@article {pmid40841806,
year = {2025},
author = {Morsy, Y and Shafie, NS and , and Amer, M},
title = {Integrative analysis of gut microbiota and metabolic pathways reveals key microbial and metabolomic alterations in diabetes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30686},
pmid = {40841806},
issn = {2045-2322},
abstract = {Type 2 diabetes mellitus (T2DM) is increasingly recognized as a condition influenced by gut microbiota composition and associated metabolic pathways. This study investigated the differences in gut microbial diversity, composition, and metabolomic profiles between diabetic and control individuals. Using 16 S rRNA gene sequencing and metabolomic analyses, we observed significantly higher microbial diversity and evenness in the diabetic group, with distinct clustering patterns as revealed by Principal Coordinate Analysis (PCoA). Taxonomic profiling demonstrated an increased relative abundance of Bacteroidaceae and Lachnospiraceae in the diabetic group, while Streptococcaceae was more prevalent in the control group. LEfSe analysis identified key microbial taxa such as Bacteroides, Blautia, and Lachnospiraceae_FCS020_group enriched in diabetic individuals, suggesting a role in metabolic dysregulation. Metabolomic pathway enrichment analysis revealed significant differences in pathways related to fatty acid metabolism, glucose homeostasis, bile acid metabolism, and amino acid biosynthesis in diabetic individuals. Enriching fatty acid elongation and β-oxidation pathways, alongside disrupted glucose metabolism, indicate profound metabolic changes associated with diabetes. Bile acid metabolism and branched-chain amino acid (BCAA) pathways were also elevated, linking these metabolites to the observed gut microbiota shifts. These findings suggest that diabetes is associated with significant alterations in the gut microbiome's composition and function, leading to disruptions in critical metabolic pathways. This study provides insights into potential microbial biomarkers and therapeutic targets for improving metabolic health in diabetic patients.},
}

@article {pmid40841760,
year = {2025},
author = {Copeland, DC and Mott, BM and Kortenkamp, OL and Erickson, RJ and Allen, NO and Anderson, KE},
title = {Image-based honey bee larval viral and bacterial diagnosis using machine learning.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30717},
pmid = {40841760},
issn = {2045-2322},
support = {2021-67013-33555//AFRI-NIFA/ ; 2021-67013-33555//AFRI-NIFA/ ; 2021-67013-33555//AFRI-NIFA/ ; 2021-67013-33555//AFRI-NIFA/ ; 2021-67013-33555//AFRI-NIFA/ ; 2021-67013-33555//AFRI-NIFA/ ; 2022-21000-021-00D//Agricultural Research Service/ ; 2022-21000-021-00D//Agricultural Research Service/ ; 2022-21000-021-00D//Agricultural Research Service/ ; 2022-21000-021-00D//Agricultural Research Service/ ; 2022-21000-021-00D//Agricultural Research Service/ ; 2022-21000-021-00D//Agricultural Research Service/ ; },
abstract = {Honey bees are essential pollinators of ecosystems and agriculture worldwide. With an estimated 50-80% of crops pollinated by honey bees, they generate approximately $20 billion annually in market value in the U.S. alone. However, commercial beekeepers often face an uphill battle, losing anywhere from 40 to 90% of their hives yearly, often by brood diseases caused by bacterial, viral, and fungal pathogens. Accurate diagnosis of brood diseases, especially distinguishing European Foulbrood (EFB) from viral infections with a superficial resemblance to EFB (EFB-like disease), remains challenging. Incorrect diagnoses often lead to prophylactic antibiotic treatment across entire apiaries, exacerbating antibiotic resistance, disrupting native gut microbiota, and increasing susceptibility to opportunistic pathogens. Correct field diagnosis of brood disease is challenging and requires years of experience to identify and differentiate various disease states according to subtle differences in larval symptomology. To explore the feasibility of an image-based AI diagnosis tool, we collaborated with apiary inspectors and researchers to generate a dataset of 2,759 honey bee larvae images from Michigan apiaries, molecularly verified through 16 S rRNA microbiome sequencing and qPCR viral screening. Our dataset included EFB cases and viral infections (ABPV, DWVA, and DWVB), which were augmented to 8,430 and 8,124 images, respectively. We leveraged transfer learning techniques, fine-tuning deep convolutional neural networks (ResNet-50v2, ResNet-101v2, InceptionResNet-v2) pre-trained on ImageNet to discriminate between EFB and viral infections. Our proof-of-concept models achieved 73-88% accuracy on the training/validation sets. When tested on an independent dataset from Illinois containing additional viral pathogens not present in training data, the models showed higher accuracy for EFB (72-88%) than viral infections (28-68%), highlighting both the promise and current limitations of this approach. Implementing AI-based diagnostic tools can reduce unnecessary antibiotic treatments and help maintain the microbiome integrity critical to colony health. However, expanding training datasets to include all major pathogens, healthy larvae, and diverse geographic regions will be essential for developing field-ready diagnostic tools.},
}

@article {pmid40841691,
year = {2025},
author = {Yau, PT and Taketani, RG and Bonnin, JM and Stewart, H and Thompson, CMA and Clark, IM and Mauchline, TH and Malone, JG and Ryan, MJ and Jones, S and Holden, N},
title = {Introducing the UK Crop Microbiome Cryobank data resource, AgMicrobiomeBase, with case studies and methods on metabarcoding analyses.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {108},
pmid = {40841691},
issn = {2524-6372},
support = {BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {BACKGROUND: Here, we describe AgMicrobiomeBase as an output of the UK Crop Microbiome Cryobank (UKCMCB) project, including details of the underlying meta-barcode sequence-based methods and three microbiome analysis case studies. The UKCMCB links genomic datasets and associated soil metadata with a cryobank collection of samples, for six economically significant crops: fava bean (Vicia faba), oil seed rape (Brassica napus), spring barley (Hordeum vulgare), spring oats (Avena sativa), spring wheat (Triticum aestivum) and sugar beet (Beta vulgaris). The crops were grown in nine agricultural soils from the UK, representing three major soil texture classes. The UKCMCB is a scalable sequence-based data catalogue linked to a cryo-preserved sample collection.

RESULTS: The focus of this paper is the amplicon sequencing, associated bioinformatics workflows, and development of the project data catalogue. Short-read amplicon sequencing (16 S rRNA gene and ITS region) was implemented to describe the rhizosphere and bulk soil communities, for the multiple crop-soil combinations. Three case studies illustrate how different biological questions in phytobiome research can be addressed using this data resource. The three case studies illustrate how to (1) determine the impact of soil texture and location on microbiome composition, (2) determine a core microbiome for a single crop across different soil types, and (3) analyse a single genus, Fusarium within a single crop microbiome. The UKCMCB data catalogue AgMicroBiomeBase (https://agmicrobiomebase.org/data) links the sequence-based data with soil metadata and to cryopreserved samples.

CONCLUSIONS: The UKCMCB provides baseline data and resources to enable researchers to assess the impact of soil type, location and crop type variables on crop soil microbiomes. The resource can be used to address biological questions and cross-study comparisons. Development of the UKCMCB will continue with the addition of metagenome and bacterial isolate genomic sequence data and has the potential to integrate additional data types including microbial phenotypes and synthetic microbial communities.},
}

@article {pmid40841660,
year = {2025},
author = {Bayraktaroglu, I and Ortí-Casañ, N and Van Dam, D and De Deyn, PP and Eisel, ULM},
title = {Systemic inflammation as a central player in the initiation and development of Alzheimer's disease.},
journal = {Immunity & ageing : I & A},
volume = {22},
number = {1},
pages = {33},
pmid = {40841660},
issn = {1742-4933},
support = {WE.03-2021-05//Alzheimer Nederland/ ; WE.03-2021-05//Alzheimer Nederland/ ; },
abstract = {Alzheimer's disease (AD) is an age-related neurodegenerative disorder and the most common cause of dementia. While the amyloid cascade hypothesis has long dominated AD research, emerging evidence suggests that neuroinflammation may play a more central role in disease onset and progression. Increasingly, AD is recognized as a multifactorial disorder influenced by systemic inflammation and immune dysregulation, shifting focus toward peripheral immune mechanisms as potential contributors to neurodegeneration. This review explores the hypothesis that inflammaging, the age-related increase in pro-inflammatory mediators, combined with lifelong exposure to infections, injuries, metabolic changes, and chronic diseases, among others, may prime the immune system, amplifying neuroinflammation and influencing the progression and exacerbation of AD pathology. To this end, we examined how systemic immune disturbances, including chronic pain, post-operative cognitive dysfunction, viral and bacterial infections, gut microbiome dysregulation, and cardiovascular disease, may act as risk factors for AD. Overall, evidence suggests that modulating peripheral inflammation, accompanied by early diagnosis, could significantly reduce the risk of developing AD. Furthermore, we highlight key immune signaling pathways involved in both central and peripheral immune responses, such as the NLRP3 inflammasome and TREM2, which represent promising therapeutic targets for modulating inflammation while preserving protective immune functions. Strategies aimed at reducing systemic inflammation, identifying early biomarkers, and intervening before significant neurodegeneration occurs may provide novel approaches to delay or prevent AD onset. In conclusion, this review underscores the crucial role of systemic inflammation in AD pathogenesis and progression. By targeting peripheral immune dysfunction, we may advance our understanding of AD mechanisms and develop more effective therapeutic interventions to mitigate disease risk and progression.},
}

@article {pmid40841578,
year = {2025},
author = {Bassu, S and Eichelsbacher, S and Giunta, F and Motzo, R and Dawid, C and Gastl, M and Schloter, M and Scherf, KA and Hör, S and De Souza, YPA and Schulz, S and Stark, TD and Mohler, V and Asseng, S},
title = {Positive impact of hydroponics and artificial light on yield and quality of wheat.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30768},
pmid = {40841578},
issn = {2045-2322},
mesh = {*Triticum/growth & development/microbiology/metabolism ; *Hydroponics/methods ; Glutens/metabolism ; *Light ; Microbiota ; Gliadin/metabolism ; Soil/chemistry ; Sunlight ; Crops, Agricultural/growth & development ; Agriculture/methods ; },
abstract = {Growing crops in controlled-environment indoor farming systems offers new ways of producing high-yield, pesticide-free, environmental-friendly food. However, it replaces soil with hydroponics and the sun with LED lights. Compared with the field, wheat grown indoors showed a much higher yield potential and bread-making quality parameters. Many mineral concentrations were higher due to the unrestricted water supply and nutrients in hydroponics. However, concentrations declined with increasing yields. The microbiome richness inside the grains of wheat grown without soil indoors was still within the range of wheat grown in the field. However, taxa were different among cultivars and treatments. There were differences in the presence of undefined secondary metabolites between indoor and outdoor wheat and across the indoor experiments. Regardless of the growing environment, immunoreactive proteins were present. Indoor-grown wheat had a higher share of ω5-gliadins but lower shares of γ-gliadins and low-molecular-weight glutenin subunits, which may affect the gluten protein immunoreactive potential for individuals with wheat-related disorders (allergy and celiac disease). Growing wheat without soil and sunlight indoors can produce high-yielding, high-quality grains. However, the food quality and health aspects associated with gluten proteins might deteriorate with a further, theoretically possible, yield increase in a controlled growing environment.},
}

*Triticum/growth & development/microbiology/metabolism
*Hydroponics/methods
Glutens/metabolism
*Light
Microbiota
Gliadin/metabolism
Soil/chemistry
Sunlight
Crops, Agricultural/growth & development
Agriculture/methods

@article {pmid40841555,
year = {2025},
author = {Wang, T and Zhang, P and Anantharaman, K and Wang, H and Zhang, H and Zhang, M and Xu, J},
title = {Metagenomic analysis reveals how multiple stressors disrupt virus-host interactions in multi-trophic freshwater mesocosms.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7806},
pmid = {40841555},
issn = {2041-1723},
support = {42377469//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32001151//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Metagenomics/methods ; Microbiota/genetics ; Lakes/microbiology/virology ; *Fresh Water/microbiology/virology ; Ecosystem ; Metagenome ; *Viruses/genetics/classification ; *Bacteria/genetics/virology ; Pesticides ; *Host Microbial Interactions/genetics ; Stress, Physiological ; Climate Change ; },
abstract = {Virus-host interactions are vital to microbiome ecology and evolution, yet their responses to environmental stressors under global change remain poorly understood. We perform a 10-month outdoor mesocosm experiment simulating multi-trophic freshwater shallow lake ecosystems. Using a fully factorial design comprising eight treatments with six replicates each, we assess the individual and combined effects of climate warming, nutrient loading, and pesticide loading on DNA viral communities and their interactions with microbial hosts. Metagenomic sequencing recovers 12,359 viral OTUs and 1628 unique prokaryotic metagenome-assembled genomes. Our analysis shows that combined nutrient and pesticide loading causes significant disruption by synergistically reducing viral alpha diversity while altering beta diversity and predator-prey linkages. Stressors lead to the simplification of virus-bacteria cross-kingdom networks, with nutrient-pesticide combinations exerting the strongest influence, although warming impacts diminish in the presence of pesticides. Stressor-driven changes also affect the abundance and composition of viral auxiliary metabolic genes, leading to complex shifts in virus-mediated metabolic pathways under multiple stress conditions. These findings underscore the importance of understanding the regulatory role of viruses on microbial communities to effectively address the challenges posed by global change.},
}

*Metagenomics/methods
Microbiota/genetics
Lakes/microbiology/virology
*Fresh Water/microbiology/virology
Ecosystem
Metagenome
*Viruses/genetics/classification
*Bacteria/genetics/virology
Pesticides
*Host Microbial Interactions/genetics
Stress, Physiological
Climate Change

@article {pmid40841315,
year = {2025},
author = {Ho, E and Wong, CP and Bouranis, JA and Shannon, J and Zhang, Z},
title = {Cruciferous Vegetables, Bioactive Metabolites, and Microbiome for Breast Cancer Prevention.},
journal = {Annual review of nutrition},
volume = {45},
number = {1},
pages = {171-195},
doi = {10.1146/annurev-nutr-062222-024321},
pmid = {40841315},
issn = {1545-4312},
mesh = {Humans ; *Breast Neoplasms/prevention & control/microbiology ; Female ; *Vegetables/chemistry ; Isothiocyanates/pharmacology ; Sulfoxides ; *Gastrointestinal Microbiome ; Phytochemicals/pharmacology ; Indoles/pharmacology ; *Brassicaceae ; Anticarcinogenic Agents ; Glucosinolates/metabolism ; Animals ; Microbiota ; },
abstract = {Breast cancer is a heterogeneous disease with varying subtypes, prognoses, and treatment responses. Cruciferous vegetables have shown promise in reducing breast cancer risk. This review discusses (a) the efficacy of sulforaphane (SFN) and indole-3-carbinol (I3C)/3,3'-diindolylmethane (DIM) on breast cancer risk, prognosis, and treatment outcomes in recent human studies through 2024; (b) preclinical studies (2018-2024) that evaluate the efficacy and synergism of SFN, DIM, and other phytochemicals with conventional breast cancer treatments as promising combination therapy strategies for validation in future clinical trials; and (c) the role of the microbiome in breast cancer and the interaction between interindividual variations in gut microbiome and glucosinolate metabolism that could modify the benefits of cruciferous vegetable consumption and breast cancer treatment efficacy. Integrating cruciferous vegetables and their bioactive compounds in light of an individual's microbiome profile as a complementary approach alongside standard treatments is a promising strategy in breast cancer care.},
}

Humans
*Breast Neoplasms/prevention & control/microbiology
Female
*Vegetables/chemistry
Isothiocyanates/pharmacology
Sulfoxides
*Gastrointestinal Microbiome
Phytochemicals/pharmacology
Indoles/pharmacology
*Brassicaceae
Anticarcinogenic Agents
Glucosinolates/metabolism
Animals
Microbiota

@article {pmid40841147,
year = {2025},
author = {Richardson, H and Alferes De Lima Headley, D and Clarke, C and Veluchamy, A and Rauchhaus, P and Pollock, J and Pembridge, T and Cassidy, D and Keir, HR and Finch, S and Hussain, F and Band, M and Smith, A and Patel, M and Paracha, M and Choudhury, G and Dhasmana, D and Chaudhuri, R and Short, PM and Chalmers, JD},
title = {The effect of different inhaled corticosteroid and long-acting bronchodilator combinations on the airway microbiome in patients with severe chronic obstructive pulmonary disease: A randomized trial (MUSIC).},
journal = {The European respiratory journal},
volume = {},
number = {},
pages = {},
doi = {10.1183/13993003.00287-2025},
pmid = {40841147},
issn = {1399-3003},
abstract = {INTRODUCTION: The microbiome is associated with exacerbation risk, quality of life and mortality in COPD. Inhaled corticosteroid (ICS) treatment has been reported to alter the microbiome through modulating host defence. How ICS alters the microbiome and whether effects are equal between different ICS preparations is debated. The aim of the MUSIC trial was to investigate whether commonly used ICS therapies have different effects on the airway microbiome in COPD.

METHODS: Multicentre randomized controlled trial. After a four-week washout period during which they withdrew from ICS, patients with COPD (FEV1 <50% predicted at baseline and/or a history of 2 or more exacerbations per year) were randomized to one of 4 treatments (budesonide/formoterol 400/12 mcg, fluticasone/salmeterol 500 mcg, fluticasone/salmeterol 250 mcg or aclidinium/formoterol 340/12 mcg, twice daily). Patients were followed-up for 3 months with monthly induced sputum, oropharyngeal and nasopharyngeal swabs for bacterial load and 16S rRNA sequencing to characterise the microbiome. Inflammatory markers were measured in sputum and blood. The primary outcome was bacterial load in oropharyngeal swabs comparing budesonide/formoterol versus fluticasone/salmeterol 500, with sputum bacterial load the key secondary endpoint.

RESULTS: 122 participants started the washout period. ICS withdrawal was poorly tolerated, 61 participants withdrew before randomization with 45 experiencing an exacerbation. 61 patients were randomized. No statistically significant differences were observed for the primary comparison of budesonide/formoterol versus fluticasone/salmeterol 500 in oropharyngeal bacterial load. There was however a significant increase in sputum bacterial load with fluticasone/salmeterol 500 compared to budesonide/formoterol by month 3. This difference was not seen with fluticasone/salmeterol 250. No significant differences in microbiome alpha diversity were observed over time. Adverse events were similar between the groups.

CONCLUSION: Fluticasone/salmeterol 500 increased sputum but not upper airway bacterial loads. ICS withdrawal was poorly tolerated in severe COPD.},
}

@article {pmid40841038,
year = {2025},
author = {Tang, Z and Zhang, Y and Shangguan, H and Xie, A and Xu, X and Jiang, Y and Breed, MF and Sun, X},
title = {Urban organic manure application enhances antibiotic resistance gene diversity and potential human pathogen abundance in invasive giant African snails.},
journal = {Journal of environmental sciences (China)},
volume = {158},
number = {},
pages = {610-620},
doi = {10.1016/j.jes.2025.02.028},
pmid = {40841038},
issn = {1001-0742},
mesh = {Animals ; *Manure ; *Drug Resistance, Microbial/genetics ; *Snails/microbiology ; Humans ; Introduced Species ; Gastrointestinal Microbiome ; Soil Microbiology ; Environmental Monitoring ; RNA, Ribosomal, 16S ; Feces/microbiology ; },
abstract = {The giant African snail (Achatina fulica) is an invasive species served as potential vectors for antibiotic resistance genes (ARGs) and potential human bacterial pathogens. Currently, urban green spaces receive extensive organic manure additions as part of their management, may intensify the biological contamination potential of these snail vectors, thereby increasing the risk of biological pollution in green spaces. However, the specific impacts of this practice on the microbial ecology of these invasive species remain poorly understood. Here, we investigated the effects of organic manure application on the gut microbiome of giant African snails, focusing on ARGs, bacterial community structure, and potential human bacterial pathogens. Microcosm experiments compared snail gut microbiomes in different treatments (Soil: soil samples collected after manure amendment, before any snail exposure. Feces: fecal samples collected from snails that lived on manure-amended soil. Control: fecal samples collected from snails that lived on unamended soil) using 16S rRNA high-throughput sequencing and metagenomic analysis. Our results show that manure application significantly altered gut bacterial community structure and increased ARG diversity by enriching specific high-risk ARGs (such as sul1 and sul2 in the Feces group increased by 2.89 and 2.43 times, respectively, compared to the Control group), and the introduction of eight novel ARG subtypes, despite decreasing overall ARG abundance. Moreover, the relative abundance of potential human pathogens, particularly Pseudomonadaceae, was greatly increased by manure application. These findings reveal that organic manure application in urban green spaces can potentially enhances their role as reservoirs and vectors of ARGs and human pathogens.},
}

Animals
*Manure
*Drug Resistance, Microbial/genetics
*Snails/microbiology
Humans
Introduced Species
Gastrointestinal Microbiome
Soil Microbiology
Environmental Monitoring
RNA, Ribosomal, 16S
Feces/microbiology

@article {pmid40841030,
year = {2025},
author = {Nie, E and He, P and Zhang, H and Lü, F},
title = {Genome-centric metagenomic analysis unveils the influence of temperature on the microbiome in anaerobic digestion.},
journal = {Journal of environmental sciences (China)},
volume = {158},
number = {},
pages = {516-526},
doi = {10.1016/j.jes.2024.10.007},
pmid = {40841030},
issn = {1001-0742},
mesh = {Anaerobiosis ; *Microbiota ; Metagenomics ; *Temperature ; *Metagenome ; Archaea/genetics ; Bacteria/genetics ; },
abstract = {Temperature plays a crucial role in shaping microbial ecosystems during anaerobic digestion. However, the specific microbial communities and their functions across a wide temperature range still remain elusive. This study employed a genome-centric metagenomic approach to explore microbial metabolic pathways and synergistic networks at temperatures of 35, 44, 53, 55, and 65 °C. A total of 84 metagenome assembled genomes (MAGs) were assembled, with over 65 % of these MAGs corresponding to novel bacterial and archaeal species (including Firmicutes, Chloroflexota, Bacteroidia and Methanobacteriota), greatly enhancing our current comprehension anaerobic digestion process. Notably, functional annotation identified that 44_bin.2 (Methanothrix_A sp. 001602645) harbors enzymes associated with hydrogenotrophic metabolism. Additionally, this microorganism exhibited diverse metabolic capabilities at 44 °C, a temperature commonly employed in industrial practice yet less explored in bench studies. Consequently, it implies a promising potential for conducting anaerobic digestion at a moderate thermophilic temperature, as opposed to the conventional mesophilic range. The microorganism exhibited a variety of metabolic capabilities at 44 °C, a temperature frequently employed in industrial applications but underexplored in laboratory investigations. The findings suggest that anaerobic digestion carried out at moderate thermophilic temperatures may have a higher potential for methane production.},
}

Anaerobiosis
*Microbiota
Metagenomics
*Temperature
*Metagenome
Archaea/genetics
Bacteria/genetics

@article {pmid40840836,
year = {2025},
author = {Young, ME and Khanna, V and Metcalfe, M and Rameshkumar, N and Harington, S and Li, LH and Doost, JS and Taegtmeyer, H and Martino, TA},
title = {A brief history of circadian time in the heart.},
journal = {Journal of molecular and cellular cardiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.yjmcc.2025.08.005},
pmid = {40840836},
issn = {1095-8584},
abstract = {This review tracks the discovery of circadian biology in cardiovascular science, starting with early clinical observations of daily changes in heart rate, blood pressure, and cardiovascular events. These patterns suggested that time of day matters, but it was not until the past two decades that the mechanisms and knowledge translation of these rhythms were uncovered. We describe the heart's intrinsic circadian properties and importantly how this leads to regulation of cardiac gene and protein expression, neuroendocrine and vascular rhythms, metabolism, cellular electrophysiology, and cell signaling pathways. Next, we explore emerging themes, including the impact of circadian timing on ischemic injury, cardiac aging, and trends in circadian desynchrony, sex, and interorgan crosstalk. Building on these discoveries, circadian medicine is beginning to reshape clinical care including timing of surgery, chronotherapies, biomarkers, ICU design, novel molecular drugs targeting the circadian clock, the role of the microbiome and time restricted eating, the new field of rest, and the concept of One Health and applications to veterinary medicine. Looking ahead we address new frontiers such as epigenetics, gene editing, and spaceflight. Together, these advances offer a roadmap for how circadian rhythms can be harnessed to improve cardiovascular health and disease outcomes, supporting longer and healthier lives.},
}

@article {pmid40840821,
year = {2025},
author = {Shah, AH and Armstrong, HK and Mittal, I and Reimer, A and Kunutsor, SK and Ducas, RA and Alizadeh, K and Tam, JW and Ravandi, A and Dhingra, S},
title = {IMpact of therapY using coleSevelam treatment reducing bile acids in patients with fonTan cIrCulation (MYSTIC): Rationale and Study Design.},
journal = {American heart journal},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ahj.2025.08.011},
pmid = {40840821},
issn = {1097-6744},
abstract = {RATIONALE: Patients with a Fontan circulation suffer from progressive multiorgan dysfunction, yet central biochemical drivers remain poorly defined. Our recent work exploring metabolomic analyses have identified markedly elevated circulating bile acids (BAs) in adult Fontan patients compared with healthy controls. Elevated BAs, especially secondary and hydrophobic ones produced by the gut microbiome were found to correlate with worse exercise capacity, greater frailty, and impaired hemodynamics.

PRIMARY HYPOTHESIS: Bile acid accumulation may contribute to Fontan pathophysiology. Colesevelam, a non-absorbed bile acid sequestrant, offers a potential targeted therapy to reduce BA levels and interrupt this disease pathway.

DESIGN: The MYSTIC trial is a prospective, randomized, double-blind, placebo-controlled cross-over pilot study in 25 adult Fontan patients (with 25 age- and sex-matched healthy controls for baseline comparisons) to evaluate the safety, tolerability, and efficacy of colesevelam in lowering plasma BA levels. Primary outcomes include safety/tolerability and change in total plasma BA levels. Secondary outcomes include changes in non-invasive hemodynamics, gut microbiome composition, fecal bile acid excretion, and biochemical profiles.

SITES: Single center. Estimated enrollment: 25 patients and 25 healthy subjects. Enrollment dates: September 2025 - August 2027 Trial Registration: NCT06197763 This manuscript describes the rationale and design of the MYSTIC study, which to our knowledge is the first interventional trial targeting a Fontan-specific metabolic derangement. The results will inform the feasibility of BA sequestration therapy in Fontan patients and guide future larger studies aimed at improving outcomes in this growing high-risk population.},
}

@article {pmid40840819,
year = {2025},
author = {Chao, NN and Zhang, L},
title = {Elucidating cellular origins and TME dynamic evolution in NSCLC through multi-omics technologies.},
journal = {Biochimica et biophysica acta. Reviews on cancer},
volume = {},
number = {},
pages = {189425},
doi = {10.1016/j.bbcan.2025.189425},
pmid = {40840819},
issn = {1879-2561},
abstract = {Non-small cell lung cancer (NSCLC) is a leading cause of cancer mortality. Despite progress in targeted therapies and immunotherapy, resistance driven by tumor heterogeneity and dynamic tumor microenvironment (TME) remodeling persists. Multi-omics (single-cell/spatial transcriptomics) reveals lung adenocarcinoma (LUAD) origins in alveolar type 2 (AT2) cells and lineage plasticity via SOX2/WNT/YAP pathways driving aggressive subtypes. The TME, a dynamic ecosystem of immune cells and fibroblasts, evolves through immune-editing phases and cancer-associated fibroblasts (CAF)/tumor-associated macrophage (TAM) crosstalk to foster immunosuppression. Multi-omics identifies key immune subsets (CXCL13[+]CD8[+]T cells, M1/M2 macrophages) and antigen-presenting cancer-associated fibroblasts (apCAFs) as therapeutic targets. Emerging strategies targeting lineage plasticity, TME reprogramming, and microbiome modulation may overcome immune checkpoint blockade (ICB)/tyrosine kinase inhibitor (TKI) resistance. Challenges in spatiotemporal heterogeneity resolution call for artificial intelligence (AI)-driven TME modeling to guide precision interventions. This review highlights multi-omics in bridging NSCLC evolution with clinical translation for personalized therapies.},
}

@article {pmid40840698,
year = {2025},
author = {Muñoz-Laiton, P and Hernandez-Valencia, JC and Isaza, JP and Correa, MM},
title = {Metatranscriptomic profiling of the bacterial and fungal microbiota of field-collected Anopheles darlingi from Colombia: Community composition and functional insights.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107795},
doi = {10.1016/j.actatropica.2025.107795},
pmid = {40840698},
issn = {1873-6254},
abstract = {Mosquitoes harbor diverse microorganisms that can influence host biology. While microbiota research in Anopheles has primarily focused on the metabarcoding approach, knowledge regarding the transcriptionally active microbiota and its functional roles in the host remains limited. This study aimed to characterize the transcriptionally active bacterial and fungal microbiota in field-collected Anopheles darlingi, a primary malaria vector in the Neotropics, and in addition, to explore its functional profile. Mosquitoes were collected in malaria-endemic regions of Colombia. Total RNA was extracted from pooled specimens to prepare cDNA libraries and sequenced by Illumina NovaSeq 6000. Results on microbiota composition showed predominance of bacterial (65%) over fungal reads (35%). The most abundant bacterial families included Enterobacteriaceae, Pseudomonadaceae, Acetobacteraceae and Moraxellaceae; the dominant genera were Halopseudomonas, Acinetobacter, Klebsiella, Escherichia and Asaia. In the fungal microbiota composition predominated Aspergillaceae and Hypoxylaceae, primarily represented by Aspergillus and Hypoxylon. Functional analysis showed transcripts encoding an MFS family transporter - an arabinose efflux permease, an ABC-type branched-chain amino acid transport system, diaminopimelate decarboxylase and O-succinylbenzoic acid-CoA ligase (MenE). These transcripts were associated with functional categories related to carbohydrate transport and metabolism, as well as the transport and biosynthesis of essential amino acids and vitamins. These findings offer valuable insights into the microbiota-mosquito dynamic and establish a foundation for further research into the role of microbiota in mosquito biology.},
}

@article {pmid40840675,
year = {2025},
author = {Choi, J and Jo, JY and Lee, J and Son, JE and Kim, SY and Lee, HE and Seong, YJ and Heo, K and Kim, Y and Park, MS and Byun, S},
title = {Lactobacillus salivarius HHuMin-U attenuates vulvovaginal candidiasis via vaginal epithelial immune enhancement mediated by NF-κB activation.},
journal = {New biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.nbt.2025.08.003},
pmid = {40840675},
issn = {1876-4347},
abstract = {Vulvovaginal candidiasis (VVC), primarily caused by Candida albicans infection, is one of the most common diseases among women and leads to various symptoms that adversely impact quality of life. VVC is conventionally treated with antifungal agents, but the high recurrence rates and the risk of inducing vaginal microbiome dysbiosis pose major concerns in effective treatment. Probiotics with immune-enhancing properties can be an effective strategy by strengthening mucosal immunity and reducing susceptibility to infection. Herein, this study investigates the therapeutic potential of Lactobacillus salivarius HHuMin-U (HMU) as a probiotic agent for treating VVC. Phenotype screening identified HMU as a top candidate with antifungal activity against C. albicans. HMU significantly upregulated immunomodulatory factors such as antimicrobial peptides, cytokines, and chemokines in human vaginal epithelial cells, which can strengthen the antifungal immune system. In an animal study, administration of HMU in a mouse VVC model significantly decreased the fungal burden and protected the mice from vaginal infection. Additionally, cellular infection models revealed that HMU reduced fungal adhesion and the cytolytic activity of C. albicans, while conditioned media from HMU-treated epithelial cells inhibited fungal growth. Transcriptomic analysis revealed that HMU treatment enriched gene sets related to epithelial barrier integrity, innate immune responses mediated by epithelial cells, and immune cell regulation. Mechanistically, the NF-κB pathway emerged as a key mediator of these responses. Collectively, HMU inhibits VVC by enhancing epithelial immunity and thus could be considered as a probiotic agent for the prevention and treatment of VVC.},
}

@article {pmid40840669,
year = {2025},
author = {Menikdiwela, KR and Lenis, M and Storch, J},
title = {The Use of Organoid Cultures in Advancing Nutrition Research.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {100489},
doi = {10.1016/j.advnut.2025.100489},
pmid = {40840669},
issn = {2156-5376},
abstract = {The importance of food and nutrients in human health and chronic disease progression has been appreciated for centuries. Crucial developments enabling understanding of the complex interactions between dietary patterns and health were made in the 20th century, owing in part to improvements in in vitro cell culture methods. Such two-dimensional (2D) cell lines remain extensively used to study the molecular mechanisms through which nutrients regulate cellular homeostasis. Nevertheless, they do not recapitulate the in vivo environment, and the complexity associated with tissues and organs, which invariably contain multiple cell types. Thus, findings from 2D cell cultures may not be directly applicable or representative of the in vivo situation. By contrast, organoids are three-dimensional (3D) tissue structures capable of mimicking structural, functional, and multicellular features of an intact organ, and are becoming increasingly used to carry out in-depth cell and molecular level studies. In particular, the use of intestinal organoids in food and nutrition research is expanding in recent years due to the greater suitability of organoids relative to 2D cultures for investigating nutrient uptake, transport, metabolism, and host-microbiome interactions. In the present review we summarize the emerging role and contributions of organoids, with emphasis on intestinal organoids, in nutrition research and intestinal health. We further highlight current limitations of organoid cultures and discuss potential future strategies to improve the use of organoids as a preferred model for investigations in the nutritional sciences.},
}

@article {pmid40840600,
year = {2025},
author = {Minaei, E and Joyce, P and Wade, SJ and Brownlee, C and Penney, C and Ranson, M and Aghmesheh, M and Sluyter, R and Vine-Perrow, KL},
title = {Gut microbial diversity is preserved through localised chemo-immunotherapy delivery in a KPC mouse model of pancreatic cancer.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {114143},
doi = {10.1016/j.jconrel.2025.114143},
pmid = {40840600},
issn = {1873-4995},
abstract = {Systemic chemotherapy and immunotherapy can disrupt gut microbial homeostasis, contributing to inflammation, treatment-related toxicity, and diminished anti-tumour immunity in pancreatic ductal adenocarcinoma (PDAC). Here, we evaluated whether localised delivery of chemo-immunotherapy via biodegradable implants could mitigate these adverse effects and preserve gut microbiota integrity. Using a syngeneic KPC mouse model of PDAC, we compared systemic versus implant-based delivery of gemcitabine/nab-paclitaxel and anti-CD40/anti-PD1 antibodies. 16S rRNA sequencing of faecal samples revealed that systemic chemo-immunotherapy significantly reduced alpha diversity, depleted immunoregulatory species (e.g. Akkermansia muciniphila, Bifidobacterium longum), and enriched pathobionts (Escherichia coli, Clostridium septicum), accompanied by elevated intestinal pro-inflammatory cytokines. In contrast, localised delivery preserved microbial diversity, maintained beneficial taxa and suppressed inflammatory cytokine levels. Further, high-dose localised chemotherapy promoted M1 macrophage polarisation while preserving microbiota more effectively than even low-dose systemic regimens. This is the first study to demonstrate that spatial control of drug exposure via localised delivery can protect the gut microbiome and modulate systemic immunity in PDAC. These findings subsequently provide proof-of-concept that implant-based approaches can enhance tolerability and efficacy of chemo-immunotherapy by minimising microbiome disruption.},
}

@article {pmid40840439,
year = {2025},
author = {He, X and Gao, Y and Zhang, Y and Yang, Z and Wang, C and Ma, Q and Lei, P and Yu, L and Fan, Y and Liu, R and Wang, W and Zhang, J and Ma, X and Zhu, F},
title = {Distinct Gut Microbial Signatures and Diminished Anti-Inflammatory Effect of Short-Chain Fatty Acids in Schizophrenia With Immune Activation.},
journal = {Schizophrenia bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1093/schbul/sbaf110},
pmid = {40840439},
issn = {1745-1701},
support = {82171505//National Natural Science Foundation of China/ ; 82230044//National Natural Science Foundation of China/ ; 82022023//National Natural Science Foundation of China/ ; 82271572//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND AND HYPOTHESIS: A subset of patients with schizophrenia (SCZ) exhibit subclinical immune activation. However, the gut microbial features of this subgroup and their interplay with the immune function remain poorly understood. This study aimed to identify the gut microbiome signature of immune-activated SCZ and elucidate the role of short-chain fatty acids (SCFAs) in the gut-immune crosstalk.

STUDY DESIGN: In this study, 297 patients with SCZ and 301 healthy controls (HCs) were assessed for 4 serum immune mediators. Immune-activated subgroups were classified based on these biomarkers. Fecal metagenomic sequencing, SCFA metabolomics, and in vitro peripheral blood mononuclear cells (PBMCs) stimulation experiments were performed to analyze the microbial composition, SCFA levels, and immune responses.

STUDY RESULTS: We found that 46.5% of the patients with SCZ exhibited elevated immune activation biomarker levels, which displayed unique bacterial signatures. Microbiome-based machine learning classifiers demonstrated robustness in SCZ and immune activation classification. Notably, microbial species abundance, functional metagenomics, and SCFA levels have confirmed an elevated capacity for SCFA production in patients with immune activation. Furthermore, in vitro PBMC stimulation experiments revealed a diminished anti-inflammatory effect of SCFAs in immune-activated patients when exposed to lipopolysaccharide-induced inflammation.

CONCLUSIONS: This study delineates the gut microbiome and SCFA metabolic profiles of immune-activated SCZ patients, revealing an association between gut microbiota dysbiosis, enhanced SCFA production capacity, and diminished anti-inflammatory effect of SCFA. These findings provide new insights into the underlying mechanisms and potential targeted treatments for SCZ patients with immune activation.},
}

@article {pmid40840314,
year = {2025},
author = {Botero, J and Cnockaert, M and Zhang, Y and Peeters, C and Vandamme, P},
title = {Carnimonas bestiolae sp. nov. and Cernens ardua gen. nov., sp. nov.: new halotolerant bacteria from the invasive solitary bee Megachile sculpturalis.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {5},
pages = {126648},
doi = {10.1016/j.syapm.2025.126648},
pmid = {40840314},
issn = {1618-0984},
abstract = {Fifteen isolates from gut samples of the invasive solitary bee Megachile sculpturalis remained unidentified after matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. Phylogenomic and overall genome relatedness indices analyses of five representative isolates demonstrated that 14 isolates represented a novel Carnimonas species for which we propose the name Carnimonas bestiolae sp. nov., with LMG 33810[T] as the type strain. A single isolate represented a distinct lineage within the Halomonadaceae family with the genera Carnimonas and Halotalea as nearest neighbor taxa and is classified as Cernens ardua gen. nov., sp. nov., with LMG 33818[T] as the type strain. Comparative genomic analysis and physiological characterization revealed functional differences between C. bestiolae, Ce. ardua and established Carnimonas and Halotalea species in central metabolism, fatty acid metabolism, and osmoregulatory pathways, the latter being consistent with adaptation to a saline environment. A reanalysis of previously published insect microbiome studies in which Carnimonas was reported, revealed 16S rRNA amplicon sequence variants with >99 % identity to C. bestiolae LMG 33810[T] 16S rRNA in gut samples of Megachile sculpturalis, Anthidium florentinum, and the psyllid Leptynoptera sulfurea. In contrast, 16S rRNA amplicon sequence variants corresponding to Ce. ardua were rarely detected and only at low relative abundances, suggesting a transient association with the insect gut.},
}

@article {pmid40840119,
year = {2025},
author = {Maldonado-Barrueco, A and Almazán-Garate, E and Armijo-Suárez, O and Iniesta-Pérez, S and Sanz-González, C and Álvarez-López, C and Cacho-Calvo, J and Quiles-Melero, I},
title = {Detection of bacterial vaginosis-associated bacteria and outcomes during clinical gynaecological conditions using qPCR: A retrospective cohort study.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {4},
pages = {117065},
doi = {10.1016/j.diagmicrobio.2025.117065},
pmid = {40840119},
issn = {1879-0070},
abstract = {Endometriosis, chronic endometritis (CE), unexplained infertility (UI), and recurrent pregnancy loss (RPL) are gynecological conditions frequently associated with inflammation and alterations in the endometrial microbiome. The presence of bacterial vaginosis-associated bacteria (BVAB) and the expression of CD138 may influence clinical outcomes. We evaluate the relationship between endometrial BVAB detection via qPCR, CD138 marker expression, prior antibiotic treatment, and the number of miscarriages. A retrospective single-center cohort study was conducted on 86 women with endometriosis, CE, UI, and/or RPL. Endometrial samples were collected and analysed using the Allplex™ Bacterial Vaginosis Plus qPCR assay (Seegene[Ⓡ]). Demographic data, CD138 expression, antibiotic usage, and miscarriage history were recorded and statistically analysed. CD138 expression was positive in 44.2% of cases. BVAB were detected in 31.4% of patients, with Lactobacillus spp. (median Log10 copies/reaction 1.56) and G. vaginalis (median Log10 copies/reaction 0.81) being the most common. A significant inverse association was found between CD138 positivity and BVAB detection (p < 0.05, OR = 0.31), suggesting reduced BVAB presence in inflamed endometria. No significant association was found between BVAB detection and prior antibiotic therapy or number of miscarriages. A significant correlation was found between negative BVAB qPCR results and positive CD138 expression, indicating a potential link between endometrial inflammation and microbiome alterations. However, antibiotic treatment did not significantly impact BVAB presence, and no association was found with miscarriage frequency. Further studies using vaginal swabs, healthy controls, and microbiome next-generation sequencing are needed to clarify these associations.},
}

@article {pmid40840010,
year = {2025},
author = {Yu, LW and Hsiao, EY},
title = {Microbial regulation of serotonin and neuroimmune interactions.},
journal = {Current opinion in immunology},
volume = {96},
number = {},
pages = {102639},
doi = {10.1016/j.coi.2025.102639},
pmid = {40840010},
issn = {1879-0372},
abstract = {Bidirectional communication between the gut microbiota and neuroimmune system is essential during host-microbiome interactions. Recent research has begun to unravel microbiome-neuroimmune crosstalk and suggest classical neurochemicals as key molecular players. Serotonin, a tryptophan-derived neurochemical found across the kingdom of life, is increasingly recognized as an important effector molecule central to interkingdom communication. Here, we focus on serotonin as a key factor for microbiome-neuroimmune interaction. We briefly summarize the serotonergic system and the role of the gut microbiome in regulating serotonin bioavailability, which leads to downstream effects on neuroimmune responses and microbial fitness.},
}

@article {pmid40839943,
year = {2025},
author = {Ngo, C and Taechamaeteekul, P and Boonprakob, R and Kamwa, R and Prapasarakul, N and Wattanaphansak, S and Tummaruk, P},
title = {Boar fecal and seminal microbiomes in relation to semen quality and probiotic supplementation in an antibiotic-free feeding program.},
journal = {Theriogenology},
volume = {249},
number = {},
pages = {117637},
doi = {10.1016/j.theriogenology.2025.117637},
pmid = {40839943},
issn = {1879-3231},
abstract = {This study aimed to investigate the fecal and seminal microbiomes of boars in relation to semen quality and the effects of transitioning from antibiotics to probiotics within an antibiotic-free feeding regimen. A total of 21 fecal and 21 semen samples were collected from seven Duroc boars at three different time points: before antibiotic withdrawal (Day 0, serving as the control), after 48 days (Day 48), and after 96 days (Day 96). The fresh semen characteristics, bacterial culture contents, and the fecal and seminal microbiomes of boars were analyzed across the three time points. The collected semen was also diluted in an antibiotic-free semen extender and stored for 4 days. Sperm quality and bacterial culture contents were assessed daily throughout the storage period. On Day 96, sperm characteristics, including total sperm motility (-17.5 %, P = 0.024), sperm viability (-20.4 %, P = 0.002), and acrosome integrity (-25.8 %, P = 0.002), were significantly lower compared to Day 0. No significant differences were observed in total bacterial count or Lactobacillus sp. count across the three time points (P > 0.05). However, following the transition from antibiotics to probiotics, the proportion of Gram-negative bacteria in fresh semen increased from 69.5 % on Day 0-88.0 % on Day 96. In addition, the percentage of E. coli rose from 18.7 % on Day 0-76.0 % on Day 96. Over the 4-day storage period, the total bacterial count and total Lactobacillus sp. count increased (P < 0.05). The seminal microbiome analysis revealed that Enterobacterales (41.4 %) were the dominant bacterial group in boars with poor semen quality, whereas Bacteroidales (14.2 %) were predominant in those with good semen quality. A cladogram of the seminal microbiome identified Gammaproteobacteria as the bacterial biomarkers on Day 96 following the transition from antibiotics to probiotics. The alpha and beta diversity of the fecal microbiome showed significant differences between Day 0 and Day 96 (P = 0.048). However, no significant differences were observed in the alpha and beta diversity of the seminal microbiome (P > 0.05). In conclusion, the increase in Gram-negative opportunistic pathogens, including Gammaproteobacteria, Enterobacterales, and E. coli, is linked to reduced semen quality after switching from antibiotics to probiotics. However, this decline is unrelated to total bacterial or Lactobacillus sp. counts. While probiotic supplementation altered fecal microbiome diversity, it had no effect on seminal microbiome diversity or semen quality, with no connection between fecal and seminal microbiome changes.},
}

@article {pmid40839618,
year = {2025},
author = {Roman, A and Linthout, C and Raymond, B and Koenraadt, CJM},
title = {Asaia spp. exposure for improving mosquito mass-rearing, and the effects on Culex pipiens pipiens vector competence for West Nile virus.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0330703},
doi = {10.1371/journal.pone.0330703},
pmid = {40839618},
issn = {1932-6203},
mesh = {Animals ; *Culex/virology/growth & development/microbiology ; *West Nile virus/physiology/pathogenicity ; *Mosquito Vectors/virology/microbiology/growth & development ; Larva/virology/growth & development/microbiology ; West Nile Fever/transmission/virology ; Mosquito Control/methods ; Female ; *Acetobacteraceae/physiology ; },
abstract = {Various vector control strategies are in place to reduce the spread of arthropod-borne viruses. Some of these, such as application of insecticides, are encountering operational challenges and a reduced overall effectiveness due to evolution of resistance. Alternative approaches for mosquito population control, such as the sterile insect technique, depend on efficient mass-rearing of healthy mosquitoes prior to mass-release in the field. Therefore, improving efficiency and quality of mass-rearing techniques is crucial to obtain fit mosquitoes. Previous studies have shown that Acetic Acid Bacteria of the genus Asaia can have a mutualistic effect on larval development in different mosquito species and can thus contribute to improved rearing output. However, whether improved performance in the larval stages may have knock-on effects in the adult stage, for example by increasing their capability to transmit arbovirus, remains unclear. Such effects may jeopardize future control efforts. We tested the effects of two Asaia species, Asaia krungthepensis and Asaia bogorensis, on development time and adult size under two rearing conditions: individual rearing and group rearing of Culex pipiens larvae. Besides investigating development and size, we also investigated whether Asaia spp. exposure during the larval stage can influence the vector competence of Culex pipiens pipiens for West Nile virus (WNV). Our work shows the potential of improving mass-rearing efficiency by employing Asaia krungthepensis as a mutualist for Culex pipiens pipiens. Importantly, this study reveals no significant increase in dissemination and transmission rate of WNV by Culex pipiens pipiens when inoculated with Asaia spp., although an increase in viral titer in the legs and the saliva was observed when the mosquitoes were inoculated with the two Asaia species. Interestingly, we confirmed that Asaia spp. bacteria did not establish as a permanent member of the microbiota of Culex pipiens pipiens. As Asaia spp. did not establish in adult mosquitoes, the observed change in WNV titers can be a result of indirect interactions of Asaia with the native Culex pipiens pipiens microbiome. Our results stress the importance of carefully evaluating host-symbiont interactions to avoid the potential of releasing mosquitoes with enhanced vector competence.},
}

Animals
*Culex/virology/growth & development/microbiology
*West Nile virus/physiology/pathogenicity
*Mosquito Vectors/virology/microbiology/growth & development
Larva/virology/growth & development/microbiology
West Nile Fever/transmission/virology
Mosquito Control/methods
Female
*Acetobacteraceae/physiology

@article {pmid40839328,
year = {2025},
author = {Bathobakae, L and Rivera, E and Mücahit, D and John, R and Atogwe, I and Phuu, P and Escobar, J and Bandaru, P and Cavanagh, Y and Ligresti, R and Robinson, MK},
title = {Pancreatic Exocrine Insufficiency After Metabolic and Bariatric Surgery.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {40839328},
issn = {1573-2568},
abstract = {Obesity is a chronic disease characterized by an abnormal or excessive accumulation of body fat. Common interventions include lifestyle changes, hypocaloric diets, and incretin mimetics, all of which have limited efficacy. Metabolic and bariatric surgery (MBS) continues to gain prominence as an effective treatment for obesity, owing to sustained weight loss and improvement in comorbid conditions. Pancreatic exocrine insufficiency (PEI) is an under-recognized but clinically significant complication of MBS. It is characterized by inadequate pancreatic enzyme secretion, resulting in fat malabsorption and micronutrient deficiencies. The true prevalence of PEI in the post-MBS population remains poorly defined due to inconsistencies in diagnostic criteria and underrecognition in clinical practice. The pathophysiology of PEI in this setting is multifactorial and includes loss of pancreaticocibal synchrony, diminished hormonal stimulation of the pancreas, and alterations in the gut microbiome such as small intestinal bacterial overgrowth. Clinical manifestations are often subtle or nonspecific, contributing to diagnostic delays. Although imperfect, the fecal elastase-1 (FE-1) test remains the most commonly used diagnostic tool in clinical practice. Current guidelines suggest that pancreatic enzyme replacement therapy (PERT) may be considered in post-bariatric patients with confirmed or suspected PEI, although data on efficacy and optimal dosing in this population are limited. This review synthesizes current evidence on epidemiology, etiopathogenesis, clinical presentation, diagnostic challenges, and management of PEI following MBS. We also summarize insights from recent studies and discuss the clinical implications of timely recognition and treatment of this underappreciated complication.},
}

@article {pmid40839319,
year = {2025},
author = {Nemec, M and Ringl, P and Spettel, K and Schneider, L and Kriz, R and Galazka, S and Sedlak, M and Jonke, E and Andrukhov, O and Makristathis, A},
title = {Correction: Exploring the impact of orthodontic appliances on the oral microbiome and inflammatory parameters.},
journal = {Progress in orthodontics},
volume = {26},
number = {1},
pages = {29},
pmid = {40839319},
issn = {2196-1042},
}

@article {pmid40839184,
year = {2025},
author = {Cardoso, MC and Lopes, TS and Lemos, MC and Figueiredo, CD and Streck, AF},
title = {Efficacy of Lacticaseibacillus rhamnosus GG in the treatment of canine atopic dermatitis: A randomized controlled study.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {40839184},
issn = {1678-4405},
}

@article {pmid40839135,
year = {2025},
author = {Khan, A and Sikdar, M and Kango, N and Srivastava, R},
title = {Synbiotics as Modulators of Developing Brain for Reproductive Development Via Estrogen Receptors in Male Coturnix Coturnix Japonica.},
journal = {Neurochemical research},
volume = {50},
number = {5},
pages = {270},
pmid = {40839135},
issn = {1573-6903},
mesh = {Animals ; Male ; *Brain/growth & development/metabolism/drug effects ; *Synbiotics/administration & dosage ; Coturnix ; *Reproduction/physiology/drug effects ; Oxidative Stress/drug effects/physiology ; *Receptors, Estrogen/metabolism ; },
abstract = {The brain-gut-microbiome axis represents a bidirectional communication linking the gastrointestinal microbiome with immunity, digestion, reproduction and nervous system. Dietary supplementation of Lactobacillus rhamnosus, Bifidobacterium longum and mannan-oligosaccharides may modulate the brain-gut-axis and also have an effect on male reproductive physiology. Therefore, the study aims to explore the reproductive and neuronal physiology potentials of synbiotics in immature male Japanese quails. To achieve this, two weeks old quails were supplemented with 1% Lactobacillus rhamnosus (L), Bifidobacterium longum (B) and mannan-oligosaccharides (M) in their diet, individually as well as in combinations (LB and LBM) for 28days. The oxidative stress markers including malondialdehyde (MDA), hydrogen peroxide (H2O2), advanced oxygen protein products (AOPPs); antioxidant enzymes {Superoxide Dismutase (SOD), Catalase}
and coenzyme Glutathione (GSH); monoamine oxidase (MAO) and acetylcholinesterase (AchE) activity were estimated in the brain. Inflammatory biomarkers (IL-10, IL-1β and NF-κB), apoptotic biomarkers (caspase-3 and caspase-7) and for reproductive aspect viz. gonadotropin releasing hormone (GnRH) and estrogen receptors (ER-α and ER-β) were analyzed by immunofluorescence in the brain. The results revealed that dietary supplementation with 1% LBM or synbiotics significantly enhances the number of neurons in the hippocampal area, antioxidant enzymes (SOD and Catalase) while it reduces MDA, H2O2 and AOPP. Synbiotics increases IL-10 expression and a substantial reduction in IL-1β and NF-κB which limits inflammation as well as apoptosis (Caspase-3 & Caspase-7) with increased AchE, MAO activity in the developing brain. Our findings indicate that synbiotics interfere and enhance neuronal development processes and are associated with fertility manifested by upregulated expression of GnRH, ER-α, ER-β in brain. Overall, combined use of pro, pre, synbiotics have a synergistic effect and serve as modulators in neuro-immune processes and fertility in developing brain of quail.},
}

Animals
Male
*Brain/growth & development/metabolism/drug effects
*Synbiotics/administration & dosage
Coturnix
*Reproduction/physiology/drug effects
Oxidative Stress/drug effects/physiology
*Receptors, Estrogen/metabolism

@article {pmid40839108,
year = {2025},
author = {Mukherjea, N and Khandelwal, A and Saluja, R and Kalra, N},
title = {The Role of the human microbiome in neurodegenerative diseases: A Perspective.},
journal = {Current genetics},
volume = {71},
number = {1},
pages = {17},
pmid = {40839108},
issn = {1432-0983},
mesh = {Humans ; *Neurodegenerative Diseases/microbiology ; *Microbiota ; Parkinson Disease/microbiology ; *Gastrointestinal Microbiome ; Alzheimer Disease/microbiology ; Inflammasomes ; Inflammation/microbiology ; },
abstract = {Advances in diagnostics, therapeutics, and large-scale clinical studies have significantly expanded our understanding how human health is shaped by the microorganisms that colonize the body since birth. This article explores the rapidly evolving field of human microbiome research, focusing upon how microbial communities influence neurological health and contribute to the development of neurodegenerative diseases (NDs). Multiple factors, including age, lifestyle, and immunological memory, are recognized as major determinants of an individual's microbiome composition, which in turn can influence the onset and the progression of disorders such as Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. These conditions have been linked to mechanisms including the aggregation of pathogenic proteins (e.g., amyloid-β and α-synuclein), inflammation driven by activation of the Toll-like receptor (TLR) signaling pathway, the NLRP3 inflammasome, as well as the modulatory effect of microbial metabolites such as short-chain fatty acids (SCFAs) and lipopolysaccharides (LPS). The article also highlights ongoing research and emerging strategies aimed at leveraging the human microbiome for better diagnosis, and management of NDs.},
}

Humans
*Neurodegenerative Diseases/microbiology
*Microbiota
Parkinson Disease/microbiology
*Gastrointestinal Microbiome
Alzheimer Disease/microbiology
Inflammasomes
Inflammation/microbiology

@article {pmid40839082,
year = {2025},
author = {Lin, S and Shi, Y and Liu, J and Luo, J and Liao, K and Liu, P and Gao, X},
title = {Gut microbiome and metabolome analysis reveal the alleviating effect of naringenin on duodenal damage in Ningdu yellow chickens caused by heat stress.},
journal = {Avian pathology : journal of the W.V.P.A},
volume = {},
number = {},
pages = {1-42},
doi = {10.1080/03079457.2025.2549360},
pmid = {40839082},
issn = {1465-3338},
abstract = {Heat stress (HS) is a major challenge to the development of the farming industry. Gut health is essential for maintaining the overall health status of the organism. Naringenin (Nar) is a natural flavonoid compound that has demonstrated considerable therapeutic potential in the treatment of a range of diseases. The aim of this study was to elucidate the effect of HS on duodenal intestinal integrity and the mitigating effect of Nar on this effect by analyzing the gut microbiome and metabolome. The results showed that HS resulted in damage to the intestinal antioxidant function and intestinal barrier in Ningdu yellow chickens, and this result was reversed with the addition of Nar, and duodenal permeability was repaired. 16S rRNA sequencing revealed that heat stress led to a substantial decline in the abundance of beneficial bacteria, including Akkermansia and Lactobacillus. Nar was found to modify the composition of the intestinal microbiota, thereby impeding the proliferation of conditionally pathogenic bacteria such as Helicobacter. Furthermore, metabolomic KEGG analysis revealed that Nar ameliorated the heat stress condition of Ningdu yellow chickens by regulating serum metabolism, primarily through the ABC transporter pathway. Correlation analysis revealed a statistically significant correlation between the gut microbiota and metabolites. The present findings demonstrate that Nar attenuates intestinal damage caused by HS in Ningdu yellow chickens, and that this effect is closely related to the effects of Nar on the composition and metabolism of intestinal flora.},
}

@article {pmid40839081,
year = {2025},
author = {Azimov, M and Cohen-Michnik, I and Rottenstreich, M and Katz, L and Zeigerman, H and Yona, AH},
title = {Distinct Clinical Phenotypes in Lactase Non-Persistence: Symptomatic, Asymptomatic, and Gassy-Asymptomatic.},
journal = {The American journal of gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ajg.0000000000003740},
pmid = {40839081},
issn = {1572-0241},
abstract = {INTRODUCTION: Lactase deficiency allows undigested lactose to reach the colon, where fermentation triggers gastrointestinal symptoms. Although lactase persistence (LP) versus non-persistence (LNP) is genetically defined, many LNP individuals are symptoms-free, suggesting additional determinants of the phenotype. We aimed to define clinically relevant LNP subgroups and examine microbiome features that differ among them.

METHODS: In 146 healthy adults, LP-associated SNPs were genotyped and a standardized 25g lactose load was administered. Breath hydrogen, methane, blood glucose, and symptom scores were collected over three hours. Microbiome composition (n=60) was profiled by 16S-rRNA sequencing of stool samples.

RESULTS: Among LNP individuals (116/146, 79%), three distinct phenotypes emerged: Symptomatic (35/116, 30%), who produced hydrogen and reported symptoms; Gassy Asymptomatic (67/116, 58%), who produced hydrogen without symptoms; and Asymptomatic (14/116, 12%), who neither produced hydrogen nor had symptoms. All LNP subgroups showed similarly low blood glucose elevations after lactose load compared to LP. A novel metric, peak hydrogen production rate (ppm/hour), improved correlation with symptom severity (R=0.49) versus the conventional hydrogen peak (R=0.34). Microbiome analyses revealed higher abundances of certain genera such as Lactobacillus and Megasphaera in asymptomatic LNP subgroups, suggesting possible microbial contributions to the absence of symptoms.

CONCLUSION: 70% of genetically LNP adults tolerate lactose without symptoms. classifying LNP individuals into distinct subgroups and incorporating hydrogen production rate into breath-test interpretation may enhance diagnostic precision, prevent unnecessary dietary restrictions and generate new hypotheses linking fermentation kinetics and symptoms. Microbiome associations remain correlative and warrant functional validation in larger, controlled studies.},
}

@article {pmid40839044,
year = {2025},
author = {Brichova, M and Dlouha, L and Tenglerova, M and Rehakova, J and Kostovcik, M and Benesova, K and Coufal, S and Pivrncova, E and Jiraskova Zakostelska, Z and Kverka, M and Skrlova, E and Svozilkova, P and Klimova, A and Kostovcikova, K and Trneny, M and Heissigerova, J},
title = {Oral, not gut microbiota diversity, reflects the inflammation and neoplasia in patients with uveitis and vitreoretinal lymphoma.},
journal = {Journal of ophthalmic inflammation and infection},
volume = {15},
number = {1},
pages = {63},
pmid = {40839044},
issn = {1869-5760},
support = {NU20-03-00253//Ministerstvo Zdravotnictví Ceské Republiky/ ; NU20-03-00253//Ministerstvo Zdravotnictví Ceské Republiky/ ; NU20-03-00253//Ministerstvo Zdravotnictví Ceské Republiky/ ; NU20-03-00253//Ministerstvo Zdravotnictví Ceské Republiky/ ; NU20-03-00253//Ministerstvo Zdravotnictví Ceské Republiky/ ; NU20-03-00253//Ministerstvo Zdravotnictví Ceské Republiky/ ; NU20-03-00253//Ministerstvo Zdravotnictví Ceské Republiky/ ; NU20-03-00253//Ministerstvo Zdravotnictví Ceské Republiky/ ; NU20-03-00253//Ministerstvo Zdravotnictví Ceské Republiky/ ; NU20-03-00253//Ministerstvo Zdravotnictví Ceské Republiky/ ; NU20-03-00253//Ministerstvo Zdravotnictví Ceské Republiky/ ; NU20-03-00253//Ministerstvo Zdravotnictví Ceské Republiky/ ; CZ.02.01.01/00/22_008/0004597//Ministry of Education, Youth and Sports of the Czech Republic/ ; CZ.02.01.01/00/22_008/0004597//Ministry of Education, Youth and Sports of the Czech Republic/ ; CZ.02.01.01/00/22_008/0004597//Ministry of Education, Youth and Sports of the Czech Republic/ ; },
abstract = {PURPOSE: Dysregulation of the microbiota on different mucosal surfaces is associated with both immune-mediated and malignant diseases. Nevertheless, the involvement of different microbial communities is still poorly characterized. The aim of our study was to compare oral and gut microbiota composition between patients with uveitis, vitreoretinal lymphoma (VRL), and controls.

METHODS: This study was designed as a prospective observational study. The inclusion criteria were treatment-naïve patients with immune-mediated uveitis or newly diagnosed VRL. The buccal swab and faecal samples were collected and bacterial 16S ribosomal RNA gene sequencing was used to identify the oral and gut microbiota.

RESULTS: We enrolled 18 patients with uveitis, median age 39 years, 16 patients with VRL, median age 67.5 years, and 16 controls, median age 63 years. In the oral microbiota, the patients suffering from uveitis showed significant enrichment of genera Pseudomonas (p < 0.0001 and p < 0.0001), and Diaphorobacter (p = 0.007 and 0.013) and reduction of Streptococcus (p < 0.0001 and p < 0.0001) when compared to patients with VRL and control subjects, respectively. In addition, these patients had also significantly higher relative abundance of the genus Enhydrobacter (p = 0.029) and lower abundance of the genera Gemella (p = 0.002), Neisseria (p = 0.008), and Prevotella (p = 0.011) when compared to patients with VRL. We found only minor changes in the gut microbiota.

CONCLUSION: Our study, as the first one, highlighted significant differences in the composition of oral microbiota among patients with uveitis, VRL, and control subjects.},
}

@article {pmid40839031,
year = {2025},
author = {Thurnher, D},
title = {[Role of the microbiome in otolaryngology].},
journal = {HNO},
volume = {73},
number = {9},
pages = {603-604},
doi = {10.1007/s00106-025-01665-6},
pmid = {40839031},
issn = {1433-0458},
}

@article {pmid40838930,
year = {2025},
author = {Luo, Y and Shi, Y and Wang, Y and Cui, Q and Ren, Y and Ding, L and Qiu, X and Zhang, B and Zhang, L and Liang, X and Guo, X},
title = {Diverse Impacts of Microplastic-derived Dissolved Organic Matter at Environmentally Relevant Concentrations on Soil Dissolved Organic Matter Transformation.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c07539},
pmid = {40838930},
issn = {1520-5851},
abstract = {Dissolved organic matter (DOM) is critical to soil ecosystems, with its dynamics influenced by exogenous substances like microplastics (MPs)-derived dissolved organic matter (MPs-DOM) from agricultural mulches. However, the impacts of MPs-DOM, especially at environmentally relevant concentrations, on soil DOM dynamics remain unclear. Here, we examined DOM transformation in yellow (YS) and black (BS) soils upon the addition of MPs-DOM, leached from biodegradable and nonbiodegradable mulches under ultraviolet irradiation (UV-MPs-DOM) and dark conditions (D-MPs-DOM), at environmentally relevant concentrations (3 mg C/kg). Results showed that extraction conditions, rather than mulch type, predominantly affected the bioavailability of MPs-DOM. UV-MPs-DOM, enriched in lipid-like and protein/amino sugar-like compounds, promoted soil DOM transformation. In YS, characterized by lower microbial diversity, UV-MPs-DOM enhanced DOM lability more than D-MPs-DOM. Conversely, in BS, with a diverse microbial community, UV-MPs-DOM with high bioavailability not only directly altered soil DOM composition but also was rapidly metabolized by the soil microbiome, particularly Proteobacteria, thereby resulting in increased soil DOM recalcitrance. However, the low bioavailability of D-MPs-DOM primarily exerted direct effects, contributing to its accumulation and increase in soil DOM lability. These findings provide novel evidence that MPs-DOM at environmentally relevant concentrations can alter soil DOM through distinct pathways, highlighting its potential long-term ecological risks.},
}

@article {pmid40838853,
year = {2025},
author = {Jiang, L and Lu, Y and He, Q},
title = {Unlocking the microbial mechanisms in fermented bean products: advances and future directions in multi-omics and machine learning approaches.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-23},
doi = {10.1080/10408398.2025.2544764},
pmid = {40838853},
issn = {1549-7852},
abstract = {Fermented bean products (FBPs) are integral to diverse global culinary traditions, prized for their distinctive flavors, nutritional benefits, and functional properties. Despite their importance, the interplay between microbial fermentation and the quality of FBPs remains incompletely understood, necessitating further investigation. This review examines the key microbial communities involved in the fermentation of various FBPs and explores the application of multi-omics technologies, such as genomics and metabolomics, to elucidate the microbiological mechanisms influencing product quality. It highlights the potential of integrating bioinformatics and machine learning to identify critical fermentation pathways and their impact on the final product. Moreover, the review anticipates the role of emerging smart technologies in enhancing the quality and efficiency of FBPs. By applying multi-omics approaches, it is possible to pinpoint core microbial consortia linked to high-quality FBPs, offering new avenues for engineering synthetic microbial communities. Such strategies may permit more precise control over fermentation processes, optimizing both the safety and consistency of FBPs. Finally, the review outlines future research directions focused on exploiting technological innovations to improve the quality, sustainability, and safety of FBPs.},
}

@article {pmid40838847,
year = {2025},
author = {Gao, X and Zheng, Y and Chang, H and Liu, J and Sun, X and Ren, Y and Li, L and Zhao, G and Cheng, Y and Ma, S and Zhao, J and Deng, J and Kang, T and Qiao, Z and Zhao, H and Xie, D and Wang, T and Li, S and Shi, H and Shi, A and Zhang, P},
title = {Metagenomic Analysis of the Tonsil Virome Highlights Its Diagnostic Potential for Rheumatoid Arthritis.},
journal = {Journal of medical virology},
volume = {97},
number = {8},
pages = {e70570},
doi = {10.1002/jmv.70570},
pmid = {40838847},
issn = {1096-9071},
support = {//The authors received no specific funding for this work./ ; },
mesh = {Humans ; *Virome ; *Arthritis, Rheumatoid/diagnosis/virology ; *Metagenomics ; Male ; Female ; Middle Aged ; *Palatine Tonsil/virology ; Adult ; *Viruses/genetics/classification/isolation & purification ; Aged ; Microbiota ; },
abstract = {Rheumatoid arthritis (RA) is a chronic autoimmune disease whose exact pathogenesis remains unclear, despite links to genetics, environmental factors, and microbial dysbiosis. Recent studies have highlighted the role of the microbiome in RA, yet the contribution of the tonsil virome remains unexplored. This study aims to investigate whether changes in the tonsil virome are associated with RA progression and assess its diagnostic potential. Using metagenomic data from 32 RA patients and 30 healthy controls (HCs), we identified 45 782 viral operational taxonomic units (vOTUs), with 14 341 classified as core vOTUs. RA patients exhibited significantly reduced virome richness and diversity, whereas Siphoviridae and Microviridae dominated both groups. Statistical analysis identified 235 RA-associated viral markers, including 13 enriched in RA and 222 in HCs. RA-enriched markers were primarily bacteriophages infecting Streptococcaceae, whereas HCs displayed more diverse viral-host interactions. Random forest models demonstrated strong discriminatory power of viral markers in distinguishing RA patients from HCs, achieving an AUC of 0.960, outperforming bacterial markers. Correlation analyses further linked viral markers to immune cell subsets, suggesting that tonsil virome alterations may influence immune dysregulation in RA. This study reveals significant changes in the tonsil virome of RA patients, highlighting its potential as a diagnostic tool and offering new insights into RA pathogenesis. These findings pave the way for future research into the virome's role in autoimmune diseases and therapeutic development.},
}

Humans
*Virome
*Arthritis, Rheumatoid/diagnosis/virology
*Metagenomics
Male
Female
Middle Aged
*Palatine Tonsil/virology
Adult
*Viruses/genetics/classification/isolation & purification
Aged
Microbiota

@article {pmid40838740,
year = {2025},
author = {Wang, J and Hashem, I and Bhonsale, S and F M Van Impe, J},
title = {Individual-based modeling (IbM) unravels spatial and social interactions in bacterial communities.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf116},
pmid = {40838740},
issn = {1751-7370},
abstract = {Bacterial interactions are fundamental in shaping community structure and function, driving processes that range from plastic degradation in marine ecosystems to dynamics within the human gut microbiome. Yet, studying these interactions is challenging due to difficulties in resolving spatiotemporal scales, quantifying interaction strengths, and integrating intrinsic cellular behaviors with extrinsic environmental conditions. Individual-based modeling addresses these challenges through single-cell-level simulations that explicitly model growth, division, motility, and environmental responses. By capturing both the spatial organization and social interactions, individual-based modeling reveals how microbial interactions and environmental gradients collectively shape community architecture, species coexistence, and adaptive responses. In particular, individual-based modeling provides mechanistic insights into how social behaviors-such as competition, metabolic cooperation, and quorum sensing-are regulated by spatial structure, uncovering the interplay between localized interactions and emergent community properties. In this review, we synthesize recent applications of individual-based modeling in studying bacterial spatial and social interactions, highlighting how their interplay governs community stability, diversity, and resilience. By linking individual-scale interactions with the ecosystem-level organization, individual-based modeling offers a predictive framework for understanding microbial ecology and informing strategies for controlling and engineering bacterial consortia in both natural and applied settings.},
}

@article {pmid40838552,
year = {2025},
author = {Szegedi, I and Bomberák, D and Éles, Z and Lóczi, L and Bagoly, Z},
title = {Cardiovascular disease and microbiome: focus on ischemic stroke.},
journal = {Polish archives of internal medicine},
volume = {},
number = {},
pages = {},
doi = {10.20452/pamw.17088},
pmid = {40838552},
issn = {1897-9483},
abstract = {Cardiovascular and cerebrovascular diseases, encompassing conditions such as ischemic heart disease and ischemic stroke (IS), remain the leading global cause of death and disability. While traditional cardiovascular risk factors (eg, hypertension, diabetes, and atherosclerosis) are well established, emerging research underscores the critical role of gut microbiota in the development and progression of both cardiac and cerebrovascular events. The microbiota-gut-brain axis is a bidirectional communication system involving neural, immune, and metabolic pathways that link gut microbial activity to vascular and brain function. Dysbiosis, marked by reduced microbial diversity and an imbalance between beneficial and pathogenic taxa, has been associated with systemic inflammation, endothelial dysfunction, increased intestinal permeability, and thrombosis. Microbial metabolites, such as trimethylamine N‑oxide (TMAO), short‑chain fatty acids, and bile acid derivatives modulate blood-brain barrier integrity, vascular tone, and neuroinflammatory responses. Both cardiovascular and cerebrovascular diseases share key microbiota‑related mechanisms, including TMAO‑mediated platelet activation and low‑grade endotoxemia, although IS is more acutely affected by gut barrier disruption and neuroinflammation. In IS, gut dysbiosis also contributes to poststroke complications, such as hemorrhagic transformation, neuropsychiatric issues, and epilepsy. Advances in sequencing and metabolomics enabled identification of microbial signatures associated with the risk for an acute ischemic event and patient prognosis. Therapeutic strategies targeting the gut microbiota-including dietary interventions, probiotics, prebiotics, and synbiotics, fecal microbiota transplantation, and intestinal epithelial stem cell therapy-show promise in mitigating vascular injury and improving recovery. This narrative review highlights current insights into microbiota‑related cardiovascular and cerebrovascular events, with a focus on IS.},
}

@article {pmid40838537,
year = {2025},
author = {Husseini, Z and Gilbert, C},
title = {Milk-Derived Extracellular Vesicles and microRNAs: Potential Modulators of Intestinal Homeostasis.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {16},
pages = {e70947},
doi = {10.1096/fj.202501630R},
pmid = {40838537},
issn = {1530-6860},
support = {30641//Fonds de recherche du Québec (FRQ)/ ; },
mesh = {*MicroRNAs/metabolism/genetics ; *Extracellular Vesicles/metabolism ; Humans ; *Homeostasis ; Animals ; *Milk/metabolism ; *Intestinal Mucosa/metabolism ; *Intestines/physiology ; },
abstract = {Milk represents a complex pool of nutrients and bioactive components that are indispensable for the growth and development of the infant. The key well-established roles played by milk's bioactive components in the infant are those at the level of the infant's intestinal and immune development. Through its bioactive components, including proteins, lipids, and oligosaccharides, milk helps the infant develop a mature intestinal identity with fully active digestive, absorptive, and barrier capacity and shapes both innate and adaptive immune responses. Recent evidence points to a new class of milk bioactive components including milk extracellular vesicles (EVs) and microRNAs, which are hypothesized to take part in contributing to infant development. The potential functions of milk microRNAs and EVs in the consumer's systems are not limited to the infant as these components can also be found in bovine milk, both raw and processed. Hence, adult consumers could also be influenced by milk EVs and microRNAs, which could affect their intestinal homeostasis particularly under pathological conditions. Nonetheless, the debate regarding the stability of milk EVs and microRNAs in the digestive tract persists, and their bioavailability and bioactivity in the consumer's tissues are still arguable. In this review, we discuss the potential functions mediated by milk microRNAs and EVs in the epithelial and immune components as well as the microbiome of the intestinal mucosa in health and disease. We also discuss the bioavailability, bioaccessibility, and bioactivity of milk EVs and microRNAs in consumer's tissues.},
}

*MicroRNAs/metabolism/genetics
*Extracellular Vesicles/metabolism
Humans
*Homeostasis
Animals
*Milk/metabolism
*Intestinal Mucosa/metabolism
*Intestines/physiology

@article {pmid40838376,
year = {2025},
author = {Grenga, L and Arntzen, MØ and Armengaud, J},
title = {Metaproteomics and Meta-Omics to Decrypt Microbiome Functionality.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e70029},
doi = {10.1002/pmic.70029},
pmid = {40838376},
issn = {1615-9861},
}

@article {pmid40838343,
year = {2025},
author = {Keller, MJ and Wang, T and Murphy, K and Serrano, MG and Kandalaft, W and Michael, I and Decety, G and McWalters, J and Buck, GA and Kelly, L and Herold, BC},
title = {Cervicovaginal Secretions in Young Women with Bacterial Vaginosis Enhance HIV Infection.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf444},
pmid = {40838343},
issn = {1537-6613},
abstract = {BACKGROUND: Bacterial vaginosis (BV) is a major health problem associated with increased HIV risk. To explore underlying mechanisms, we assessed the cervicovaginal mucosal immune environment before and after metronidazole treatment in women with BV and healthy controls.

METHODS: Women with BV diagnosed clinically by Amsel criteria were treated with oral or intravaginal metronidazole. Vaginal swabs and cervicovaginal lavage (CVL) were obtained at enrollment and approximately two and four weeks later for assessment of immune mediators, antiviral activity, and 16s rRNA gene sequencing. Healthy controls had sampling at enrollment and four weeks.

RESULTS: Vaginal pH, Nugent score, Shannon alpha diversity index, and vaginal community state types (CST) differed significantly at enrollment comparing women with clinical BV (n=19) and controls (n=13) (p<0.001). BV cases had significantly higher CVL IL-1α and TNF-α, but lower IgG at enrollment compared to controls, which improved following treatment. Similar results were observed if participants with discordant molecular results (n=3) were excluded. Most notably, CVL from BV cases enhanced whereas control CVL inhibited HIV infection of cells relative to buffer (138.4 ± 109.8% vs 30.9 ±37.9%, p=0.001). There was a transient reduction in HIV enhancement following treatment, which was not sustained. Enhancement correlated with CST and markers of dysbiosis. Specifically, decreases in lactobacilli and increases in Prevotella, Dialister micraerophilus, and Peptoniphilus lacrimalis were associated with enhancement.

CONCLUSIONS: These findings provide a potential mechanistic link that may contribute to the increased risk of HIV in association with BV and highlight the importance of early diagnosis and improved treatments.},
}

@article {pmid40838329,
year = {2025},
author = {Regueira-Iglesias, A and Suárez-Rodríguez, B and Blanco-Pintos, T and Sánchez-Barco, A and Relvas, M and Balsa-Castro, C and Tomás, I},
title = {Diversity and random forest models of oral microbiomes in periodontal health using publicly available data.},
journal = {Journal of periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jper.70000},
pmid = {40838329},
issn = {1943-3670},
support = {PI24/00222//Instituto de Salud Carlos III/ ; },
abstract = {BACKGROUND: Evidence on the 16S metabarcoding of supragingival, subgingival, and salivary microbiomes in periodontal health remains limited. We aimed to analyze the diversity and potential of machine-learning models of supragingival, subgingival, and salivary microbiomes in periodontal health.

METHODS: A total of 848 samples (supragingival = 210; subgingival = 155; saliva = 483) from 491 periodontally healthy subjects were included. Publicly available Illumina sequences were processed with mothur, and taxonomy was assigned using an oral-specific database. Random forest (RF) models were built on the training set (2/3 of the samples) using a 3-fold cross-validation. They were tested on the test set (1/3).

RESULTS: A total of 121 amplicon sequence variants (ASVs) presented with differential abundances between the two types of plaque, 212 between the supragingival and saliva samples, and 160 between the subgingival and saliva (p < 0.01). Furthermore, the supragingival versus subgingival model consisted of five ASVs. The performance parameters on the test set were area under the curve (AUC) = 0.908, accuracy (ACC) = 84.30%, sensitivity = 95.71%, and specificity = 68.63%. Both the supragingival and subgingival versus saliva models also had five ASVs. These two models revealed similar performance (AUC = 0.992 and 0.986, ACC > 95%, sensitivity > 90%, specificity > 95%).

CONCLUSION: Although supragingival and subgingival bacterial profiles diverged only modestly, primarily due to taxa with small effect sizes, they were both compositionally distinct from the salivary microbiome. RF models accurately classified samples by niche, with higher performance in distinguishing saliva from plaques. Specific ASVs from Escherichia, Fusobacterium, Granulicatella, Treponema, Peptostreptococcaceae [XI][G-9], and Prevotella were identified in subgingival plaque, while Oribacterium and Solobacterium were identified in saliva, indicating potential niche-specific microbial signatures in periodontal health.

PLAIN LANGUAGE SUMMARY: Mapping oral microbes in relation to periodontal health is essential for microbiome-based diagnostics and the development of new preventive/therapeutic strategies. Our two-by-two predictive models demonstrated that a small set of bacterial ASVs can accurately classify periodontally healthy samples according to their oral niche. Notably, models distinguishing saliva from dental plaques achieved superior performance compared to those discriminating between plaques. This likely reflects the greater resemblance in dominant microbial taxa between the two plaque niches. These findings underscore the potential of machine-learning approaches to identify key microbial signatures and highlight the predictive ASVs as promising biomarkers for characterizing oral niches in periodontal health.},
}

@article {pmid40838261,
year = {2025},
author = {Lange, UG and Lehr, K and Thieme, R and Hoffmeister, A and Feisthammel, J and Gockel, I and Link, A and Jansen-Winkeln, B},
title = {The influence of antibiotic and mechanical bowel preparation on the microbiome in colorectal cancer surgery: A pilot study.},
journal = {Surgery in practice and science},
volume = {22},
number = {},
pages = {100302},
pmid = {40838261},
issn = {2666-2620},
abstract = {BACKROUND: The extent to which bowel preparation mechanical (MBP) or oral antibiotic (OA) or in combination (MBP/OA)) should be performed prior to elective colorectal surgery is the subject of ongoing debate. The aim of our study was to investigate the effect of MPB/OA [with single-shot intravenous antibiotic administration before incision (MPB/OA+ivAB)] on the microbiome of patients with colorectal carcinoma (CRC) operated minimally-invasive.

METHODS: We were studying 16 consecutive patients who underwent elective resection surgery for CRC at our centre in a prospective panel study. MBP was performed and 1 g parmomomycin/500 mg metronidazole was administered orally one day preoperatively; 1 g ertapenem was administered intravenously 30 min prior incision. Three mucosal samples were taken preoperatively during colonoscopy and intraoperatively and analysed by 16S rRNA V1-V2 gene sequencing.

RESULTS: Before MPB/OA+ivOA, the genera Phocaeicola (10 %), Bacteroides (7 %) and unclassified Ruminococcaceae (6 %) were predominant. After preparation, all bacteria were reduced except Enterococcus (7 %) and Escherichia/Shigella (6 %), which had increased. Significant reductions were seen for Bacteroides (p = 0.01), Haemophilus (p = 0.047), Holdemanella (p = 0.004), Neisseria (p = 0.004), Odoribacter (p = 0.027), unclassified Clostridiales (p = 0.008) and unclassified Ruminococcacaeae (p = 0.009). Large effect sizes (Cohens'd) were seen for Bacteroidetes (d = 0.864) and unclassified Ruminococcacaeae (d = 0.909).

CONCLUSIONS: In our pilot study, we observed a significant reduction in seven bacterial genera after MBP/OA+ivAB in patients with CRC. Some of these bacterial genera have been associated with anastomotic insufficiency. Further, large in-depth analyses are needed to evaluate perioperative microbial drift with postoperative complications.},
}

@article {pmid40838083,
year = {2025},
author = {Sekikawa, A and Wharton, W and Murray-Krezan, C and Wu, M and Chang, Y and Snitz, BE and Coccari, M and Yang, S and Love, ML and Cusick, D and Wang, R and Li, M and Park, C and Li, J and DeConne, TM and Smith, C and Verble, DD and Lancet, MQ and Foroud, T and Kim, T and Nadkarni, NK and Mettenburg, JM and Zamora, E and Lopez, OL and Hughes, TM},
title = {ACE trial design: Equol targeting estrogen receptor-β in vascular and cognitive aging.},
journal = {Alzheimer's & dementia (New York, N. Y.)},
volume = {11},
number = {3},
pages = {e70144},
pmid = {40838083},
issn = {2352-8737},
abstract = {INTRODUCTION: Equol, a gut microbiome-derived metabolite of soy isoflavone daidzein, functions as a selective estrogen receptor beta (ERβ) agonist. In preclinical studies, it has demonstrated vascular protective and antioxidant effects, with emerging evidence suggesting potential neuroprotective properties. However, its role in preventing vascular aging and cognitive decline in humans remains unexplored. The Arterial Stiffness, Cognition, and Equol (ACE) trial investigates whether daily equol supplementation can slow the progression of arterial stiffness, brain white matter lesions, and cognitive decline in older adults without dementia.

METHODS: ACE is a multicenter, randomized, double-blind, placebo-controlled clinical trial conducted at the University of Pittsburgh, Wake Forest University, and Emory University. Community-dwelling adults aged 65 to 85 years without dementia were enrolled and randomized 1:1 to receive either 10 mg/day of equol or placebo for 24 months. The primary outcome is arterial stiffness assessed by carotid-femoral pulse wave velocity. Secondary outcomes include white matter lesions detected on the brain magnetic resonance imaging and cognitive function as assessed by the Preclinical Alzheimer Cognitive Composite. Power calculations were based on a planned sample size of 400 participants, accounting for an anticipated 20% attrition rate.

RESULTS: A total of 1783 individuals were pre-screened, and 764 underwent in-person eligibility assessment. Of these, 369 participants were randomized into two groups: Arm A (n = 185) and Arm B (n = 184). The randomized sample self-reported as 52% women and 22% Black/African American participants. Baseline demographic and clinical characteristics were well balanced between the two arms, indicating successful randomization.

DISCUSSION: ACE successfully enrolled a racially diverse population of older adults and achieved near-target recruitment. ACE is the first large-scale trial to evaluate whether equol, a selective ERβ agonist, can impact vascular and cognitive aging, paving the way for precision nutrition strategies in dementia prevention.

HIGHLIGHTS: We detail the first randomized controlled trial of equol, an estrogen receptor beta (ERβ) agonist, for vascular and cognitive aging.The study tested equol's effects on arterial stiffness, white matter lesions, and cognition.The multisite trial enrolled 369 self-reported White and Black older adults aged 65 to 85 years.The trial investigated a novel dietary metabolite targeting ERβ pathways.},
}

@article {pmid40838009,
year = {2025},
author = {Yuan, S and Jia, W and Liu, X and Liu, R and Cao, M and Wu, Y and Li, Y and Xu, W and Xiao, C and Hong, Z and Zhang, B},
title = {Therapeutic effect of fecal microbiota transplantation on hyperuricemia mice by improving gut microbiota.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1599107},
pmid = {40838009},
issn = {1664-302X},
abstract = {OBJECTIVE: The primary objective of this study was to assess the impact of fecal microbiota transplantation (FMT) on serum biochemical parameters, renal injury, and gut microbiota in hyperuricemia (HUA) mice.

METHODS: Six-week-old male C57BL/6 J mice were given a high-purine diet and potassium oxonate injections to induce HUA, followed by a two-week FMT treatment. Regular body weight checks, serum biochemical analyses, and fecal sampling for 16S rRNA gene sequencing were conducted to evaluate the treatment's impact on gut microbiota.

RESULTS: The model group showed significant increases in uric acid (UA), creatinine (Cr), blood urea nitrogen (BUN) levels, and increased xanthine oxidase (XOD) activity compared to controls (p < 0.05). FMT treatment effectively reduced these levels and XOD activity (p < 0.05). At the genus level, specific taxa like Muribaculaceae and Prevotellaceae_UCG-001 were less abundant, while Blautia and Ruminiclostridium_9 were more abundant in the model group. Following FMT, gut microbiota composition returned to near-normal levels, with significant differences from the model group (p < 0.05).

CONCLUSION: This study demonstrates that FMT holds therapeutic potential for HUA mice by reducing UA levels, alleviating renal damage, and restoring gut microbiota balance.},
}

@article {pmid40837691,
year = {2025},
author = {Zhai, ZQ and Yang, LK and Zhu, LB and Zhao, FJ and Xie, WY and Wang, P},
title = {Early Life Exposure to Manure-Fertilized Soil Shapes the Gut Antibiotic Resistome.},
journal = {Environment & health (Washington, D.C.)},
volume = {3},
number = {8},
pages = {931-941},
pmid = {40837691},
issn = {2833-8278},
abstract = {The global rise of antimicrobial resistance (AMR) presents a pressing public health challenge with agricultural practices such as the use of manure fertilization, excessive antibiotic use in livestock, and the irrigation of crops with contaminated water contributing to the spread of antibiotic resistance genes (ARGs). Despite growing concerns, the pathways through which ARGs migrate from environmental reservoirs to animal microbiomes are poorly understood. In this study, we raised mice from birth in pig manure-fertilized red (Ultisols) and black (Mollisols) soils or unfertilized controls, sampling their gut microbiomes at 8 weeks, to show that early life exposure to manure-fertilized soil profoundly shapes the gut antibiotic resistome in mice. Application of organic manure significantly enriched tetracycline-resistant ARGs in both red and black soils. Mice living in these environments harbored markedly higher abundances of ARGs, particularly the tet-(Q) gene, compared to those in nonfertilized environments. Notably, Muribaculaceae and Bacteroidaceae were identified as key hosts of tet-(Q), with evidence suggesting a horizontal gene transfer between these families. These findings indicate that manure fertilization not only increases ARG abundance in soils but also facilitates its transfer to animal microbiomes, thereby amplifying the risk of AMR dissemination. This research underscores the importance of improved agricultural management practices to mitigate the environmental transmission of AMR.},
}

@article {pmid40837523,
year = {2025},
author = {Miao, X and Cao, H and Chen, J and Gao, Y and Li, J and Zhang, B and Nie, M and Yu, M},
title = {Supragingival microbial profiles in caries-free and caries-active adolescents treated with fixed orthodontics.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100455},
pmid = {40837523},
issn = {2666-5174},
abstract = {BACKGROUND: Dental caries occur primarily due to the formation of excessive dental plaque biofilm on teeth surfaces. This study aims to analyze the supragingival microbial profiles of permanent teeth in caries-free and caries-active adolescents with fixed orthodontic appliances and to identify bacterial biomarkers that may be indicative of caries activity in specific population.

METHODS: Twelve-year-old adolescents treated with fixed orthodontic appliances were selected as the study population, with 5 caries-free and 5 caries-active subjects. Supragingival plaque samples were collected from the first permanent molars for the 16S rRNA high-throughput sequencing analysis of the V3-V4 region.

RESULTS: There was no significant difference in alpha diversity and beta diversity between the caries-free and caries-active groups. LEfSe analysis showed that differentially abundant genera such as Selenomonas_3 (S. haemophilus, S. abiotrophia and S. streptococcus), Oribacterium, Dialister, and Olsenella species in the caries-free group, and Streptococcus mutans (S. mutans), Neisseria, Haemophilus, Granulicatella, and Abiotrophia species in the caries-active group, could be identified as potential biomarkers (P < 0.05). Co-occurrence network analysis revealed significant synergistic relationships among bacteria, with Streptococcusspp. displaying the strongest associations with other genera.

CONCLUSIONS: Increases in S. mutans and bacteria from the genera Neisseria, Haemophilus, Granulicatella, and Abiotrophia were strongly associated with the caries-active status of adolescents undergoing orthodontic treatment with fixed appliances. While increases in Selenomonas_3, Oribacterium, Dialister, and Olsenella were linked to caries-free status. These findings highlight the importance of managing the oral microbiome in adolescents with fixed orthodontic appliances, as certain bacterial species can serve as indicators of caries risk.},
}

@article {pmid40837385,
year = {2025},
author = {Liu, J and Dong, K and Deng, Q and Zou, Z and Chen, S and Feng, N and Wang, J and Huang, H and Wu, Q},
title = {Regulation of aging-related chronic diseases by dietary polyphenols: An updated overview.},
journal = {Current research in food science},
volume = {11},
number = {},
pages = {101163},
pmid = {40837385},
issn = {2665-9271},
abstract = {With the aging of the population, diseases of aging such as Alzheimer's disease, diabetes and coronary heart disease are gradually becoming a key concern in global health. Dietary polyphenols, as a natural antioxidant with biological activities such as anti-inflammatory, anti-glycation, and anticancer, can effectively prevent and treat these diseases through a variety of mechanisms. However, the current means of prevention and control for these age-related diseases are still insufficient, especially the lack of reviews and studies on systematic regulation from a dietary perspective. Therefore, in this paper, we will review the bioactivity of dietary polyphenols and their regulatory mechanisms on aging-related diseases, the relationship between dietary polyphenols and cell signaling pathways and the microbiome, and the creation of polyphenol-based functional anti-aging foods, so as to provide new ideas and methods for the intervention of geriatric diseases from the perspective of dietary regulation.},
}

@article {pmid40837218,
year = {2025},
author = {Zhang, X and He, T and Zhou, J and Zhang, X},
title = {Viruses are a key regulator of the microbial carbon cycle in the deep-sea biosphere.},
journal = {Environmental science and ecotechnology},
volume = {27},
number = {},
pages = {100609},
pmid = {40837218},
issn = {2666-4984},
abstract = {The marine biosphere profoundly influences atmospheric chemistry and climate through its carbon cycle. Viruses, the most abundant and diverse entities in marine ecosystems, significantly shape global carbon dynamics by infecting microbes and altering their metabolism. Both DNA and RNA viruses drive these processes in surface oceans, yet their roles in the deep sea-a sunlight-independent ecosystem that stores vast carbon reserves-remain largely unexplored. Here we show that viruses regulate the microbial carbon cycle in the deep-sea biosphere, based on viromic analysis of 66 global sediment samples spanning 1900 to 24,000 years. We identified 324,772 DNA viruses and 61,066 RNA viruses, revealing high diversity and long-term persistence. These viruses co-participate in host carbon metabolism via synergistic genes that encode carbohydrate-active enzymes, with DNA viruses primarily aiding synthesis and RNA viruses supporting decomposition. Integrated virome and microbiome data indicate that viral genes form novel metabolic branches, compensating for host deficiencies and enhancing pathway efficiency in processes like fructose-mannose and pyruvate metabolism. Our findings position deep-sea viruses as key regulators of marine microbial carbon cycling, with implications for global biogeochemical models and climate resilience. This work offers the first holistic perspective on DNA and RNA viruses in deep-sea carbon dynamics, illuminating their ecological significance across geological timescales.},
}

@article {pmid40836907,
year = {2025},
author = {Snelson, M and Rhys-Jones, D and Jama, HA and Creek, DJ and Mackay, CR and Muir, J and Marques, FZ},
title = {Preintervention Intake of Whole Grains Versus Refined Grains, and the Gut Microbiome, Discriminate the Antihypertensive Effect of Prebiotic Fiber.},
journal = {Circulation. Genomic and precision medicine},
volume = {},
number = {},
pages = {e005019},
doi = {10.1161/CIRCGEN.124.005019},
pmid = {40836907},
issn = {2574-8300},
}

@article {pmid40836857,
year = {2025},
author = {Zhong, L and Ren, P and Wang, H and Fu, C and Feng, D and Wang, M and Zeng, L and Yao, P and Wang, T},
title = {Potential association between altered oral microbiota and oxidative stress in individuals with autism.},
journal = {Autism : the international journal of research and practice},
volume = {},
number = {},
pages = {13623613251362259},
doi = {10.1177/13623613251362259},
pmid = {40836857},
issn = {1461-7005},
abstract = {Autism spectrum disorders are potentially associated with gastrointestinal dysfunction, although the underlying mechanisms remain unclear. Recently, the oral cavity has gained attention as the starting point of the digestive tract. We aim to explore the potential association between altered oral microbiota and oxidative stress in individuals with autism spectrum disorders. We conducted a case-control study involving 54 subjects with autism spectrum disorders and 46 typically developing participants. Oral epithelial cells and saliva samples were collected to analyze oxidative stress markers and oral microbiota composition using 16S rDNA sequencing. Compared with typically developing participants, individuals with autism spectrum disorders exhibited suppressed mRNA levels of superoxide dismutase 2 and RAR-related orphan receptor α, increased H3K9me2 modifications at superoxide dismutase 2 promoter, elevated levels of 8-oxo-dG in oral epithelial cells, and a reduced ratio of reduced glutathione/oxidized glutathione (GSH/GSSG) ratio in saliva. In addition, alpha and beta diversity analyses showed significant differences in microbial richness, evenness, and intersample variation between the autism spectrum disorder and typically developing groups. Statistical analyses confirmed marked distinctions in microbial diversity and community structure between the two groups. Individuals with autism spectrum disorders show increased oxidative stress and altered oral microbiota compared with typically developing participants. While the underlying mechanisms remain unclear, these findings suggest that altered oral microbiota may be linked to oxidative stress, providing insights into autism spectrum disorder pathology and potential avenues for clinical intervention.Lay AbstractAutism spectrum disorders are linked to gut-related issues, but the exact causes are still unclear. Recent research focuses on the mouth, the first part of the digestive system, to understand how it may play a role. This study looked at how the oral microbiome (the community of microorganisms in the mouth) and oxidative stress (an imbalance between harmful free radicals and antioxidants in the body) differ in people with autism spectrum disorders compared with typically developing individuals. Researchers studied 54 people with autism spectrum disorders and 46 typically developing individuals by analyzing their saliva and oral cells. Results showed that people with autism spectrum disorders had higher levels of oxidative stress markers and noticeable differences in their oral microbiota diversity and structure. These findings suggest a potential connection between changes in oral bacteria and oxidative stress in autism spectrum disorders, opening the door for new ways to study and treat autism spectrum disorders-related health issues.},
}

@article {pmid40836656,
year = {2025},
author = {Federici, B and Dell'isola, GB and Striano, P and Verrotti, A},
title = {Intestinal microbiome and epilepsy: a new therapeutic approach?.},
journal = {Expert review of clinical pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17512433.2025.2550724},
pmid = {40836656},
issn = {1751-2441},
}

@article {pmid40836634,
year = {2025},
author = {Van Dijck, L and Esposto, D and Huelsmann, C and Malisic, M and Piro, A and Giehl, RFH and Balcke, GU and Tissier, A and Parker, JE},
title = {Cooperation between a root fungal endophyte and host-derived coumarin scopoletin mediates Arabidopsis iron nutrition.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70476},
pmid = {40836634},
issn = {1469-8137},
support = {//Cluster of Excellence on Plant Sciences/ ; //Max-Planck-Gesellschaft/ ; SPP 2125 DECRyPT//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Iron acquisition is a critical challenge for plants, especially in iron-deficient soils. Recent research underscores the importance of root-exuded coumarins in modulating the root microbiome community structure and facilitating iron uptake. However, interactions between root-associated fungi and coumarins in plant iron nutrition remain unknown. We investigated the mechanism by which a fungal endophyte, Macrophomina phaseolina (F80), enhances Arabidopsis iron nutrition. Fungal-coumarin interactions were assessed by profiling metabolites and measuring iron mobilisation in F80 cultures supplemented with specific coumarins, alongside quantifying growth performance and iron content in Arabidopsis coumarin-biosynthesis mutants inoculated with F80. Our findings reveal that an interaction between the coumarin scopoletin and F80 in the rhizosphere rescues plant growth under iron-limiting conditions by resolving the iron mobility bottleneck. F80 exhibits a capacity to modify scopoletin into iron-chelating catechol coumarin esculetin, thereby releasing available iron. We conclude that Arabidopsis-produced scopoletin functions as a precursor for fungal conversion into iron-chelating coumarins. By extending the role of coumarins from bacterial to fungal members of the root microbiota, this study places coumarins at the centre of commensal-mediated enhancement of plant iron nutrition across microbial kingdoms.},
}

@article {pmid40836512,
year = {2025},
author = {Wu, X and Chen, H and Ding, R and Chen, G and Jia, H and Zhong, S and Gu, R},
title = {Integrating Transcriptome, Metabolome and Microbiome to Explore the Molecular Mechanism of Phenotypic Plasticity in P. rotata During Low-Altitude Domestication.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70138},
pmid = {40836512},
issn = {1365-3040},
support = {//This study was supported by the National Key Research and Development Program of the Ministry of Science and Technology./ ; },
abstract = {The endangered Tibetan herb Phlomoides rotata is threatened by overharvesting and slow natural regeneration. To support its sustainable utilisation, we investigated the mechanisms underlying its phenotypic plasticity during low-altitude adaptation using an integrated multi-omics approach. Specifically, rhizosphere soils and leaf tissues were collected from P. rotata cultivated at high-, mid-, and low altitudes for multi-omics analysis, including bacterial and fungal profiling, and phenotypic, transcriptomic, and metabolomic assessments. Altitude-dependent shifts were observed in microbial community composition. Functional profiling suggests that rhizosphere microbial communities of P. rotata at low altitude possess enhanced metabolic activity and nutrient cycling capacity. Procrustes analysis revealed strong concordance between potential microbial indicators and phenotypic traits (R[2] = 0.84, p = 0.002 for bacteria, R[2] = 0.82, p = 0.005 for fungi). Transcriptomic analysis identified 3336 and 9208 unigenes associated with phenotypic variation. GO enrichment revealed that low-altitude samples were dominated by growth-related functions, while high-altitude samples favoured defence responses. KEGG enrichment of hub genes supported this pattern, highlighting enhanced developmental and biosynthetic pathways at low altitudes and stress-regulatory processes at high altitudes. Metabolomic analysis identified 658 altitude-associated differential metabolites. KEGG enrichment showed zeatin biosynthesis was prominent at high altitudes, while butanoate, starch, and sucrose metabolism were enriched at low altitudes. Furthermore, random forest analysis of phenotype-associated metabolites revealed that phenylpropanoids and organic acids were characteristic of high-altitude samples, while organoheterocyclic compounds were more typical of low-altitude environments. Mantel test and PLS-SEM modelling jointly revealed that altitude-driven shifts in rhizosphere microbiome function regulate host gene expression and secondary metabolism, ultimately shaping phenotypic variation. This comprehensive research provides novel insights into the environmentally induced phenotypic plasticity of alpine medicinal plants during low-altitude adaptation and offers a deeper understanding of the key drivers of this process.},
}

@article {pmid40836410,
year = {2025},
author = {Quan, J and Liu, X and Liang, S and Nie, L and Zhang, L and Hong, X and He, M and Lei, S and Duan, L and Zhang, Y and Zhuang, L},
title = {Electroacupuncture suppresses motor impairments via microbiota-metabolized LPS/NLRP3 signaling in 6-OHDA induced Parkinson's disease rats.},
journal = {International immunopharmacology},
volume = {162},
number = {},
pages = {115089},
doi = {10.1016/j.intimp.2025.115089},
pmid = {40836410},
issn = {1878-1705},
mesh = {Animals ; *NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; *Electroacupuncture ; *Gastrointestinal Microbiome ; Lipopolysaccharides/metabolism ; Male ; Rats ; Oxidopamine ; Signal Transduction ; Rats, Sprague-Dawley ; Dopaminergic Neurons ; *Parkinson Disease/therapy ; Disease Models, Animal ; Fecal Microbiota Transplantation ; },
abstract = {Emerging evidence indicates that electroacupuncture (EA) exerts significant therapeutic effects on Parkinson's disease (PD)-related symptoms, with the immune mechanisms of the gut-brain axis playing a pivotal role in PD pathophysiology. This study aimed to explore whether EA mitigated PD-related symptoms and conferred neuroprotection to dopaminergic neurons in a 6-hydroxydopamine (6-OHDA) rat model by modulating the microbiota-metabolized lipopolysaccharide (LPS)/NLRP3 pathway. EA treatment ameliorated motor and anxiety symptoms in 6-OHDA rats and elevated the levels of TH. Metabolomic analysis indicated that the therapeutic effects of EA are associated with the gut microbiota and the NOD-like receptor signaling pathway. 16S rRNA sequencing demonstrated that EA significantly modified the composition of the gut microbiota, evidenced by alterations in the relative abundance of 16 genera, and led to the downregulation of the LPS and NOD-like receptor signaling pathways. Additionally, EA was found to attenuate intestinal inflammation, decrease serum inflammatory markers, reduce neuroinflammation, and suppress the overexpression of microglia and astrocytes, while concurrently preserving the integrity of the intestinal and blood-brain barriers. Fecal microbiota transplantation experiments further substantiated the pivotal role of gut microbiota in mediating the anti-PD effects of EA. In summary, EA has the potential to alleviate PD-related symptoms and safeguard dopaminergic neurons by rectifying gut microbiota dysbiosis and downregulating the LPS/NLRP3 immune pathway along the gut-brain axis in PD rat models.},
}

Animals
*NLR Family, Pyrin Domain-Containing 3 Protein/metabolism
*Electroacupuncture
*Gastrointestinal Microbiome
Lipopolysaccharides/metabolism
Male
Rats
Oxidopamine
Signal Transduction
Rats, Sprague-Dawley
Dopaminergic Neurons
*Parkinson Disease/therapy
Disease Models, Animal
Fecal Microbiota Transplantation

@article {pmid40836363,
year = {2025},
author = {Hass, JK and Fernandes, AG and Montague, MJ and Burgos-Rodriguez, A and Martinez, MI and Brent, LJN and Snyder-Mackler, N and Danias, J and Wollstein, G and Higham, JP and Melin, AD},
title = {The ocular surface microbiome of rhesus macaques.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {88},
pmid = {40836363},
issn = {2524-4671},
support = {R01AG060931, R56AG071023, R01AG084706/AG/NIA NIH HHS/United States ; R01AG060931, R56AG071023, R01AG084706/AG/NIA NIH HHS/United States ; R01AG060931, R56AG071023, R01AG084706/AG/NIA NIH HHS/United States ; G2020047//Bright Focus Foundation/ ; G2020047//Bright Focus Foundation/ ; G2020047//Bright Focus Foundation/ ; G2020047//Bright Focus Foundation/ ; 035174/EY/NEI NIH HHS/United States ; NFRFE-2018-02159//New Frontiers Grant/ ; NFRFE-2018-02159//New Frontiers Grant/ ; 950-231257//Canada Excellence Research Chairs, Government of Canada/ ; },
abstract = {BACKGROUND: The ocular surface microbiota (OSM) is important for eye health, and variations in OSM composition have been associated with multiple diseases in humans. Studies of OSM-disease dynamics in humans are confounded by lifestyle factors. Animal models provide a complementary approach to understanding biological systems, free from many confounds of human studies. Here, we provide the first study of the OSM of rhesus macaques, a premier animal model for eye health and disease. We describe the taxonomy of the rhesus macaque OSM, and explore compositional correlations with age, sex, and living condition.

METHODS: We analyzed eyelid and conjunctival microbiota swabs from 132 individual rhesus macaques (Macaca mulatta) (57 males, 75 females, 1-26 years old) from one captive and one free-ranging group using 16 S rRNA V3/V4 MiSeq sequencing. We investigated alpha diversity, beta diversity, and differential abundance.

RESULTS: We found several similarities between the top Phyla and Genera of the rhesus macaque OSM and those reported in human literature. Significantly higher alpha diversity, which may reflect age-related ocular surface mucous membrane integrity and immune function, was present in younger individuals compared to older ones. Higher alpha diversity was also present in free-ranging rhesus macaques compared to ones in captivity, possibly related to differences in diet, exercise, and medical exposures between macaques in different living conditions. Beta diversity was most strongly influenced by individual identity, followed by living conditions. Sex did not correlate with any OSM variation.

CONCLUSIONS: In this study we describe the taxonomic composition of the rhesus macaque OSM, and identify significant differences in alpha and beta diversity according to individual nonhuman primate host variables and the surrounding environment. Our findings suggest composition of the nonhuman primate OSM is shaped by age-related physiology, individual identity, and external living conditions. Our results offer novel insights into an underexplored region of the primate microbiome and highlight the utility of rhesus macaques as a model system for investigating the links between the OSM, ocular health, and disease.},
}

@article {pmid40836357,
year = {2025},
author = {Lieberman, OJ and Yao, V and Velasquez, G and Otero, M and Bao, K and Peterson, K and Kobeissy, FH and Pan, JZ and Guan, Z and Hinson, HE and Baranzini, SE and Hemphill, JC and Singhal, NS and Amorim, E},
title = {Higher circulating short-chain fatty acids are associated with good neurologic outcome after cardiac arrest.},
journal = {Critical care (London, England)},
volume = {29},
number = {1},
pages = {371},
pmid = {40836357},
issn = {1466-609X},
}

@article {pmid40836305,
year = {2025},
author = {Zhou, Y and Dong, J and Wang, Z and Huang, C and Yu, X and Wang, X and Yang, B and Wu, Y and Peng, Q},
title = {From background diabetic retinopathy to its proliferative stage. What is the role of gut microbiota in the trajectory of DR? a Mendelian randomization study with mediation analysis.},
journal = {Diabetology & metabolic syndrome},
volume = {17},
number = {1},
pages = {346},
pmid = {40836305},
issn = {1758-5996},
support = {SY-XKZT-2021-1015//Subject Boosting Program of the Shanghai Fourth People's Hospital Affiliated to Tongji University/ ; },
abstract = {BACKGROUND: Growing evidence suggests that gut microbiota (GM) plays a role in diabetic retinopathy (DR), but the causal microbial drivers and their stage-dependent roles during DR progression remain poorly characterised. Using genetic causality methods, we aim to depict a longitudinal GM mapping and stage-stratified GM signatures across the DR trajectory, spanning initial background DR (BDR) through non-proliferative form (NPDR), to advanced proliferative stage (PDR).

METHODS: GWAS data of 207 GM taxa (from phylum to species) were acquired from the Dutch Microbiome Project (N = 7,824), and DR from FinnGen (over 300,000 individuals). A bidirectional two-sample Mendelian Randomization (TSMR) analysis was conducted to elucidate directional causality between GM and DR. Multiple sensitivity evaluations were performed for pleiotropy, heterogeneity, and stability. Additionally, two-step MR and multivariable MR (MVMR) were performed to dissect causal GM-DR relationships using 1400 candidate circulating metabolite level/ratio data from a Canadian cohort (N = 8,299).

RESULTS: We identified 11 causal GM taxa (1 family, 3 genera, and 7 species) during the progression of DR. Notably, species_Bacteroides_dorei and species_Dorea_longicatena demonstrated pan-stage pathogenicity (BDR and PDR, all OR>1, PIVW<0.05), while family_Clostridiaceae (OR = 1.540, 95%CI: 1.110-2.135), genus_Clostridium (OR = 1.473, 95%CI: 1.086-1.997), and species_Eubacterium_ramulus (OR = 1.382, 95%CI: 1.000-1.911) specifically promoted NPDR. Six causal protective GM taxa, comprising four species, Bifidobacterium_longum (OR = 0.540, 95%CI: 0.370-0.788), Bacteroides_stercoris (OR = 0.633, 95%CI: 0.407-0.986), Ruminococcus_torques (OR = 0.771, 95%CI: 0.627-0.948), Roseburia_hominis (OR = 0.652, 95%CI: 0.501-0.849), and two genera, Escherichia (OR = 0.799, 95%CI: 0.638-0.999) and Flavonifractor (OR = 0.825, 95%CI: 0.685-0.993), mitigate NPDR or PDR risks. Among the 76, 90, and 86 causal DR stage-specific metabolites, the mannose-to-hydroxyproline ratio was the only metabolite universally linked to all DR stages, with the other 31 metabolites influencing dual phases. Mediation analysis validated five metabolites (asparagine, cystine, gamma-glutamylglycine, ximenoylcarnitine (C26:1) levels, and androsterone glucuronide to etiocholanolone glucuronide ratio) as key mediators bridging causal GM-DR links, with considerable mediating proportions of 6.75%, 14.90%, 3.03%, 7.25%, and 11.97%, respectively.

CONCLUSION: This study pioneers causal longitudinal mapping of GM dynamics across DR progression through integrated genetic prediction and metabolomic mediation analyses, delineating stage-specific microbial drivers, pan-stage pathogens, and metabolite mediators that collectively orchestrate DR pathogenesis. The identified GM-metabolite-DR axis establishes an actionable roadmap for targeted microbiome modulation and metabolite-based therapeutic strategies, bridging observational associations to mechanistic intervention opportunities.},
}

@article {pmid40836244,
year = {2025},
author = {Yu, LC and Wei, SC and Li, YH and Huang, CY and Pai, YC and Hung, YM and Lai, LC and Ni, YH},
title = {Phenotypic characterization and complete genome of a tumorigenic pathobiont Escherichia coli LI60C3.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {63},
pmid = {40836244},
issn = {1757-4749},
support = {NHRI-EX111/112/113-11108BI//National Health Research Institute, Taiwan/ ; NHRI-EX111/112/113-11108BI//National Health Research Institute, Taiwan/ ; NHRI-EX111/112/113-11108BI//National Health Research Institute, Taiwan/ ; NHRI-EX111/112/113-11108BI//National Health Research Institute, Taiwan/ ; NSTC 113-2320-B002-062-MY3, MoST 110-2320-B-002-011-MY3//National Science and Technology Council, Taiwan/ ; },
abstract = {BACKGROUND: Symbiotic microbes benefit the host, but the emergence of pathobionts leads to disease. An invasive Escherichia coli LI60C3, isolated from mouse colonocytes, shows colitogenic and tumorigenic properties. Despite extensive research on the role of microbiota in colorectal cancer (CRC) development, the genetic markers associated with this pathobiont remain elusive. The objective is to characterize the tumorigenic E. coli through whole-genome sequencing (WGS) and phenotypic assays, and validate their presence in human CRC.

METHODS: The intracellular bacterial counts and proliferation rates of human intestinal epithelial cells were evaluated after exposure to various E. coli strains. Tumor burden was assessed in mice orally administered LI60C3. WGS of LI60C3 was performed on a PacBio Sequel II platform, and the long reads were assembled de novo for gene annotation and detection of virulence factors and antibiotic resistance. Bacteria-specific genes were assessed in CRC specimens by qPCR analysis.

RESULTS: A 100-fold increase in intracellular bacterial count was observed in epithelial cells exposed to LI60C3 compared to commensal E. coli strains. LI60C3 resulted in a threefold increase in epithelial cell cycle rate and a fourfold rise in mouse tumor numbers. WGS revealed a circular chromosome of 4,863,930 bases for LI60C3, demonstrating a high sequence homology to adherent-invasive E. coli LF82 (91%) and NC101 (87%) and to uropathogenic E. coli 536 (88%). Two extrachromosomal plasmids, pTra and pCoMb, were identified. While pTra exhibits sequence homology with other commensal E. coli plasmids, pCoMb has partial matches with those found in pathogenic bacteria. LI60C3 is classified as phylogroup B2 and expresses virulence factors, including Type 1 and P fimbriae, contact-dependent growth inhibition system, iron acquisition system, and hemolysin. Unique gene clusters, named Epm and Phz islands, were identified in the LI60C3 genome. The emergence of LI60C3-specific genes was observed in mouse tumors induced by chemicals and gene mutation, and higher levels of LI60C3 markers were validated in human CRC specimens compared with healthy mucosal samples.

CONCLUSION: Genetic signatures of LI60C3 were detected in mouse and human CRC. The comparative genome analysis for LI60C3 helps identify pathobionts and may be used as cancer predictors.},
}

@article {pmid40791484,
year = {2025},
author = {Caetano-Silva, E and Hilt, M and Valishev, I and Lim, C and Kasperek, M and Shrestha, A and McCusker, R and Armstrong, H and Loman, B and Bailey, M and Allen, JM},
title = {Social stress worsens colitis through β-adrenergic-driven oxidative stress in intestinal mucosal compartments.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40791484},
issn = {2692-8205},
abstract = {Psychological stress is a known risk factor for inflammatory bowel disease (IBD), but the mechanisms linking stress to worsened disease remain unclear. Because distinct stress paradigms activate different neuroimmune circuits, it is critical to investigate model-specific effects. We examined how social stress primes the gut for heightened inflammation and whether this is mediated by specific neuroendocrine pathways, including α2-/β-adrenergic (sympathetic) or glucocorticoid/ corticotropin-releasing hormone receptor (CRHR1) (HPA axis) signaling. Mice were exposed to social disruption (SDR) stress and pretreated with pharmacological antagonists targeting α2-adrenergic receptors (idazoxan), β-adrenergic receptor (β-AR) (propranolol), glucocorticoid receptor (mifepristone), or CRHR1 (antalarmin). Intestinal epithelial cell (IEC) gene expression and microbiota composition were assessed following SDR. To determine disease impact, SDR was combined with either Citrobacter rodentium infection or dextran sulfate sodium (DSS)-induced colitis, with interventions including the β-AR inhibitor propranolol and the NADPH oxidase inhibitor apocynin. SDR significantly upregulated expression of Dual oxidase 2 (Duox2), Dual oxidase maturation factor 2 (Duoxa2), and inducible nitric oxide synthase 2 (Nos2) in IECs (2- to 8-fold, p < 0.0001), effects reversed by β-AR blockade but not α2-adrenergic, CRH, or glucocorticoid inhibition. SDR also induced microbial dysbiosis, characterized by reduced alpha-diversity and compositional shifts, which was rescued by propranolol. Stress exacerbated disease severity in both infectious (C. rodentium) and chemically induced (DSS) colitis, amplifying colonic expression of Duox2, Nos2, and Ccl2, especially. Apocynin mitigated stress-induced ROS/RNS production and body weight loss even prior to colitis onset, reduced colonic gene expression of key oxidative enzymes, and alleviated both chemically and infectious colitis severity. These findings provide strong evidence that social stress sensitizes the gut to inflammation through β-adrenergic and NADPH oxidase-driven oxidative stress, highlighting potential therapeutic targets for mitigating stress-exacerbated IBD.},
}

@article {pmid40836091,
year = {2025},
author = {Linares-Otoya, L and Shirkey, JD and Chhetri, BK and Mira, A and Biswas, A and Neff, SL and Linares-Otoya, MV and Chen, Y and Campos-Florian, JV and Ganoza-Yupanqui, ML and Jeffrey, PD and Hughson, FM and Donia, MS},
title = {Discovery of a widespread chemical signalling pathway in the Bacteroidota.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40836091},
issn = {1476-4687},
abstract = {Considerable advances have been made in characterizing bioactive molecules secreted by bacteria, yet the regulatory elements controlling their production remain largely understudied. Here we identify and characterize the N-acyl-cyclolysine (ACL) system-a cell-density-dependent chemical signalling system specific to and widespread in the phylum Bacteroidota (formerly Bacteroidetes)-and show that it regulates the expression of co-localized operons encoding diverse secreted molecules. Using genetic and biochemical analyses, combined with structural studies of a key biosynthetic enzyme, AclA, we elucidate the molecular structure of various ACLs and their complete biosynthetic pathway involving L-lysine acylation and ATP-dependent cyclization. Furthermore, we find that secreted ACLs are sensed by a dedicated transcription factor, AclR, resulting in the expression of associated operons and the autoinduction of ACL biosynthesis. Moreover, we show that different Bacteroidota strains produce structurally diverse ACLs and encode transcription factors with varying ligand specificities. Finally, we find that the acl circuit is widely distributed and transcribed in human gut and oral microbiome samples, with clear evidence for an active role in regulating associated operons under host colonization conditions. Understanding the function of the ACL system in different contexts has the potential to reveal details about the biology, ecology and chemistry of the Bacteroidota and how members of this phylum interact with their environments and hosts.},
}

@article {pmid40836070,
year = {2025},
author = {Lim, A and Baek, J and Seo, M and Kim, KY and Kim, S and Kwak, W and Lee, J and Kwak, J and Yoon, WJ and Kim, W and Yoon, S},
title = {Atopic dermatitis-alleviating effects of lactiplantibacillus plantarum LRCC5195 paraprobiotics through microbiome modulation and safety assessment via genomic characterization and in vitro analysis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30545},
pmid = {40836070},
issn = {2045-2322},
abstract = {The efficacy of paraprobiotics from Lactiplantibacillus plantarum LRCC5195 (LP5195-P) in alleviating atopic dermatitis (AD) through microbiome modulation and its safety were evaluated in AD-induced mice. Oral administration of LP5195-P to mice for 8 weeks after AD induction was used to investigate changes in microbiota, immune regulation, and symptoms of dermatitis. Taxonomic analysis of the gut microbiota revealed substantially higher bacterial diversity and abundance in LP5195-P treated group compared to that in negative control. Metabolic analysis revealed significant changes in short-chain fatty acid levels. These microbiome changes correlated with alterations in immune modulation. Furthermore, LP5195-P treatment decreased gene expression related to Treg and Th2 responses in the ileum and skin. Improvements in AD symptoms, including edema and erythema, were observed, and inhibitory effects on histamine release and β-hexosaminidase activity were demonstrated. In conclusion, LP5195-P administration induced a balanced immune response involving gut microbiota and short-chain fatty acids, highlighting its potential as a therapeutic candidate for AD.},
}

@article {pmid40835817,
year = {2025},
author = {Carlberg, C and Blüthner, A and Schoeman-Giziakis, I and Oosting, A and Cocolin, L},
title = {Modulating biological aging with food-derived signals: a systems and precision nutrition perspective.},
journal = {npj aging},
volume = {11},
number = {1},
pages = {76},
pmid = {40835817},
issn = {2731-6068},
support = {952601//European Union's Horizon Europe research and innovation program/ ; 2023/49/B/NZ9/00402//Polish National Science Centre/ ; },
abstract = {Lifespan extension has not prevented age-related decline. We propose that diet acts as a molecular modulator of aging, influencing inflammation, the microbiome, and systemic resilience. Biological age markers and AI-powered multi-omics reveal actionable dietary targets, including food-derived signals and Nutrition Dark Matter. We highlight precision nutrition and the EIT Food Healthy Aging Think & Do Tank as pathways to align science, policy, and practice for healthy aging.},
}

@article {pmid40835787,
year = {2025},
author = {Nguyen, TT and Kim, YK and Nguyen, TVT and Kwon, J and Bang, YJ},
title = {Metabolic profiling and genetic tool development in the mucosal bacterium Selenomonas sputigena.},
journal = {Genes & genomics},
volume = {},
number = {},
pages = {},
pmid = {40835787},
issn = {2092-9293},
support = {Creative-Pioneering Researchers Program//Seoul National University/ ; RS-2023-00217157//Ministry of Education, Science and Technology/ ; 800-20240293//College of Medicine, Seoul National University/ ; },
abstract = {BACKGROUND: Selenomonas sputigena is an anaerobic mucosa-associated bacterium with dual roles in human health-acting as a pathobiont in periodontal disease and exhibiting protective effects in allergic airway inflammation. Despite its clinical significance, its metabolic functions and underlying mechanisms remain poorly defined.

OBJECTIVE: This study aimed to systematically characterize S. sputigena's metabolic capacity and develop genetic tools for functional studies.

METHODS: We reconstructed central carbon metabolic networks through in silico analysis. Growth kinetics, substrate utilization, and fermentation profiles were evaluated experimentally across five carbon sources: glucose, gluconate, glycerol, glutamate, and succinate. Expression of key metabolic genes was quantified by qRT-PCR. Native promoter constructs were developed and tested for GFP reporter expression.

RESULTS: Selenomonas sputigena displayed glucose-preferential growth with rapid consumption (0.70 ± 0.05 mM h⁻[1]) and substantial acetate production (17.76 ± 2.05 mM). Gluconate and glycerol supported moderate growth, while glutamate and succinate were poorly utilized. Gene expression analysis revealed strong substrate-dependent regulation of glycolytic genes, with gap expression correlating with growth performance, while TCA cycle genes maintained constitutive basal expression. Four native promoters successfully drove reporter expression, with Pgap demonstrating superior performance as a growth-responsive reporter.

CONCLUSIONS: This study establishes the first comprehensive metabolic and genetic framework for S. sputigena, revealing glucose-dependent fermentation with high acetate production that may contribute to host interactions. The validated promoter system enables future investigations of host-microbe interactions and therapeutic applications in mucosal environments.},
}

@article {pmid40835614,
year = {2025},
author = {Ma, H and Cornadó, D and Raaijmakers, JM},
title = {The soil-plant-human gut microbiome axis into perspective.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7748},
pmid = {40835614},
issn = {2041-1723},
support = {32201402//National Natural Science Foundation of China (National Science Foundation of China)/ ; 202206205006//China Scholarship Council (CSC)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Soil Microbiology ; *Plants/microbiology ; Soil/chemistry ; Ecosystem ; Animals ; },
abstract = {Microbiomes of soil, plants, and the animal gut are pivotal for key life processes such as nutrient cycling, stress resilience, and immunity. While studies have hinted at a shared microbial reservoir connecting these environments, compelling evidence of a soil-plant-gut microbiome axis is scarce. This perspective explores the potential continuum and diversification of microbes along this axis, highlighting specific microorganisms capable of moving from soil to plants to the human gut. A conceptual framework is proposed to better understand the mechanisms driving interactions among these microbiomes. We also examine how soil, plant, and gut microbiomes may co-evolve and influence one another through reciprocal effects. We consider external environmental factors that could strengthen their interconnections, potentially creating beneficial feedback loops that impact ecosystem and human health.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Soil Microbiology
*Plants/microbiology
Soil/chemistry
Ecosystem
Animals

@article {pmid40835534,
year = {2025},
author = {Song, B and Shi, W and Jia, D},
title = {A bidirectional tango between drugs and bugs.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.08.004},
pmid = {40835534},
issn = {1878-4380},
abstract = {Beyond the commonly considered factor of diet, small-molecule drugs have been identified as effectors of microbiota composition. Recently, two studies (Grießhammer et al. and Kumar et al.) reported that non-antibiotics, like antibiotics, could disrupt gut microbial homeostasis, reducing colonization resistance and facilitating pathogen invasion. These findings hold profound implications for our understanding of drug-host-microbiome interactions.},
}

@article {pmid40835328,
year = {2025},
author = {Cox, DD and Stiffler, AK and Hervé, V and Léger-Pigout, M and Powers, LC and Lopez, PJ and Sosa, OA and Parsons, RJ},
title = {Sailing together: A review of the pelagic Sargassum microbiome.},
journal = {Harmful algae},
volume = {148},
number = {},
pages = {102904},
doi = {10.1016/j.hal.2025.102904},
pmid = {40835328},
issn = {1878-1470},
mesh = {*Sargassum/microbiology ; *Microbiota ; },
abstract = {Pelagic Sargassum, denoting the two species S. natans and S. fluitans, has become a focal point of both scientific and public interest due to recent superbloom events. As a result, investigation into the dynamics of Sargassum-associated microbiota, which was previously quite limited, has regained momentum in the past five years. This review collates the current state of knowledge relating to the Sargassum microbiome as well as synthesizes relevant biogeochemical findings which may aid future efforts in this field. We explore microbiome composition and functional roles within this holobiont, specifically in terms of taxonomic diversity, macronutrient cycling, and the fate of Sargassum-derived organic matter. Despite progress, significant gaps remain in our understanding of the dynamic interactions within these microbial communities and their broader ecological significance. Future research directions are identified alongside recommendations for standardized protocols, emphasizing the need for more in-depth studies utilizing advanced molecular and biogeochemical techniques to unravel the full complexity of the Sargassum microbiome.},
}

*Sargassum/microbiology
*Microbiota

@article {pmid40835113,
year = {2025},
author = {Ullah, W and Alsaiari, M and Jalalah, M and Harraz, FA and Thakur, N and Zidan, NS and Sakran, M and Eraky, M and Salama, ES},
title = {Digestibility, microbiome dynamics, and biogas generation in anaerobic digestion with integrated additives and artificial intelligence.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122640},
doi = {10.1016/j.envres.2025.122640},
pmid = {40835113},
issn = {1096-0953},
abstract = {Addition of abiotic and biotic factors as single or combined in anaerobic digestion (AD) improves the substrate hydrolysis, microbial nexus, and enzymatic activity. The effect of a single abiotic (salinity, micronutrients, and conductive material) or biotic factor (bacteria, fungi, and archaea) on AD has been reviewed previously. However, the recent research trend on combined factors strategies (CFSs) (abiotic with biotic or two abiotic or biotic) in AD has not been reviewed. Thus, this review aims to collect, summarize, and compare the recent studies on CFSs in AD. The impact of CFSs on substrate digestion, biomethanation, microbial abundance, enzyme production, and metabolic pathways is elaborated. The time (initial, middle, and end) of CFSs addition, artificial intelligence (AI) approaches, and technoeconomic analysis are also discussed. Biochar+ micronutrients were the most studied coupled abiotic factors, followed by magnetite+ activated carbon, which are reported to improve the hydrolysis efficiency, biomethane production, and microbial abundance. Combined biotic factors (bacteria+ archaea) improved key methanogens (Methanothrix and Methanosarcina). The majorly reported integrated abiotic and biotic factors were biochar+ archaea, which promoted microbial growth and direct inter-species electron transport, resulting in increased biomethane production (14.4-79%). Modelling, prediction, and optimization of CFSs in AD through artificial intelligence (AI) has high potential. CFSs also offer a short payback period and return on investment. However, further research is required to understand the substrate-specific CFSs, addition time, and mechanisms in AD.},
}

@article {pmid40835099,
year = {2025},
author = {Igudesman, D and Yu, G and Dutta, T and Carnero, EA and Krajmalnik-Brown, R and Smith, SR and Corbin, KD},
title = {Global metabolite profiling in feces, serum, and urine yields insights into energy balance phenotypes induced by diet-driven microbiome remodeling.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajcnut.2025.08.003},
pmid = {40835099},
issn = {1938-3207},
abstract = {BACKGROUND: Preclinical literature and behavioral human data suggest that diet profoundly impacts the human gut microbiome and energy absorption-a key determinant of energy balance. To determine whether these associations are causal, domiciled controlled feeding studies with precise measurements of dietary intake and energy balance are needed. Metabolomics can serve as a readout of microbiome function, helping to identify putative mechanisms mediating these effects. We previously demonstrated that a high-fiber Microbiome Enhancer Diet (MBD) limited in processed foods and fed at energy balance decreased energy absorption and increased microbial biomass relative to a calorie-matched, fiber-poor, highly processed Western Diet (WD).

OBJECTIVE: We aimed to identify metabolomic signatures distinguishing MBD from WD feeding and potential mechanisms mediating the MBD-induced negative energy balance.

METHODS: We deployed global metabolomics in feces, serum, and urine using samples collected at the end of a randomized crossover controlled feeding trial delivering 22 days of an MBD and a WD to 17 persons without obesity. Samples were collected while participants were domiciled on a metabolic ward and analyzed using Ultrahigh Performance Liquid Chromatography-Tandem Mass Spectroscopy. Linear mixed effects models tested metabolite changes by diet. Weighted gene network correlation analysis identified metabolite modules correlated with energy balance phenotypes.

RESULTS: Numerous metabolites were consistently altered by MBD relative to WD feeding in the feces, fasting serum, and urine. Fecal diet-microbiota co-metabolites decreased by an MBD correlated with reduced energy absorption and increased microbial biomass. An MBD shifted the urinary metabolome from sugar degradation to ketogenesis-evidence of negative energy balance.

CONCLUSIONS: Precisely controlled diets disparate in microbiota-accessible substrates led to distinct metabolomic signatures in feces, fasting serum, and/or urine. These diet-microbiota co-metabolites may be biomarkers of a "fed" (MBD) or "starved" (WD) gut microbiota associated with energy balance. These findings lay the foundation for unveiling causal pathways linking diet-microbiota co-metabolism to energy absorption.

NCT02939703https://clinicaltrials.gov/study/NCT02939703?term=NCT02939703&rank=1.},
}

@article {pmid40835086,
year = {2025},
author = {Chan, AA and Noguti, J and Ramirez, NM and Navarrete, M and Lee, DJ},
title = {Primary Cutaneous Melanoma Microbiome is Associated with Overall Survival and Recurrence.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2025.07.028},
pmid = {40835086},
issn = {1523-1747},
abstract = {Melanoma contributes to the highest deaths from skin cancer. The primary melanoma intratumoral microbiome association with clinical outcomes has not been described. We hypothesized that specific microbes may be associated with clinical outcomes as found in other cancers. We performed 16S V1-V3 rRNA gene based microbial profiling of primary melanoma FFPE specimens and found that the bacterial composition of cutaneous melanoma (β-Diversity analysis) was associated with both overall survival and recurrence (P=0.024 and P=0.025), and higher effective number of species (α-Diversity) was associated with both worse overall survival (P=0.048; HR=2.13, 95% CI: [1.15, 6.02]) and earlier time-to-recurrence (P=0.016; HR=2.13, 95% CI: [1.15, 3.94]). Cutibacterium granulosum was associated with better overall survival and lower recurrence. Lower recurrence was also associated with Cutibacterium acnes, Corynebacterium kefirresidentii, and an unclassified Corynebacterium. Conversely, both higher recurrence and worse overall survival were associated with Leuconostoc inhae, Streptococcus salivarius, Collinsella sp900764415, and an unclassified Porphyromonas. While the bacterial microbiome for nasal and oral melanomas was not associated with clinical outcomes, five bacterial OTUs were significantly associated with recurrence versus no recurrence by supervised β-Diversity analysis (P=0.023). These findings highlight a potential role of microbes in the pathophysiology of melanoma.},
}

@article {pmid40835055,
year = {2025},
author = {Ntuli, L and Mtshali, A and Mzobe, G and Pillay, N and Happel, AU and Ngcapu, S},
title = {Developmental challenges in infants WHO are HIV-exposed uninfected.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106078},
doi = {10.1016/j.bbi.2025.106078},
pmid = {40835055},
issn = {1090-2139},
abstract = {INTRODUCTION: The global HIV epidemic continues to affect millions of people and significantly affects children. Approximately 16 million children born to HIV-positive women, categorized as HIV-exposed uninfected (HEU), face unique developmental hurdles despite not contracting the virus. These children are more likely to experience developmental issues due to factors such as exposure to maternal HIV, antiretroviral therapy (ART), nutritional shortages, and adverse social conditions. Research indicates that children who are HIV-exposed but uninfected (HEU) may have subpar neurodevelopmental outcomes compared to those born to HIV-negative women. Despite the growing awareness of HEU children's challenges, there remains a gap in comprehensive reviews that synthesize knowledge about the influences on their development, especially with current ART protocols. This review examines these developmental challenges, focusing on growth and neurodevelopmental outcomes; the effects of maternal HIV infection and ART; and the influence of nutrition, socio-environmental factors, and biological mechanisms on health outcomes in HEU infants.

DISCUSSION: Children with HEU are at higher risk of growth deficits and neurodevelopmental delays. Maternal health issues, such as poor nutrition and mental health disorders, adversely affect fetal and postnatal development. Socioenvironmental conditions also shape the developmental outcomes of HEU children. In-utero exposure to HIV and antiretroviral drugs (ARVs), along with neonatal ARV exposure during breastfeeding, can negatively affect an infant's immune function, brain structure, growth patterns, and neurodevelopment. While studies have shown differences between children born HIV-uninfected but exposed to HIV/ARV and their unexposed peers, several limitations have been noted. Much of the immunological, neurological, and mortality data in children born HIV-uninfected but exposed to HIV/ARV lacks non-HIV-exposed and ARV-exposed controls, making it challenging to distinguish between the effects of ARVs and HIV exposure. These limitations emphasize the need for future studies with well-defined control groups to isolate the effects of ARVs from HIV exposure better.

CONCLUSION: HEU infants face multifactorial developmental challenges arising from the interplay of biological factors, including maternal immune activation, systemic inflammation, ART-related mitochondrial toxicity, and altered infant immune function and socio-environmental determinants such as nutritional deficiencies, food insecurity, and maternal mental health disorders. These interacting factors collectively impair growth, neurodevelopment, and immune competence. To mitigate these adverse outcomes, targeted interventions are urgently needed, including optimizing ART regimens to reduce infant toxicity, implementing comprehensive nutritional and food security support for mothers and children, addressing maternal mental health and psychosocial wellbeing, and strengthening early childhood development programs alongside improved healthcare access. Future research must employ rigorous longitudinal designs with well-matched control groups to disentangle the effects of HIV and ART exposure and to inform effective, integrated strategies that promote optimal health and development in HEU children.},
}

@article {pmid40835054,
year = {2025},
author = {Wu, Y and Tao, S and Xiao, L and Zhang, J and Tang, Y and Zhang, M and Liu, S and Huang, Y and Liu, Y and Xie, M and Zhao, Z and Lv, Q and Cai, J and Pei, K and Ma, Q and Yin, Y and Dai, M and Wei, M and Chen, Y and Wang, Q},
title = {Gut virome alterations in schizophrenia: identifying viral biomarkers associated with schizophrenia and treatment response.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106080},
doi = {10.1016/j.bbi.2025.106080},
pmid = {40835054},
issn = {1090-2139},
abstract = {BACKGROUND: The gut virome is an important component of the microbiome with potential implications for schizophrenia. However, its role in disease pathology and treatment response remains unclear.

METHODS: We performed metagenomic sequencing on fecal samples from 49 first-episode schizophrenia patients and 49 healthy controls. Viral diversity and taxonomic profiles were compared between groups. Within patients, we assessed associations between viral alpha diversity and symptom severity, as well as between specific viral taxa and treatment outcomes, including short- and long-term PANSS reduction and response trajectories. Response trajectories were identified by clustering patients based on the longitudinal PANSS reduction patterns.

RESULTS: There were no significant differences in alpha diversity between schizophrenia patients and healthy controls. Among patients, higher viral diversity was associated with more severe negative symptoms. Although several viral taxa showed nominal associations with schizophrenia, none remained significant after FDR correction. Regarding treatment outcomes, the abundance of Brigitvirus was negatively associated with the 6-week symptom reduction rate (FDR = 0.012), and two viral species were reduced in the low-response trajectory group.

CONCLUSIONS: Although virome differences between patients with schizophrenia and healthy controls were modest, associations between viral features and both symptom severity and treatment response indicate potential clinical relevance.},
}

@article {pmid40834540,
year = {2025},
author = {Sun, T and Delaplace, P and Li, G and James, A and Pan, J and Zhang, J},
title = {Biosolids application to agricultural soil: Heavy metal as key driver of antibiotic resistance under co-occurrence of multiple selective pressures.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139603},
doi = {10.1016/j.jhazmat.2025.139603},
pmid = {40834540},
issn = {1873-3336},
abstract = {The application of biosolids can improve soil fertility and nutrient cycling but also can pose risks of heavy metals and antibiotics introduction. The individual effects of heavy metals and antibiotics accumulation on soil microbial communities and functions have been reported, however, their combined effects during biosolids application to agricultural soil remain unclear. In order to explore the effects of long-term biosolids application on soil microbial communities, we sampled soil from a field experiment spanning 16 years of biosolids application and determined the abundance of resistance genes in the soil. The results showed that long-term biosolids application significantly increased the abundance of antibiotic resistance genes (ARGs) and metal resistance gene (MRGs), especially of aminoglycoside and Zn resistance genes. Based on these results we conducted a microcosm experiment that involved the addition of both a heavy metal and an antibiotic to the soil. This experiment showed that both heavy metals and antibiotics significantly affected soil microbial communities, with heavy metals acting as the primary selective pressure, potentially driving the simultaneous enrichment of both metal and antibiotic resistance genes. Further, core microbiome abundance was positively related to ARGs, MRGs and mobile genetic elements (MGEs) abundance, and explained the variations in antibiotic genes. In addition, core microbiome abundance showed positive relationship with microbial community stability. These findings emphasize the need for careful management of biosolids application to mitigate the risks associated with resistance genes accumulation, which could pose long-term ecological and agricultural challenges. Additionally, the positive relationship between core microbiome abundance and microbial community stability underscores the potential role of microbial communities in enhancing soil resilience against environmental stressors.},
}

@article {pmid40834509,
year = {2025},
author = {Poshvina, DV and Balkin, AS and Dilbaryan, DS and Vasilchenko, AS},
title = {Unravelling the response of the soil microbiome to macrolactin A: A metagenomic study.},
journal = {Chemosphere},
volume = {387},
number = {},
pages = {144645},
doi = {10.1016/j.chemosphere.2025.144645},
pmid = {40834509},
issn = {1879-1298},
abstract = {The development of environmentally sustainable biopreparations for crop protection requires comprehensive assessment of their microbiome impacts. This study investigates how macrolactin A (McA)-a polyketide antibiotic produced by plant-beneficial Bacillus velezensis-shapes soil microbial communities and antibiotic resistance gene (ARG) profiles under various agricultural scenarios. Using high-throughput metagenomics and network analysis, we compared untreated soils with those exposed to two McA concentrations: a high dose (10 mg/kg soil, representing potential point-source accumulation) and a low dose (1 mg/kg, mimicking natural rhizosphere levels). While overall ARG α- and β-diversity remained stable, we observed significant taxonomic restructuring, with Pseudomonadota increasing by 1.36-2.15 % and Actinomycetota declining by 1.14-1.74 % across treatments. Resistome analysis showed dose-dependent ARG selection: control soils favored target alteration mechanism, whereas McA promoted efflux, inactivation, and protection mechanisms. Network analysis demonstrated disruption of complex ARG-host associations, as control-dominant genera belonging to Actinomycetota (Conexibacter, Baekduia, and Capillimicrobium) maintaining 16-21 ARGs per genome decreased, while genera belonging to Pseudomonadota (Bradyrhizobium, Mesorhizobium, Paraburkholderia, and Piscinibacter) with streamlined resistomes (1-2 ARGs) became prevalent. Functional gene profiling (COGs) and annotation of MAGs revealed dose-dependent restructuring: low-dose McA enriched chemotaxis systems and broad-spectrum efflux pumps, facilitating motile escape and energy-efficient resistance, whereas high-dose exposure selected for secondary metabolite synthesis, metal transporters, and cell wall remodeling genes, indicating defensive countermeasures. These findings demonstrate McA's biphasic selection: low doses favor avoidance strategies (efflux/motility), while high doses enforce biosynthetic defenses and structural resilience. The results support the hypothesis that narrow-spectrum antibiotics act as ecosystem engineers through metabolic trade-offs, highlighting the need to evaluate resistome restructuring in biocontrol agent risk assessments.},
}

@article {pmid40834321,
year = {2025},
author = {Busenitz, K and Lundgren, JG},
title = {No effects of human-grade probiotics on Apis mellifera (Hymenoptera: Apidae) health metrics.},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toaf210},
pmid = {40834321},
issn = {1938-291X},
abstract = {Dietary-administered probiotics may address poor health and performance in honey bees (Apis mellifera L. [Hymenoptera: Apidae]). Human-grade probiotics are an affordable source of general probiotics. We examined the effects of human-grade probiotics by comparing colony and individual level health and performance between colonies administered a probiotic every other week, and those not given probiotic supplementation (control treatment group). We found that probiotics did not statistically increase individual honey bee health and performance as measured by body lipid level, tibial length, and weight of bees, nor colony performance as measured by monthly assessments of brood area, colony weight, and Varroa destructor Anderson and Trueman (Mesostigmata: Varroidae) mite infestation rate.},
}

@article {pmid40834262,
year = {2025},
author = {Lee, SH and Lopes, E and Colombel, JF and Ungaro, R},
title = {Identifying Potential Targets for the Interception of Inflammatory Bowel Disease: Toward Precision Prevention.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf168},
pmid = {40834262},
issn = {1536-4844},
support = {1K23DK136977-01A1/NH/NIH HHS/United States ; },
abstract = {There is growing recognition that inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), is preceded by a prolonged preclinical phase marked by subtle but measurable changes in the immune system, gut microbiome, and epithelial barrier function. These early alterations, often detectable years before diagnosis, offer a window of opportunity for disease interception. In this review, we examine the current evidence for environmental, microbial, and molecular factors that may contribute to the initiation of IBD, with a particular focus on modifiable risk pathways. We discuss preventive strategies across different levels of risk-from lifestyle and environmental interventions in the general population to more targeted approaches in individuals with familial predisposition, such as first-degree relatives. We also highlight recent findings on emerging biomarkers, including anti-flagellin antibodies, anti-GM-CSF autoantibodies, glycome, and integrin-targeted immune responses, that could guide precision prevention efforts. While most evidence to date has focused on CD, we also review preclinical insights relevant to UC. As the field moves toward earlier identification of at-risk individuals, the concept of "precision prevention"-matching interventions to individual risk and biology-may ultimately shift the paradigm of IBD care from treatment to prevention.},
}

@article {pmid40833852,
year = {2025},
author = {Vander Donck, L and Victor, M and Van Beeck, W and Van Rillaer, T and Dillen, J and Ahannach, S and Wittouck, S and Allonsius, CN and Lebeer, S},
title = {Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli.},
journal = {Cell reports},
volume = {44},
number = {9},
pages = {116171},
doi = {10.1016/j.celrep.2025.116171},
pmid = {40833852},
issn = {2211-1247},
abstract = {The human vagina is a unique microbiome, typically predominated by Lactobacillus species in healthy women. However, we currently lack an understanding of why lactobacilli predominate in this environment and how these bacteria interact, aspects that are crucial for developing microbiome-based therapeutics. In this study, we used cost-efficient synthetic communities (SynComs) to investigate the stability and dynamics of Lactobacillus-predominated vaginal communities from healthy women independent of host influence. Reproducible communities of Lactobacillus crispatus co-occurring with Limosilactobacillus species and Lactobacillus jensenii were established in top-down experiments. Co-occurrence was verified with compositional correlation patterns in metagenome sequencing data and reproduced through a bottom-up approach. This co-occurrence pattern was independent of strain selection, host factors, and inoculation ratio. Genome-scale metabolic models predicted potential cross-feeding involving amino acids (e.g., L-arginine, L-lysine, and γ-aminobutyric acid [GABA]) and vitamins as mechanisms mediating their co-occurrence. This study provides a framework for developing reproducible synthetic vaginal Lactobacillus communities and informs future microbiome-based therapies.},
}

@article {pmid40833644,
year = {2025},
author = {AlBeshri, S},
title = {Perspectives on tongue coating: etiology, clinical management, and associated diseases - a narrative review.},
journal = {The Saudi dental journal},
volume = {37},
number = {7-9},
pages = {41},
pmid = {40833644},
issn = {1013-9052},
abstract = {Tongue coating (TC) is a biofilm comprising desquamated epithelial cells, food debris, and microorganisms. TC is commonly found across populations and may hold significant implications for both oral and systemic health. Factors such as age, diet, smoking, and systemic conditions influence its formation. TC is a primary reservoir for pathogenic bacteria and is closely linked to halitosis and periodontal disease. Beyond oral health, TC has been associated with systemic diseases, including aspiration pneumonia, cardiovascular disease, and diabetes, through mechanisms involving microbial translocation and low-grade inflammation. Literature search was performed using search engines and databases including, PubMed, Google Scholar, Web of Science and Medline, utilizing key words such as "Tongue coating," "Tongue cleaning," "Halitosis and Oral malodor". This review assesses the etiology, composition, and health implications of TC, highlighting its microbial diversity and correlation with oral and systemic conditions. Additionally, it examines interventions such as mechanical cleaning, chemical treatments, and dietary modifications to manage TC effectively. Emphasizing tongue hygiene as part of routine oral care is crucial for enhancing oral health, mitigating systemic risks, and improving quality of life.},
}

@article {pmid40833633,
year = {2025},
author = {Castillo-Lopez, E and Hartinger, T and Ricci, S and Xu, K and Schwartz-Zimmerman, H and Berthiller, F and Reisinger, N and Zebeli, Q},
title = {The severity of subacute ruminal acidosis of primiparous transition cows affects the fecal metabolome, without affecting the fecal microbiome of the cows or their calves.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf213},
pmid = {40833633},
issn = {1365-2672},
abstract = {AIMS: To evaluate the effects of the severity of subacute ruminal acidosis (SARA) on the fecal microbiome and metabolome of primiparous transition cows, and the fecal microbiome and blood composition of the offspring; to investigate the effect of transition from gestation to lactation on the fecal microbiome of cows.

METHODS AND RESULTS: The study included 24 cows; three SARA severities were evaluated: low, moderate, and high. Analyses of the fecal microbiome and metabolome of cows were performed from week 3 before parturition until week 10 in lactation; fecal microbiome of calves was evaluated at 1 week of age. Blood composition of calves was evaluated at days 1 and 7. Compared to low, greater SARA severity did not affect the fecal microbial diversity or abundance in cows, but increased concentrations of fecal amino acids and their derivatives in high SARA, resulting in enrichment of metabolic pathways for amino acid metabolism. No negative effects of SARA severity were found on the offsprings' fecal microbiome or blood composition. Fecal amylolytic bacteria increased in cows post-calving at the expense of fibrolytic and methanogenic taxa.

CONCLUSION: SARA severity influenced the fecal metabolome of transition cows, but no negative impacts were found on the fecal microbiome of cows or on the microbiome and blood composition of the offspring.},
}

@article {pmid40833598,
year = {2025},
author = {Cai, T and Su, D and Tang, Z and Liu, J and Tang, W and Wu, Y and Wang, F},
title = {Biotransformation and disposition of C[14]-labeled sonrotoclax ([[14]C]BGB-11417) in preclinical safety species and characterization of unique contribution from gut microbiome.},
journal = {Cancer chemotherapy and pharmacology},
volume = {95},
number = {1},
pages = {82},
pmid = {40833598},
issn = {1432-0843},
mesh = {Animals ; Dogs ; Mice ; Biotransformation ; *Gastrointestinal Microbiome/physiology ; Tissue Distribution ; Humans ; Carbon Radioisotopes ; Male ; Feces/microbiology/chemistry ; Female ; *Antineoplastic Agents/pharmacokinetics ; },
abstract = {INTRODUCTION: Sonrotoclax (BGB-11417), a second-generation B-cell lymphoma-2 (BCL-2) inhibitor currently in clinical development, requires comprehensive verification of its biotransformation and disposition profiles in safety species.

METHODS: [[14]C]BGB-11417 was employed to assess its pharmacokinetics, excretion, tissue distribution and metabolite profiles in mice and dogs. Radioactivity in plasma and excreta were analyzed to determine pharmacokinetics and mass balance. The metabolite profiles were generated by the chromatographic separation coupled with radioactivity detector/ mass spectrometry. Quantitative whole-body autoradiography (QWBA) was performed to assess tissue distribution in both pigmented or albino mice. Anaerobic human fecal incubation was conducted to evaluate the biotransformation contribution of gut microbiome.

RESULTS: Tmax of [[14]C]BGB-11417 radioactivity was observed at 4 h, with a T1/2 ranging 6.5-7.2 h in both species. The highest tissue exposure was noted in metabolic and excretory organs, with 90% of the administered radioactivity eliminated through mouse excreta within 48 h. Prolonged excretion kinetics accompanied by marked inter-individual variability were observed in dog excreta. A distinct nitro-reduction pathway was detected exclusively in dogs. These metabolites were also detected in anaerobic incubations of [[14]C]BGB-11417 with human feces. Aerobic incubation of the nitro-reduction metabolite with dog feces directly yielded lipid-conjugated products, confirming that conjugation occurs spontaneously post-reduction rather than on the parent drug.

CONCLUSION: The concordance between dog fecal metabolites and human fecal incubations underscored cross-species gut microbiome similarities. These findings offer a mechanistic insight into the fate of sonrotoclax in organisms and guide the interpretation of metabolic clearance in human.},
}

Animals
Dogs
Mice
Biotransformation
*Gastrointestinal Microbiome/physiology
Tissue Distribution
Humans
Carbon Radioisotopes
Male
Feces/microbiology/chemistry
Female
*Antineoplastic Agents/pharmacokinetics

@article {pmid40833556,
year = {2025},
author = {Yuan, Y and Zhao, L and Ding, H and Hua, Y and Wang, H and Zhao, M},
title = {Characterization of intestinal microbiota in patients with psoriasis combined with metabolic syndrome.},
journal = {Molecular and cellular biochemistry},
volume = {},
number = {},
pages = {},
pmid = {40833556},
issn = {1573-4919},
support = {2023129//Tianjin Municipal Health Committee/ ; 2022003//Scientific Research Program of Tianjin Key Area of Traditional Chinese Medicine/ ; },
abstract = {The co-morbidity of psoriasis (PsO) and metabolic syndrome (MetS) is prevalent. While the mechanisms causing PsO in MetS remain unknown, it is understood that gut microbiota plays a critical role in maintaining immune and metabolic balance. However, the specific mechanisms and whether biomarkers are involved in the pathophysiological process of PSO in MetS patients have yet to be elucidated. This study involved 29 patients with PSO and MetS (PM) and 29 with MetS (M). It analyzed their clinical parameters, microbial composition, function, diagnostic, and predictive performance. The results unveiled significant differences between the two groups concerning microbial diversity and community composition. Most of the differential microbiota in the PM group exhibited a negative correlation with high-density lipoprotein (HDL) and a positive correlation with serum uric acid (SUA). In contrast, the opposite was observed in the M group. Sixteen MetaCyc pathways showed significance in the PM group, encompassing peptidoglycan biosynthesis II (staphylococci), the super pathway of L-arginine and L-ornithine degradation, teichoic acid (poly-glycerol) biosynthesis, and palmitic biosynthesis II (bacteria and plants). Six KEGG pathways were enriched in the M group, such as flavone, flavonol biosynthesis, and carotenoid biosynthesis. Most importantly, we determined that eight biomarkers, represented by Akkermansia, demonstrated robust diagnostic predictive power. This study elucidates the potential mechanism through which metabolic disorders impact the onset and progression of psoriasis via intestinal microbiota. Furthermore, it offers novel strategies for preventing, diagnosing, and treating PsO in MetS.},
}

@article {pmid40833490,
year = {2025},
author = {Pang, S and Yu, S and Zhang, J},
title = {Methodological considerations in gut microbiota research on IgA vasculitis: terminology, data presentation, and evidence limitations.},
journal = {International urology and nephrology},
volume = {},
number = {},
pages = {},
pmid = {40833490},
issn = {1573-2584},
support = {No. 2025ZD01//2025 Key Research Project of Shanghai Sanda University/ ; },
}

@article {pmid40833093,
year = {2025},
author = {Lai, Z-L and Su, Y-D and Lin, H-H and Wang, S-Y and Lin, Y and Liang, S and Chen, W-C and Hsueh, P-R},
title = {Deciphering the impact of contaminating microbiota in DNA extraction reagents on metagenomic next-generation sequencing workflows.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0311924},
doi = {10.1128/spectrum.03119-24},
pmid = {40833093},
issn = {2165-0497},
abstract = {UNLABELLED: The widespread adoption of metagenomic next-generation sequencing has revolutionized microbial detection, yet contaminating DNA in laboratory reagents poses significant challenges for result interpretation. This study investigated microbial contamination profiles across four commercial DNA extraction reagent brands (M, Q, R, and Z) and assessed batch-to-batch variability. Extraction blanks were generated using molecular-grade water or ZymoBIOMICS Spike-in Control I as input materials. Analysis revealed distinct background microbiota profiles between brands, with some containing common pathogenic species that could affect clinical interpretation. Notably, background contamination patterns varied significantly between different lots of the same brand, highlighting the need for lot-specific microbiota profiling. Site-specific environmental contaminants were identified through analysis of 30 control samples from a single study site. Additionally, comparison of blood samples from healthy individuals with control samples suggested no evidence of a consistent blood microbiome, suggesting that "extraction blanks" may serve as negative controls in clinical metagenomic testing of sterile liquid biopsy samples. These findings emphasize the importance of including negative controls in every run and underscore the need for manufacturers to provide comprehensive background microbiota data for each reagent lot to optimize clinical interpretation and minimize false-positive results.

IMPORTANCE: Metagenomic next-generation sequencing (mNGS) has revolutionized pathogen detection and microbiome studies, but contamination from DNA extraction reagents remains a critical challenge. This study highlights the significant variability in background microbiota profiles across reagent brands and manufacturing lots, emphasizing the need for manufacturers to provide detailed contamination profiles. Our findings underscore the importance of implementing extraction blanks as standard controls and incorporating bioinformatics tools to account for background noise. These measures are essential to enhance the reliability of mNGS results and prevent diagnostic errors, particularly in clinical settings where contamination could mask or mimic pathogen signals. Additionally, our confirmation that healthy blood lacks a consistent microbiome helps streamline control selection in clinical testing protocols, potentially reducing costs and complexity in clinical mNGS workflows.},
}

@article {pmid40832934,
year = {2025},
author = {McDonald, JT and Rogers, CJ and Nishita, D and Ghandhi, SA and Taraboletti, A and Morton, SR and Shuryak, I and Bakke, J and Gahagan, J and Pannkuk, EL and Authier, S and Aryankalayil, MJ and Chopra, S and Sproull, M and Shankavaram, U and Camphausen, K and Garty, G and Amundson, SA and Brenner, DJ and Turner, HC and Schaaf, GW and Olson, JD and Cline, JM and Menon, N and Laiakis, EC and Fornace, AJ and Chang, P},
title = {Multicentered Biospecimen Analyses after 4 Gy Sublethal Total Body Irradiation in Rhesus.},
journal = {Radiation research},
volume = {},
number = {},
pages = {},
doi = {10.1667/RADE-24-00008.1},
pmid = {40832934},
issn = {1938-5404},
abstract = {In the event of a large-scale radiological emergency, delivering timely medical aid to individuals receiving potentially lethal doses of radiation will result in improved survival and decreased severity of injuries. While it may be possible to reconstruct a dose estimate based on a location during the event and/or early symptoms presenting after the event, limitations with readily available information and inaccuracy of that estimate may not provide enough certainty for successful medical triage. Thus, individual biodosimetry assessments would assist medical professionals in providing prompt care to those who would benefit the most. In this study, a variety of accessible biospecimens (blood, plasma, serum, feces, saliva, and urine) from eight rhesus macaques irradiated with a single total body sublethal dose of 4 Gy of 60Co γ rays were collected before and up to 60 days after exposure for distribution to 10 different investigators' work sites for site-specific analyses. Results showing statistically significant changes in hematology parameters as well as gene, protein, and metabolite expression have since been published. Here, these results are combined and integrated with new data from microRNA (miRNA) expression in plasma samples as well as 16S rRNA sequencing and metabolomics data from fecal samples. A total of 40 unique miRNAs were significantly expressed on days 3, 6, 30, or 60. Metabolomic analysis of fecal samples found changes in multiple pathways, including steroid hormones, C18 (sex) hormones, and bile acid synthesis. Temporal changes were found in the gut microbiome for microbial abundance and richness. Finally, a retrospective view of the collective results demonstrated common overlapping pathways that were enriched from significantly altered biomarkers. This large, collaborative study from a single irradiated cohort demonstrates the utility of multiple timepoints, biospecimen types, and omics technologies that collectively identified 61 common biomarkers across 4 omics platforms that were enriched for pathways relevant to an acute radiation injury to the hematopoietic system that may aid future radiation biodosimetry efforts.},
}

@article {pmid40832705,
year = {2025},
author = {Heymsfield, SB and Atherton, PJ and Christensen, S and Tewksbury, C and Velazquez, A and Walter, J and Blaak, EE},
title = {Evolution of multidisciplinary obesity treatments: past, present, and future role of nutrition.},
journal = {Obesity (Silver Spring, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1002/oby.24340},
pmid = {40832705},
issn = {1930-739X},
support = {//Abbott Nutrition Medical Affairs and Research/ ; },
abstract = {Obesity is a complex chronic disease requiring lifelong comprehensive treatment. In addition to lifestyle counseling that improves nutrition and physical activity, a promising new generation of obesity medications has been added to bariatric procedures as therapeutic options to achieve weight reduction and improve health outcomes. With the promise of effective and safe treatments comes the need to emphasize maximal reduction of body fat and minimal loss of vital body components, including skeletal muscle and bone. Nutrition is a critical aspect of obesity care and is leveraged to support preservation of lean tissues, such as skeletal muscle, through adequate, daily, high-quality protein intake and intake of key micronutrients. More targeted nutrition approaches that promote muscle protein synthesis include amino acid supplementation with leucine and its metabolite β-hydroxy β-methylbutyrate. Another potential target for support is the gut microbiome, as its adequate function is increasingly seen as playing a role in human health and metabolism. Obesity is a heterogenous disease, and there is considerable interest in specific metabolic phenotypes that might be used to tailor nutrition strategies. As research advances on these and other fronts, there is the potential to identify precision nutrition strategies for individualized, more effective approaches to lifelong obesity management.},
}

@article {pmid40832693,
year = {2025},
author = {Kret, Z and Akinola, OM and Ahlidja, W and Joe, B},
title = {Food as Medicine for Hypertension: Microbiota as Mediators.},
journal = {Hypertension (Dallas, Tex. : 1979)},
volume = {},
number = {},
pages = {},
doi = {10.1161/HYPERTENSIONAHA.125.17950},
pmid = {40832693},
issn = {1524-4563},
abstract = {Hypertension is the single largest modifiable risk factor for chronic cardiovascular and renal diseases and strokes. Approximately 47% of American adults have hypertension. Despite the existence of pharmacological treatments, we remain highly vulnerable to the incidence of hypertension. Research in the past decade has identified microbiota as a previously unrecognized factor that regulates blood pressure. Because microbiota depends on the host food for its sustenance, diet presents as a potential factor to remodel microbiota composition and, thereby, affect blood pressure. Here, we survey the dietary sources of the 6 major food components: carbohydrates, proteins, fats, minerals, vitamins, and water for their ability to influence gut microbiota-mediated blood pressure regulation. Furthermore, beyond food components per se, we discuss how food additives and chemicals used in current agricultural practices could adversely remodel gut microbiota composition and contribute to hypertension. The goal of our work here is 2-prong: (1) to better understand why certain dietary components are beneficial over others for hypertensives because of their ability to remodel gut microbiota composition and (2) to advocate for further research and implementations of dietary interventions in the treatment of hypertension based on their ability to modulate gut microbiota.},
}

@article {pmid40832679,
year = {2025},
author = {Liang, L and Liu, P and Song, D},
title = {Fretibacterium: Exploring Its Pathogenic Potential in Oral Infectious Diseases.},
journal = {Molecular oral microbiology},
volume = {},
number = {},
pages = {e70004},
doi = {10.1111/omi.70004},
pmid = {40832679},
issn = {2041-1014},
support = {2025ZNSFSC0767//the Natural Science Foundation of Sichuan Province/ ; //Technological Innovation and Development Project/ ; 2024-YF05-00565-SN//Chengdu Science and Technology Bureau/ ; },
abstract = {Oral infectious diseases, particularly inflammatory periodontal lesions, exert a substantial impact on healthcare systems and economies, as acknowledged by the World Health Organization. The prevailing consensus attributes the onset of oral infectious diseases to dysbiosis within the intricate oral microbiome. In this context, Fretibacterium-a strictly anaerobic genus whose representative species, Fretibacterium fastidiosum, was classified in 2013 as the third human oral species within the Synergistetes phylum-has garnered attention for its progressive enrichment in periodontitis and distinct abundance profiles in health versus disease. This review synthesizes current knowledge on Fretibacterium's role in periodontal disease, dental caries, endodontic infections, and peri-implantitis, with emphasis on its virulence mechanisms. Then further explore its clinical associations with systemic conditions (e.g., diabetes) and evaluate conventional and emerging therapeutic strategies. By providing evidence-based insights, this work aims to guide clinical management and future research directions.},
}

@article {pmid40832633,
year = {2025},
author = {Ma, Y and Ke, J and Wang, Y and Zhou, Y and Gao, X and Wang, X and Shen, Q},
title = {The improvement effect of insoluble dietary fiber of Polygonatum sibiricum on hyperlipidemia in high-fat diet mice via gut microbiota and metabolites.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1601867},
pmid = {40832633},
issn = {2296-861X},
abstract = {OBJECTIVE: Polygonatum sibiricum is rich in insoluble dietary fiber (IDF), but its antihyperlipidemic effect remains unclear. This study investigated the antihyperlipidemic effect of Polygonatum sibiricum's IDF (PIDF) in high-fat diet mice.

METHODS: Male C57BL/6 J mice were fed with a high-fat diet continuously for 8 weeks. At the same time, the low-dose and high-dose groups were supplemented with 0.5 g/kg·BW and 1.0 g/kg·BW of PIDF, respectively. The weight and food intake of the mice were measured during the experiment. After 8 weeks of feeding, the organ weight, serum indexes, and liver function were investigated. Furthermore, the mechanism of antihyperlipidemic was explained by analyzing the gut microbiota and metabolites.

RESULTS: The results of the LIDF and HIDF showed that the PIDF treatment significantly alleviated the liver and kidney weight and body fat index. PIDF administration remarkably increased the high-density lipoprotein cholesterol level and enhanced hepatic superoxide dismutase activity in high-fat diet-fed mice. The levels of total cholesterol, triglycerides, low-density lipoprotein cholesterol, glucose, and aspartate transaminase in the HIDF were significantly lower than in the high-fat diet group. In addition, PIDF supplements also decreased the ratio of Bacillota to Bacteroidota, increasing the relative abundance of Alistipes and Akkermansia. Furthermore, metabolites suggest that dietary increases in PIDF can promote lipid and amino acid metabolism. Hence, PIDF improves lipid metabolism by regulating the gut microbiome and influencing host metabolism.

CONCLUSION: It can be concluded that PIDF may alleviate hyperlipidemia by regulating cholesterol metabolism, increasing the abundance of beneficial microorganisms, and controlling its metabolites. The results of this study accelerated the application of PIDF in the health food industry.},
}

@article {pmid40832481,
year = {2025},
author = {Kim, J and Kim, Y and Lee, YJ and Lee, HJ and Sim, I and Koh, S and Suh, DH and Jung, ES and Jo, JC},
title = {Gut Microbiome and Metabolome Dynamics as Predictors of Clinical Outcomes in Hematopoietic Stem Cell Transplantation.},
journal = {MedComm},
volume = {6},
number = {9},
pages = {e70334},
pmid = {40832481},
issn = {2688-2663},
abstract = {Hematopoietic stem cell transplantation (HSCT) profoundly disrupts the gut microbiome and metabolome, which in turn influence immune-related complications and patient outcomes. To systematically characterize these perturbations, we performed a longitudinal analysis of fecal microbiota composition and metabolite profiles in HSCT recipients at three critical timepoints: pre-transplant (T1), peri-transplant (T2), and post-transplant (T3). We observed that reduced microbial diversity at T1 and T3 was strongly associated with increased incidence of graft-versus-host disease (GVHD), progressive disease (PD), and decreased overall survival (OS). Metabolomic profiling revealed a significant decline in short-chain fatty acids (SCFAs), particularly acetate, from T1 to T2, which correlated with adverse clinical outcomes including GVHD, diarrhea, PD, and lower OS. Elevated levels of uric acid at T2 were predictive of GVHD onset, while decreased 1-phenylethylamine was linked to transplant-associated diarrhea. Furthermore, enrichment of beneficial bacterial taxa such as Lachnospiraceae and Ruminococcaceae was associated with improved survival. Together, these findings highlight the gut microbiome-metabolome axis as a dynamic biomarker for HSCT prognosis. This integrated insight offers potential avenues for microbiota-targeted diagnostics and interventions aimed at mitigating transplant-related complications and improving patient survival.},
}

@article {pmid40832390,
year = {2025},
author = {Levy, S and McCauley, KE and Strength, R and Robbins, ES and Chen, Q and Namasivyam, S and Maxwell, G and Hourigan, SK},
title = {Colibactin genes are highly prevalent in the developing infant gut microbiome.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.12.25333511},
pmid = {40832390},
abstract = {Early-life exposure to colibactin-producing pks + gut bacteria is hypothesized to imprint mutations on the colorectal epithelium, increasing the risk of colorectal cancer later in life. We demonstrate an extremely high prevalence of pks+ bacteria (>50% of infants) during the first two years of life, suggesting carriage is likely normal during early-life microbiome development. Further research is needed into the conditions in which carriage can lead to mutagenesis.},
}

@article {pmid40832318,
year = {2025},
author = {Reasoner, SA and Frainey, BT and Hale, OF and Borden, A and Graham, MK and Turner, E and Brenes, LR and Soderstrom, CBW and Green, H and Schmitz, JE and Laub, MT and Kelly, MS and Clayton, DB and Hadjifrangiskou, M},
title = {Unmasking Pathogen Traits for Chronic Colonization in Neurogenic Bladder Patients.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.14.669717},
pmid = {40832318},
issn = {2692-8205},
abstract = {Individuals with neurogenic bladder are particularly susceptible to both chronic bacterial colonization of the bladder and urinary tract infections (UTIs). Neurogenic bladder can arise from a variety of diseases such as diabetes, spinal cord injuries, and spina bifida. To study the ecological and evolutionary dynamics of the microbiome in neurogenic bladder, we developed a longitudinal cohort of 77 children and young adults with spina bifida from two medical centers. We used enhanced urine culture, 16S rRNA sequencing, and whole genome sequencing to characterize the microbial composition of urine and fecal samples. In addition to prospective sample collection, we retrieved prior bacterial isolates from enrolled patients from Vanderbilt's clinical microbial biobank, MicroVU. This allowed us to compare bacterial isolates from the same patients over a period of five years. Urine samples were characterized by high abundance of urinary pathogens, such as E. coli and Klebsiella . From longitudinal isolates from individual patients, we identified two common patterns of urinary tract colonization. We observed either the rapid cycling of strains and/or species, often following antibiotic treatment, or we observed the persistence of a single strain across timepoints. Neither persistence of a strain nor colonization with a new strain or species was associated with increased antibiotic resistance. Rather, in paired longitudinally collected strains from the same patients, mutations were identified in genes that code for cell envelope components associated with immune or phage evasion. Experimental testing revealed that O-antigen/LPS biosynthesis mutations confer protection from the immune system while altering susceptibility to phage predation, reflecting a fitness trade-off. We argue that this unparalleled cohort offers the opportunity to identify mechanisms of bacterial adaptation to the urinary tract that can be exploited in future therapeutic approaches.},
}

@article {pmid40832203,
year = {2025},
author = {Amitabh, P and Parthasarathy, R},
title = {Characterizing trajectories of innate immune cells in larval zebrafish.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.12.669957},
pmid = {40832203},
issn = {2692-8205},
abstract = {It is well established from in vitro studies of immune cells that stimulation by a wide range of potential signals leads to motility and morphology changes. How these physical behaviors manifest inside a living animal remains unclear due to limitations of conventional imaging and analysis approaches. Here, we establish a quantitative framework for imaging and tracking neutrophil and macrophage dynamics in larval zebrafish, spanning a large fraction of the animal for multi-hour timescales with few-minute temporal resolution. We focus especially on the gut, examining innate immune responses to different preparations of the intestinal microbiome. Using light sheet fluorescence microscopy and trajectory analysis of hundreds of individual cells, we characterize speeds, directional persistence measures, and cellular morphology to reveal distinct population behaviors. Individual immune cells exhibit stable motility phenotypes, favoring predominantly motile or non-motile states rather than frequent transitions between them. Gut architecture constrains migration patterns as demonstrated by preferential anterior-posterior movement and a high probability of cells remaining in the vicinity of the gut throughout the imaging duration. Macrophages display significantly reduced sphericity during motile periods compared to non-motile periods, providing a morphological signature that may enable inference of dynamic behavior from static snapshots. Surprisingly, migration patterns remain consistent across diverse microbial conditions - germ-free, conventionally reared, and colonized by two strains of a zebrafish-native Vibrio species - indicating that tissue structure exerts a stronger influence than bacterial stimuli on immune surveillance dynamics. Previously observed tissue damage by the wild-type Vibrio strain, and the resulting recruitment of immune cells towards the damage site, provided the only microbe-specific cellular behavior. These findings reveal innate immune surveillance as a stereotyped process whose characteristics reflect both cellular decision-making and larger-scale anatomical structure.},
}

@article {pmid40832181,
year = {2025},
author = {Chen, L and Camargo, AP and Qin, Y and Koonin, EV and Wang, H and Zou, Y and Duan, Y and Li, H},
title = {A prevalent huge phage clade in human and animal gut microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.10.669567},
pmid = {40832181},
issn = {2692-8205},
abstract = {Huge phages are widespread in the biosphere, yet their prevalence and ecology in the human gut remain poorly characterized. Here, we report Jug (Jumbo gut) phages with genomes of 360-402 kilobase pairs that comprise ~1.1% of the reads in human gut metagenomes, and are predicted to infect Bacteroides and/or Phocaeicola. Although three of the four major groups of Jug phages shared >90% genome-wide sequence identity, their large terminase subunits exhibited only 38-57% identity, suggesting horizontal acquisition from other phages. Over 1,500 genomes of Jug phages were recovered from human and animal gut metagenomes, revealing their broad distribution, with largely shared gene content suggestive of frequent cross-animal-host transmission. Jug phages displayed high gene transcription activities, including the gene for a calcium-translocating P-type ATPase not detected previously in phages. These findings broaden our understanding of huge phages and highlight Jug phages as potential major players in gut microbiome ecology.},
}

@article {pmid40832167,
year = {2025},
author = {Gordon, M and Akyol, TY and Amos, B and Andersen, SU and Williams, C},
title = {KeySDL: Sparse Dictionary Learning for Keystone Microbe Identification.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.07.669165},
pmid = {40832167},
issn = {2692-8205},
abstract = {Identification of microbes with large impacts on their microbial communities, known as keystone microbes, is a topic of long-standing interest in microbiome research. However, many approaches to identify keystone microbes are limited by the inherent nonlinearity and state-dependence of microbial dynamics. Machine learning approaches have been applied to address these shortcomings but often require more data than is available for a given microbial system. We propose a keystone identification approach called KeySDL which reduces the amount of data required by incorporating assumptions about the type of microbial dynamics present in the experimental system. The data are modeled as originating from a Generalized Lotka-Volterra (GLV) model, an architecture commonly used to simulate microbial systems. The parameters of this model are then estimated using Sparse Dictionary Learning (SDL) Compared to existing methods, this approach allows accurate prediction of keystone microbes from small numbers of samples and provides an output interpretable as reconstructed system dynamics. We also propose a self-consistency score to help evaluate whether the assumption of GLV dynamics is reasonable for a given dataset, either through the application of KeySDL or other analysis tools validated using GLV simulation.},
}

@article {pmid40831636,
year = {2025},
author = {Wen, X and Fang, C and Huang, L and Miao, J and Lin, Y},
title = {Mapping total microbial communities and waterborne pathogens in household drinking water in China by citizen science and metabarcoding.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1609070},
pmid = {40831636},
issn = {1664-302X},
abstract = {INTRODUCTION: Access to safe drinking water remains a critical public health priority, as waterborne diseases continue to pose global health risks. In China, microbial contamination in household water supplies is of particular concern. Traditional culture-based monitoring methods are limited in sensitivity and scope, and scaling such efforts nationwide would demand significant resources. Comprehensive, culture-independent microbiome assessments are therefore needed to better characterize microbial risks in tap water.

METHODS: To address this gap, we developed a cost-effective, citizen science-based approach for monitoring the tap water microbiome. Between December 2020 and August 2021, 50 household tap water samples were collected by volunteers across 19 provinces and regions in China, including several samples obtained before and/or after extreme weather events including the 2021 Henan Floods and Typhoon In-Fa. A low-biomass sampling protocol was developed and adopted, and DNA was extracted and analyzed via 16S rRNA gene metabarcoding targeting the V4 region.

RESULTS: Of the 50 samples, 22 were successfully amplified and yielded DNA with a significant number of sequencing reads. High-throughput amplicon sequencing identified 7,635 Amplicon Sequence Variants (ASVs), revealing a diverse microbiome in household tap water. Opportunistic pathogens, including Mycobacterium, Acinetobacter, and Legionella, were detected in all PCR-positive samples. Alarmingly, post-typhoon samples from Changzhou showed a marked increase in the relative abundance of Escherichia coli.

DISCUSSION: Although based on a limited number of sequenced samples, this study highlights potential microbial risks in household tap water, particularly following extreme weather events. The presence of multiple opportunistic and potentially pathogenic taxa underscores the limitations of traditional indicator-based monitoring. Our findings demonstrate the feasibility and scalability of citizen science for microbial water quality survey, offering a complementary tool for national monitoring and informing future public health strategies for water safety.},
}

@article {pmid40831630,
year = {2025},
author = {Martin de Bustamante, MG and Plummer, CE and Caddey, B and Gomez, DE},
title = {The effect of topical antibiotic or antibiotic-corticosteroid treatment on the ocular surface microbiota of healthy horses.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1535095},
pmid = {40831630},
issn = {1664-302X},
abstract = {INTRODUCTION: Information regarding the impact of topical antibiotics with or without corticosteroids on the microbiota of the horses' eyes is limited. This study aimed to describe the bacterial ocular surface microbiota in healthy horses and evaluate the effect of topical antibiotics or antibiotic-corticosteroid medication on the ocular surface microbiota.

METHODS: This was a prospective, randomized, longitudinal, blinded study in which one eye of 12 horses was treated 3 times daily for 7 days with neomycin, polymyxin B and bacitracin ophthalmic ointment (n = 6) or neomycin, polymyxin B and dexamethasone ophthalmic ointment (n = 6). The contralateral eyes operated as untreated controls. The inferior conjunctival fornix of both eyes was sampled at baseline before antibiotic administration (day 0), on days 3, 7, 9, 14, and 30. The ocular surface microbiota was characterized by amplifying the V4 region of the 16S ribosomal RNA gene.

RESULTS: Alpha- (richness and diversity) and beta-diversity (weighted and unweighted UniFrac distances) measurements of the ocular surface microbiota varied similarly after treatments starting on day 1, returning to baseline measurements by day 30. At baseline, the main phyla detected in the ocular microbiota was Proteobacteria, representing 75% relative abundance, followed by Firmicutes and Bacteroidetes. After treatments, Proteobacteria declined in all groups, and Firmicutes and Bacteroidete's relative abundance increased, returning to baseline levels on day 30. The main genera detected on the ocular surface on day 0 were Suttonella, Nicoletella, Pasteurella, and members of the family Moraxellaceae. After treatment, the relative abundance of this bacteria declined in all groups, returning to baseline levels on day 30, although some alterations were still present.

DISCUSSION: Here we show that topical antibiotics administered with or without corticosteroids induce changes in the ocular surface of horses' eyes, and the microbiota appears to return to baseline approximately three weeks after treatment discontinuation.},
}

@article {pmid40831599,
year = {2025},
author = {Armstrong, CN and Saha, S and Aagard, MA and Mahmoud, MY and Varki, NM and Gilbert, NM and Frieboes, HB and Lewis, WG and Lewis, AL},
title = {Preclinical validation of electrospun fibers to achieve vaginal colonization by Lactobacillus crispatus.},
journal = {Frontiers in bacteriology},
volume = {4},
number = {},
pages = {},
pmid = {40831599},
issn = {2813-6144},
abstract = {Communities of bacteria collectively known as the vaginal microbiota reside in the human vagina. Bacterial vaginosis (BV) describes an imbalance of this microbiota, affecting more than 25% of women worldwide, and is linked to health problems such as infertility, cervical cancer, and preterm birth. Following antibiotic treatment, BV becomes recurrent in many individuals. Lactobacillus crispatus is widely believed to contribute to a healthy vaginal microbiome, and its therapeutic application has shown promise in early clinical trials investigating adjunct therapies for lasting treatment of conditions such as BV. There is a pressing need for therapeutic platforms that apply biologically active agents such as probiotic bacteria, to the vagina with little user effort but lasting effect. Here, we use a mouse model to investigate the functional utility and potential harms of soft, slow-dissolving fibers made by electrospinning polyethylene oxide (PEO) and poly(lactic-co-glycolic acid) (PLGA). Blank electrospun fibers that passed quality control checkpoints were administered vaginally in a murine model and compared to animals receiving mock procedures. Fiber administration had no significant effects on mucus glycan markers, vaginal epithelial exfoliation, keratinization, tissue edema or neutrophil infiltration. L. crispatus-loaded fibers enabled L. crispatus colonization in most animals for more than one week. Mice receiving L. crispatus-loaded fibers had significantly higher measured concentrations of lactate in vaginal washes at 48 hrs compared to pre-colonization washes. These data provide pre-clinical proof of concept that vaginal administration of electrospun fibers can achieve viable delivery and vaginal colonization by metabolically active L. crispatus, without eliciting inflammation or injury.},
}

@article {pmid40831218,
year = {2025},
author = {Zhou, L and Wang, C and Gao, J and Wu, X and Li, G and Jiang, X and Xia, Y and Zhang, J and Lv, B and Zhao, F and Zhang, H and Pi, H and Qiu, J and Xu, S and Zou, Z and Chen, C},
title = {Novel Role of Gut-Derived Roseburia Intestinalis in Safeguarding Intestinal Barrier Integrity and Microenvironment Homeostasis During Arsenic Exposure.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e11895},
doi = {10.1002/advs.202511895},
pmid = {40831218},
issn = {2198-3844},
support = {82473594//National Natural Science Foundation of China/ ; KJQN 202200448//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; W0043//Future Medical Youth Innovation Team of Chongqing Medical University/ ; 2023DBXM006//Chongqing Medical Scientific Research Project, Joint project of Chongqing Health Commission and Science and Technology Bureau/ ; CSTB2023NSCQ-LZX0059//Natural Science Foundation of Chongqing/ ; },
abstract = {As a well-known metalloid, arsenic usually causes human intestinal disorders via contaminated drinking water. However, the mechanisms underlying how arsenic induces intestinal injury remain unresolved, and the effective means of intervention are very limited. By establishing an acute arsenic exposure animal model, this work shows that arsenic disrupts the mechanical, chemical, immunological, and biological barriers of the intestine, and thereby changes the microenvironment in the gut. We further verify that the administration of fecal microbiota transplantation with a healthy gut microbiome alleviates the intestinal damage induced by arsenic. Intriguingly, by using 16S rRNA sequencing and anaerobic culture, we identify a novel role of gut-derived strain, Roseburia intestinalis, which exhibits significant protection against arsenic-induced intestinal toxicity in mice. By applying non-targeted metabolomics after arsenic exposure, this work further establishes the beneficial effects and the potential metabolites associated with Roseburia intestinalis, including cacodylic acid, carindone, 3-hydroxymelatonin and L-galacto-2-heptulose, etc. Transcriptomic analysis reveals that the protective effects of Roseburia intestinalis against arsenic-induced intestinal injury include mainly immune-related pathways. Taken together, these findings highlight that supplementation with gut-derived Roseburia intestinalis is an alternative strategy that could be used in the prevention and treatment of arsenic-related intestinal disorders.},
}

@article {pmid40830911,
year = {2025},
author = {Qi, Q and Gao, C and Meng, X and Liu, W and Xue, Y and Yan, Y},
title = {Oral Microbiota Dynamics Across the Lifespan: Age, Sex, Race and Socioeconomic Influences in the US Population.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.70016},
pmid = {40830911},
issn = {1600-051X},
support = {82473650//National Natural Science Foundation of China/ ; 82073572//National Natural Science Foundation of China/ ; 20230484467//Beijing Nova Program/ ; },
abstract = {AIM: The oral microbiota, a complex and dynamic ecosystem, plays a crucial role in human health, yet systematic studies across the lifespan remain limited. This study aimed to investigate variations in the oral microbiota and the effects of key influencing factors on the oral microbiota at different age groups.

MATERIALS AND METHODS: In this study, we analysed the oral microbiota of 9662 individuals aged 14-69 years from the US National Health and Nutrition Examination Survey (NHANES) to explore the impact of demographic, lifestyle and environmental factors on microbial diversity and composition. Microbiological characterisation was done using the participants' oral rinses by 16S ribosomal RNA gene sequencing.

RESULTS: Our findings revealed a clear age-related trend in microbial diversity, with Shannon diversity peaking in middle-aged and declining in older adults. The composition of the oral microbiota also varied significantly with age, as different genera exhibited distinct abundance patterns across the lifespan. Gender and race emerged as key influencing factors, with males showing greater Shannon diversity and greater relative abundances of Atopobium, Megasphaera and Porphyromonas spp., and Whites were enriched in Rothia and Veillonella. Socioeconomic factors and lifestyle, particularly smoking, were strongly associated with shifts in microbial communities.

CONCLUSIONS: These findings provide a comprehensive overview of the dynamic changes in the oral microbiota throughout life and underscore the intricate interplay between host and environmental factors in shaping microbial composition, offering a foundation for future research on microbiota-related health interventions.},
}

@article {pmid40830709,
year = {2025},
author = {Wang, JS and Arrowsmith, ER and Beck, JT and Friedmann, J and Jamal, R and McHale, D and Gardner, H and Chisamore, MJ and Ulahannan, SV},
title = {Phase 1/2, open-label study of oral bacterial supplementation (EDP1503) plus pembrolizumab in participants with advanced or metastatic microsatellite-stable colorectal cancer, triple-negative breast cancer, and checkpoint inhibitor-relapsed tumors.},
journal = {Investigational new drugs},
volume = {},
number = {},
pages = {},
pmid = {40830709},
issn = {1573-0646},
abstract = {We report a phase 1/2 study evaluating EDP1503 (capsule containing Bifidobacterium animalis lactis) ± pembrolizumab in participants with microsatellite-stable colorectal cancer (MSS CRC), triple-negative breast cancer (TNBC), or other tumor types that relapsed after responding to immunotherapy (KEYNOTE-939/EDP1503-101; NCT03775850). Participants (≥ 18 years) had confirmed advanced/metastatic tumors and progressive disease (PD), were intolerant/nonresponsive to recommended treatment, and had measurable disease (RECIST v1.1). Cohorts were: MSS CRC (Cohort A), metastatic/locally advanced TNBC (Cohort B), and PD following partial response/stable disease for ≥ 6 months during anti‒PD-(L)1 therapy (≥ 8 months during anti‒PD-(L)1 therapy plus chemotherapy for non-small-cell lung cancer) (Cohort C). Participants received oral EDP1503 (2 or 4 capsules twice daily [BID]) for 2 weeks, then EDP1503 (2 or 4 capsules BID) plus intravenous pembrolizumab 200 mg every 3 weeks until PD, participant withdrawal, investigator decision, intolerable toxicity, or completion of 35 cycles. Primary endpoints were safety/tolerability, objective response rate (RECIST v1.1), and immune-response rate. Secondary endpoints included duration of clinical benefit, progression-free survival (PFS), and overall survival (OS). Of 69 participants, objective responses were observed in 3 (2 in Cohort B and 1 in Cohort C with partial responses received 4 capsules BID). For participants receiving 4 capsules BID, median duration of clinical benefit (95% CI) was 8.7 months (5.5 months‒not evaluable), median PFS was 1.8 (1.7‒1.9) months, and median OS was 7.8 (2.5‒13.5) months. Grade ≥ 3 adverse events occurred in 28 participants (40.6%), with no new safety signals. EDP1503 plus pembrolizumab had manageable safety but limited clinical activity.Trial registration: KEYNOTE-939, EDP1503-101 trial: ClinicalTrials.gov NCT03775850.},
}

@article {pmid40830705,
year = {2025},
author = {Oulkhir, FE and Allaoui, A and Idbella, A and Danouche, M and Bargaz, A and Biskri, L and Idbella, M},
title = {Bacillus subtilis ED24 Controls Fusarium culmorum in Wheat Through Bioactive Metabolite Secretion and Modulation of Rhizosphere Microbiome.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {89},
pmid = {40830705},
issn = {1432-184X},
mesh = {*Triticum/microbiology/growth & development ; *Fusarium/growth & development/drug effects/physiology ; *Bacillus subtilis/physiology/metabolism ; *Rhizosphere ; *Plant Diseases/microbiology/prevention & control ; *Microbiota ; Soil Microbiology ; Plant Roots/microbiology ; Endophytes/physiology ; Fungicides, Industrial/pharmacology ; },
abstract = {Fusarium culmorum is a soil-borne fungal pathogen causing root and stem rot, seedling blight, and significant yield losses in small grain cereals, including wheat. This study aimed to evaluate the antifungal potential of Bacillus subtilis ED24, an endophytic strain isolated from Ziziphus lotus (L.) roots, and its effects on wheat growth and yield under controlled conditions. In vitro assays demonstrated that B. subtilis ED24 inhibited F. culmorum mycelial growth by up to 87%, associated with the secretion of 37 distinct secondary metabolites, predominantly involved in carbon cycling. In pot experiments, B. subtilis ED24 significantly enhanced wheat germination (85%) and growth compared to infected plants treated with the chemical fungicide tebuconazole. Although nutrient analysis showed significantly higher shoot nitrogen (32.34 mg/pot) and phosphorus (2.41 mg/pot) contents in the B. subtilis ED24 treatment compared to tebuconazole (8.11 and 0.18 mg/pot, respectively), no significant differences were observed when compared to the infected control (C-). Similarly, B. subtilis ED24 led to improved thousand grain weight (40.4 g), protein content (19.98%), and ash content (1.95%) relative to tebuconazole (29.1 g, 18.31%, and 1.74%, respectively), yet these values did not differ significantly from the infected control (C-). Notably, the number of seeds per pot was significantly increased by B. subtilis ED24 compared to the infected control (C-) (113.8 seeds/pot vs. 54.2 seeds/pot). Additionally, B. subtilis ED24 modulated the wheat rhizosphere microbiome, enriching beneficial taxa such as Eurotiomycetes fungal class and the bacterial genus Paramesorhizobium. These findings suggest that the antifungal activity and growth-promoting effects of B. subtilis ED24 are likely mediated through the synthesis of unique bioactive metabolites and microbiome modulation, offering a promising sustainable alternative to chemical fungicides in wheat production.},
}

*Triticum/microbiology/growth & development
*Fusarium/growth & development/drug effects/physiology
*Bacillus subtilis/physiology/metabolism
*Rhizosphere
*Plant Diseases/microbiology/prevention & control
*Microbiota
Soil Microbiology
Plant Roots/microbiology
Endophytes/physiology
Fungicides, Industrial/pharmacology