechanisms. By integrating current pathophysiologic understanding with evolving clinical data, these insights inform strategies for optimizing long-term cardiovascular health in patients with autoimmune disease.},
}

@article {pmid41080185,
year = {2025},
author = {Shahzad, M and Ahmad, HA and Ghani, M and Al Nabhani, Z},
title = {Animal models for understanding the mechanisms of malnutrition: a literature review.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1655811},
pmid = {41080185},
issn = {2296-861X},
abstract = {Malnutrition, encompassing undernutrition, micronutrient deficiencies, and overnutrition, remain a pervasive global health challenge. This underprivileged condition contributes significantly to worldwide morbidity and mortality and causes profound impairments in growth, development, immune function, and metabolic health. Understanding the underlying biological mechanisms is critical, and animal models are indispensable tools for dissecting these complex pathways and for evaluating potential nutritional interventions under controlled conditions that are infeasible in humans. This literature review comprehensively examines rodent models and explores other diverse animal models used to investigate malnutrition, ranging from invertebrates (e.g., Drosophila) and fish (zebrafish) to mammals (piglets and non-human primates). We highlight how each model has yielded mechanistic insights into malnutrition-induced pathophysiology, i.e., from altered metabolic signaling to immune dysfunction and critically evaluate their strengths and limitations in replicating the multifactorial nature of human malnutrition. Key considerations include the extent to which each model mimics human nutritional deficits or excesses, appropriate developmental stages, species-specific metabolic differences, and the influence of comorbid factors such as infection or gut microbiome alterations. We emphasize translational relevance by identifying where animal-derived findings align with clinical observations and where they diverge, underscoring the challenges in extrapolating preclinical results to human disease. Overall, this review provides a comprehensive resource to guide researchers in selecting appropriate animal models and interpreting their findings, with the ultimate goal of enhancing the translation of preclinical insights into improved strategies to address malnutrition.},
}

@article {pmid41080169,
year = {2025},
author = {Lin, X and Li, Z and Zheng, D and Du, R and Zhong, R and Lin, C and Meng, H},
title = {Effects of resistant starch consumption on anthropometric and serum parameters in adults with metabolic syndrome-related risks: a systematic review and meta-analysis.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1655664},
pmid = {41080169},
issn = {2296-861X},
abstract = {BACKGROUND: The effects of resistant starch (RS) consumption on anthropometric and serum biomarkers in adults with metabolic syndrome (MetS)-related risks, each component of which similarly increases the incidence of cardiovascular disease, have yielded inconclusive results when compared to anticipated outcomes. The heterogenous effects of RS type, delivery mode, participant characteristics, intervention conditions, and the quality of study design on the observed outcomes are considered to be insufficiently understood.

METHODS: A comprehensive search was conducted in five public databases and 30 previously published meta-analyses up to January 21, 2025, following the PRISMA guidelines. A total of 23 parallel or crossover randomized controlled trials were included for qualitative analysis via Cochrane Risk of Bias tool and the Jadad scale. Among, 19 studies were included for synthesizing effect sizes of changes in anthropometric parameters, glycemic and lipid profiles, inflammatory markers, and oxidative stress biomarkers using a random-effects model. Subgroup analysis was performed to explore contributes of heterogeneity. Sensitivity analysis and publication bias analysis were conducted.

RESULTS: RS consumption was associated with significant reductions in hip circumference (MD = -1.83 cm; 95% CI: -2.03 to -1.64), total cholesterol (MD = -0.20 mmol/L; 95% CI: -0.32 to -0.08), low-density lipoprotein cholesterol (MD = -0.11 mmol/L; 95% CI: -0.18 to -0.04), and improved superoxide dismutase levels (SMD = 0.29; 95% CI: 0.08-0.51). Waist circumference, fasting insulin, HOMA-IR, and TNF-α were reduced by RS with high heterogeneity yet. High quality of study design, participants with younger age and overweight, a supplement as delivery, a dose of up to 30 g/day, and lasting over 8 weeks partly influenced the effects.

CONCLUSION: Steady effects of RS were observed on hip circumference, total cholesterol, low-density lipoprotein cholesterol, and superoxide dismutase in adults with MetS-related risks. For the intervention with RS, it is recommended that participants be younger and overweight, with a dosage of at least 30 g/day, and over a period of 8 weeks. Future studies should be designed with high methodological quality, with considerations of delivery mode, properties, as well as gut microbiome and metabolome.

https://www.crd.york.ac.uk/PROSPERO/view/CRD420251014654 CRD420251014654.},
}

@article {pmid41080149,
year = {2025},
author = {Xu, H and Li, S and Liu, S and Zuo, YG},
title = {A Conceptual Review of Gut, Skin, and Oral Microbiota in Autoimmune Bullous Diseases: From Dysbiosis to Therapeutic Potential.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {13925-13943},
pmid = {41080149},
issn = {1178-7031},
abstract = {Autoimmune bullous diseases (AIBDs), including pemphigus and bullous pemphigoid, are chronic inflammatory skin disorders characterized by dysregulated immune responses mediated by autoantibodies that target adhesion molecules in the skin and mucous membranes. Emerging evidence highlights the pivotal role of host microbiota dysbiosis in AIBDs pathogenesis, offering novel insights into disease mechanisms and therapeutic strategies. This review systematically synthesizes the current findings on gut, skin, and oral microbiota alterations in AIBDs, emphasizing their contributions via the gut-skin axis, microbial metabolites, and pathogen-host interactions. Key innovations include uncovering how specific pathogenic and commensal microbiota influence disease progression through intriguing skin inflammation and direct barrier impairment. Notably, while some microbiota changes overlap with other dermatoses, AIBDs exhibit distinct microbial signatures associated with their unique autoimmune mechanisms targeting adhesion molecules. Furthermore, we explore microbiota-targeted therapies, such as antibiotics, probiotics, and fecal microbiota transplantation, and demonstrate their potential to restore microbial homeostasis and improve clinical outcomes. By integrating multi-omics evidence and clinical data, this review bridges mechanistic insights with translational applications, proposing microbiota modulation as a promising adjunctive therapy for AIBDs. Our analysis identifies critical research gaps, including the need for longitudinal studies and personalized microbial interventions, positioning this review at the forefront of microbiome-inflammation-autoimmunity research.},
}

@article {pmid41080146,
year = {2025},
author = {He, X and Yang, F and Qu, G and Zhang, H and Yi, M and Wang, X and Sun, S},
title = {Integrated microbial and proteomic analysis elucidates quality degradation mechanisms of fresh milk through the industrial processing stage.},
journal = {Food chemistry: X},
volume = {31},
number = {},
pages = {103062},
pmid = {41080146},
issn = {2590-1575},
abstract = {Fresh milk quality deterioration during processing is a major dairy challenge, with microbial-driven protein degradation mechanisms unclear. This study pioneers an integrated microbiome-proteome approach to systematically elucidate the dynamic interplay between microbial succession and protein quality changes during industrial processing. Microbial community analysis revealed oscillatory richness, with 2.3-fold and 1.8-fold increases during pre-treatment (PL) and refrigerated transport (RC), respectively. Pseudomonas (12.4 % → 31.7 %) and Acinetobacter (8.1 % → 19.3 %) dominated key phases, with proteomics showing significant nutrient loss (IgM: -69.8 %; IgG: -54.15 %). Integrating microbial metagenomics with proteolytic pathway analysis identified proteases from Pseudomonas and Acinetobacter as key drivers of protein degradation (68 % activity). Pasteurization cut microbial load by 82 % but paradoxically intensified nutrient loss via protein denaturation. Crucially, our data establish a time-dependent degradation model, revealing that combined microbial enzymatic action and thermal effects account for 76 % of total protein hydrolysis, providing a theoretical framework for developing targeted intervention strategies in dairy processing optimization.},
}

@article {pmid41079947,
year = {2025},
author = {Teh, Z and Garcia-Maurino Alcazar, C and Bhatia, K},
title = {Overcoming barriers to gut microbiome development through nutritional factors in the first 1,000 days of life: strategies and implications for preventing non-communicable diseases.},
journal = {Gut microbiome (Cambridge, England)},
volume = {6},
number = {},
pages = {e18},
pmid = {41079947},
issn = {2632-2897},
abstract = {Current efforts to reduce the incidence of non-communicable disease (NCD) are slow, but increasing evidence highlights the microbiome as a potential target for prevention. The majority of microbial development occurs in the first 1,000 days of life, presenting opportunities for strategic intervention to reduce the prevalence of future NCDs. In this review, we explore the social, structural, and political barriers that may hinder physiological gut microbial development in the first 1,000 days in the context of current scientific knowledge, focusing on nutritional factors in pregnancy, and during the exclusive breastfeeding and complementary feeding periods. We summarise emerging evidence and explore obstacles to nutritional choices affecting microbial development, and unpack the rhetoric that healthy eating to develop a microbiome that supports optimum health is an individual choice. As evidence on the role of the microbiome in health and disease grows, specific attention must be applied to existing social, structural, and political barriers that may hinder optimal microbial development. Addressing the role of corporate actors and social determinants influencing dietary choices and barriers surrounding breastfeeding must be prioritised, alongside efforts to advance basic scientific research. Until a wider public health perspective is taken, the success of interventions and recommendations will be limited.},
}

@article {pmid41079946,
year = {2025},
author = {Campisi, SC and Zhang, F and Seo, M and Muha, J and Schumacher, A and De Luca, I and Bradley-Ridout, G and Merriman, K and Parkinson, J and Korczak, DJ},
title = {The gut microbiome and child and adolescent depression and anxiety: a systematic review and meta-analysis with youth consultation.},
journal = {Gut microbiome (Cambridge, England)},
volume = {6},
number = {},
pages = {e17},
pmid = {41079946},
issn = {2632-2897},
abstract = {Decreased gut microbial diversity is associated with greater depression symptoms in adults. Findings on the relationship between the gut microbiome and depression or anxiety in children and adolescents are mixed, and evidence syntheses are needed. Seven databases were searched for peer-reviewed studies on the gut microbiome and internalizing symptoms, depression, or anxiety, in children and adolescents (<19 years). Random-effects meta-analyses of alpha diversity indices were performed. Youth advisors validated the research findings' relevance to their experiences and contributed to dissemination planning. Eight studies were included, representing 2,865 participants (mean age = 11.4 years, SD = 4.3). Study designs were cross-sectional (n = 5), longitudinal (n = 2), and interventional (n = 1). No association was found between alpha or beta diversity and internalizing problems, depression, or anxiety. Increased abundance of genera within phyla Bacillota (e.g., Fusicatenibacter) and Pseudomonadota (e.g., Escherichia), along with decreased abundance of other Bacillota genera (e.g., Faecalibacterium), were associated with depression and anxiety symptoms. This review identified preliminary associations between specific bacterial taxa and depression and anxiety in children and adolescents. Larger studies using comprehensive analytical approaches are needed to explore the role of the gut microbiome in the genesis and treatment of internalizing disorders.},
}

@article {pmid41079945,
year = {2025},
author = {Mweetwa, MN and Ahsan, K and Louis-Auguste, J and Besa, E and Posma, JM and McNulty, N and Barrat, MJ and Gordon, J and Kelly, P},
title = {Intestinal microbiome changes in response to amino acid and micronutrient supplementation: secondary analysis of the AMAZE trial.},
journal = {Gut microbiome (Cambridge, England)},
volume = {6},
number = {},
pages = {e16},
pmid = {41079945},
issn = {2632-2897},
abstract = {Microbial dysbiosis has been linked to environmental enteropathy (EE) and alterations in nutrient absorption; however, compositional modifications following exposure to supplementary nutrients are poorly understood. Here, we report the effect of amino acid and micronutrient supplementation on the gut microbiome of adults with EE. In the AMAZE trial, adults with EE were randomized to amino acids (AA) and/or micronutrients (MM) for 16 weeks in a 2 × 2 factorial design against placebo. Endoscopy was performed before and after intervention, during which duodenal aspirates were collected as well as fecal samples. 16S rRNA amplicon sequencing was performed on both these samples, and differences in bacterial community composition before and after interventions were investigated using differential abundance analysis, corrected using false discovery rate, plus alpha and beta diversity measurements. HIV seropositive participants exhibited lower alpha and beta diversity at baseline. AA and/or MM supplementation did not show significant changes in abundance or diversity of genera post-intervention compared to placebo. Micronutrient supplementation resulted in an increase in the pyruvate fermentation to acetone MetaCyc pathways compared to the placebo arm. This study provides insights into the responsiveness of the gut microbiome to micronutrient and amino acid supplementation in adults with EE.},
}

@article {pmid41079925,
year = {2025},
author = {Jin, J and Cheng, K and Chen, M and Liang, H and Zhang, W},
title = {Immunotherapy resistance in MASLD-related hepatocellular carcinoma: special immune microenvironment and gut microbiota.},
journal = {International journal of biological sciences},
volume = {21},
number = {13},
pages = {5666-5690},
pmid = {41079925},
issn = {1449-2288},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Carcinoma, Hepatocellular/therapy/immunology/microbiology/etiology ; *Liver Neoplasms/therapy/immunology/microbiology/etiology ; *Immunotherapy/methods ; *Tumor Microenvironment/immunology ; Animals ; *Non-alcoholic Fatty Liver Disease/complications/immunology ; },
abstract = {Obesity represents a major global public health challenge. Consequently, metabolic dysfunction-associated steatotic liver disease (MASLD) has become the primary driver of chronic liver disease globally and is currently the most rapidly accelerating factor contributing to hepatocellular carcinoma (HCC). However, current evidence indicates that immunotherapy, a cornerstone of HCC management, yields suboptimal results specifically in MASLD-related HCC (MASLD-HCC) cases. Various immune components constitute a special immune microenvironment in MASLD-HCC, including heterogeneous myeloid cells, lymphocytes and platelets. Furthermore, disruptions in the intestinal barrier, along with the ectopic presence of intestinal flora and metabolites, also influence the immune microenvironment in MASLD-HCC. Elucidating immune cells functions and their interplay with gut microbiota is critical to deciphering MASLD progression to carcinogenesis and immunotherapy resistance. This review synthesizes current insights into the immune microenvironment and gut microbiome in MASLD-HCC, identifies factors influencing the efficacy of immunotherapy, and summarizes potential therapeutic targets to provide detailed guidance for developing effective immunotherapy strategies for MASLD-HCC.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Carcinoma, Hepatocellular/therapy/immunology/microbiology/etiology
*Liver Neoplasms/therapy/immunology/microbiology/etiology
*Immunotherapy/methods
*Tumor Microenvironment/immunology
Animals
*Non-alcoholic Fatty Liver Disease/complications/immunology

@article {pmid41079904,
year = {2025},
author = {Gao, Y and Li, X and Luo, F and Chen, R and Zhang, X},
title = {Integrative mass spectrometry-driven multi-omics and single cell technologies in ankylosing spondylitis: insights into pathogenesis, biomarker discovery, and precision medicine.},
journal = {Journal of translational autoimmunity},
volume = {11},
number = {},
pages = {100319},
pmid = {41079904},
issn = {2589-9090},
abstract = {Ankylosing spondylitis (AS), a chronic inflammatory arthritis primarily affecting the axial skeleton, presents significant clinical challenges due to its complex pathogenesis, delayed diagnosis, and heterogeneous therapeutic responses. This review highlights the pivotal role of mass spectrometry (MS)-based multi-omics technologies in elucidating AS pathogenesis, identifying disease-specific biomarkers, and advancing precision medicine for AS. The fundamental principles of MS are outlined, encompassing ionization methods like electrospray and matrix-assisted laser desorption/ionization, mass analyzers such as orbitrap and time-of-flight, and separation systems including liquid and gas chromatography. These technologies enable highly sensitive and comprehensive profiling of proteomes, metabolomes, and lipidomes. Proteomics analyses have revealed dysregulated pathways and identified key biomarkers, including complement components, matrix metalloproteinases and the panel "C-reactive protein + serum amyloid A1", for distinguishing active AS from healthy controls and stable AS. Metabolomics studies emphasize disturbances in tryptophan-kynurenine metabolism and gut microbiome-derived metabolites, including short-chain fatty acids, thereby linking microbial imbalance to inflammatory responses. A combination of three metabolites (3-amino-2-piperidone, hypoxanthine, and octadecylamine) has shown promise as serum biomarkers for AS diagnosis. Lipidomics profiling reveals significant changes in phospholipid composition. Furthermore, emerging single cell technologies (e.g., mass cytometry) have dissected immune heterogeneity in AS, revealing chemokine signaling dysregulation in monocyte and T-cell subclusters. Persistent challenges and future advancements, such as data heterogeneity, cohort limitations, and the interpretability of artificial intelligence models for multi-omics integration were discussed. By integrating technological innovation with clinical insights, this review systematically summarizes multiple potential biomarker panels for AS, in which multi-omics-driven strategies facilitate early diagnosis, mechanistic subtyping, and personalized therapies, ultimately improving patient outcomes in AS.},
}

@article {pmid41079737,
year = {2025},
author = {Shan, N and Wang, L and Duan, C and Wu, Y and Jing, Y and Fan, H and Wang, S and Wang, Y and Wang, S and Liu, H and Cheng, K and Liu, L and Liu, S and Zhuang, R},
title = {Pretreatment with Astragalus polysaccharide alleviates heat stroke-induced intestinal injury in mice.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1612852},
pmid = {41079737},
issn = {1663-9812},
abstract = {BACKGROUND: Heat stroke (HS) is a life-threatening illness. For HS, prevention is more important than treatment. Astragalus polysaccharides (APS), a major active ingredient of Astragalus membranaceus (Fisch.) Bunge, has multiple bioactivities, including anti-inflammatory and immunoregulation. This study aimed to evaluate the protective effects of APS on intestinal injury caused by HS.

METHODS: Mice were randomized to different groups. After 1 week of APS treatment, a mouse HS model was constructed and evaluated. Intestinal injury was assessed via histopathological examination, and the inflammation level was quantified via quantitative PCR. Flow cytometry and immunofluorescence analyses were used to detect neutrophil infiltration. Gut microbiota was analyzed via 16S rRNA sequencing. Moreover, network pharmacology was employed to analyze the potential targets and functional enrichment of APS. The apoptosis levels were detected in mouse intestinal tissues and IEC-6 intestinal epithelial cells.

RESULTS: APS pretreatment (50 mg/kg BW) prolonged the survival time, delayed the increasing rate of core temperature, and markedly improved organ injuries of HS mice. APS pretreatment improved the pathological changes in the intestine, inhibited inflammation, and reduced neutrophil infiltration. APS enhances the richness of intestinal flora and may shift microbiota functions, thereby benefiting vitamin B metabolism. Network pharmacology analysis indicated the apoptosis pathway as a potential target of APS. In vivo experiments using mouse HS model and in vitro experiments using IEC-6 cells confirmed the inhibitory effect of APS on apoptosis.

CONCLUSION: The preventive effects of APS on HS-induced intestinal injury include the alteration of intestinal microbiota composition and anti-inflammatory and antiapoptotic capacity.},
}

@article {pmid41079703,
year = {2025},
author = {Akinnola, OO and Samuel, AE and Omonhinmin, CA},
title = {Dataset on characterisation of microbiome of prostate tissue and expressed prostatic secretions.},
journal = {Data in brief},
volume = {63},
number = {},
pages = {112098},
pmid = {41079703},
issn = {2352-3409},
abstract = {Prostate cancer (PCa) is the second most prevalent cancer in men, particularly affecting those of Black African descent. Nigeria currently has the fourth highest risk for PCa mortality in the world. The microbiome of the prostate has emerged as a critical factor in understanding the aetiology and progression of prostate diseases, such as prostate cancer (PCa), benign prostatic hyperplasia (BPH) , benign stromal hyperplasia (BSH) and prostatitis (PRO). This study to comparatively characterise the microbiome present in prostate tissue and expressed prostatic secretion (EPS) from 30 study subjects diagnosed with PCa, BPH, BSH and PRO and sampled from the urology clinic of Lagos State University Teaching Hospital Ikeja. Bacterial species community composition and diversity were analysed based on 16S rRNA metagenome nucleotide data to ensure the accuracy, reproducibility, and broader applicability of microbiological and genomic research. Data information allows for precise identification of organisms at the species or strain level, essential for verifying experimental results and comparisons of the isolated organism's genome with related strains, providing insights into genetic diversity, virulence factors, and metabolic pathways of the sample population microbiome.},
}

@article {pmid41079637,
year = {2025},
author = {Tóth, AG and Nagy, SÁ and Lakatos, I and Solymosi, N and Stágel, A and Paholcsek, M and Posta, K and Gömbös, P and Ferenczi, S and Szőke, Z},
title = {Impact of mycotoxins and glyphosate residue on the gut microbiome and resistome of European fallow deer.},
journal = {iScience},
volume = {28},
number = {10},
pages = {113539},
pmid = {41079637},
issn = {2589-0042},
abstract = {Some mycotoxins and herbicide residues pose threats to animal health. These toxins might affect the gut microbiome of fallow deer. The analyzation of the intestinal content samples of this valuable game species exposed to varying levels of zearalenone (ZEA) and other toxic compounds such as aflatoxin B1, deoxynivalenol, fumonisin B1, and glyphosate residues was performed. Metagenomic analysis revealed significant alterations in the bacterial community composition. Higher ZEA levels were associated with decreased alpha diversity, whereas higher aflatoxin levels had the opposite effect. Changes in the abundance of antibiotic resistance genes (ARGs) were also observed, suggesting a potential link between mycotoxin exposure and antimicrobial resistance. Furthermore, five complete bacterial genomes were assembled from the metagenomic data. These findings highlight the complex interplay between environmental toxins, gut microbiota, and animal health. Understanding these interactions is crucial for developing strategies to mitigate the negative effects of toxin exposure on wildlife populations.},
}

@article {pmid41079634,
year = {2025},
author = {Ren, S and Zhang, D and Shi, X and Li, T and Hu, Q and Feng, Y and Hu, C and Feng, S and Zhu, Y and Gao, F},
title = {Gut virome characteristics associated with early onset of anemia and neurodevelopmental delay in preterm infants.},
journal = {iScience},
volume = {28},
number = {10},
pages = {113578},
pmid = {41079634},
issn = {2589-0042},
abstract = {Early-onset anemia (EOA) and neurodevelopmental delay (NDD) are highly prevalent in preterm infants, causing substantial long-term health impacts. This study aimed to identify distinctive gut virome characteristics and their associations with EOA and NDD. We hypothesized that gut microbial colonization types and bacteriophage profiles may be risk factors for NDD in preterm infants with EOA. Fecal samples from 107 healthy preterm infants within the first week of life underwent virome and 16S rRNA sequencing. Consensus clustering of viral species signatures divided infants into four groups. The high EOA risk group showed significantly higher virome alpha diversity. Enriched Circoviridae sp. and uncultured Caudoviridae phage, along with reduced CRESS virus sp., were linked to elevated NDD risk. Geobacillus virus Tp84-the only bacteriophage exhibiting both temperate and virulent lifestyles-was associated with high EOA risk but low NDD risk. These findings highlight the role of gut virome in EOA and NDD pathogenesis, suggesting potential for targeted bacteriophage-based interventions to mitigate EOA-related NDD in preterm infants.},
}

@article {pmid41079626,
year = {2025},
author = {Papadopoulou, KΚ and Chatzinotas, A and Diaz-Otero, BG and Brader, G and Karpouzas, DG and Garces Ruiz, M and Alonso Prados, JL and Declerck, S and Kellari, LM and Sessitsch, A},
title = {Benefits and challenges of upcoming microbial plant protection applications sustaining planetary health.},
journal = {iScience},
volume = {28},
number = {10},
pages = {113557},
pmid = {41079626},
issn = {2589-0042},
abstract = {Plant disease outbreaks pose severe risks to global food security. Due to climate change, new diseases are expected to emerge, and the current use of chemical pesticides poses risks to environmental and human health. In the last decade, alternative plant protection agents of microbial origin have been developed, which also raise great expectations in the industry. Current products primarily represent individual microbial strains, either fungi or bacteria, which occasionally fail under field conditions due to various factors while their regulatory status differs globally. Recently, more diverse applications have started to emerge, ranging from microbial consortia, phages and protists to microbiome modulation or soil translocation. Integrated solutions, incorporating artificial intelligence are also proposed. In this review, we discuss the opportunities and challenges of these solutions, providing specific examples and discuss the regulatory needs for their market entry as well as their relevance for improving food security and planetary health.},
}

@article {pmid41078999,
year = {2025},
author = {Xu, Q and Huang, Y and Chen, X and Lin, C},
title = {A Cross-Sectional Study on the Relationship Between Urinary Enterolactone and Sleep Quality in American Obese Adults.},
journal = {Nature and science of sleep},
volume = {17},
number = {},
pages = {2529-2540},
pmid = {41078999},
issn = {1179-1608},
abstract = {OBJECTIVE: This study aimed to appraise the association between urinary enterolactone and sleep quality in American obese adults.

METHODS: Our study analyzed data from 913 obese adults (2005-2008) in the National Health and Nutrition Examination Survey (NHANES) database. Enterolactone was tested in urine specimens. The Pittsburgh Sleep Quality Index (PSQI)-like measure reconstructed for NHANES based on prior literature was used to assess sleep quality. Multivariable logistic regression models were used to calculate the associations between urinary enterolactone and sleep quality in American obese adults. We also carried out linear tests utilizing restricted cubic splines to investigate the dose-response relationship between urinary enterolactone and sleep quality. Furthermore, we conducted stratified and interaction analyses to determine whether this relationship remained consistent across various subgroups.

RESULTS: A total of 913 obese participants were included in the analyses. After adjusting for potential confounding factors, each one-unit change in log-transformed urinary enterolactone was associated with 8% lower odds of poor sleep quality (OR=0.92, 95% CI: 0.85-0.99, p=0.027). When urinary enterolactone was presented in tertiles, this inversely correlation became more significant with increasing levels of urinary enterolactone. Moreover, in stratified analyses, the relationship between urinary enterolactone and sleep quality persisted.

CONCLUSION: Urinary enterolactone, an indicator of gut microbiome health, is inversely associated with poor sleep quality in American obese adults.},
}

@article {pmid41078571,
year = {2025},
author = {Nelson, AE and Arbeeva, L and Johnson, K and Savage-Guin, S and Walker, T and Enomoto, M and Stevens, C and Koskinen, M and Cole, T and Aker, S and Thonen-Fleck, C and Azcarate-Peril, MA and Loeser, RF and Renner, JB and Golightly, YM and Lascelles, BDX},
title = {Cross-sectional associations of radiographic multiple joint osteoarthritis and symptoms, laboratory values and the gut microbiota: A multimodal study in humans and pet dogs.},
journal = {Osteoarthritis and cartilage open},
volume = {7},
number = {4},
pages = {100682},
pmid = {41078571},
issn = {2665-9131},
abstract = {OBJECTIVE: To describe the frequency of multiple joint osteoarthritis (MJOA) and symptoms, and associations with fecal microbial diversity and composition, in cohorts of humans and dogs.

DESIGN: Human participants enrolled in the community-based Johnston County Health Study (JoCoHS), and an independent cohort of pet dogs, were included. Questionnaires, functional assessments, standardized multiple joint radiographs, and pain assessments, blood and fecal samples were obtained. Microbiome analysis was done by 16S rRNA amplicon sequencing. MJOA was defined as ≥3 unique joint sites involved; symptom burden was based on self-reported/proxy measures of pain. Descriptive statistics and Spearman correlations with Benjamini-Hochberg correction were used to determine relationships among lab tests, pain, and microbiome diversity measures.

RESULTS: Human participants (n ​= ​100, 63 ​% women, mean age 56 years, mean body mass index 34 ​kg/m[2]) and 115 pet dogs (40 ​% spayed females, 57 ​% neutered males, mean age 8 years, mean weight 27 ​kg) were included; 20 ​% had radiographic MJOA (rMJOA). Microbial α-diversity did not differ between participants with or without rMJOA. However, lower levels of the Christensenellaceae R-7 group and Lachnoclostridium in humans, and the butyrate-producing bacterium, Faecalibacterium in dogs, were moderately correlated with greater pain severity, as were higher levels of Escherichia-Shigella in dogs. Faecalibacterium was more abundant in humans without rMJOA.

CONCLUSIONS: These two cohorts demonstrated remarkably similar frequencies of rMJOA (∼20 ​%), supporting the use of dogs to model naturally occurring MJOA. Taxa potentially related to rMJOA and pain were identified in this preliminary analysis, providing new insights into links between dysbiosis and MJOA.},
}

@article {pmid41078567,
year = {2025},
author = {Cavaillon, JM and Carlet, J},
title = {Reassessing sepsis research: new clues for old players and new players for an old symptom to improve patient outcomes.},
journal = {EXCLI journal},
volume = {24},
number = {},
pages = {1143-1192},
pmid = {41078567},
issn = {1611-2156},
abstract = {Sepsis remains a global health problem that causes millions of deaths each year. A rapid and accurate diagnosis is highly desired to allow a rapid use of appropriate antibiotics. A better understanding of the associated pathophysiology has been achieved these recent years. The initial appropriate immune response to infection evolves towards an overwhelmed inflammatory response involving both pro- and anti-inflammatory players that act concomitantly. It also includes cell deaths and cellular dysfunctions of leukocytes, endothelial cells and epithelial cells, associated with mitochondrial dysfunction. These dysregulations are responsible for organ impairment and alteration of immune status of circulating leukocytes. In contrast, within the tissues, an over-activation exists as illustrated by transcriptomic analyses of organs of patients deceased of sepsis, and revealed by the presence of a macrophage activation syndrome within the bone marrow. Despite progresses in understanding the mechanisms underlying sepsis and despite successful therapies in animal models, no real new therapies have emerged these recent decades. This failure may reflect the yin yang aspect of the same players of the host response such as fever, release of cytokines, or coagulation which can display both a beneficial or a detrimental role. Great hopes are now expected from precision medicine, based on patients' endotypes which should help to decipher the patient's sub-groups who could benefit from the different treatments, or to define some appropriate time windows for a given treatment. See also the graphical abstract(Fig. 1).},
}

@article {pmid41078547,
year = {2025},
author = {Hussain, A and Mojgani, N and Shah, SMA and Kousar, N and Ali, SA},
title = {The emerging role of probiotics in the management and treatment of diabetic foot ulcer: a comprehensive review.},
journal = {AIMS microbiology},
volume = {11},
number = {3},
pages = {649-678},
pmid = {41078547},
issn = {2471-1888},
abstract = {Diabetic foot ulcer (DFU) is a complex complication characterized by tissue damage and neurological problems in the lower extremities. Poor wound healing intensifies the severity of DFU, which currently has a 15%-20% prevalence and thus poses a significant healthcare challenge. DFU treatment is often considered complicated due to multifaceted problems, including high cost, low stability, and prolonged healing time. Thus, there is a need to find multidisciplinary, cost-effective, and potential treatment options. In parallel, the role of skin and gut microbiota has been highlighted, influencing the progression of DFU. Probiotics, when used in sufficient amounts, confer a health benefit to the host and are found to have a promising treatment potential for DFU. Probiotics exert beneficial effects that help to improve the management and healing of DFU, following various mechanisms like controlling hyperglycemia, enhancing immune function, modulating the microbiota, and maintaining glucose homeostasis, all of which contribute to improved management and healing of DFU. Despite the potential of probiotics in DFU treatment, their precise mechanisms, optimal strains, dosages, and experimental validation remain underexplored. To fully explore the probiotic potential for DFU, extensive animal studies and clinical trials are needed. This article provides a comprehensive overview of the current status of DFU, existing treatment options, current limitations, and the growing importance of probiotic therapy. It also emphasizes the application of advanced technologies, including artificial intelligence (AI) and machine learning (ML), in advancing DFU treatment strategies.},
}

@article {pmid41078543,
year = {2025},
author = {Vijayaram, S and Mahendran, K and Razafindralambo, H and Ringø, E and Kannan, S and Sun, YZ},
title = {Probiotics, gut microbiota, and brain health: Exploring therapeutic pathways.},
journal = {AIMS microbiology},
volume = {11},
number = {3},
pages = {501-541},
pmid = {41078543},
issn = {2471-1888},
abstract = {The gut microbiome plays a significant role in regulating gastrointestinal (GI) function and modulating the gut-brain axis, which describes the bidirectional communication between the GI tract and the central nervous system (CNS). Its involvement in digestion, immunity, and neurophysiology is well recognized. This study offers novel insights by focusing on psychobiotics, a class of probiotics with targeted neuroactive properties. These microorganisms influence brain function through defined mechanisms, including modulation of neuroinflammation, neurotransmitter production (GABA, serotonin), regulation of the hypothalamic-pituitary-adrenal (HPA) axis, and vagus nerve signaling. Our work critically examines recent advances in applications of psychobiotics for neurological disorders such as Parkinson's disease, Alzheimer's disease, multiple sclerosis, and autism spectrum disorder. By integrating evidence from microbiome research, neuroimmunology, and clinical studies, we identify promising microbial strains and mechanistic pathways with therapeutic potential. This study contributes original perspectives by highlighting underexplored microbe-host interactions and proposing targeted microbial interventions as adjuncts to conventional neurotherapies. Further research is needed to validate strain-specific effects, long-term efficacy, and safety profiles in clinical settings.},
}

@article {pmid41078532,
year = {2025},
author = {Taha, H and Issa, A and Muhanna, Z and Al-Shehab, M and Wadi, T and Awamleh, S and Ateiwi, YA and Abusido, M and Berggren, V},
title = {Microbiota-based interventions for autism spectrum disorder: a systematic review of efficacy and clinical potential.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1648118},
pmid = {41078532},
issn = {1664-302X},
abstract = {PURPOSE: Autism spectrum disorder (ASD) is increasingly linked to gut microbiota imbalances, influencing both behavioral and gastrointestinal (GI) symptoms. This systematic review assesses the efficacy of microbiota-based interventions, including probiotics, prebiotics, synbiotics, and fecal microbiota transplantation (FMT), in improving ASD-related symptoms, aiming to provide insights into their therapeutic potential and inform future clinical applications.

METHODS: A comprehensive systematic review was conducted following PRISMA guidelines and registered in PROSPERO (CRD42024615043). A structured literature search was performed in PubMed, Cochrane Library, and Scopus to identify peer-reviewed English-language studies. Eligible studies included randomized controlled trials (RCTs), non-randomized trials (NRTs), and retrospective studies assessing the impact of microbiota-based interventions on ASD-related behavioral and GI outcomes. Two independent reviewers conducted study selection, data extraction, and quality assessment using standardized risk-of-bias tools.

RESULTS: 33 studies were included, consisting of 16 RCTs, 14 NRTs, and 3 retrospective studies. Among them, 15 assessed probiotics, 4 prebiotics, 5 synbiotics, and 9 FMT. Probiotics showed moderate behavioral improvements in ASD, with multi-strain formulations being more effective than single strains. Prebiotics and synbiotics yielded mixed results, with some studies indicating benefits in behavioral and GI symptoms. FMT demonstrated the most consistent and sustained improvements in both ASD-related behaviors and GI function. Adverse events were minimal, primarily involving transient GI symptoms.

CONCLUSION: Microbiota-targeted interventions, particularly FMT, hold promise for managing ASD symptoms, though probiotics, prebiotics, and synbiotics present variable efficacy. Standardized protocols, larger controlled trials, and personalized microbiome-based approaches are necessary to refine these therapeutic strategies and enhance clinical applicability.

https://www.crd.york.ac.uk/PROSPERO/view/CRD42024615043, identifier CRD42024615043.},
}

@article {pmid41078529,
year = {2025},
author = {Ceretto, A and Weinig, C},
title = {Rhizosphere microbiomes of field-grown B. stricta exhibit minimal diel changes in microbial membership and protein synthesis potential.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1609057},
pmid = {41078529},
issn = {1664-302X},
abstract = {The rhizosphere microbiome has a significant impact on plant health and fitness. Quantifying bacterial responses to fine-scale plant-mediated changes in the rhizosphere, such as those associated with diel cycling in host plant physiology, will increase our understanding of microbial community assembly patterns. Here, we used 16S rRNA biomarker gene (DNA) and transcript (RNA) sequencing to characterize changes in the rhizosphere community membership and PSP over short timescales in field-grown Boechera stricta (B. stricta) plants. Microbial communities characterized by 16S-rRNA-transcripts, which serve as a proxy for microbial protein synthesis potential (PSP), showed greater sensitivity to fine-scale environmental changes than did communities characterized by 16S-rRNA biomarker gene sequencing, which reflects microbial presence/absence. Significant differences were observed between communities characterized by RNA vs. DNA, with RNA-derived communities showing greater alpha and beta diversity differences between the rhizosphere vs. control soil communities within phyla and in differential abundance analysis of genera. Communities reconstructed from RNA were more sensitive to the effects of field blocks and collection timepoints. Differential abundance analysis revealed significant differences (p < 0.05) between the pre-dawn (AM) and early afternoon (PM) timepoints for five genera based on 16S rRNA transcripts. This included the plant-associated genus Curtobacterium. However, when variance was partitioned between days of collection, the amplitude of the signal between diel timepoints was non-significant. In summary, community composition and protein synthesis potential were highly sensitive to abiotic factors expressed over the small spatial scale of field blocks and short 24-h periods between collection days but showed minimal to no diel patterning.},
}

@article {pmid41078525,
year = {2025},
author = {Taggart, MG and Baah, DS and Allen, S and Khan, Z and Arnscheidt, J and Jordan, P and O'Hagan, BMG and Ibrahim, AD and Rao, JR and Ternan, NG},
title = {Fitting soil extracellular enzyme activity into the complex network of abiotic and biotic soil properties often associated with soil health.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1638267},
pmid = {41078525},
issn = {1664-302X},
abstract = {In this mini review we examine how soil extracellular enzymes play a key role in nutrient cycling, but stress that their activity alone does not fully represent ecosystem processes. We emphasize the need for more contextual environmental data-such as pH, temperature, moisture and nutrient availability-for accurate interpretation of the significance of enzyme activity in carbon and nutrient (N, P) cycling in soil ecosystems. The importance of enzymes within the soil microbiome determines its inherent capacity to support crop growth and often reflects soil quality and soil health, which are in turn governed by multiple different soil properties. Soil enzymes (e.g., phosphatase, glucosidases, glycosaminidases) activity have been used as key soil health bio indicators for monitoring soil nutrient transformations in overgeneralized statements. Although soil enzymes constitute important attributes that are closely linked to the dynamics of soil nutrient transformation and make nutrients available to plants, we suggest a multi-factor assessment for soil health measurement. We propose that this can give a pulse reading of soil nutrient health at crucial times of soil, land use, and crop management practices but that care is required to incorporate temporal soil and land use properties for correct interpretation.},
}

@article {pmid41078520,
year = {2025},
author = {Mumtaz, MZ and Castellane, TCL and Shahid, I and Tamburini, E and Bouizgarne, B},
title = {Editorial: Plant mineral microbe interactions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1677458},
doi = {10.3389/fmicb.2025.1677458},
pmid = {41078520},
issn = {1664-302X},
}

@article {pmid41078518,
year = {2025},
author = {Liu, J and Wang, L and Su, L and Chen, J and Su, R},
title = {Exploring the gut microbiota-Parkinson's disease link: preliminary insights from metagenomics and Mendelian randomization.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1654418},
pmid = {41078518},
issn = {1664-302X},
abstract = {INTRODUCTION: The relationship between the gut microbiome and Parkinson's disease (PD) has recently attracted significant attention, with most studies focused on analyzing microbial composition. However, our understanding of the potential causal relationship between the gut microbiota and PD remains limited.

METHODS: We extracted microbiome data from the metagenome for broad taxonomic coverage and accurate functional analysis. Subsequently, Mendelian randomization was employed to elucidate the causal relationship between the gut microbiome and PD.

RESULTS: The gut microbiota in PD patients was found to be systemically imbalanced, characterized by an abnormal enrichment of potential pathogenic bacteria, a significant reduction in key beneficial bacteria, and a reorganization of intestinal metabolic functions. This state of imbalance involves significant abnormalities in multiple metabolic and regulatory pathways, including the glucose metabolism, oxidative stress response, protein homeostasis regulation, and immune signaling pathways. These findings suggest that dysbiosis may influence host neural function through multilevel metabolic interventions. Additionally, specific microbial communities are clearly associated with disease risk, with some bacterial populations promoting disease onset and others demonstrating a potentially protective effect. Although metagenomic findings require validation in larger cohorts, the results of this study indicate that changes in gut microbiota composition and function are closely related to PD onset and progression.

CONCLUSION: This study revealed that certain microorganisms traditionally considered beneficial may contribute to PD risk. This finding challenges previous assumptions and highlights the complexity of host-microbiome interactions. The identification of altered metabolic and immune pathways, particularly those involving bacteria that produce short-chain fatty acids, underscores the critical role of the gut microbiota in PD pathophysiology. However, the relatively small sample size of the current metagenomic analysis limits the generalizability of these findings. Larger, more diverse cohorts are needed to validate these results. Despite this limitation, the study provides important insights into microbiome-targeted therapeutic strategies, emphasizing the need to reconsider the roles of both beneficial and harmful microorganisms in PD.},
}

@article {pmid41078508,
year = {2025},
author = {Huang, B and Li, B and Pan, G and Huang, D and Yang, G and Ma, Y and Ya, F and Rao, M and Wei, Y},
title = {Bacillus amyloliquefaciens G02 enhances selenium uptake in lettuce (Lactuca sativa) by improving soil selenium availability and rhizosphere microbiome regulation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1656037},
pmid = {41078508},
issn = {1664-302X},
abstract = {Selenium (Se) is an essential trace element for human, but its low availability in soils results in its inadequacy in edible crops, thereby limiting its human intake. However, the role of the plant growth-promoting bacteria in soil Se availability and the pathways involved in biofortification in edible plants remain poorly understood. In this study, a Se-tolerant, plant growth-promoting bacterium, Bacillus amyloliquefaciens strain G02, which activates Se was isolated from the soils in Se-rich fields in Guangxi, China. We employed soil microcosm and potted experiments, along with metabolomics and 16S rRNA sequencing, to investigate how strain G02 incubation promotes elemental Se (0) solubilization, soil Se activation, and Se enrichment in lettuce. The strain G02 exhibited high phosphate solubilization (87.36 mg/L), IAA production (8.35 mg/L), as well as siderophore and ACC deaminase activities. Strain G02 is capable of dissolved Se(0) and Se minerals, increased pH, and secreted metabolites enhancing Se solubility. Soil microcosm experiments showed that the incubation of strain G02 increased available Se forms [soluble selenium (SOL-Se) and exchangeable selenium (EXC-Se)] in soil. Moreover, potted experiments revealed that the incubation of strain G02 increased biomass, Se concentration in lettuce, soil enzyme activities, beneficial microbial abundance and the native bacterial taxa. The strain G02 enhances soil Se availability through metabolites secretion, Se solubilization, and rhizosphere microbial regulation, improving ability of lettuce to absorb and transport Se. This study provides novel insights into the microbially mediated Se biofortification.},
}

@article {pmid41078442,
year = {2025},
author = {Yang, J and Chen, J and Liu, Z and Qu, Y and Yue, X and Yuan, B and Li, M},
title = {The Role of the Intestinal Microbiome in the Pathogenesis and Treatment of Hyperuricemia: A Review.},
journal = {Food science & nutrition},
volume = {13},
number = {10},
pages = {e70982},
pmid = {41078442},
issn = {2048-7177},
abstract = {Hyperuricemia (HUA), characterized by elevated blood uric acid (UA) levels, is a major risk factor for gout, UA nephropathy, metabolic syndrome, and other related disorders. Traditional drug therapy for HUA includes medications (e.g., allopurinol and febuxostat) and dietary changes; however, it is limited and may be accompanied by adverse side effects such as allergies, prompting the investigation of alternative therapeutic approaches. Although the newly researched "in-situ graft polymerization" protein drug modification technology and the emerging gut microbiota transplantation technology have demonstrated innovation in regulating blood UA, they still need to overcome bottlenecks in immunogenicity, individual variability, and formulation technology. Recent research has highlighted the potential of modulating the intestinal microbiome as a promising strategy for managing HUA. Nevertheless, the mechanism by which different intestinal microbiomes affect HUA pathogenesis remains unclear. To bridge this gap, this review firstly outlines the characteristics and prevailing conditions of HUA, followed by the current status of treatment. Besides, this review integrates the findings from clinical trials and animal studies to explore in depth the pathogenic mechanisms of HUA and the potential roles and regulatory pathways of the gut microbiota in mitigating HUA. The gut microbiota act as multi-functional factors that affect HUA by reducing UA production, enhancing purine metabolism, influencing amino acid transport, and increasing UA excretion. This review addresses critical gaps in the extant literature regarding microbiota-mediated UA homeostasis and provides new perspectives for the future treatment of HUA.},
}

@article {pmid41078363,
year = {2025},
author = {Su, S and Ni, X and Lin, Y},
title = {The oral-gut microbiota axis in cardiovascular diseases: mechanisms, therapeutic targets, and translational challenges.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1658502},
pmid = {41078363},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Cardiovascular Diseases/microbiology/therapy/etiology ; *Dysbiosis/complications/microbiology ; *Mouth/microbiology ; Animals ; },
abstract = {The oral-gut microbiota axis, a newly recognized regulatory system, has emerged as a pivotal factor in the development of cardiovascular diseases (CVDs). This review comprehensively synthesizes the latest evidence on how the dysbiosis of oral and gut microbiota, along with their metabolic and immunological cross-talk, contributes to CVD pathogenesis, including atherosclerosis, hypertension, and heart failure. We highlight the novel "microbiota-metabolism-immunity"tri-dimensional regulatory network and explore innovative therapeutic strategies, such as precision microbiome modulation and non-invasive biomarker development. By bridging the gap between basic research and clinical translation, this review provides new insights into preventing and treating CVDs through targeting the oral-gut axis.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Cardiovascular Diseases/microbiology/therapy/etiology
*Dysbiosis/complications/microbiology
*Mouth/microbiology
Animals

@article {pmid41078307,
year = {2025},
author = {He, H and Xiao, M and Song, L and Tian, Y and Jia, Y},
title = {Lipidome-microbiome crosstalk as an outer niche in the skin: regulatory networks in health and disease.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjd/ljaf353},
pmid = {41078307},
issn = {1365-2133},
support = {//Beijing Technology and Business University/ ; //Beijing Municipal Education Commission/ ; 32100254//National Science Foundation of China/ ; },
abstract = {The skin is the outermost barrier to organisms from the external environment. This natural role, endowed by evolution, results in a nutrient-poor skin surface that enables microbial nutrition-dependent lipids to shape microbial ecology by survival pressure and nutrient preference. In turn, the skin microbiota produce microorganism-metabolized bioactive molecules (MBMs) to increase molecular diversity. This crosstalk functions as a crucial component of niche-regulating skin properties via multiple mechanisms. Furthermore, the local and remote effects of different barrier sites provide a more comprehensive explanation for the crosstalk from a global perspective. The variable function and mechanism of crosstalk may represent an evolutionary means by which the skin uses fluctuating commensal signals - the highly dynamic MBMs - to calibrate skin status and provide heterologous protection against invasive pathogens. Elucidating the reasons for the differing selectivity and catalytic efficiency of lipid-metabolizing enzymes in microorganisms and revealing the biologic processes and regulatory mechanisms of the 'co-metabolic systems' on the skin will advance diagnostic and therapeutic strategies for local cutaneous disorders and comorbid diseases of distant organs.},
}

@article {pmid41078233,
year = {2025},
author = {Ardila, CM and Vivares-Builes, AM and Pineda-Vélez, E},
title = {Molecular Biomarkers and Machine Learning in Oral Cancer: A Systematic Review and Meta-Analysis.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.70121},
pmid = {41078233},
issn = {1601-0825},
abstract = {OBJECTIVE: This systematic review and meta-analysis aimed to synthesize diagnostic and prognostic performance metrics of machine learning (ML)-based biomarker models in oral squamous cell carcinoma (OSCC) and to integrate biological insights through a functional metasynthesis.

METHODS: Following PRISMA 2020 guidelines, a comprehensive search was conducted up to July 2025. Eligible studies applied ML algorithms to molecular or imaging biomarkers from OSCC patients. Data synthesis incorporated meta-analysis when endpoints and designs were sufficiently comparable; otherwise, study-level results were summarized narratively.

RESULTS: Twenty-five studies encompassing 4408 patients were included. Diagnostic performance was strongest for salivary DNA methylation (AUC up to 1.00), metabolomics (AUC ≈0.92), and FTIR imaging (AUC ≈0.91), while autoantibody and microbiome models showed more variable accuracy. Prognostic models based on immune-feature signatures outperformed conventional scores, while multimodal approaches integrating imaging and metabolomics retained strong performance under external validation. Models based on pathomics and MRI radiomics also achieved clinically meaningful accuracy across independent cohorts. Functional metasynthesis revealed convergent biological processes-metabolic reprogramming, immune-inflammatory remodeling, microbiome dysbiosis, and epithelial/extracellular matrix disruption-that underpin predictive accuracy.

CONCLUSION: ML models leveraging molecular and imaging biomarkers show strong potential to improve OSCC diagnosis, risk stratification, and prognosis, particularly through multimodal integration.},
}

@article {pmid41078163,
year = {2025},
author = {Turpin, W and Kalili, H and Halfvarson, J and Croitoru, K},
title = {IBD Prediction Is Possible, but How Far Are We from Implementing It?.},
journal = {Inflammatory bowel diseases},
volume = {31},
number = {Supplement_2},
pages = {S41-S50},
doi = {10.1093/ibd/izaf197},
pmid = {41078163},
issn = {1536-4844},
support = {//Crohn's and Colitis Canada/ ; CMF108031/CAPMC/CIHR/Canada ; //Helmsley Charitable Trust/ ; //Canada Research Chair in Inflammatory Bowel Diseases/ ; 2020-02021//Swedish Research Council/ ; //Crohn's and Colitis Foundation/ ; },
mesh = {Humans ; *Biomarkers/analysis ; *Inflammatory Bowel Diseases/diagnosis ; Metabolomics ; Proteomics ; Risk Assessment ; },
abstract = {Crohn's disease and ulcerative colitis, collectively known as inflammatory bowel diseases (IBDs), are chronic gastrointestinal diseases with poorly characterized pathophysiology. Recent advancements in the identification of preclinical biomarkers of IBD have shed some insight into our ability to predict or prevent these conditions. This review discusses the growing body of research on biomarkers ranging from genetics, measures of gut permeability, and microbiome signatures to circulating proteomics and metabolomics. In addition, the review will highlight the potential application of these biomarkers for early detection and risk stratification of IBD. Notably, proteomic markers such as CXCL9 and MMP-10, along with metabolic perturbations detectable prior to clinical diagnosis, provide promising avenues for understanding IBD pathogenesis and guiding prevention strategies. Furthermore, the development of integrative risk scores, combining multiomic data with demographic and lifestyle factors, could offer a personalized approach to disease prediction and prevention. While these advances present significant opportunities, challenges remain in data complexity and variability of biomarkers. This review emphasizes the importance of continued longitudinal studies and clinical trials to validate predictive models. Ultimately, the integration of early risk prediction holds the potential to reduce IBD incidence through targeted, proactive strategies.},
}

Humans
*Biomarkers/analysis
*Inflammatory Bowel Diseases/diagnosis
Metabolomics
Proteomics
Risk Assessment

@article {pmid41078161,
year = {2025},
author = {Ribeiro-Mourão, F and Agrawal, M and Torres, J and Peter, I},
title = {Intervention(s) in the Early-Life Period to Modulate Inflammatory Bowel Disease Risk: What Could Be the Impact?.},
journal = {Inflammatory bowel diseases},
volume = {31},
number = {Supplement_2},
pages = {S27-S40},
doi = {10.1093/ibd/izaf205},
pmid = {41078161},
issn = {1536-4844},
support = {101194780//Innovative Health Initiative Joint Undertaking/ ; },
mesh = {Humans ; *Inflammatory Bowel Diseases/prevention & control/etiology ; Pregnancy ; Female ; Gastrointestinal Microbiome ; Risk Factors ; Breast Feeding ; *Prenatal Exposure Delayed Effects/prevention & control ; Infant, Newborn ; },
abstract = {The rising incidence of pediatric-onset inflammatory bowel disease (IBD) has intensified focus on the early-life period as a critical window for prevention. Accumulating observational evidence links prenatal, perinatal, and early childhood exposures to later IBD risk. Several mechanisms underpin this relationship, including gut microbiome development, immune system maturation, epigenetic modulation, and metabolic and endocrine programming. Building on this framework, this review outlines potential intervention strategies across key developmental stages-from maternal nutrition and microbiome modulation during pregnancy to delivery-related factors such as birth mode, intrapartum antibiotic use, and early breastfeeding practices. Postnatal strategies include breastfeeding promotion, timely and diverse dietary introduction, antibiotic stewardship, and minimization of detrimental environmental exposures. Such approaches may be particularly relevant for high-risk groups, notably children born to individuals with IBD. Practical guidance is provided for families affected by IBD, alongside a discussion on how universal and risk-stratified strategies may be integrated. However, it is important to note that most of these strategies remain hypothetical, with limited validation. Emerging research areas include maternal dietary interventions, microbiome-based therapies, and the utilization of digital tools for risk monitoring. This review also addresses ethical and implementation challenges inherent to early-life prevention research and intervention.},
}

Humans
*Inflammatory Bowel Diseases/prevention & control/etiology
Pregnancy
Female
Gastrointestinal Microbiome
Risk Factors
Breast Feeding
*Prenatal Exposure Delayed Effects/prevention & control
Infant, Newborn

@article {pmid41078159,
year = {2025},
author = {Torres, J and Moss, A},
title = {Introduction to the IBD Journal Supplement: "Prevention of IBD: Forecasting and Forestalling Inflammatory Bowel Disease Onset".},
journal = {Inflammatory bowel diseases},
volume = {31},
number = {Supplement_2},
pages = {S1-S2},
doi = {10.1093/ibd/izaf207},
pmid = {41078159},
issn = {1536-4844},
mesh = {Humans ; *Inflammatory Bowel Diseases/prevention & control/etiology ; Risk Factors ; Biomarkers/analysis ; Forecasting ; },
abstract = {Despite significant therapeutic advances in inflammatory bowel disease (IBD), patients still experience diagnostic delays, suboptimal outcomes, and low remission rates-highlighting the urgent need for new approaches. This IBD journal supplement gathers leading experts to examine critical aspects of disease prediction and prevention. Topics include the genetic architecture of IBD, early-life environmental risk factors and their influence on disease risk, and emerging predictive biomarkers such as microbiome signatures, gut permeability, and proteomics, among others. Insights from type 1 diabetes research inform potential strategies for disease interception in IBD. Several targets are proposed for interception and prevention of disease, and the optimal design of an IBD-prevention trial is discussed. While landmark initiatives across the globe are currently paving the way for biomarker validation and trial implementation, harmonizing terminology and defining preclinical stages are essential next steps. Ultimately, understanding disease initiation may enable transformative strategies, shifting the paradigm from treatment to true prevention and potentially altering the course of IBD.},
}

Humans
*Inflammatory Bowel Diseases/prevention & control/etiology
Risk Factors
Biomarkers/analysis
Forecasting

@article {pmid41078118,
year = {2025},
author = {Wang, Y and Yang, J and Hou, H and Song, L and Cheng, X and Liu, YX},
title = {Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.70379},
pmid = {41078118},
issn = {1467-7652},
support = {32470055//National Natural Science Foundation of China/ ; U23A20148//National Natural Science Foundation of China/ ; CAAS-BRC-CB-2025-01//Basic Research Center for Crop Biosafety Sciences/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; },
abstract = {Plants provide ecological habitats for diverse microorganisms, making accurate metagenomic sequencing essential for understanding the complex interactions that support plant growth, development and disease resistance. However, host DNA contamination poses a major challenge in plant microbiome studies, obscuring microbial genetic signatures and complicating the accurate analysis of microbial genomes. This review provides a comprehensive overview of current host DNA depletion strategies, including physical separation (e.g., filtration, gradient centrifugation), selective lysis and enzymatic treatments targeting plant cell walls. Advanced techniques such as targeted sequence capture with magnetic beads, methylation-based enrichment and nanopore selective sequencing offer additional options for host DNA removal. Despite these advances, current methods still face challenges in efficiency, specificity and applicability, emphasising the need for tailored strategies and the exploration of novel approaches for microbial enrichment. Innovations like CRISPR-Cas9 and chromatin immunoprecipitation-based host DNA depletion methods are proposed to provide novel directions for addressing current limitations. The development and refinement of host depletion techniques tailored to plant systems are crucial for enabling high-resolution, cost-effective metagenomic studies. These efforts promise to deepen our understanding of microbial diversity and functionality, ultimately accelerating microbiome-based innovations in crop improvement, sustainable agriculture and ecosystem resilience.},
}

@article {pmid41078079,
year = {2025},
author = {Shibata, R and Li, Y and Yaskolka Meir, A and Cregeen, SJ and Ross, MC and Espinola, JA and Sullivan, AF and Liang, L and Hasegawa, K and Camargo, CA and Zhu, Z},
title = {Nasopharyngeal Microbiome-Epigenome-Wide Association Analysis in Infants With Severe Bronchiolitis.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70102},
pmid = {41078079},
issn = {1398-9995},
support = {/NH/NIH HHS/United States ; //Environmental influences on Child Health Outcomes (ECHO) Program Opportunities and Innovation Fund (OIF)/ ; //Massachusetts General Hospital/ ; //the Harvard University William F. Milton Fund/ ; //American Lung Association Innovation Award/ ; },
abstract = {BACKGROUND: Bronchiolitis exposes infants to both acute burdens (e.g., hospitalization in cases of severe bronchiolitis) and increased risks for chronic respiratory sequelae (e.g., asthma). In severe bronchiolitis, recent evidence suggests distinct pathobiological roles of microbiota (e.g., viruses, bacteria) and host responses influenced by genetic and epigenetic factors. However, the relationship of airway microbiota with host DNA methylation (DNAm) in infants with severe bronchiolitis remains unknown.

METHODS: In a multi-center prospective cohort of 504 multi-ethnic infants with severe bronchiolitis (age < 1 year), using nasopharyngeal microbiome (exposure) and blood DNAm (outcome, Infinium MethylationEPIC BeadChip, Illumina) data within 24 h of the hospitalization, we conducted microbiome-epigenome-wide association studies (mbEWAS). We examined microbiota-associated differentially methylated CpGs (mbDMCs, false discovery rate [FDR] < 0.05), regions (mbDMRs, FDR < 0.05), and DNAm age acceleration. We also determined the associations of DNAm age acceleration with asthma development by age 6 years. Furthermore, we focused on asthma-related pathogenic bacteria-Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae-for functional analyses by examining serum mbDMR-related proteins (Proseek Multiplex, Olink) and their enriched pathways (FDR < 0.10).

RESULTS: Across 23 common taxa-observed at least in 25% of the infants, we identified 1 mbDMC (S. pneumoniae, cg16594639, chr20: 39528675) and 96 mbDMRs (e.g., S. pneumoniae, chr5:27038497-27038802, CDH9; chr6:48068669-48068940, PTCHD4). A higher H. influenzae abundance was associated with DNAm age deceleration, and the deceleration was associated with a higher risk of developing asthma. In 29 mbDMRs of the asthma-related pathogenic bacteria, we identified 156 mbDMR-related proteins (e.g., MMP9, XCL1). These proteins were enriched in immune response-related pathways (e.g., regulation of ERBB signaling and eosinophil chemotaxis and migration pathways).

CONCLUSIONS: In this multi-center prospective cohort study of severe bronchiolitis, our mbEWAS suggested the microbiota-host associations that regulate immune responses.},
}

@article {pmid41077905,
year = {2025},
author = {Hernández-Terán, A and Escalante, AE and Rebolleda-Gómez, M},
title = {Plant domestication does not reduce diversity in rhizosphere bacterial communities.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70588},
pmid = {41077905},
issn = {1469-8137},
support = {LT 0047/2023-L//Human Frontier Science Program/ ; IN214124//UNAM-PAPIIT/ ; //University of California President's Postdoctoral Fellowship/ ; //School of Biological Sciences at the University of California, Irvine/ ; },
abstract = {Domestication has profoundly shaped the genetic makeup of numerous plant and animal species. While its genetic and phenotypic effects are well documented, the impact on the plant microbiome remains less understood. Two primary hypotheses have been proposed: a reduction in microbial diversity resulting from the domestication process and the diminished ability of host plants to control their microbiomes. We tested these hypotheses by comparing wild and domesticated plants across maize, wheat, barley, sunflower, tomato, cotton, bean, soybean, sorghum, rice, potato, and agave. We conducted a meta-analysis comparing the rhizosphere bacterial communities of domesticated plants and their wild relatives. Analyses focused on microbial diversity, community composition, and the degree of host influence on bacterial assemblages. Our results indicate that the effects of domestication are species-specific and context-dependent, with most domesticated plants exhibiting increased bacterial diversity and more structured communities. This study provides evidence that plant domestication does not lead to a uniform reduction in bacterial diversity or a consistent loss of host influence in bacterial assemblages. From these findings, we discuss new perspectives and the need for future studies incorporating native soils and host genetic variation, as well as analyzing diversity and microbiome function.},
}

@article {pmid41077825,
year = {2025},
author = {Yin, R and Sargsyan, D and Wu, R and Hudlikar, R and Li, S and Kuo, HC and Sarwar, MS and Zhou, Y and Gao, Z and Howell, A and Chen, C and Blaser, MJ and Tony Tong Kong, AN},
title = {Microbiome and Metabolome Alterations in Nrf2 Knockout Mice With Induced Gut Inflammation and Fed With Phenethyl Isothiocyanate and Cranberry Enriched Diets.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70283},
doi = {10.1002/mnfr.70283},
pmid = {41077825},
issn = {1613-4133},
abstract = {Cranberries contain phytochemicals with potent antioxidant properties. Phenethyl isothiocyanate (PEITC) is abundant in crucifers and possesses anti-cancer and anti-inflammatory properties. These food additives can alter gut microbiota and improve the host's health. Microbiome and microbial metabolome interactions with the host's cells help maintain gastrointestinal (GI) tract homeostasis. Cranberry and PEITC enriched diets were fed to wild-type (WT) and Nrf2 knockout (KO) mice, including those challenged with dextran sulfate sodium (DSS), and their gut microbiomes and metabolomes were examined. Relative abundances of Deferribacteres, Epsilonbacteraeota, and Proteobacteria decreased, while Firmicutes and Verrucomicrobia increased in the DSS-challenged mice samples. These trends were reversed by PEITC and cranberry enriched diets. The diets also preserved the Firmicutes-to-Bacteroidetes ratio, an endpoint associated with gut inflammation and obesity. DSS challenge altered production of several metabolites. Nrf2 KO mice samples had lower concentrations of short-chain fatty acids (SCFA) and amino acids, and higher concentrations of secondary bile acids.Nrf2 KO mice microbiomes exhibited higher richness and diversity. PEITC and cranberry enriched diets positively affected hosts' microbiomes and boosted several microbial metabolites. Phenotypic expression of Nrf2 impacted the microbiota and metabolic reprogramming induced by DSS-mediated inflammation and dietary supplements of cranberry and PEITC.},
}

@article {pmid41077748,
year = {2025},
author = {Lee, HK and Shin, CM and Chang, YH and Jo, H and Choi, J and Choi, Y and Jun, YK and Yoon, H and Park, YS and Kim, N and Lee, DH},
title = {Predictors of Treatment Response to Fecal Microbiota Transplantation in Irritable Bowel Syndrome: A Pilot Study.},
journal = {Journal of neurogastroenterology and motility},
volume = {31},
number = {4},
pages = {462-476},
doi = {10.5056/jnm24183},
pmid = {41077748},
issn = {2093-0879},
abstract = {BACKGROUND/AIMS: We aim to investigate the effectiveness, safety, and predictors of treatment response to fecal microbiota transplantation (FMT) in Korean irritable bowel syndrome (IBS) patients.

METHODS: Patients with moderate to severe diarrhea-predominant IBS (IBS-D) or mixed-type IBS (IBS-M) received FMT from one healthy donor via esophagogastroduodenoscopy. IBS-symptom severity score (IBS-SSS), Bristol stool form scale (BSFS), IBS Quality of Life (IBS-QoL) questionnaires, Hospital Anxiety and Depression Scale (HADS), and gut microbiome profiles were assessed at baseline, 4 weeks and 12 weeks post-FMT.

RESULTS: Among the 46 enrolled IBS patients, 37 patients (IBS-D:IBS-M = 28:9) completed a 12-week follow-up. Significant improvements were observed in IBS-SSS, IBS-QoL, and BSFS after 12 weeks. FMT led to increased microbial diversity and a sustained increase in beneficial bacterial genera, including Holdemanella, Ruminococcus, and Faecalibacterium. In terms of β-diversity, the distance between the patient's gut microbiome and that of the donor decreased after FMT; greater reduction in distance to donor microbiota was associated with greater symptom improvement (Unweighted UniFrac distance, P < 0.05). Responders (IBS-SSS reduction > 50 points) exhibited lower baseline relative abundances of Roseburia and Subdoligranulum, and more profound microbiome shifts toward the donor profile after FMT.

CONCLUSIONS: FMT appears to be a potentially effective treatment for moderate to severe IBS, with significant symptom relief and gut microbiota changes. Lower baseline abundances of Roseburia and Subdoligranulum and greater shifts of gut microbiome profile toward donor microbiota after FMT may predict favorable FMT response. Long-term follow-up is on the way to assessing the durability of these effects.},
}

@article {pmid41077690,
year = {2025},
author = {Peng, Y and Lee, JH and Kim, CY and Lee, J},
title = {Halophyte-Derived Kushneria Strains Enhance Salt Tolerance and Rhizosphere Dynamics in Cabbage.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70234},
pmid = {41077690},
issn = {1365-3040},
support = {//This study was supported by the Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program (KGM5282533) and the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT, RS-2024-00352429)./ ; },
abstract = {Halophytic plants harbour salt-tolerant bacteria that enhance resilience to salinity. In this study, two highly halotolerant Kushneria isolates, K. konosiri (Kk) and K. marisflavi (Km), were obtained from the halophyte Suaeda maritima. Both strains tolerated up to 25% NaCl and promoted Arabidopsis thaliana growth under salt stress by producing indole-3-acetic acid, proline, and extracellular polysaccharides that mitigated osmotic stress. Inoculation with Kk or Km increased shoot and root biomass and reduced intracellular Na[+] and reactive oxygen species. Their agricultural potential was tested in cabbage (Brassica rapa), where both isolates alleviated salinity-induced growth inhibition. A combined inoculum (Kkm) showed enhanced efficacy, significantly increasing shoot biomass (1.26-fold vs. Kk; 1.23-fold vs. Km) and dry weight (1.19-fold vs. Kk; 1.13-fold vs. Km). Kkm treatment also improved the K[+]/Na[+] ratio and proline accumulation. Microbial profiling revealed that Kkm enriched Bacillus species in the rhizosphere and promoted greater biofilm formation than single strains. These findings demonstrate that Kushneria isolates function as salt-tolerant plant growth-promoting bacteria, enhancing ion homoeostasis, stress protection, and rhizosphere restructuring. This study highlights the potential of halophyte-derived microbial consortia to improve crop salt tolerance in agriculture.},
}

@article {pmid41077635,
year = {2025},
author = {Noel, S and Patel, SK and White, J and Verma, D and Menez, S and Raj, D and Parikh, C and Rabb, H and , },
title = {Metagenomic Profiling of Gut Microbiota in Kidney Precision Medicine Project Participants With CKD and AKI.},
journal = {Comprehensive Physiology},
volume = {15},
number = {5},
pages = {e70058},
doi = {10.1002/cph4.70058},
pmid = {41077635},
issn = {2040-4603},
support = {U01DK133081//KPMP/ ; U01DK133091//KPMP/ ; U01DK133092//KPMP/ ; U01DK133093//KPMP/ ; U01DK133095//KPMP/ ; U01DK133097//KPMP/ ; U01DK114866//KPMP/ ; U01DK114908//KPMP/ ; U01DK133090//KPMP/ ; U01DK133113//KPMP/ ; U01DK133766//KPMP/ ; U01DK133768//KPMP/ ; U01DK114907//KPMP/ ; U01DK114920//KPMP/ ; U01DK114923//KPMP/ ; U01DK114933//KPMP/ ; U24DK114886//KPMP/ ; UH3DK114926//KPMP/ ; UH3DK114861//KPMP/ ; UH3DK114915//KPMP/ ; UH3DK114937//KPMP/ ; R01DK104662/DK/NIDDK NIH HHS/United States ; R01DK123342/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Renal Insufficiency, Chronic/microbiology ; *Acute Kidney Injury/microbiology ; Metagenomics/methods ; Precision Medicine/methods ; Female ; Male ; Middle Aged ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: The gut microbiome plays an important role in human health and disease. Kidney Precision Medicine Project (KPMP) is a well-phenotyped, kidney biopsy-proven cohort of AKI and CKD patients. Comprehensive profiling of gut microbiota can uncover novel mechanistic, diagnostic, and therapeutic strategies for CKD and AKI patients.

METHODS: We performed metagenomic whole genome sequencing (mWGS; > 25 million reads) on KPMP stool samples. mWGS data of healthy controls from 4 published studies was used. Kraken2 and MetaPhlAn3 were used for taxonomic assignment, and HUMAnN3 for functional annotation.

RESULTS: Kraken2 analysis showed significantly higher abundance of Ruminococcus bicirculans in CKD (6.47) compared to AKI (1.82) and healthy individuals (2.42; p = 0.01). Furthermore, the abundance of Gordonibacter pamelaeae increased in CKD (0.30) compared to AKI (0.07; p = 0.05) and healthy individuals (0.03). The percent mean abundance of genus Chryseobacterium was slightly higher in CKD (0.07) compared to AKI (0.05; p = 0.05) but reduced compared to healthy individuals (0.20; p < 0.001). MetaPhlAn3 identified alterations in Gordonibacter, Bacteroides, and Faecalibacterium with a significant increase in Clostridium asparagiforme in AKI (11.68) compared to CKD (0.03; p = 0.06) and healthy (0.01; p = 0.001) individuals. Roseburia hominis, Roseburia intestinalis, Dorea longicatena, and Gemmiger formicilis were significantly reduced in AKI compared to CKD and healthy individuals. LDA/HUMAnN3 analysis showed a significant correlation between several metabolites and bacterial species in this KPMP population.

CONCLUSION: Kidney biopsy-proven CKD and AKI patients show a distinct gut microbiota profile compared to healthy individuals. This high-quality dataset is a valuable resource for developing microbiome-based diagnostics and therapies for CKD and AKI.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Renal Insufficiency, Chronic/microbiology
*Acute Kidney Injury/microbiology
Metagenomics/methods
Precision Medicine/methods
Female
Male
Middle Aged
Adult
Feces/microbiology

@article {pmid41077600,
year = {2025},
author = {Xiang, X and Liu, S and Wang, H and Wang, C and Zhou, W and Chen, H and Feng, Y and He, X and Xu, G and Zhao, Q and Li, T and Liu, D and Yin, Y and He, L},
title = {Glutathione contributes to alleviating hepatic injury via host-microbiome interaction and CAR-dependent pathway.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {41077600},
issn = {1869-1889},
abstract = {Glutathione (GSH) is a potent antioxidant regulating oxidative stress, but whether exogenous GSH supplementation mitigates stress injury through host-microbiome and liver interactions remains unclear. This study aimed to determine the regulatory mechanism of GSH using in vivo (28-day-old weaned piglets) and in vitro (alpha mouse liver 12 (AML12) cells) stress injury models. Thirty-five healthy weaned piglets (mean body weight (9.52±0.20) kg) were fed diets supplemented with 0.01%, 0.03%, or 0.06% GSH for 4 weeks, followed by being injected intraperitoneally with paraquat (PQ) on days 28, 30, and 32. AML12 cells exposed to tert-butyl hydroperoxide (tBHP) were used to evaluate related mechanisms, and CINPA1was used to inhibit constitutive androstane receptor (CAR) activity. Our results showed that PQ challenge induced hepatic morphological and functional impairments, accompanied by suppression of antioxidant capacity and immune function. Notably, exogenous GSH treatment significantly increased CD4[+]/CD8[+] T lymphocyte ratio, GSH, immunoglobulin A and interleukin-10 levels in serum, reduced the secretion and gene expression of pro-inflammatory factors to alleviate liver injury. Moreover, GSH treatment significantly promoted CAR nuclear translocation and regulated the expression of detoxification genes in response to liver inflammation. Additionally, GSH treatment improved the diversity and relative abundance of colonic probiotic bacteria such as UCG_002, Christensenellaceae_R_7_group, Prevotellaceae_NK3B31_group, Prevotella, Oscillospira, and unclassified_UCG_010. Furthermore, in vitro results showed that 3 mmol L[-1] GSH administration could increase the expression of CAR pathway and antioxidant related genes, and inhibit cellular ROS production in tBHP-induced AML12 cells. However, CAR inhibition by CINPA1 prevented GSH from alleviating tBHP-induced oxidative stress injury in AML12 cells. Our results indicate that exogenous GSH treatment alleviated liver injury in piglets through host-microbiome interaction and a CAR-dependent signaling pathway.},
}

@article {pmid41077555,
year = {2025},
author = {Bazany, K and Dhar, A and Otto, K and Jing, Y and Trivedi, P},
title = {Water Deficit Stress Alters the Microbial Community Assembly, Structure, and Sources in Corn and Sugar Beet.},
journal = {Environmental microbiology},
volume = {27},
number = {10},
pages = {e70186},
doi = {10.1111/1462-2920.70186},
pmid = {41077555},
issn = {1462-2920},
support = {COL007760A//Colorado Agriculture Experimental Station/ ; 2020-67013-31801//US Department of Agriculture, National Institute of Food and Agriculture/ ; },
mesh = {*Zea mays/microbiology ; *Beta vulgaris/microbiology ; *Microbiota ; Bacteria/classification/genetics/isolation & purification ; Plant Roots/microbiology ; Soil Microbiology ; Fungi/genetics/classification/isolation & purification ; Stress, Physiological ; Plant Leaves/microbiology ; Rhizosphere ; Water/metabolism ; Droughts ; Osmotic Pressure ; },
abstract = {Plant-associated microbes can improve plant fitness under abiotic stress conditions like drought by providing stress-relieving benefits to the host; however, there is limited research on the complex ways in which microbial communities assemble in plants under varying environmental conditions. In a field study, we examined the bacterial, fungal, and protist communities of the rhizospheres, roots, and leaves of corn and sugar beet grown under irrigated and water deficit conditions. We hypothesised that water deficit would alter the community composition and structure of plant microbiomes by shifting the relative importance of community assembly processes and the patterns of movement from microbial sources to sinks. Using amplicon sequencing and modelling approaches, we found that the water deficit treatment led to key differences in microbial community structure and that these changes were likely driven by differences in community assembly processes and microbial source communities. Altogether, these results indicate that plant microbiome communities are shaped by available microbial sources, host selection factors, microbial interactions, and stochastic forces, and that each of these factors is influenced by osmotic stress. These findings highlight the importance of applying ecological concepts to plant microbiome research in order to elucidate the impacts of environmental factors on microbial community assembly.},
}

*Zea mays/microbiology
*Beta vulgaris/microbiology
*Microbiota
Bacteria/classification/genetics/isolation & purification
Plant Roots/microbiology
Soil Microbiology
Fungi/genetics/classification/isolation & purification
Stress, Physiological
Plant Leaves/microbiology
Rhizosphere
Water/metabolism
Droughts
Osmotic Pressure

@article {pmid41077541,
year = {2025},
author = {Mazhar, Z and Bashir, H},
title = {Microbiome-genetic interplay in intraductal papillary mucinous neoplasms: A critical appraisal of emerging evidence.},
journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pan.2025.10.001},
pmid = {41077541},
issn = {1424-3911},
}

@article {pmid41077440,
year = {2025},
author = {Shogan, BD},
title = {The Microbiome and Surgery: A New Frontier.},
journal = {The Surgical clinics of North America},
volume = {105},
number = {5},
pages = {xi-xii},
doi = {10.1016/j.suc.2025.07.010},
pmid = {41077440},
issn = {1558-3171},
}

@article {pmid41077439,
year = {2025},
author = {Schenarts, PJ},
title = {Rethinking Everything: The Impact of the Microbiome.},
journal = {The Surgical clinics of North America},
volume = {105},
number = {5},
pages = {ix-x},
doi = {10.1016/j.suc.2025.07.002},
pmid = {41077439},
issn = {1558-3171},
}

@article {pmid41077438,
year = {2025},
author = {Alverdy, J},
title = {Preparing the Bowel for Surgery in the Era of Microbiome Sciences.},
journal = {The Surgical clinics of North America},
volume = {105},
number = {5},
pages = {965-974},
doi = {10.1016/j.suc.2025.06.004},
pmid = {41077438},
issn = {1558-3171},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Preoperative Care/methods ; *Cathartics/administration & dosage ; },
abstract = {The concept that a "one-size-fits-all" approach can be universally applied to all patients undergoing colorectal surgery is waning in enthusiasm especially given the variation in risk perception among patients and surgeons. In this review, we discuss the scientific rationale in generating a microbiome readout that will inform how to selectively eliminate problematic pathogens while preserving those beneficial bacterial strains that may enhance recovery from surgery. We also provide the reader with practical decision points with which to contemplate the need for a bowel preparation with your patient.},
}

Humans
*Gastrointestinal Microbiome
*Preoperative Care/methods
*Cathartics/administration & dosage

@article {pmid41077437,
year = {2025},
author = {Barat, B and Shogan, BD},
title = {The Microbiome's Role in Driving Anastomotic Leak and Cancer Recurrence Following Colorectal Surgery.},
journal = {The Surgical clinics of North America},
volume = {105},
number = {5},
pages = {953-964},
doi = {10.1016/j.suc.2025.06.003},
pmid = {41077437},
issn = {1558-3171},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Anastomotic Leak/microbiology/etiology/prevention & control ; *Neoplasm Recurrence, Local/microbiology/etiology ; *Colorectal Neoplasms/surgery/microbiology ; },
abstract = {The intestinal microbiota is composed of diverse microbial species that interact with the host, playing a vital role in immune regulation and maintaining homeostasis. Colorectal surgery has been shown to alter the gut microbiota, contributing to post-operative complications. Emerging evidence suggests that these microbial shifts influence the incidence of anastomotic leaks. In this review, we examine how the gut microbiota composition is altered in patients undergoing colon surgery, leading to anastomotic leaks, the role of collagenolytic bacteria in tissue breakdown at the anastomotic site, the connection between anastomotic leaks and cancer recurrence, and microbially based therapeutic approaches to prevent leaks.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Anastomotic Leak/microbiology/etiology/prevention & control
*Neoplasm Recurrence, Local/microbiology/etiology
*Colorectal Neoplasms/surgery/microbiology

@article {pmid40885534,
year = {2025},
author = {Gagnon, DJ and Burkholder, KM and Weissman, AJ and Riker, RR and Ryzhov, S and May, TL and DiPalazzo, J and deKay, JT and Knudsen, L and Moore, MW and Pozzessere, NA and Weatherbee, M and Kelly, M and Nigatu, AS and Sevigny, JL and Simpson, S and Thomas, WK and Callaway, CW and Geller, BJ and Sawyer, DB and Seder, DB},
title = {Ceftriaxone to Prevent Early-Onset Pneumonia in Comatose Patients Following Out-of-Hospital Cardiac Arrest: A Pilot Randomized Controlled Trial and Resistome Assessment (PROTECT).},
journal = {Chest},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chest.2025.08.007},
pmid = {40885534},
issn = {1931-3543},
support = {R01 HL173118/HL/NHLBI NIH HHS/United States ; },
abstract = {BACKGROUND: Antibiotic prophylaxis following out-of-hospital cardiac arrest (OHCA) reduces early-onset pneumonia. However, it has an uncertain impact on mortality and noninfectious outcomes, with ongoing concerns about the subsequent development of antibiotic resistance.

RESEARCH QUESTION: Does prophylactic ceftriaxone reduce the incidence of early-onset pneumonia without increasing the acquisition of antibiotic resistance genes after OHCA?

STUDY DESIGN AND METHODS: Comatose survivors of OHCA treated with targeted temperature management without a clinical diagnosis of pneumonia at admission were randomized to receive ceftriaxone 2 g or matching placebo every 12 hours for 3 days. The primary outcome was early-onset pneumonia occurring ≤ 4 days following intubation confirmed by masked adjudicators. Abundance of antibiotic resistance genes recovered from rectal swabs before-and-after study drug administration were analyzed with metagenomic sequencing.

RESULTS: A total of 411 participants were screened; 53 (13%) were randomized to treatment, and one participant withdrew, leaving 26 in each group in the final analysis. Early-onset pneumonia was diagnosed in 10 (38%) participants receiving ceftriaxone and 18 (69%) participants receiving placebo (risk ratio, 0.57; 95% CI, 0.21-1.001; P = .05). Open-label antibiotics were administered to 14 (54%) participants receiving ceftriaxone and 22 (85%) receiving placebo (risk ratio, 0.64; 95% CI, 0.43-0.94); most of the antibiotics were broad-spectrum agents (93% and 100%, respectively). After adjusting for differences in abundance of antibiotic resistance genes prior to study drug administration, participants randomized to receive ceftriaxone acquired significantly fewer antibiotic resistance genes to frequently used antibiotics in the ICU compared with those randomized to receive placebo (incidence risk ratio, 0.30; 95% CI, 0.13-0.70). Serious adverse drug effects were not reported in either treatment group.

INTERPRETATION: This trial was inconclusive regarding the impact of ceftriaxone prophylaxis on reducing the incidence of early-onset pneumonia following OHCA. However, ceftriaxone was associated with less frequent administration of open-label antibiotics and reduced acquisition of antibiotic resistance genes to frequently used antibiotics in the ICU.

CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov; No.: NCT04999592; URL: www.

CLINICALTRIALS: gov.},
}

@article {pmid41077436,
year = {2025},
author = {Dalal, SR},
title = {The Microbiome and Inflammatory Bowel Diseases.},
journal = {The Surgical clinics of North America},
volume = {105},
number = {5},
pages = {941-951},
doi = {10.1016/j.suc.2025.06.007},
pmid = {41077436},
issn = {1558-3171},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology/therapy/immunology ; Dysbiosis/microbiology/complications ; },
abstract = {Inflammatory Bowel Diseases (IBD) are associated with a less diverse, dysbiotic intestinal microbiome that leads to alterations in immune modifying microbial metabolites. Genetic and environmental risk factors for IBD likely exert their effects through alterations of the microbiome. Transfer of synthetic microbial communities and targeted dietary interventions hold some promise in altering underlying causes of IBD.},
}

Humans
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases/microbiology/therapy/immunology
Dysbiosis/microbiology/complications

@article {pmid41077435,
year = {2025},
author = {Galbraith, NJ and White, MG},
title = {Microbiome of Young and Later-Onset Colorectal Cancer.},
journal = {The Surgical clinics of North America},
volume = {105},
number = {5},
pages = {925-939},
doi = {10.1016/j.suc.2025.06.002},
pmid = {41077435},
issn = {1558-3171},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/epidemiology ; *Gastrointestinal Microbiome ; Age of Onset ; },
abstract = {Young-onset colorectal cancer (YOCRC) is increasingly common in the Western world. This has been attributed to changes in diet, lifestyle, and other environmental factors which all influence the gut microbiome. This review summarizes a small number of studies that have demonstrated differences in the microbiome of YOCRC, assessed in the stool and tumoral compartment. These populations are distinct from LOCRC and are prognostically important. Further research may reveal their role in the pathogenesis of this epidemic, and microbiological interventions can alter or augment existing treatment responses.},
}

Humans
*Colorectal Neoplasms/microbiology/epidemiology
*Gastrointestinal Microbiome
Age of Onset