@article {pmid40267905,
year = {2025},
author = {Zhang, J and Wang, B and Xu, H and Liu, W and Yu, J and Wang, Q and Yu, H and Wei, JW and Dai, R and Zhou, J and He, Y and Zou, D and Yang, J and Ban, X and Hu, Q and Meng, X and Liu, YX and Wang, B and Hu, B and Wang, M and Xin, P and Chu, J and Li, C and Garrido-Oter, R and Yu, P and van Dijk, ADJ and Dong, L and Bouwmeester, H and Gao, S and Huang, A and Chu, C and Li, J and Bai, Y},
title = {Root microbiota regulates tiller number in rice.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.03.033},
pmid = {40267905},
issn = {1097-4172},
abstract = {Rice tillering is an important agronomic trait regulated by plant genetic and environmental factors. However, the role and mechanism of the root microbiota in modulating rice tillering have not been explored. Here, we examined the root microbiota composition and tiller numbers of 182 genome-sequenced rice varieties grown under field conditions and uncovered a significant correlation between root microbiota composition and rice tiller number. Using cultivated bacterial isolates, we demonstrated that various members of the root microbiota can regulate rice tillering in both laboratory and field conditions. Genetic, biochemical, and structural analyses revealed that cyclo(Leu-Pro), produced by the tiller-inhibiting bacterium Exiguobacterium R2567, activates the rice strigolactone (SL) signaling pathway by binding to the SL receptor OsD14, thus regulating tillering. The present work provides insight into how the root microbiota regulates key agronomic traits and offers a promising strategy for optimizing crop growth by harnessing the root microbiota in sustainable agriculture.},
}

@article {pmid40267755,
year = {2025},
author = {Situ, Y and Zhang, P and Zhang, C and Jiang, A and Zhang, N and Zhu, L and Mou, W and Liu, Z and Wong, HZH and Zhang, J and Cheng, Q and Lin, A and Luo, P},
title = {The metabolic dialogue between intratumoural microbes and cancer: implications for immunotherapy.},
journal = {EBioMedicine},
volume = {115},
number = {},
pages = {105708},
doi = {10.1016/j.ebiom.2025.105708},
pmid = {40267755},
issn = {2352-3964},
abstract = {The tumour microenvironment (TME) exerts a profound influence on cancer progression and treatment outcomes. Recent investigations have elucidated the crucial role of intratumoural microbiota and their metabolites in shaping the TME and modulating anti-tumour immunity. This review critically assesses the influence of intratumoural microbial metabolites on the TME and cancer immunotherapy. We systematically analyse how microbial-derived glucose, amino acid, and lipid metabolites modulate immune cell function, cytokine secretion, and tumour growth. The roles of specific metabolites, including lactate, short-chain fatty acids, bile acids, and tryptophan derivatives, are comprehensively examined in regulating immune responses and tumour progression. Furthermore, we investigate the potential of these metabolites to augment the efficacy of cancer immunotherapies, with particular emphasis on immune checkpoint inhibitors. By delineating the mechanisms through which microbial metabolites influence the TME, this review provides insights into novel microbiome-based therapeutic strategies, thereby highlighting a promising frontier in personalised cancer medicine.},
}

@article {pmid40267682,
year = {2025},
author = {Deokar, GS and Pathak, VA and Kshirsagar, SJ and Al-Asmari, F and Nirmal, N},
title = {Enhancement of vitamin B12 in plant-based food through microbial fermentation-a sustainable food system.},
journal = {Food chemistry},
volume = {484},
number = {},
pages = {144437},
doi = {10.1016/j.foodchem.2025.144437},
pmid = {40267682},
issn = {1873-7072},
abstract = {Vitamin B12 deficiency represents a notable health concern, especially among individuals adhering to plant-based dietary patterns. Understanding the biochemical mechanisms of in-situ B12 synthesis by gut microbiome and prebiotic supplementation is important for microbial fermentation strategies. This article discusses the mechanisms and applications of microbial fermentation in augmenting B12 levels, focusing on its significance in fortifying plant-derived food products. Microbial fermentation stands as a promising avenue for enhancing vitamin B12 content in plant-based foods, addressing a critical dietary concern among vegetarians and vegans. Moreover, bioavailability, regulatory considerations, and large-scale production remain a challenge and provide a scope for improvements. Future research should be focused on optimizing fermentation conditions, improving B12 stability in fortified foods, and assessing its long-term impact on human health.},
}

@article {pmid40267563,
year = {2025},
author = {Jian, Z and Wu, H and Yan, S and Li, T and Zhao, R and Zhao, J and Zi, X and Wang, K and Huang, Y and Gu, D and Zhao, S and Ge, C and Jia, J and Liu, L and Xu, Z and Dou, T},
title = {Species and functional composition of cecal microbiota and resistance gene diversity in different Yunnan native chicken breeds: A metagenomic analysis.},
journal = {Poultry science},
volume = {104},
number = {7},
pages = {105138},
doi = {10.1016/j.psj.2025.105138},
pmid = {40267563},
issn = {1525-3171},
abstract = {The gut microbiota of chickens not only modulates host immune function and production performance through nutrient metabolism but also serves as a reservoir for antibiotic resistance genes (ARGs), whose accumulation exacerbates bacterial resistance. This study integrated 108 cecal microbiome samples from six Yunnan native chicken breeds under free-range and caged farming systems, constructing a comprehensive catalog comprising 12,715 microbial genomes. We systematically revealed the dual mechanisms by which the gut microbiota regulates host phenotypes and ARG dissemination. Metagenomic analysis demonstrated that Alistipes, Prevotella, and Spirochaeta synergistically regulate body weight and immune indices through metabolic networks, which are linked to the significant enrichment of carbohydrate-active enzymes. GH23 and GT2 presented the greatest abundance, highlighting their pivotal role in dietary fiber metabolism. A total of 1327 ARGs were identified, spanning seven resistance mechanisms dominated by antibiotic efflux and target alteration. Alistipes_sp._CAG:831 presented the highest ARG abundance and diversity, with ARG levels strongly correlated with host bacterial abundance. Metagenomic-phenotype association networks further revealed that environmental stress drives disparities in ARG enrichment by altering the microbial community structure. This study elucidates the gut microbiota-host interaction network in Yunnan native chickens and provides critical insights into ARG transmission dynamics, offering a theoretical foundation for antibiotic resistance risk assessment and sustainable poultry farming strategies.},
}

@article {pmid40267504,
year = {2025},
author = {Hu, X and Gu, X and Li, H and Wang, H and Tang, D},
title = {Global Trends in Artificial Intelligence and Sepsis-Related Research: A Bibliometric Analysis.},
journal = {Shock (Augusta, Ga.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/SHK.0000000000002598},
pmid = {40267504},
issn = {1540-0514},
abstract = {BACKGROUND: In the field of bibliometrics, although some studies have conducted literature reviews and analyses on sepsis, these studies mainly focus on specific areas or technologies, such as the relationship between the gut microbiome and sepsis, or immunomodulatory treatments for sepsis. However, there are still few studies that provide comprehensive bibliometric analyses of global scientific publications related to AI in sepsis research.

OBJECTIVE: The aim of this study is to assess the global trend analysis of AI applications in sepsis based on publication output, citations, co-authorship between countries, and co-occurrence of author keywords.

METHODS: A total of 4,382 papers published from 2015 to December 2024 were retrieved and downloaded from the SCIE database in WOS. After selecting the document types as articles and reviews, and conducting eligibility checks on titles and abstracts, the final bibliometric analysis using VOSviewer and CiteSpace included 4,209 papers.

RESULTS: The number of published papers increased sharply starting in 2021, accounting for 58.14% (2,447/4,209) of all included papers. The United States and China together account for approximately 60.16% (2,532/4,209) of the total publications. Among the top 10 institutions in AI research on sepsis, seven are located in the United States. Rishikesan Kamaleswaran is the most contributing author, with PLOS ONE having more citations in this field than other journals. SCIENTIFIC REPORTS is also the most influential journal (NP = 106, H-index = 23, IF: 3.8).

CONCLUSION: This study highlights the popular areas of AI research, provides a comprehensive overview of the research trends of AI in sepsis, and offers potential collaboration and future research prospects. To make AI-based clinical research sufficiently persuasive in sepsis practice, collaborative research is needed to improve the maturity and robustness of AI-driven models.},
}

@article {pmid40267287,
year = {2025},
author = {Chen, D and Zhang, T and Cui, H and Gu, J and Xuan, P},
title = {KNDM: A Knowledge Graph Transformer and Node Category Sensitive Contrastive Learning Model for Drug and Microbe Association Prediction.},
journal = {Journal of chemical information and modeling},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jcim.5c00186},
pmid = {40267287},
issn = {1549-960X},
abstract = {It has been proven that the microbiome in human bodies can promote or inhibit the treatment effects of the drugs by affecting their toxicities and activities. Therefore, identifying drug-related microbes helps in understanding how drugs exert their functions under the influence of these microbes. Most recent methods for drug-related microbe prediction are developed based on graph learning. However, those methods fail to fully utilize the diverse characteristics of drug and microbe entities from the perspective of a knowledge graph, as well as the contextual relationships among multiple meta-paths from the meta-path perspective. Moreover, previous methods overlook the consistency between the entity features derived from the knowledge graph and the node semantic features extracted from the meta-paths. To address these limitations, we propose a knowledge-graph transformer and node category-sensitive contrastive learning-based drug and microbe association prediction model (KNDM). This model learns the diverse features of drug and microbe entities, encodes the contextual relationships across multiple meta-paths, and integrates the feature consistency. First, we construct a knowledge graph consisting of drug and microbe entities, which aids in revealing similarities and associations between any two entities. Second, considering the heterogeneity of entities in the knowledge graph, we propose an entity category-sensitive transformer to integrate the diversity of multiple entity types and the various relationships among them. Third, multiple meta-paths are constructed to capture and embed the semantic relationships based on similarities and associations among drug and microbe nodes. A meta-path semantic feature learning strategy with recursive gating is proposed to capture specific semantic features of individual meta-paths while fusing contextual relationships among multiple meta-paths. Finally, we develop a node-category-sensitive contrastive learning strategy to enhance the consistency between entity features and node semantic features. Extensive experiments demonstrate that KNDM outperforms eight state-of-the-art drug-microbe association prediction models, while ablation studies validate the effectiveness of its key innovations. Additionally, case studies on candidate microbes associated with three drugs-curcumin, epigallocatechin gallate, and ciprofloxacin-further showcase KNDM's capability to identify potential drug-microbe associations.},
}

@article {pmid40267282,
year = {2025},
author = {Yang, Z and Chen, H and Zhong, GH and Liu, J},
title = {cAMP-Mediated Biofilm eDNA Transfer Facilitates the Resilience of Soil Microbiome to Agrochemical Stress.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c00961},
pmid = {40267282},
issn = {1520-5118},
abstract = {Soil microorganisms utilize extracellular DNA (eDNA)-based biofilms as a defense against xenobiotics. However, the specific effects and transfer pathways of eDNA under persistent agrochemical exposure remain unclear. This study examined the transfer dynamics of carbofuran-hydrolase gene pchA from Pseudomonas stutzeri PS21. During biofilm formation, pchA was released from eDNA, leading to an enrichment of beneficial microorganisms such as Acidobacteria and Elusimicrobia, which enhanced organic compound metabolism and improved soil microbiome resilience. An increase in the pchA-associated mobile genetic elements and the colocalization of pchA with other bacterial species indicated the potential horizontal gene transfer (HGT) under carbofuran exposure. Additionally, carbofuran triggered a cAMP-dependent apoptotic pathway, leading to a 59.6% increase in pchA copy number, which suggested that cAMP played a role in initiating HGT. In conclusion, the cAMP-mediated interspecific transfer of pchA could enhance microbial coadaptation to carbofuran contamination, thereby strengthening the collective defense of soil microbiome against agrochemical stress.},
}

@article {pmid40267215,
year = {2025},
author = {Gabby, ME and Bandara, A and Outrata, LM and Ebohon, O and Ahmad, SS and Dressler, JM and McClune, ME and Trimble, RN and Mullen, L and Jutras, BL},
title = {A high-resolution screen identifies a preexisting beta-lactam that specifically treats Lyme disease in mice.},
journal = {Science translational medicine},
volume = {17},
number = {795},
pages = {eadr9091},
doi = {10.1126/scitranslmed.adr9091},
pmid = {40267215},
issn = {1946-6242},
mesh = {Animals ; *Lyme Disease/drug therapy/microbiology ; Borrelia burgdorferi/drug effects ; Mice ; *beta-Lactams/therapeutic use/pharmacology ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Humans ; Microbial Sensitivity Tests ; Drug Evaluation, Preclinical ; },
abstract = {Lyme disease, caused by Borrelia burgdorferi in the United States, is an escalating human health problem that can cause severe disease if not properly treated. Doxycycline is the primary treatment option for Lyme disease; however, several concerns are associated with high-dose doxycycline treatment. For example, doxycycline is a broad-spectrum antibiotic and kills beneficial bacteria. Doxycycline is also known to produce unwanted off-target effects in eukaryotic cells. Some at-risk populations such as young children cannot be prescribed doxycycline, and in addition to these shortcomings, the treatment appears to fail in 10 to 20% of cases. We reasoned that safe, alternative therapies may currently exist but have not yet been found because of the challenges associated with drug screening approaches. We screened nearly 500 US Food and Drug Administration-approved compounds using an array of physiological, cellular, and molecular techniques. Top-performing candidates were counter screened to identify compounds that did not affect other bacterial phyla. Piperacillin emerged as a compound that eradicated B. burgdorferi at low-nanomolar concentrations by specifically interfering with the unusual, multizonal peptidoglycan synthesis pattern common to the Borrelia clade. Mechanistic in vitro studies identified the cellular target of piperacillin in B. burgdorferi and produced key insights that may explain both the specificity and efficacy of the compound. Further, in vivo studies using an experimental mouse infection model demonstrated that piperacillin treated animals at a 100-fold lower dose than the effective dose of doxycycline without affecting the murine microbiome. Our findings suggest that piperacillin may offer clinicians another therapeutic option for Lyme disease.},
}

Animals
*Lyme Disease/drug therapy/microbiology
Borrelia burgdorferi/drug effects
Mice
*beta-Lactams/therapeutic use/pharmacology
*Anti-Bacterial Agents/therapeutic use/pharmacology
Humans
Microbial Sensitivity Tests
Drug Evaluation, Preclinical

@article {pmid40267015,
year = {2025},
author = {Incharoen, T and Charoensook, R and Tartrakoon, W and Numthuam, S and Sunanta, Y and Jimenez, G and Loor, JJ},
title = {Dietary Bacillus toyonensis BCT-7112[T] Supplementation Influences Performance, Egg Quality, Ammonia Emission, and Cecal Microbiome in Laying Ducks.},
journal = {Veterinary sciences},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/vetsci12030259},
pmid = {40267015},
issn = {2306-7381},
support = {R2561A064//Rubinum S.A., Spain, and Center of Excellence for Agricultural and Livestock Innovation, Faculty of Agriculture Natural Resources and Environment, Naresuan University, Phitsanulok, Thailand/ ; },
abstract = {This study evaluated the effects of Bacillus toyonensis BCT-7112[T] on laying duck performance, egg quality, ammonia emission, and cecal microbiota. Two hundred twenty 32-week-old Khaki Campbell ducks were assigned to four dietary treatments (0, 200, 500, or 1000 ppm Toyocerin[®] 10[9] premixture, containing 1 × 10[9] B. toyonensis BCT-7112[T] CFU/g) with five replicate pens of eleven birds each. Data on productivity, egg quality, and ammonia emissions were collected weekly, and cecal microbiota were analyzed at 44 weeks of age. Supplementation with 1000 ppm B. toyonensis BCT-7112[T] significantly increased average egg weight (p < 0.001) and eggshell thickness (p = 0.007). Egg mass also improved at higher supplementation levels (p < 0.05), though feed intake, feed conversion, daily egg production, and most egg quality parameters were unaffected (p > 0.05). Ammonia emissions in litter decreased significantly (p < 0.05) with probiotic inclusion. Cecal microbiota analysis revealed higher diversity in ducks fed 1000 ppm, with a notable shift in predominant phyla from Bacteroidetes (35.12%) and Firmicutes (34.93%) in the controls to Bacteroidetes (40.52%), Firmicutes (34.08%), and Deferribacteres (9.54%) in the treated ducks. The findings suggest that 1000 ppm B. toyonensis BCT-7112[T] enhances egg production, eggshell quality, and microbial diversity while reducing ammonia emissions in laying duck systems.},
}

@article {pmid40266957,
year = {2025},
author = {Sun, J and Liang, S and Gu, X and Xu, J and Wang, X and Wang, Z and Tao, H and Wang, J and Han, B},
title = {Effects of Dietary Supplementation with Yeast Hydrolysate on Immune Function, Fecal Short Chain Fatty Acids, and Intestinal Health in Cats.},
journal = {Veterinary sciences},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/vetsci12030239},
pmid = {40266957},
issn = {2306-7381},
support = {CAAS-ASTIP-2023-IFR-14//Central Public-interest Scientific Institution Basal Research Fund/ ; },
abstract = {Yeast hydrolysate (YH) is rich in amino acids and other nutrients, and as a nutritional supplement it has been widely used in daily nutritional supplements for livestock. However, the role of YH in domestic pets, especially cats, has not yet been determined. The objective of this research was to study the effects of different concentrations of YH on the healthy cats. All cats were randomly divided into four treatments: the control group (T0, n = 6, without YH), treatment 1 (T1, the low concentration group, 0.8% of YH, n = 6), treatment 2 (T2, the middle concentration group, 1.5% of YH, n = 6), and treatment 3 (T3, the high concentration group, 4% of YH, n = 6), and the blood biochemistry, immune indexes and odorous substances in the feces, and microbiome of cats were determined on day 28. Our results showed that YH could increase the immunoglobulin G (IgG) level in the serum (p < 0.01) and reduce 3-methylindole content in the feces (p < 0.01). The acetic acid in the feces of T2 treatment (1.5%YH) was apparently increased compared to the control treatment (p < 0.05). The blood biochemistry indexes were not affected by the YH. Compared to the control group, there was no significant difference in the abundance at the phylum level. On the genus level, the abundance of g_Ruminocococcaceae and g_Lachnospiraceae, the beneficial bacteria in the gut, were decreased in the treatment T3 compared to treatment T1 (p < 0.05), but there was no significance between T1 and T2, which suggested that a high concentration of YH may be negative for gut health. So, the research showed that 1.5% of YH could be the best concentration for the improvement of immunity and gut health for cats.},
}

@article {pmid40266944,
year = {2025},
author = {Herzog, F and Crissman, KR and Beckers, KF and Zhou, G and Liu, CC and Sones, JL},
title = {Lactobacillus Genus Complex Probiotic-Induced Changes on the Equine Clitoral Microbiome.},
journal = {Veterinary sciences},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/vetsci12030232},
pmid = {40266944},
issn = {2306-7381},
support = {2022//Louisiana State University Charles V. Cusimano/ ; },
abstract = {Dysbiosis of the lower reproductive tract (LRT) in mares may play a role in clinical diseases, including endometritis and placentitis. Metagenomic/metagenetic analysis of bacterial DNA can identify organisms that are not readily cultured and, thus, may go undetected. In this study, we tested the following hypotheses: (1) the clitoris of estrual mares harbors a unique resident microbiome, (2) topical Lactobacillus genus complex (LGC)-containing probiotic will alter the equine clitoral microbiome, and (3) early pregnancy rates following clitoral LGC application will not differ significantly from industry standards. Mares (n = 12) in estrus had sterile clitoral swabs collected (0) prior to daily topical LGC for 4 days. Second (12 h) and third clitoral swabs (48 h) were collected following final LGC application. During the next estrus, the mares were bred by artificial insemination. Genomic DNA was extracted and used for 16S rRNA sequencing via the Illumina Miseq platform. Abundance was evaluated via Friedman test with pairwise Dunn's post hoc comparisons. Statistical significance was set at p < 0.05. Compared to time 0, Desulfobacterota decreased and Corynebacterium spp. increased at 12 h and 48 h compared to 0, while Actinobacillus and Fusobacterium spp. increased in a time-dependent manner. Furthermore, Mobiluncus spp. and Christensenellacea_R-7_group decreased at 12 h and 48 h compared to 0. LGC changed the beta but not alpha diversity at both 12 h and 48 h. Mares with LGC application achieved an 85% pregnancy rate in the subsequent estrus. Future investigations are needed to understand the role of the LRT microbiome and probiotics in equine breeding.},
}

@article {pmid40266930,
year = {2025},
author = {Bakker, J and Nederlof, RA and Stumpel, J and de la Garza, MA},
title = {Recent Advances in the Etiology, Diagnosis, and Treatment of Marmoset Wasting Syndrome.},
journal = {Veterinary sciences},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/vetsci12030203},
pmid = {40266930},
issn = {2306-7381},
abstract = {One of the primary challenges encountered in managing captive callitrichids is a group of gastrointestinal disorders that are collectively known as Marmoset Wasting Syndrome (MWS). Unfortunately, MWS is still not well understood. It is suggested that MWS has a multifactorial etiology; stress, infection, malnutrition, malabsorption, and enteritis or colitis may be associated with MWS. Usually, animals demonstrate more than one of the following clinical signs: progressive weight loss, alopecia, chronic diarrhea, muscle atrophy, hypoproteinemia, and anemia. Recent advances in diagnostics, mostly noninvasive fecal and urine tests, yielded promising results. Good treatment results have been achieved with the administration of glucocorticoids and tranexamic acid, although no cure has been found yet. Probiotics and gel diets also demonstrated to be potentially useful. However, once animals are affected by MWS, treatments eventually become ineffective, and animals will inevitably require euthanasia to prevent further suffering. Preventative measures should be aimed at reducing stress and optimizing housing, husbandry, and diets. More research is warranted to elucidate the pathogenesis of MWS in captive callitrichids and to refine diagnostic and treatment methods.},
}

@article {pmid40266902,
year = {2025},
author = {Kerek, Á and Román, I and Szabó, Á and Pézsa, NP and Jerzsele, Á},
title = {Antibiotic Resistance Gene Expression in Veterinary Probiotics: Two Sides of the Coin.},
journal = {Veterinary sciences},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/vetsci12030217},
pmid = {40266902},
issn = {2306-7381},
support = {RRF-2.3.1-21-2022-00001//National Recovery Fund/ ; },
abstract = {The rapid proliferation of antimicrobial resistance has emerged as one of the most pressing animal and public health challenges of our time. Probiotics, extensively employed in human and veterinary medicine, are instrumental in maintaining a balanced microbiome and mitigating its disruption during antibiotic therapy. While their numerous benefits are well documented, probiotics also present potential risks, notably the capacity to harbor antimicrobial resistance genes. This genetic reservoir could contribute to the emergence and spread of antimicrobial resistance by facilitating the horizontal transfer of resistance genes to pathogenic bacteria within the gut. This review critically examines the presence of antimicrobial resistance genes in commonly used probiotic strains, explores the underlying mechanisms of resistance, and provides a balanced analysis of the benefits and risks associated with their use. By addressing these dual aspects, this paper highlights the need for vigilant evaluation of probiotics to preserve their therapeutic potential while minimizing public health risks.},
}

@article {pmid40266732,
year = {2025},
author = {Duque-Granda, D and Vivero-Gómez, RJ and González Ceballos, LA and Junca, H and Duque, SR and Aroca Aguilera, MC and Castañeda-Espinosa, A and Cadavid-Restrepo, G and Gómez, GF and Moreno-Herrera, CX},
title = {Exploring the Diversity of Microbial Communities Associated with Two Anopheles Species During Dry Season in an Indigenous Community from the Colombian Amazon.},
journal = {Insects},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/insects16030269},
pmid = {40266732},
issn = {2075-4450},
support = {Hermes 57545//Universidad Nacional de Colombia/ ; },
abstract = {Malaria disease affects millions of people annually, making the Amazon Basin a major hotspot in the Americas. While traditional control strategies rely on physical and chemical methods, the Anopheles microbiome offers a promising avenue for biological control, as certain bacteria can inhibit parasite development and alter vector immune and reproductive systems, disrupting the transmission cycle. For this reason, this study aimed to explore the bacterial communities in An. darlingi and An. triannulatus s.l., including breeding sites, immature stages, and adults from San Pedro de los Lagos (Leticia, Amazonas) through next-generation sequencing of the 16S rRNA gene. The results revealed a higher bacterial genus richness in the L1-L2 larvae of An. triannulatus s.l. Aeromonas and Enterobacter were prevalent in most samples, with abundances of 52.51% in L3-L4 larvae and 48.88% in pupae of An. triannulatus s.l., respectively. In breeding site water, Verrucomicrobiota bacteria were the most dominant (52.39%). We also identified Delftia (15.46%) in An. triannulatus s.l. pupae and Asaia (98.22%) in An. triannulatus, linked to Plasmodium inhibition, and Elizabethkingia, in low abundances, along with Klebsiella and Serratia, known for paratransgenesis potential. Considering the high bacterial diversity observed across the different mosquito life stages, identifying bacterial composition is the first step towards developing new strategies for malaria control. However, the specific roles of these bacteria in anophelines and the malaria transmission cycle remain to be elucidated.},
}

@article {pmid40266727,
year = {2025},
author = {Ngando, FJ and Tang, H and Zhang, X and Zhang, X and Yang, F and Shang, Y and Cai, J and Guo, Y and Zhao, L and Zhang, C},
title = {Effects of Feeding Sources and Different Temperature Changes on the Gut Microbiome Structure of Chrysomya megacephala (Diptera: Calliphoridae).},
journal = {Insects},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/insects16030283},
pmid = {40266727},
issn = {2075-4450},
support = {No.82371895//National Natural Science Foundation of China/ ; No. 2022JJ40671//the Human Natural Science Foundation/ ; },
abstract = {Chrysomya megacephala (Diptera: Calliphoridae), commonly referred to as the oriental latrine fly, is a synanthropic blowfly species frequently associated with decomposing organic matter. This study sought to investigate the influence of various feeding substrates and temperature conditions, specifically constant temperatures of 15, 25, 35 °C, and variable temperatures averaging 23.31 °C, on the gut microbiome of C. megacephala. The microbiome analysis was conducted using the Illumina HiSeq platform for 16S rRNA gene sequencing in Changsha, China. Across all experimental conditions, the gut microbiome of C. megacephala yielded 1257 operational taxonomic units (OTUs), which were categorized into 26 phyla, 72 classes, 165 orders, 270 families, 516 genera, and 794 species. The study showed significant differences in the gut microbiome of C. megacephala between different feeding sources and temperature conditions across the lifespan. Low temperature had the potential to reduce the proportion abundance of bacterial communities in the gut microbiome, while high and variable temperature increased them. Metabolism was the main predicted function with diverse phenotypic characters in the gut microbiota of C. megacephala. The presence of diverse bacterial phenotypes in the gut microbiome of C. megacephala highlights its significant interest for medicine and offers promising applications in industry and agriculture.},
}

@article {pmid40266445,
year = {2025},
author = {Chellappoo, A and Baedke, J and Meloni, M},
title = {From genetic to postgenomic determinisms: The role of the environment reconsidered : Introduction to the collection 'Postgenomic determinisms: Environmental narratives after the century of the gene'.},
journal = {History and philosophy of the life sciences},
volume = {47},
number = {2},
pages = {23},
pmid = {40266445},
issn = {1742-6316},
support = {BA 5808/2-1//Deutsche Forschungsgemeinschaft/ ; BA 5808/2-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Humans ; *Environment ; *Genetic Determinism ; *Genomics ; *Gene-Environment Interaction ; *Genetics/history ; },
abstract = {In the past twenty years, conceptual and technological shifts in the life sciences have unseated the causal primacy of the gene. The picture emerging from 'postgenomic' science is one that emphasises multifactorial dependencies between the environment, development, and the genome, and blurs boundaries between biological individuals, and between the body and the environment. Despite the rejection of genetic determinism within postgenomics, forms of determinism nevertheless persist. The environment is often conceptualised in postgenomic research in a narrow and constrained way, affording an outsized causal role to certain environmental factors while neglecting the influence of others. This carries ethical and social implications, including for understandings of race and motherhood. This topical collection interrogates the environmental determinisms developing within postgenomic science, through investigation of their conceptual foundations, histories, and social contexts across a range of postgenomic fields.},
}

Humans
*Environment
*Genetic Determinism
*Genomics
*Gene-Environment Interaction
*Genetics/history

@article {pmid40266410,
year = {2025},
author = {van Boom, KM and Kohn, TA and Tordiffe, ASW},
title = {Methionine, threonine and glutamic acid adapted pathways in captive cheetahs on a glycine-supplemented diet.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {21},
number = {3},
pages = {56},
pmid = {40266410},
issn = {1573-3890},
mesh = {Animals ; *Glycine/metabolism/administration & dosage ; *Acinonyx/metabolism/blood ; *Threonine/metabolism/blood ; Dietary Supplements ; *Methionine/metabolism/blood ; *Glutamic Acid/metabolism/blood/urine ; Diet ; Animal Feed/analysis ; Male ; Female ; },
abstract = {BACKGROUND: Captive cheetahs are prone to a range of unusual diseases potentially linked to unnatural diets high in muscle meat and low in collagen-rich animal fibre. In the wild, cheetahs typically eat whole prey diets not easily replicated in a captive setting. Glycine is the most abundant amino acid in collagen with a key role in several metabolic pathways such as collagen biosynthesis. Several recent studies suggest that endogenous glycine production may be limited in several species.

OBJECTIVES: Using untargeted [1]H- nuclear magnetic resonance, the metabolic changes in the urine and serum of 10 adult captive cheetahs on a glycine-supplemented diet were investigated.

METHODS: Cheetahs were fed either a meat only (control) or glycine-supplemented meat diet (30 g glycine per 1 kg meat) for four weeks, followed by a four-week cross-over. Urine and blood samples were collected at baseline and after each intervention.

RESULTS: A total of 151 and 60 metabolites were identified in the urine and serum, respectively. Specifically, dimethylsulphone, proline, fructose, dimethylamine, trimethylamine, pyroglutamic acid, 1,3-diaminopropane, dihydrothymine, methylmalonic acid and pimelic acid contributed to metabolome differences in the urine. In serum, glutamic acid, threonine, α-aminobutyric acid, glucose-6-phosphate, ethanolamine, methionine and propionic acid were highlighted. These metabolites play various metabolic roles in energy production, immune function, protein and collagen biosynthesis or as products of gut microbiome fermentation.

CONCLUSION: Glycine supplementation influenced threonine sparing, pyrimidine biosynthesis pathways and bacterial fermentation products, although the implications of these findings on the health of captive cheetahs is unknown. Future studies should use a targeted approach to further elaborate on these pathways.},
}

Animals
*Glycine/metabolism/administration & dosage
*Acinonyx/metabolism/blood
*Threonine/metabolism/blood
Dietary Supplements
*Methionine/metabolism/blood
*Glutamic Acid/metabolism/blood/urine
Diet
Animal Feed/analysis
Male
Female

@article {pmid40266381,
year = {2025},
author = {Cuny, MAC and Gloder, G and Bourne, ME and Kalisvaart, SN and Verreth, C and Crauwels, S and Cusumano, A and Lievens, B and Poelman, EH},
title = {Parasitoid Calyx Fluid and Venom Affect Bacterial Communities in Their Lepidopteran Host Labial Salivary Glands.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {33},
pmid = {40266381},
issn = {1432-184X},
support = {ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; },
mesh = {Animals ; *Salivary Glands/microbiology ; *Wasps/physiology ; *Bacteria/classification/genetics/isolation & purification/drug effects ; *Microbiota ; Larva/parasitology/microbiology ; Host-Parasite Interactions ; *Butterflies/microbiology/parasitology ; Hemolymph/microbiology ; Polydnaviridae/physiology ; *Wasp Venoms/pharmacology ; *Moths/microbiology/parasitology ; },
abstract = {The influence of gut and gonad bacterial communities on insect physiology, behaviour, and ecology is increasingly recognised. Parasitism by parasitoid wasps alters many physiological processes in their hosts, including gut bacterial communities. However, it remains unclear whether these changes are restricted to the gut or also occur in other tissues and fluids, and the mechanisms underlying such changes are unknown. We hypothesise that host microbiome changes result from the injection of calyx fluid (that contain symbiotic viruses known as polydnaviruses) and venom during parasitoid oviposition and that these effects vary by host tissue. To test this, we microinjected Pieris brassicae caterpillars with calyx fluid and venom from Cotesia glomerata, using saline solution and natural parasitism by C. glomerata as controls. We analysed changes in the bacterial community composition in the gut, regurgitate, haemolymph, and labial salivary glands of the host insects. Multivariate analysis revealed distinct bacterial communities across tissues and fluids, with high diversity in the salivary glands and haemolymph. Parasitism and injection of calyx fluid and venom significantly altered bacterial communities in the salivary glands. Differential abundance analysis showed that parasitism affected bacterial relative abundance in the haemolymph, and that Wolbachia was only found in the haemolymph of parasitized caterpillars. Altogether, our findings reveal that parasitism influences the host haemolymph microbiome, and both parasitism and injection of calyx fluid and venom drive changes in the bacterial community composition within the host salivary glands. Given that the composition of salivary glands can influence plant response to herbivory, we discuss these results in the broader context of plant-parasitoid interactions.},
}

Animals
*Salivary Glands/microbiology
*Wasps/physiology
*Bacteria/classification/genetics/isolation & purification/drug effects
*Microbiota
Larva/parasitology/microbiology
Host-Parasite Interactions
*Butterflies/microbiology/parasitology
Hemolymph/microbiology
Polydnaviridae/physiology
*Wasp Venoms/pharmacology
*Moths/microbiology/parasitology

@article {pmid40266380,
year = {2025},
author = {Çakır, B and Sönmezoğlu, BG and Şahin, EÖ and Köroğlu, M and Aksoy, NÖ},
title = {Evaluation of ocular surface microbiota in children with blepharoconjunctivitis.},
journal = {Graefe's archive for clinical and experimental ophthalmology = Albrecht von Graefes Archiv fur klinische und experimentelle Ophthalmologie},
volume = {},
number = {},
pages = {},
pmid = {40266380},
issn = {1435-702X},
support = {2022-09-32-106//Sakarya Üniversitesi/ ; },
abstract = {PURPOSE: To investigate the conjunctival and eyelid margin bacterial microbiota in children with blepharoconjunctivitis by using 16S rDNA amplicon sequencing.

METHODS: In this prospective cross-sectional study, 20 children aged between 3-15 years with blepharoconjunctivitis or blepharokeratokonjunctivitis formed Blepharitis Group and 21 children aged between 3-15 years without any ocular and sysemic diseases except mild refractive errors formed Control Group. Swap samples from all children were taken. The alpha diversity of the ocular surface microbiota within each group were evaluated by using Shannon's, Simpson, and Chao index. Beta diversity was evaluated by Bray Curtis index.

RESULTS: Microbiological diversity was higher in the patient group than in the control group. According to Shannon's, Simpson, and Chao index, there were statistically difference between groups (p: 0.000013, p:000003 p: 0.00235, respectively). According to the Bray Curtis index, the healthy eye microbiome in the control group is observed to be highly similar, consistent with other analyses, and the overlapping cluster with the blepharitis eye microbiome is quite low (pco1: 40.93%). Sphingoblump, Micrococus, Lacnospiracebacterium, Stenothermophilus, Aurelmonass, Micrococus, Blatiabeum, Delfiacdiovorans and Vellonella densities were found to be higher in the patient group.

CONCLUSION: Both alpha and beta diversity analyses were significantly higher in pediatric age group patients with blepharitis. In addition, Lacnospiracebacterium, Stenothermophilus, Aurelmonass, Micrococus, Blatiabeum, Delfiacdiovorans and Vellonella densities were found to be higher, which may lead to future studies focused on diagnosis and treatment.},
}

@article {pmid40266093,
year = {2025},
author = {Zou, Y and Pu, L and Guo, A and Li, Y and Liu, Y and Wang, Y and Ding, Y and Du, X and Guo, X and Zhang, S and Cai, X and Wang, S},
title = {Helminth reshapes host gut microbiota and immunoregulation by deploying an antimicrobial program of innate immunity.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2496447},
doi = {10.1080/19490976.2025.2496447},
pmid = {40266093},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/immunology ; Animals ; *Immunity, Innate ; Mice ; Macrophages/immunology ; T-Lymphocytes, Regulatory/immunology ; Antimicrobial Cationic Peptides/immunology ; Mice, Inbred C57BL ; Lactobacillus ; },
abstract = {Helminths can manipulate their host's gut microbiota, with the expansion of the lactobacilli population being a common feature. This process profoundly influences host immunoregulation, yet the underlying mechanisms remain almost unknown. Using a tissue-dwelling helminth model (larval Echinococcus multilocularis) while validating key findings from other helminth infections, we show that helminths harness the antibacterial program of host innate immunity to transform the host gut microbiome and control gut microbiota-mediated immunity. Using multifaceted techniques, we elucidate that cathelicidin-related antimicrobial peptide (CRAMP), derived from the expanded CD11b[+]CD206[+] macrophages rather than the intestinal epithelial cells, is the key component that enters into the gut ecological system and enhances the fitness of Lactobacillus by selectively killing gram-negative microbes like enterobacteria. Furthermore, through in vitro cell culturing and in vivo dietary intervention experiments, we demonstrate that this regulation from innate immunity is boosted via toll-like receptor signaling by helminth's secretory products, which could be sufficiently tuned down by dietary vitamin D through its receptor and cyp27b1. Importantly, using microbiota-targeted treatment methods, we prove that this signaling bolsters gut microbiota-mediated host intestinal Foxp3[+] Treg cell expansion and parasite survival and that therapies targeting this signaling are effective in treating infection. We outline a dietary micronutrient-dependent mechanism by which helminths leverage host innate immunity to edit the host gut microbiome and thereby control immunosuppression precisely.},
}

*Gastrointestinal Microbiome/immunology
Animals
*Immunity, Innate
Mice
Macrophages/immunology
T-Lymphocytes, Regulatory/immunology
Antimicrobial Cationic Peptides/immunology
Mice, Inbred C57BL
Lactobacillus

@article {pmid40265782,
year = {2025},
author = {Soultatos, SK and Chatzaki, A and Karas, PA and Papadaki, AA and Kalantzakis, GS and Psarras, G and Goumas, DE and Karpouzas, DG and Markakis, EA},
title = {Biocontrol Potential of Raw Olive Mill Waste Against Verticillium dahliae in Vegetable Crops.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/plants14060867},
pmid = {40265782},
issn = {2223-7747},
abstract = {Verticillium wilt caused by the soil-borne fungus Verticillium dahliae causes severe losses to a broad range of economically important crops worldwide. Chemical disease management is ineffective; thus, alternative control strategies are needed. Olive-producing countries face the challenge of managing olive mill wastewater (OMW) in an environmentally friendly and agronomically beneficial manner. The proper use of OMW supported by scientific research has been proposed as a valuable means for successful disease management. In this respect, we tested whether soil application of raw OMW can protect vegetable crops against V. dahliae and investigated the potential disease-suppressive mechanisms. OMW inhibited significantly fungal growth, sporulation, hyphae width, and conidial and microsclerotial germination in vitro, and these effects were dose-dependent. Moreover, the addition of OMW in the soil provided sufficient protection of eggplant and tomato against V. dahliae in planta. The high OMW-conferred protection of eggplant was gradually decreased, possibly due to the decreased phenolic content in OMW over time. Bioassays with sterilized soil substrate and OMW, along with isolated microbial strains, revealed that soil- and OMW-originated microbes had no role in disease suppression. Moreover, split-root set-ups suggested a non-systemic OMW-induced resistance mechanism. Root-drench application of OMW in eggplant and tomato plants did not cause significant alterations in the structure of the plant microbiome that could be associated with disease suppressiveness.},
}

@article {pmid40265726,
year = {2025},
author = {Rawat, A and Han, B and Patel, N and Allehaibi, H and Rosado, AS and Hirt, H},
title = {Symbiotic plant-bacterial-fungal interaction orchestrates ethylene and auxin signaling for optimized plant growth.},
journal = {The Plant journal : for cell and molecular biology},
volume = {122},
number = {2},
pages = {e70174},
doi = {10.1111/tpj.70174},
pmid = {40265726},
issn = {1365-313X},
support = {BAS/1/1062-01-01//King Abdullah University of Science and Technology/ ; },
mesh = {*Symbiosis/physiology ; *Arabidopsis/microbiology/growth & development/physiology ; *Indoleacetic Acids/metabolism ; *Ethylenes/metabolism ; Signal Transduction ; *Enterobacter/physiology ; *Basidiomycota/physiology ; Endophytes/physiology ; Plant Growth Regulators/metabolism ; Rhizosphere ; Plant Development ; Plant Roots/microbiology ; },
abstract = {The complex and mutual interactions between plants and their associated microbiota are key for plant survival and fitness. From the myriad of microbes that exist in the soil, plants dynamically engineer their surrounding microbiome in response to varying environmental and nutrient conditions. The notion that the rhizosphere bacterial and fungal community acts in harmony with plants is widely acknowledged, yet little is known about how these microorganisms interact with each other and their host plants. Here, we explored the interaction of two well-studied plant beneficial endophytes, Enterobacter sp. SA187 and the fungus Serendipita indica. We show that these microbes show inhibitory growth in vitro but act in a mutually positive manner in the presence of Arabidopsis as a plant host. Although both microbes can promote plant salinity tolerance, plant resilience is enhanced in the ternary interaction, revealing that the host plant has the ability to positively orchestrate the interactions between microbes to everyone's benefit. In conclusion, this study advances our understanding of plant-microbiome interaction beyond individual plant-microbe relationships, unveiling a new layer of complexity in how plants manage microbial communities for optimal growth and stress resistance.},
}

*Symbiosis/physiology
*Arabidopsis/microbiology/growth & development/physiology
*Indoleacetic Acids/metabolism
*Ethylenes/metabolism
Signal Transduction
*Enterobacter/physiology
*Basidiomycota/physiology
Endophytes/physiology
Plant Growth Regulators/metabolism
Rhizosphere
Plant Development
Plant Roots/microbiology

@article {pmid40265594,
year = {2025},
author = {Zhang, D and Zhang, Z and Liao, L and Dong, B and Xiong, X and Qin, X and Fan, X},
title = {Impact of fecal microbiota transplantation on lung function and gut microbiome in an ARDS rat model: A multi-omics analysis including 16S rRNA sequencing, metabolomics, and transcriptomics.},
journal = {International journal of immunopathology and pharmacology},
volume = {39},
number = {},
pages = {3946320251333982},
doi = {10.1177/03946320251333982},
pmid = {40265594},
issn = {2058-7384},
mesh = {Animals ; *Gastrointestinal Microbiome ; Rats, Sprague-Dawley ; *Fecal Microbiota Transplantation/methods ; *Respiratory Distress Syndrome/therapy/microbiology/metabolism/physiopathology/genetics ; *Lung/metabolism/physiopathology/microbiology ; *RNA, Ribosomal, 16S/genetics ; Metabolomics/methods ; Disease Models, Animal ; Rats ; Male ; *Transcriptome ; Multiomics ; },
abstract = {OBJECTIVE: Acute respiratory distress syndrome (ARDS) is a severe pulmonary condition characterized by inflammation and lung damage, frequently resulting in poor clinical outcomes. Recent studies suggest that the gut-lung axis, mediated by gut microbiota, is critical in ARDS progression. This study investigates the therapeutic potential of fecal microbiota transplantation (FMT) in an ARDS rat model (n = 6).

INTRODUCTION: The pathogenesis of ARDS involves complex interactions between the lungs and gut, with microbiota playing a key role. Understanding the effects of FMT on lung function and gut microbiota may provide new therapeutic strategies for ARDS management.

METHODS: Sprague-Dawley rats were pre-treated with a broad-spectrum antibiotic cocktail to create a germ-free state and subsequently exposed to intranasal lipopolysaccharide to induce ARDS. The rats then received FMT treatment. Lung samples were analyzed using histopathology and transcriptomics. Fecal samples were analyzed using 16S rRNA sequencing and metabolomics.

RESULTS: FMT treatment significantly reduced lung injury and improved pulmonary function, as evidenced by increased partial pressure of arterial oxygen (PaO2) and decreased partial pressure of arterial carbon dioxide (PaCO2). FMT also significantly altered in gut microbiota composition by regulating the gut microbiota composition of Akkermansia and Lactobacillus, restoring the abundance of genera such as Muribaculaceae, Clostridia_UCG-014, Prevotella, and Adlercreutzia, while reducing Romboutsia. FMT restored key metabolic pathways involved in lipid metabolism, amino acid biosynthesis, and immune regulation, including the modulation of immune pathways like mTOR signaling. These alterations contribute to reduced lung injury and improved pulmonary function.

CONCLUSION: These findings indicate that FMT may exert its beneficial effects in ARDS by modulating the gut microbiota and enhancing metabolic and immune responses. However, given that this study remains in the preclinical stage, further validation in clinical studies is necessary before considering clinical application.},
}

Animals
*Gastrointestinal Microbiome
Rats, Sprague-Dawley
*Fecal Microbiota Transplantation/methods
*Respiratory Distress Syndrome/therapy/microbiology/metabolism/physiopathology/genetics
*Lung/metabolism/physiopathology/microbiology
*RNA, Ribosomal, 16S/genetics
Metabolomics/methods
Disease Models, Animal
Rats
Male
*Transcriptome
Multiomics

@article {pmid40265492,
year = {2025},
author = {Wang, B and Zheng, X and Zhang, X},
title = {Extracorporeal Shock Wave Therapy (ESWT) in burn scar microbiome modulation: critical analysis of methodological rigor and translational potential.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000002411},
pmid = {40265492},
issn = {1743-9159},
}

@article {pmid40265464,
year = {2025},
author = {Yan, X and Xie, F and Yang, S and Sun, Y and Lei, Y and Ren, Q and Si, H and Li, Z and Qiu, Q},
title = {Metagenomic Insights into the Rumen Microbiome in Solid and Liquid Fractions of Yaks and their Differences Compared to Other Ruminants.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.12984},
pmid = {40265464},
issn = {1749-4877},
support = {32225009//National Natural Science Foundation of China/ ; 32122083//National Natural Science Foundation of China/ ; 32402780//National Natural Science Foundation of China/ ; XDA26040301//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
abstract = {The rumen microbiome plays a critical role in nutrient metabolism and adaptation of the yak (Bos grunniens), an import livestock animal of the Qinghai-Tibet Plateau renowned for their superior plant fiber degradation capacity. However, the microbiome among the different ecological niches within yak's rumen remains unelucidated. Through shotgun sequencing of rumen solid and liquid fractions from five yaks, we identified significant differences in the microbial communities and their genetic functions between the solid and liquid fractions. Solid fractions exhibited dominance by Ruminococcus, Succiniclasticum, and Aspergillus, while Prevotella, Paludibacter, Parabacteroides, and Bacteroides prevailed in liquid fractions. Comparative CAZyme profiling revealed solid fractions were significantly enriched in cellulose/hemicellulose-targeting enzymes (GH5, GH11, and CBM63), implicating their specialization in breaking down the fibrous grasses. In contrast, liquid fractions showed higher abundances of starch-degrading enzymes (GH13, CBM48) and host-glycan utilizers (GH92), suggesting roles in soluble nutrient extraction and host-microbe interactions. Comparative analysis of 574 metagenome-assembled genomes suggested that Methanomethylophilaceae_UBA71 and nitrate-respiring Ruminococcaceae_Firm-04 preferentially colonized in the solids, whereas propionate-producing Quinella and animal glycan-degrading Bacteroides were more prevalent in the liquids. Moreover, compared to Hu sheep, yak's rumen microbiome showed significantly enhanced utilization of plant polysaccharide capacity. Comparative analysis across 10 ruminant species further highlighted host phylogeny as a key driver of rumen microbiome variation. These findings advance our understanding of niche differentiation and functional specialization within the unique yak rumen ecosystem.},
}

@article {pmid40265160,
year = {2025},
author = {Fässler, D and Heinken, A and Hertel, J},
title = {Characterising functional redundancy in microbiome communities via relative entropy.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {1482-1497},
pmid = {40265160},
issn = {2001-0370},
abstract = {Functional redundancy has been hypothesised to be at the core of the well-evidenced relation between high ecological microbiome diversity and human health. Here, we conceptualise and operationalise functional redundancy on a single-trait level for functionally annotated microbial communities, utilising an information-theoretic approach based on relative entropy that also allows for the quantification of functional interdependency across species. Via constraint-based microbiome community modelling of a public faecal metagenomic dataset, we demonstrate that the strength of the relation between species diversity and functional redundancy is dependent on specific attributes of the function under consideration such as the rarity and the occurring functional interdependencies. Moreover, by integrating faecal metabolome data, we highlight that measures of functional redundancy have correlates in the host's metabolome. We further demonstrate that microbiomes sampled from colorectal cancer patients display higher levels of species-species functional interdependencies than those of healthy controls. By analysing microbiome community models from an inflammatory bowel disease (IBD) study, we show that although species diversity decreased in IBD subjects, functional redundancy increased for certain metabolites, notably hydrogen sulphide. This finding highlights their potential to provide valuable insights beyond species diversity. Here, we formalise the concept of functional redundancy in microbial communities and demonstrate its usefulness in real microbiome data, providing a foundation for a deeper understanding of how microbiome diversity shapes the functional capacities of a microbiome.},
}

@article {pmid40264979,
year = {2025},
author = {Zhong, Y and Chi, H and Wu, T and Fan, W and Su, H and Li, R and Jiang, W and Du, X and Ma, Z},
title = {Diversity of rhizosphere microbial communities in different rice varieties and their diverse adaptive responses to saline and alkaline stress.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1537846},
pmid = {40264979},
issn = {1664-302X},
abstract = {Rice rhizosphere microbiota plays a crucial role in crop yield and abiotic stress tolerance. However, little is known about how the composition and function of rhizosphere soil microbial communities respond to soil salinity, alkalinity, and rice variety in rice paddy ecosystems. In this study, we analyzed the composition and function of rhizosphere soil microbial communities associated with two rice varieties (Jida177 and Tongxi933) cultivated in soils with different levels of salinity-alkalinity in Northeast China using a metagenomics approach. Our results indicate that the rhizospheres of Jida177 and Tongxi933 rice varieties harbor distinct microbial communities, and these microbial communities are differentiated based on both soil salinity-alkalinity and rice varieties. Furthermore, the observed differences in rice yield and grain quality between the Jida177 and Tongxi933 rice varieties suggest that these changes may be attributed to alterations in the rhizosphere microbiome under varying salinity conditions. These findings may pave the way for more efficient soil management and deeper understanding of the potential effects of soil salinization on the rice rhizosphere system.},
}

@article {pmid40264974,
year = {2025},
author = {Wong, SH and Wu, WKK},
title = {Editorial: Roles of gut microbiota in cancers of the gastrointestinal tract.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1585090},
pmid = {40264974},
issn = {1664-302X},
}

@article {pmid40264836,
year = {2025},
author = {Fiala, O and Hanzlova, M and Borska, L and Fiala, Z and Holmannova, D},
title = {Beyond physical exhaustion: Understanding overtraining syndrome through the lens of molecular mechanisms and clinical manifestation.},
journal = {Sports medicine and health science},
volume = {7},
number = {4},
pages = {237-248},
pmid = {40264836},
issn = {2666-3376},
abstract = {BACKGROUND: Overtraining Syndrome (OTS) is a condition resulting from excessive physical activity without adequate recovery, predominantly affecting elite athletes and military personnel. While overreaching can be a temporary state, non-functional overreaching may progress to chronic OTS. This review explores various hypotheses regarding the pathogenesis of OTS, including glycogen depletion, dysregulated cytokine response, oxidative stress, and alterations in the autonomic nervous system function. It also highlights the systemic impact of OTS on multiple organ systems, immune function, and overall health, linking the condition to chronic inflammation and an increased disease susceptibility. Additionally, it addresses the role of the gut microbiome in health modulation through physical activity.

METHODS: This narrative review was conducted through a structured search of peer-reviewed journal articles in databases such as PubMed, Web of Science, and Google Scholar, focusing on studies involving human participants and published in English.

RESULTS: OTS has systemic effects on multiple organ systems, immune function, and overall health, leading to chronic inflammation and increased disease susceptibility. Athletes with OTS exhibit higher morbidity rates, influenced by factors such as sleep deprivation and stress. The review also emphasizes the role of the gut microbiome as a significant modulator of health through physical activity.

CONCLUSION: Balanced training and recovery are crucial for preventing OTS and maintaining optimal health and quality of life in physically active individuals. Understanding the complex pathophysiology of OTS is essential for developing effective prevention and treatment strategies.},
}

@article {pmid40264799,
year = {2025},
author = {Dadi, P and Pauling, CW and Shrivastava, A and Shah, DD},
title = {Synthesis of versatile neuromodulatory molecules by a gut microbial glutamate decarboxylase.},
journal = {iScience},
volume = {28},
number = {4},
pages = {112289},
pmid = {40264799},
issn = {2589-0042},
abstract = {Dysbiosis of the microbiome correlates with many neurological disorders, yet very little is known about the chemistry that controls the production of neuromodulatory molecules by gut microbes. Here, we found that an enzyme glutamate decarboxylase (BfGAD) of a gut microbe Bacteroides fragilis forms multiple neuromodulatory molecules such as γ-aminobutyric acid (GABA), hypotaurine, taurine, homotaurine, and β-alanine. We evolved BfGAD and doubled its taurine productivity. Additionally, we increased its specificity toward the substrate L-glutamate. Here, we provide a chemical strategy via which the BfGAD activity could be fine-tuned. In future, this strategy could be used to modulate the production of neuromodulatory molecules by gut microbes.},
}

@article {pmid40264541,
year = {2025},
author = {Wu, Y and Azevedo, P and Jin, S and Xu, H and Lei, H and Verschuren, L and Rodas-Gonzalez, A and Nyachoti, M and Yang, C},
title = {Feed efficiency and fecal microbiome of nursery pigs from parents with divergent breeding value for feed conversion ratio.},
journal = {Translational animal science},
volume = {9},
number = {},
pages = {txaf026},
pmid = {40264541},
issn = {2573-2102},
abstract = {Improving feed efficiency (FE) is essential for the swine industry's economic and environmental sustainability. Genetic selection, particularly through estimating breeding values for feed conversion ratio (EBV_FCR), is a common strategy to enhance FE. However, the biological mechanisms underlying phenotypic variations in FE between pigs with different EBV_FCR values are not fully understood. This study investigates these mechanisms by examining growth performance, nutrient and energy digestibility, and fecal microbiota composition and functionality of pigs at the nursery stage. The study involved 128 pigs, weaned at 21 d (±2 d) and with an initial body weight of 6.87 kg (±0.34 kg). These pigs, selected from dam and sire lines with divergent EBV_FCR values, were randomly assigned to 32 pens with four pigs each. Pigs were fed a corn and soybean meal-based diet, divided into two feeding phases of 2 wk each, under similar rearing conditions. Results indicated no significant differences in average daily feed intake (ADFI), average daily body weight gain (ADG), or feed efficiency (FE, gain:feed) between pigs from different EBV_FCR lines (P > 0.05). Similarly, nutrient digestibility showed no significant variation (P > 0.05). While the overall fecal microbiota taxonomic composition was similar between the groups, there was a trend toward higher beta diversity in the microbiota of pigs from parents with lower EBV_FCR (high efficiency pigs, H pigs) (P < 0.083). Carbohydrate and amino acid metabolism were predominant in all pigs, regardless of genetic background, with similar predicted microbiota functionality across groups. The study concluded that genetic differences based on parents divergent EBV_FCR did not affect growth performance, nutrient utilization, or microbiota characteristics at the nursery stage. This suggests that while EBV_FCR based genetic selection does not impact early-stage performance or microbiome responses, its effects may differ in older pigs, warranting further research.},
}

@article {pmid40264335,
year = {2025},
author = {Barasarathi, J and Perveen, K and Khan, F and Muthukumaran, M and Debnath, A and Behera, M and Pongen, M and Sayyed, R and Mastinu, A},
title = {Targeting Agrobacterium tumefaciens: A Computational Study on Quorum Sensing Inhibition.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70041},
doi = {10.1002/jobm.70041},
pmid = {40264335},
issn = {1521-4028},
support = {//King Saud University, Riyadh, Saudi Arabia, Researchers Supporting Project Number RSP2025R358 and University of Brescia, "ex 60% - Mastinu"./ ; },
abstract = {Crown gall disease, caused by Agrobacterium tumefaciens, results in significant loss in agricultural productivity losses due to induced tumor-like growths on various crops. The virulence of A. tumefaciens is controlled by its quorum sensing (QS) system, specifically through the TraR protein, which regulates the expression of genes essential for pathogenicity and plasmid transfer. Beyond pathogenic interactions, QS plays a crucial role in the plant microbiome, influencing symbiosis, competition, and plant health. This study aimed to identify QS inhibitors (QSIs) that disrupt TraR-mediated signaling as a novel approach to mitigate crown gall disease while exploring broader implications for plant-microbe interactions. Using a combination of molecular docking, molecular dynamics (MD) simulations, and protein-protein interaction analysis, we screened a library of potential QSIs and identified N-phenylselenourea as a potent candidate with a binding affinity of -8 kcal/mol to TraR. MD simulations confirmed the stability of this compound within the TraR binding pocket, with strong interactions observed with key residues such as Tyr53 and Asp70. Gene Ontology (GO) enrichment analysis supported these findings, highlighting the disruption of critical pathogenic pathways. Our findings underscore the dual benefits of QSIs, offering a targeted strategy to control A. tumefaciens infections while potentially enhancing plant-microbiome interactions for improved plant health. This study lays the groundwork for developing sustainable agricultural practices by leveraging QS disruption to manage plant diseases and promote beneficial microbial communities.},
}

@article {pmid40264322,
year = {2025},
author = {Jain, MS and Prasanthi, S and Bommala, ND and Goudanavar, P and Naveen, NR},
title = {Harnessing the Human Microbiome for Innovative Drug Delivery Systems: Exploring Pharmacomicrobiomics and Targeted Therapies.},
journal = {Current pharmaceutical design},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113816128354250250326045943},
pmid = {40264322},
issn = {1873-4286},
abstract = {The human gut microbiome has emerged as a crucial component of health and disease, presenting novel opportunities for the development of drug delivery systems based on microbiome interactions. This paper explores advanced strategies utilizing microorganisms, engineered bacteria, viruses, and bacteria-encapsulated nanoparticles as next-generation therapeutic vehicles. Focusing on analytical approaches to phage therapy and bio-hybrid bacteria for targeted drug delivery, the article highlights recent breakthroughs in colon-specific targeting for gastrointestinal disorders. The study also delves into the emerging field of pharmacomicrobiomics, with an emphasis on applications in cancer, cardiovascular, digestive, and nervous system treatments, specifically targeting key drug classes such as ACE inhibitors, proton-pump inhibitors, and NSAIDs. Challenges related to cytotoxicity and toxicity are addressed, offering proposals for safer therapeutic applications. This review underscores the transformative potential of the microbiome in personalized medicine and targeted drug delivery, with a focus on its integration with advanced technologies to optimize therapeutic outcomes.},
}

@article {pmid40264268,
year = {2025},
author = {Yang, Q and Zhang, X and Luo, Y and Jiang, Y and You, J and Li, C and Ye, F and Chen, T and Chen, Q},
title = {Ameliorative effect of "intestinal-vaginal" probiotics on 5-fluorouracil-induced microbial dysbiosis in colorectal cancer.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo00940e},
pmid = {40264268},
issn = {2042-650X},
abstract = {The interaction between the gut microbiome and cancer chemotherapy has been extensively studied. However, the exact role of the vaginal microbiome in chemotherapy remains unknown. To address this issue, we established a colorectal cancer chemotherapy mouse model. Here, we confirmed that 5-fluorouracil induced dysbiosis in both the vaginal and gut microbiomes, presenting a new challenge for conventional chemotherapy. Therefore, we innovatively propose an "intestinal-vaginal" probiotics administration strategy, which involves the simultaneous delivery of probiotics to both the gut and vagina, aiming to enhance chemotherapy efficacy while alleviating dysbiosis and associated side effects. Our results indicate that, compared to gut-only probiotic intervention, "intestinal-vaginal" probiotics administration significantly enhanced the anticancer efficacy of 5-fluorouracil by upregulating the p53 pathway. Furthermore, regarding gastrointestinal side effects, "intestinal-vaginal" probiotics more effectively reduced the release of vomit-associated neurotransmitters (e.g., 5-HT and SP), while also alleviating mucositis by downregulating the NF-κB pathway. Additionally, "intestinal-vaginal" probiotics outperformed the oral probiotic by increasing beneficial microbiota and reducing pathogenic bacteria. Notably, regarding vaginal side effects, "intestinal-vaginal" probiotics significantly inhibited the NF-κB inflammatory pathway and pro-apoptotic proteins, and improved vaginal dysbiosis compared to vaginal-only probiotics. These findings provide the first evidence of the significant potential of the "intestinal-vaginal" probiotics delivery approach as an adjunctive cancer therapy, which offers a novel perspective on the synergistic interactions between host microbiota communities.},
}

@article {pmid40264255,
year = {2025},
author = {Allkja, J and Bakri, A and Short, B and Gilmour, A and Brown, JL and Bal, AM and Newby, KJM and Jenkins, T and Short, RD and Williams, C and Ramage, G},
title = {Investigating the Prevalence of Fungi in Diabetic Ulcers: An Under-Recognised Contributor to Polymicrobial Biofilms.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {133},
number = {4},
pages = {e70025},
doi = {10.1111/apm.70025},
pmid = {40264255},
issn = {1600-0463},
support = {EP/V005839/1//Engineering and Physical Sciences Research Council/ ; },
mesh = {Humans ; *Biofilms/growth & development ; *Diabetic Foot/microbiology ; Female ; Male ; *Fungi/isolation & purification/classification/genetics ; Middle Aged ; Aged ; *Coinfection/microbiology/epidemiology ; Prevalence ; Real-Time Polymerase Chain Reaction ; Aged, 80 and over ; Adult ; },
abstract = {Diabetic foot ulcers (DFUs) are common complications for diabetic patients, often exacerbated by complex polymicrobial biofilm infections. While the majority of DFU studies are bacterial focused, fungi have also been identified. This study aims to investigate the prevalence of fungi in DFUs, as well as their potential role and influence on persistence and wound healing. Consecutive DFU swabs were collected from 128 patients (n = 349). Fungal positivity was assessed using enhanced culture and real-time qPCR. Routine microbiology cultures were carried out as part of standard care in the clinics, and their results were then compared to our laboratory investigation. Routine and enhanced culture resulted in similar rates of fungal detection (~9%), whereas qPCR resulted in a higher rate of detection (31%). Notably, the predominant yeast Candida parapsilosis was present in ischaemic and penetrating bone wounds. These findings support existing evidence of fungal presence in DFUs. We demonstrated that routine diagnostic methods are sufficient for fungal detection, but enhanced culture methods allow for more precise fungal identification. Finally, while fungal presence does not appear to impact patient outcomes in our study, their role within these infections remains poorly understood, and further studies are needed to fully understand their relationship to the microbiome.},
}

Humans
*Biofilms/growth & development
*Diabetic Foot/microbiology
Female
Male
*Fungi/isolation & purification/classification/genetics
Middle Aged
Aged
*Coinfection/microbiology/epidemiology
Prevalence
Real-Time Polymerase Chain Reaction
Aged, 80 and over
Adult

@article {pmid40264170,
year = {2025},
author = {Mayer, T and Teutloff, E and Unger, K and Lehenberger, P and Agler, MT},
title = {Deterministic colonization arises early during the transition of soil bacteria to the phyllosphere and is shaped by plant-microbe interactions.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {102},
pmid = {40264170},
issn = {2049-2618},
support = {390713860//Deutsche Forschungsgemeinschaft/ ; 390713860//Deutsche Forschungsgemeinschaft/ ; 390713860//Deutsche Forschungsgemeinschaft/ ; 390713860//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Soil Microbiology ; *Plant Leaves/microbiology ; *Bacteria/classification/genetics/isolation & purification/growth & development ; Germination ; Phylogeny ; Pseudomonas/genetics ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Host Microbial Interactions ; },
abstract = {BACKGROUND: Upon seed germination, soil bacteria are activated to transition to the plant and eventually colonize mature tissues like leaves. These bacteria are poised to significantly influence plant health, but we know little about their colonization routes. We studied the mechanisms of the transition of soil bacteria to germinating plants and leaves using an in-planta isolation approach and by experimentally manipulating inoculation times. We then tested how plant-microbe-microbe interactions shape assembly mechanisms in natural soil communities by amending soil with a trackable, labeled strain of the opportunistic pathogen Pseudomonas viridiflava (Pv3D9).

RESULTS: We identified 27 diverse genera of leaf-associated bacteria that could transition alone from a few cells near a germinating plant to mature leaves, suggesting that the soil-to-leaf transition is probably important for them in nature. Indeed, when plants were only inoculated by soil after the emergence of true leaves, less diverse bacteria transitioned to mature leaves via different colonization mechanisms than when plants germinated in the presence of soil microorganisms. In particular, deterministic processes drove the colonization of phylogenetic bins dominated by Pedobacter, Enterobacter, Stenotrophomonas, Janthinobacterium, Pseudomonas, and Chryseobacterium only in the natural soil-to-leaf transition. Host genotype and soil amendments with Pv3D9, both of which affect host physiology, had strong effects on mainly deterministic colonization.

CONCLUSIONS: Diverse bacteria transition from soil to leaves during natural colonization, resulting in characteristic diversity in healthy leaf microbiomes. The mechanisms of colonization are a mix of stochastic processes, which will be largely shaped by competition, and deterministic processes which are more responsive to factors that shape host physiology. In the chase toward targeted manipulation of microbiomes, identifying these mechanisms for a given host and environment provides important information. Developing targeted treatments, however, will require further dissection of the pathways by which host factors drive stochastic and deterministic transitions from soil to leaves. Video Abstract.},
}

*Soil Microbiology
*Plant Leaves/microbiology
*Bacteria/classification/genetics/isolation & purification/growth & development
Germination
Phylogeny
Pseudomonas/genetics
Microbiota
RNA, Ribosomal, 16S/genetics
Soil/chemistry
Host Microbial Interactions

@article {pmid40264132,
year = {2025},
author = {Zhou, M and Wu, L and Sun, X and Liu, M and Wang, Y and Yang, B and Ai, H and Chen, C and Huang, L},
title = {Assessing the relationship between the gut microbiota and growth traits in Chinese indigenous pig breeds.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {284},
pmid = {40264132},
issn = {1746-6148},
support = {3226200298//National Natural Science Foundation of China/ ; 2022YFA1304204//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Swine/growth & development/microbiology ; Feces/microbiology ; China ; RNA, Ribosomal, 16S/genetics ; Cecum/microbiology ; Bacteria/classification/genetics ; East Asian People ; },
abstract = {BACKGROUND: Gut microbiota plays crucial roles in host metabolism, diseases and development. It has also been reported to be associated with growth performance in pigs. However, the bacterial species influencing pig growth performance have not been isolated, and the mechanisms remain unclear.

RESULTS: In this study, we collected 500 gut microbial samples from two Chinese indigenous pig breeds, including 244 fecal samples from Bamaxiang (BMX) pigs and 256 cecum content samples from Erhualian (EHL) pigs, to investigate the relationship between gut microbiota and pig growth traits. Bacterial compositions were determined by 16 S rRNA gene sequencing, and association analysis was performed using a two-part model. We found that the Firmicutes-to-Bacteroidota ratio in fecal samples from BMX pigs was negatively associated with average daily gain (P = 0.0085). Amplicon sequence variants (ASVs) belonging to Prevotella and three ASVs annotated to Oscillospiraceae were negatively associated with pig growth traits, while ASVs annotated to Muribaculaceae and Rikenellaceae showed positive correlations with growth traits in BMX fecal samples. In cecum content samples from EHL pigs, ASVs belonging to Prevotella, Lactobacillus delbrueckii, and Lachnospiraceae were negatively associated with growth performance, whereas one ASV belonging to Rikenellaceae demonstrated a positive association. Predicted functional capacity analysis revealed that metabolic pathways related to the digestive system, glycan biosynthesis and metabolism, signaling molecules and interactions, and xenobiotics biodegradation and metabolism were positively associated with pig growth traits. Conversely, the excretory system pathway showed a negative correlation. These pathways were found to correlate with growth trait-associated bacterial ASVs, suggesting that alterations in gut bacterial composition led to functional capacity shifts in the gut microbiome, subsequently affecting porcine growth.

CONCLUSIONS: Our results gave significant insights about the effect of gut microbiota on pig growth and provided important evidence to support further isolation of bacterial taxa that influence pig growth for elucidating their mechanisms.},
}

Animals
*Gastrointestinal Microbiome
Swine/growth & development/microbiology
Feces/microbiology
China
RNA, Ribosomal, 16S/genetics
Cecum/microbiology
Bacteria/classification/genetics
East Asian People

@article {pmid40264013,
year = {2025},
author = {Peng, Y and Zhang, X and Wang, G and Li, Z and Lai, X and Yang, B and Chen, B and Du, G},
title = {The gut microbial community structure of the oriental armyworm Mythimna separata (Walker) (Lepidoptera: Noctuidae) affects the the virulence of the entomopathogenic fungus Metarhizium rileyi.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {232},
pmid = {40264013},
issn = {1471-2180},
support = {202202AE090036//Major Science and Technology Project of Yunnan and Kunming/ ; 202301AT070487//Science and Technology Department of Yunnan Province Basic Research Project/ ; },
mesh = {Animals ; *Metarhizium/pathogenicity ; *Gastrointestinal Microbiome ; Virulence ; Larva/microbiology ; *Moths/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Mythimna separata, the oriental armyworm, is a lepidopteran pest that threatens cereal crops. In the current study, two strains (XSBN200920 and JHML200710) of entomopathogenic fungus Metarhizium rileyi were tested for virulence against oriental armyworms. When treated with spore suspensions of both strains at a concentration of 1.0 × 10[8] spores/mL, the 3rd instar larvae's survival rate was considerably different (P < 0.01). The median lethal time of the insects exposed to XSBN200920 was about 3 d longer than that of JHML200710. The results of 16S ribosomal RNA sequencing showed that Chao1 richness in the JHML200710 treatment group was significantly decreased compared with the CK (0.02% Tween 80). The dominant gut bacteria species at the phylum level were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidota in the three groups. The CK group had a much higher associated abundance of cyanobacteria than the other two fungal treatment groups. Sixteen genera revealed significant variations in the gut bacteria of the insects at the genus level. The Kyoto Encyclopedia of Genes and Genomes (KEGG) functional gene and enzyme analysis showed that when compared with the CK group, the XSBN200920 treatment group showed a significant reduction in six aspects, including betalain biosynthesis, spliceosome, and neuroactive ligand-receptor interaction. These findings suggested that healthy and fungus-infected insects' intestinal microbial community structure differed significantly. And the virulence of M. rileyi is closely linked to its ability to alter the structure of the intestinal microbiome of insects. The results offer a starting point for examining the relationship between the gut microbial diversity of oriental armyworms and variations in the virulence of pathogenic fungi.},
}

Animals
*Metarhizium/pathogenicity
*Gastrointestinal Microbiome
Virulence
Larva/microbiology
*Moths/microbiology
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics/isolation & purification

@article {pmid40263877,
year = {2025},
author = {Qu, C and Liang, S and Wang, K and He, Y and Ju, W and Sun, Y and Miao, J},
title = {EPA-enriched lipid from Apostichopus japonicus byproducts mitigates UVB-induced oxidative stress and inflammation by gut-skin axis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {208},
number = {},
pages = {116085},
doi = {10.1016/j.foodres.2025.116085},
pmid = {40263877},
issn = {1873-7145},
mesh = {Animals ; *Ultraviolet Rays/adverse effects ; *Oxidative Stress/drug effects/radiation effects ; *Skin/drug effects/radiation effects/metabolism ; *Stichopus/chemistry ; Gastrointestinal Microbiome/drug effects ; *Inflammation/prevention & control ; *Eicosapentaenoic Acid/pharmacology ; *Lipids/pharmacology/chemistry ; Antioxidants/pharmacology ; },
abstract = {The tremendous byproducts from sea cucumber processing discarded as waste bring serious environmental and economic challenges. The abundant EPA in sea cucumber intestines indicates the potential for lipid development. However, there is little study on how these lipids affect skin health. Using REM techniques, this study prepared lipids from Apostichopus japonicus intestines (AJIL) with a 26.63 % EPA content, which displayed DPPH scavenging capacity in vitro. Administration of AJIL showed significant skin repair effects by reducing the symptoms of UVB-induced skin tissue damage, preventing epidermal thickening and increasing hydroxyproline content to protect collagen. AJIL suppressed oxidative stress and inflammation by significantly reducing ROS and MDA levels and enhancing GPx and CAT activity, as well as inhibiting the expression of inflammatory cytokines such as TNF-α, NF-κB, IL-1β and IL-6. By upregulating Nrf2, HO-1 and NQO-1 and downregulating Keap1, AJIL activated the Keap1-Nrf2 signaling pathways. Furthermore, AJIL regulated the composition and structure of gut microbiome, especially significantly increasing the SCFA-producing and anti-inflammatory bacteria like Muribacuclaceae, Alloprevotella, Bacteroides and Prevotellaceae, then improved key metabolic pathways. Overall, AJIL mediated the gut-skin axis to prevent UVB-induced skin damage and revealed potential as a natural skin protection candidate, which transformed discarded sea cucumber intestines into valuable resources for skin health.},
}

Animals
*Ultraviolet Rays/adverse effects
*Oxidative Stress/drug effects/radiation effects
*Skin/drug effects/radiation effects/metabolism
*Stichopus/chemistry
Gastrointestinal Microbiome/drug effects
*Inflammation/prevention & control
*Eicosapentaenoic Acid/pharmacology
*Lipids/pharmacology/chemistry
Antioxidants/pharmacology

@article {pmid40263874,
year = {2025},
author = {Huang, X and Li, R and Xu, J and Kang, J and Chen, X and Han, B and Xue, Y},
title = {Integrated multi-omics uncover viruses, active fermenting microbes and their metabolic profiles in the Daqu microbiome.},
journal = {Food research international (Ottawa, Ont.)},
volume = {208},
number = {},
pages = {116061},
doi = {10.1016/j.foodres.2025.116061},
pmid = {40263874},
issn = {1873-7145},
mesh = {*Fermentation ; *Microbiota ; Fungi/metabolism/genetics ; *Bacteria/metabolism/genetics ; *Viruses/genetics/classification ; Metagenomics ; Food Microbiology ; *Fermented Foods/microbiology/virology ; Bacteriophages/genetics ; *Metabolome ; Multiomics ; },
abstract = {The coexistence and coevolution of viruses and fermenting microbes have a significant impact on the structure and function of microbial communities. Although the presence of viruses in Daqu, the fermentation starter for Chinese Baijiu, has been documented, their specific effects on the community composition and metabolic functions of low, medium, and high-temperature Daqu remain unclear. In this study, we employed multi-omics technology to explore the distribution of viruses and active bacteria and fungi in various Daqu and their potential metabolic roles. Viral metagenomic sequencing showed a predominance of Parvoviridae in High-Temperature Daqu (HTQ), while Genomoviridae were dominant in Medium-Temperature Daqu (MTQ) and Low- Temperature Daqu (LTQ). Phages belonging to the Siphoviridae, Podoviridae, Herelleviridae, and Myoviridae families showed significantly different abundances across three Daqu groups. Metatranscriptomic analysis showed that fungal communities were most active in LTQ, whereas bacterial communities were dominant in MTQ and HTQ. By employing the CRISPR-Cas spacer, a higher predicted number of phage-host linkages was identified in LTQ, particularly with hosts including Lactobacillus, Staphylococcus, Acinetobacter, Enterobacter, and Bacillus. Correlation analysis showed that bacteria like Acinetobacter, Lactobacillus, and Streptococcus exhibited the strongest associations with metabolites, particularly amino acids and organic acids. The potential phage-induced metabolic differences in the three Daqu groups were mainly linked to pathways involved in the metabolism of amino acids, sugars, and organic acids. Overall, our study elucidates the impact of viruses on shaping microbial composition and influencing metabolic functions in Daqu. These results improve our comprehension of viruses and microbes in Daqu microbial communities and provide valuable insights for enhancing quality control in Daqu production.},
}

*Fermentation
*Microbiota
Fungi/metabolism/genetics
*Bacteria/metabolism/genetics
*Viruses/genetics/classification
Metagenomics
Food Microbiology
*Fermented Foods/microbiology/virology
Bacteriophages/genetics
*Metabolome
Multiomics

@article {pmid40263778,
year = {2025},
author = {Peng, L and Zeng, H and Wan, L and Yang, X and Bai, Q and Huang, J and Liu, Z},
title = {Effects of microbial fermentation on tea in alleviating obesity symptoms: Insights from microbiome and metabolomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {208},
number = {},
pages = {116111},
doi = {10.1016/j.foodres.2025.116111},
pmid = {40263778},
issn = {1873-7145},
mesh = {*Fermentation ; *Tea/chemistry/microbiology ; *Obesity/metabolism ; *Metabolomics ; Animals ; Polyphenols/analysis ; Male ; *Microbiota ; Camellia sinensis/microbiology/chemistry ; Mice ; Anti-Obesity Agents/pharmacology ; Mice, Inbred C57BL ; },
abstract = {Previous studies imply that dark tea has more advantages in facilitating the growth of Akkermansia which may be beneficial to anti-obesity. However, whether those benefits are affected by the unique processing (microbial fermentation) of dark tea remains unclear. Moreover, although there are many reports regarding the comparison of anti-obesity effects among different types of tea, the insights into the relationship between tea pharmacological component and the therapeutic effects are still limited due to the ununified tea raw material. In our study, the anti-obesity effects of non-microbial fermentation tea (NFT) and microbial fermentation tea (FT) are investigated and compared. By controlling for the raw material source, the effects of microbial fermentation on tea in alleviating obesity symptoms are effectively isolated. Our results suggested that even though NFT and FT showed distinctive differences in terms of ingredients, they exerted similar properties in attenuating overweight, regulating glucolipid metabolism, and alleviating hepatic dysfunction. The underlying mechanisms could be that NFT and FT displayed similar effects in promoting the proliferation of Akkermansia as well as enhancing the production of short-chain fatty acids. Furthermore, tea chemical constituent analyses exhibited that although microbial fermentation caused differences in polyphenol profiling between NFT and FT, it didn't remarkably influence the polyphenol content in tea which is strongly associated with the growth of Akkermansia. This might be root cause of the comparable effects on alleviating obesity symptoms between NFT and FT groups. Together, the current data supplied valuable information on the relationship among the microbial fermentation of tea, tea bioactivities, and obesity symptoms for mankind to understand.},
}

*Fermentation
*Tea/chemistry/microbiology
*Obesity/metabolism
*Metabolomics
Animals
Polyphenols/analysis
Male
*Microbiota
Camellia sinensis/microbiology/chemistry
Mice
Anti-Obesity Agents/pharmacology
Mice, Inbred C57BL

@article {pmid40263590,
year = {2025},
author = {Kadibalban, AS and Künstner, A and Schröder, T and Zauleck, J and Witt, O and Marinos, G and Kaleta, C},
title = {Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota.},
journal = {Molecular systems biology},
volume = {},
number = {},
pages = {},
pmid = {40263590},
issn = {1744-4292},
support = {EXC2167//Deutsche Forschungsgemeinschaft (DFG)/ ; KA 3541/20-1//ExoMod/ ; },
abstract = {Type 2 diabetes (T2D) presents a global health concern, with evidence highlighting the role of the human gut microbiome in metabolic diseases. This study employs metabolic modelling to elucidate changes in host-microbiome interactions in T2D. Glucose levels, diet, 16S sequences and metadata were collected for 1866 individuals. In addition, microbial community models, and ecological interactions were simulated for the gut microbiomes. Our findings revealed a significant decrease in metabolic fluxes provided by the host's diet to the microbiome in T2D patients, accompanied by increased within-community exchanges. Moreover, the diabetic microbiomes shift towards increased exploitative ecological interactions at the expense of collaborative interactions. The reduced microbiome-to-host butyrate flux, along with decreased fluxes of amino acids (including tryptophan), nucleotides, and B vitamins from the host's diet, further highlight the dysregulation in microbial-host interactions in diabetes. In addition, microbiomes of T2D patients exhibit enrichment in energy metabolism, indicative of increased metabolic activity and antagonism. This study sheds light on the increased microbiome autonomy and antagonism accompanying diabetes, and provides candidate metabolic targets for intervention studies and experimental validation.},
}

@article {pmid40263502,
year = {2025},
author = {Canderan, J and Ye, Y},
title = {Identification of microbial species and proteins associated with colorectal cancer by reanalyzing CPTAC proteomic datasets.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13926},
pmid = {40263502},
issn = {2045-2322},
support = {R01AI143254//U.S. Department of Health & Human Services | NIH | Center for Information Technology (Center for Information Technology, National Institutes of Health)/ ; EF-202545//National Science Foundation (NSF)/ ; },
mesh = {*Colorectal Neoplasms/microbiology/metabolism ; Humans ; *Proteomics/methods ; *Bacterial Proteins/metabolism ; Aspergillus/metabolism ; },
abstract = {Microbiome research has revealed associations between microbial species and colorectal cancer (CRC). Most of the existing research relied on metagenomic data. We leveraged a tool that we recently developed for detecting human and microbial peptides from (meta)proteomics data to reanalyze Clinical Proteomic Tumor Analysis Consortium CRC proteomics datasets. Our analyses revealed potential microbial species and proteins that are associated with CRC, especially when analyzing multiplexed proteomics data consisting of cancerous and healthy tissue taken from the same individuals. Many of the identified proteins are associated with species with known links to CRC, such as the fungi Aspergillus kawachii, but many are unstudied or their specific roles unknown. Proteins from other microbial species, such as Paenibacillus cellulosilyticus, were also identified in the samples. We showed that Aspergillus kawachii and others are depleted overall in cancer samples, which is consistent with a previous genomic-based multi-cohort study. Our analysis also revealed that some proteins belonging to this species are more abundantly detected, while others in this and other species are not. Further, we showed that microbial identifications could be used to build predictive models for tumor detection, but caution needs to be taken when applying such models trained on one dataset to another due to the substantial impacts of different experimental techniques on peptide detection profiles.},
}

*Colorectal Neoplasms/microbiology/metabolism
Humans
*Proteomics/methods
*Bacterial Proteins/metabolism
Aspergillus/metabolism

@article {pmid40263165,
year = {2025},
author = {Tan, J and Chen, R and Gan, D and Ou, M and Wu, Y and Jie, H and Xu, Y and Huang, J},
title = {Correlation between Lactobacillus of Vaginal Microbiota and the Pregnancy Outcomes for Patients Experiencing Recurrent Miscarriage.},
journal = {Reproductive sciences (Thousand Oaks, Calif.)},
volume = {},
number = {},
pages = {},
pmid = {40263165},
issn = {1933-7205},
support = {2022A1515012599//Basic and Applied Basic Research Foundation of Guangdong Province/ ; },
abstract = {The etiology of recurrent miscarriage (RM) is complex, with the vaginal microbiota (VM) being an important factor associated with RM. We aimed to establish the VM composition in both patients with RM and healthy women and further investigate relationship between the subsequent pregnancy outcomes of patients with RM and VM, to explain the potential mechanism of VM in RM to some extent. A cohort study compared the VM between 34 patients with RM and 15 healthy women using a sequencing technique based on Type IIB restriction enzymes for the microbiome (2bRAD-M). Further comparison was made between 11 patients with clinical miscarriages (CM) and 13 patients with ongoing pregnancies (OP) in the RM group who conceived naturally. To determine the VM composition, the 2bRAD-M library was prepared, and sequence and bioinformatics analyses were conducted. The composition of the VM exhibited notable differences between the non-RM and RM groups, with significant findings for alpha diversity (p < 0.05) and beta diversity (p = 0.01). Further analysis between the RM-OP and RM-CM groups revealed a significant difference in Lactobacillus (97.81% ± 2.71% vs. 53.37% ± 46.42%, p = 0.03). Other uncommon species, such as Cutibacterium acnes (C. acnes) (p = 0.04) were found significantly increase in the RM-CM group. Functional annotation analysis revealed 47 related signaling pathways between the two groups. The results of this study indicate that Lactobacillus is associated with subsequent miscarriages and that C. acnes is closely related to pregnancy outcomes of patients with RM.},
}

@article {pmid40263059,
year = {2025},
author = {Sarnaik, D and Krishnakumar, A and Nejati, S and Sullivan, CR and Cross, TL and Campbell, WW and Johnson, JS and Rahimi, R},
title = {A smart capsule with a bacteria- and pH-triggered enteric polymer coating for targeted colonic microbiome sampling.},
journal = {Acta biomaterialia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.actbio.2025.04.025},
pmid = {40263059},
issn = {1878-7568},
abstract = {The gut microbiome is recognized as a critical factor in advancing precision nutrition and medicine for health and in developing dietary recommendations and targeted therapies for gastrointestinal (GI) health and diseases. However, conventional sampling methods, such as fecal analysis and colonoscopy, often fail to capture microbial information from specific regions of the GI tract or require invasive procedures, thereby limiting accuracy and clinical utility. As a non-invasive alternative, passive sampling capsules have been developed for site-specific microbiome analysis by employing pH-sensitive enteric coatings that delay sampling until the capsule reaches the targeted intestinal region. Although this approach has been successful in the small intestine, colonic sampling remains challenging due to the high interpersonal variability in intestinal pH, which makes it difficult to rely solely on a pH-triggering mechanism. To overcome this challenge, a dual bacterially and pH triggered polymeric enteric coating was created by blending lactulose and N,N-dimethylaminoethyl methacrylate, enabling complete dissolution within the colonic region. Through systematic characterization of multiple polymer blend compositions using Fourier Transform Infrared Spectroscopy, Thermogravimetric Analysis, and Differential Scanning Calorimetry, an optimized design was identified that provides both suitable physical integrity and rapid (∼2 h) degradation in the presence of colonic bacteria, across a pH range of 5 to 8. The optimized blend was subsequently applied as a double-layer enteric coating on a sampling capsule, enabling the dissolution of the outer layer in the small intestine and complete dissolution of the inner layer in the colon. In-vitro and in-vivo pig model studies were conducted to validate the capsule's sampling performance and to ensure the preservation of the microbial environment. Furthermore, 16S rRNA sequencing revealed a taxonomic similarity between samples collected by the capsule and the colonic microbiome (residing between the ileum and fecal matter). Overall, this technology provides an effective approach to targeted microbial sampling and may pave the way for more comprehensive colonic microbiome analyses and improved diagnostic capabilities for GI diseases. STATEMENT OF SIGNIFICANCE: Precise monitoring of the gut microbiome is vital for understanding health and disease, yet current sampling techniques often lack precision or require invasive procedures. Our work introduces a novel, non-invasive capsule that targets the colon using a dual-trigger polymer system activated by both pH and colonic bacteria. This design enables localized sampling of gut microbiota, overcoming the limitations of fecal analysis, endoscopy, and earlier pH-triggered capsule designs. By capturing microbial communities directly from the colon, our technology provides deeper insights into colonic health and conditions such as inflammatory bowel disease and colorectal cancer. This breakthrough represents a significant advancement in precision nutrition and medicine for human health, and advanced diagnostics and targeted therapies to support dietary guidance, clinical practice and biomedical research.},
}

@article {pmid40262895,
year = {2025},
author = {Lind, AL and McDonald, NA and Gerrick, ER and Bhatt, AS and Pollard, K},
title = {Contiguous and complete assemblies of Blastocystis gut microbiome-associated protists reveal evolutionary diversification to host ecology.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279080.124},
pmid = {40262895},
issn = {1549-5469},
abstract = {Blastocystis, an obligate host-associated protist, is the most common microbial eukaryote in the human gut and is widely distributed across vertebrate hosts. The evolutionary transition of Blastocystis from its free-living stramenopile ancestors to a radiation of host-associated organisms is poorly understood. To explore this, we cultured and sequenced eight strains representing the significant phylogenetic diversity of the genus using long-read, short-read, and Hi-C DNA sequencing, alongside gene annotation and RNA sequencing. Comparative genomic analyses revealed significant variation in gene content and genome structure across Blastocystis Notably, three strains from herbivorous tortoises, phylogenetically distant from human subtypes, have markedly larger genomes with longer introns and intergenic regions, and retain canonical stop codons absent in the human-associated strains. Despite these genetic differences, all eight isolates exhibit gene losses linked to the reduced cellular complexity of Blastocystis, including losses of cilia and flagella genes, microtubule motor genes, and signal transduction genes. Isolates from herbivorous tortoises contained higher numbers of plant carbohydrate-metabolizing enzymes, suggesting that like gut bacteria, these protists ferment plant material in the host gut. We find evidence that some of these carbohydrate-metabolizing enzymes were horizontally acquired from bacteria, indicating that horizontal gene transfer is an ongoing process in Blastocystis that has contributed to host-related adaptation. Together, these results highlight substantial genetic and metabolic diversity within the Blastocystis genus, indicating different lineages of Blastocystis have varied ecological roles in the host gut.},
}

@article {pmid40262772,
year = {2025},
author = {Wang, Y and Zhang, R and Wang, C and Yan, W and Zhang, T and Ju, F},
title = {Metabolic Segregation and Functional Gene Clusters in Anaerobic Digestion Consortia.},
journal = {Environmental microbiology},
volume = {27},
number = {4},
pages = {e70091},
doi = {10.1111/1462-2920.70091},
pmid = {40262772},
issn = {1462-2920},
support = {22241603//National Science Foundation of China/ ; LR22D010001//Zhejiang Provincial Natural Science Foundation of China/ ; WU2022C030//Research Center for Industries of the Future (RCIF)/ ; },
abstract = {A combined enrichment experiment and genome-centric meta-omics analysis demonstrated that metabolic specificity, rather than flexibility, governs the anaerobic digestion (AD) ecosystem. This study provides new insights into interspecies electron transfer in the AD process, highlighting a segregation in the metabolism of H2 and formate. Our findings show that H2 acts as the primary electron sink for recycling redox cofactors, including NAD[+] and oxidised ferredoxin (Fdox), during primary fermentation, while formate is the dominant electron carrier in secondary fermentation, especially under conditions with elevated H2 concentrations. Importantly, no evidence of biochemical interconversion between H2 and formate was identified in the primary fermenting bacteria or in syntrophs enriched in this study. This segregation of H2 and formate metabolism likely benefits the anaerobic oxidation of butyrate and propionate with a higher tolerance to H2 accumulation. Moreover, this study highlights the functional partitioning among microbial populations in key AD niches: primary fermentation, secondary fermentation (syntrophic acetogenesis), hydrogenotrophic methanogenesis, and acetoclastic methanogenesis. Genome-centric analysis of the AD microbiome identified several key functional gene clusters, which could enhance genome-centric genotype-phenotype correlations, particularly for strict anaerobes that are difficult to isolate and characterise in pure culture.},
}

@article {pmid40262540,
year = {2025},
author = {Zung, JL and McBride, CS},
title = {Sebaceous origins of human odor.},
journal = {Current biology : CB},
volume = {35},
number = {8},
pages = {R303-R313},
doi = {10.1016/j.cub.2025.03.031},
pmid = {40262540},
issn = {1879-0445},
abstract = {The compounds that make up human body odor have been catalogued by researchers in many fields. Yet few are aware of exactly where these molecules come from. Volatile body-odor compounds are often cited as being produced primarily via microbial activity from precursors in sweat. While this is a source of many human volatiles, here we synthesize data showing that some of the most distinctive and abundant components of human odor instead originate from precursors in sebum, via reactions that do not involve the skin microbiome. We also review the unique biochemistry of human sebaceous glands and discuss evolutionary hypotheses that may partly explain why human sebum is so unique. Finally, we discuss how sebum-derived volatiles intersect with human health and disease, for example, via attraction of disease-vector mosquitoes or use in medical diagnostics. Our review draws insights from multiple fields, which together provide surprising clarity on some of the proximate and ultimate mechanisms underlying the distinctive composition of human odor.},
}

@article {pmid40262434,
year = {2025},
author = {Lima, RAT and Garay, AV and Frederico, TD and de Oliveira, GM and Quirino, BF and Barbosa, JARG and Freitas, SM and Krüger, RH},
title = {Biochemical and structural characterization of a family-9 glycoside hydrolase bioprospected from the termite Syntermes wheeleri gut bacteria metagenome.},
journal = {Enzyme and microbial technology},
volume = {189},
number = {},
pages = {110654},
doi = {10.1016/j.enzmictec.2025.110654},
pmid = {40262434},
issn = {1879-0909},
abstract = {Glycosyl hydrolases (GH) are enzymes involved in the degradation of plant biomass. They are important for biorefineries that aim at the sustainable utilization of lignocellulosic residues to generate value-added products. The termite Syntermes wheeleri gut microbiota showed an abundance of bacteria from the phylum Firmicutes, a phylum with enzymes capable of breaking down cellulose and degrading lignin, facilitating the use of plant materials as a food source for termites. Using bioinformatics techniques, cellobiohydrolases were searched for in the gut metagenome of the termite Syntermes wheeleri, endemic to the Cerrado. After selecting sequences of the target enzymes, termite gut microbiome metatranscriptome data were used as the criteria to choose the GH9 enzyme sequence Exo8574. Here we present the biochemical and structural characterization of Exo8574, a GH9 enzyme that showed activity with the substrate p-nitrophenyl-D-cellobioside (pNPC), consistent with cellobiohydrolase activity. Bioinformatics tools were used to perform phylogeny studies of Exo8574 and to identify conserved families and domains. Exo8574 showed 48.8 % homology to a protein from a bacterium belonging to the phylum Firmicutes. The high-quality three-dimensional (3D) model of Exo8574 was obtained by protein structure prediction AlphaFold 2, a neural network-based method. After the heterologous expression of Exo8574 and its purification, biochemical experiments showed that the optimal activity of the enzyme was at a temperature of 55 ºC and pH 6.0, which was enhanced in the presence of metal ions, especially Fe[2 +]. The estimated kinetic parameters of Exo8574 using the synthetic substrate p-nithrophenyl-beta-D-cellobioside (pNPC) were: Vmax = 9.14 ± 0.2 x10[-5] μmol/min and Km = 248.27 ± 26.35 μmol/L. The thermostability test showed a 50 % loss of activity after 1 h incubation at 55 °C. The secondary structure contents of Exo8574 evaluated by Circular Dichroism were pH dependent, with greater structuring of protein in β-antiparallel and α-helices at pH 6.0. The similarity between the CD results and the Ramachandran plot of the 3D model suggests that a reliable model has been obtained. Altogether, the results of the biochemical and structural characterization showed that Exo8574 is capable of acting on p-nithrophenyl-beta-D-cellobioside (pNPC), a substrate that mimics bonds cleaved by cellobiohydrolases. These findings have significant implications for advancing in the field of biomass conversion while also contributing to efforts aimed at overcoming challenges in developing more efficient cellulase cocktails.},
}

@article {pmid40262063,
year = {2025},
author = {Elkrief, A and Routy, B and Derosa, L and Bolte, L and Wargo, JA and McQuade, JL and Zitvogel, L},
title = {Gut Microbiota in Immuno-Oncology: A Practical Guide for Medical Oncologists With a Focus on Antibiotics Stewardship.},
journal = {American Society of Clinical Oncology educational book. American Society of Clinical Oncology. Annual Meeting},
volume = {45},
number = {3},
pages = {e472902},
doi = {10.1200/EDBK-25-472902},
pmid = {40262063},
issn = {1548-8756},
abstract = {The gut microbiota has emerged as a critical determinant of immune checkpoint inhibitor (ICI) efficacy, resistance, and toxicity. Retrospective and prospective studies profiling the taxonomic composition of intestinal microbes of patients treated with ICI have revealed specific gut microbial signatures associated with response. By contrast, dysbiosis, which can be caused by chronic inflammatory processes (such as cancer) or comedications, is a risk factor of resistance to ICI. Recent large-scale meta-analyses have confirmed that antibiotic (ATB) use before or during ICI therapy alters the microbiota repertoire and significantly shortens overall survival, even after adjusting for prognostic factors. These results underscore the importance of implementing ATB stewardship recommendations in routine oncology practice. Microbiota-centered interventions are now being explored to treat gut dysbiosis and optimize ICI responses. Early-phase clinical trials evaluating fecal microbiota transplantation (FMT) from ICI responders or healthy donors have shown that this approach is safe and provided preliminary data on potential efficacy to overcome both primary and secondary resistance to ICI in melanoma, non-small cell lung cancer, and renal cell carcinoma. More targeted interventions including live bacterial products including Clostridium butyricum and Akkermansia massiliensis represent novel microbiome-based adjunct therapies. Likewise, dietary interventions, such as high-fiber diets, have shown promise in enhancing ICI activity. In this ASCO Educational Book, we summarize the current state-of-the-evidence of the clinical relevance of the intestinal microbiota in cancer immunotherapy and provide a practical guide for ATB stewardship.},
}

@article {pmid40261735,
year = {2025},
author = {Rogers, AB and Kale, V and Baldi, G and Alberdi, A and Gilbert, MTP and Gupta, D and Limborg, MT and Li, S and Payne, T and Petersen, B and Rasmussen, JA and Richardson, L and Finn, RD},
title = {HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production.},
journal = {Database : the journal of biological databases and curation},
volume = {2025},
number = {},
pages = {},
doi = {10.1093/database/baae112},
pmid = {40261735},
issn = {1758-0463},
mesh = {Animals ; *Chickens/microbiology ; *Microbiota ; *Salmon/microbiology ; *Databases, Genetic ; *Host Microbial Interactions ; Metadata ; *Gastrointestinal Microbiome ; },
abstract = {The HoloFood project used a hologenomic approach to understand the impact of host-microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project's raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues. The HoloFood Data Portal is a web resource that simplifies access to the project datasets. For example, users can conveniently access multiomic datasets derived from the same individual or retrieve host phenotypic data with a linked gut microbiome sample. Project-specific metagenome-assembled genome and viral catalogues are also provided, linking to broader datasets in MGnify. The portal stores only data necessary to provide these relationships, with possible linking to the underlying repositories. The portal showcases a model approach for how future multiomics datasets can be made available. Database URL: https://www.holofooddata.org.},
}

Animals
*Chickens/microbiology
*Microbiota
*Salmon/microbiology
*Databases, Genetic
*Host Microbial Interactions
Metadata
*Gastrointestinal Microbiome

@article {pmid40261569,
year = {2025},
author = {Basili, M and Randazzo, B and Caccamo, L and Guicciardi O Guizzardi, S and Meola, M and Perdichizzi, A and Quero, GM and Maricchiolo, G},
title = {Effect of graded inclusion of black soldier fly (Hermetia illucens, Linnaeus, 1758) pre-pupae meal in diets for gilthead seabream (Sparus aurata, Linnaeus, 1758) on gut microbiome and liver morphology.},
journal = {Fish physiology and biochemistry},
volume = {51},
number = {3},
pages = {85},
pmid = {40261569},
issn = {1573-5168},
mesh = {Animals ; *Sea Bream/anatomy & histology/microbiology/physiology ; *Gastrointestinal Microbiome ; *Animal Feed/analysis ; *Liver/anatomy & histology ; *Diet/veterinary ; Animal Nutritional Physiological Phenomena ; },
abstract = {Over the last decades, an insect meal has received great attention for finfish diets, due to its nutritional composition and low ecological footprint. In the present study, we assessed the response of gut microbiota composition and liver histology of gilthead seabream (Sparus aurata) fed four experimental diets including the black soldier fly (Hermetia illucens) meal (HI) used to replace 0 (HI0), 25 (HI25), 35 (HI35) and 50 (HI50) percent of fish meal in a 131-day feeding trial. At the end of the experiment, a remarkable change in gut microbiota composition related to HI inclusion was observed, with a preponderance of Cyanobacteriain the control and low HI groups (HI0, HI25) while Chloroflexi became prevalent in the higher HI inclusion groups (HI35, HI50). Predictive analysis on bacterial metabolic pathways showed a clear separation between HI0-HI25 and HI35-HI50 groups. The microbiota shifts observed suggest a pivotal role of HI in inducing a bacterial-mediated physiological response in this fish species, probably due to chitin content and the fatty acid profile of this ingredient. Liver histology showed a higher hepatocyte size in fish from the HI50 group, suggesting lipid dysmetabolism due to the HI meal fatty acid profile, while a marginal adaptive response was observed in the HI25 group. In conclusion, while up to 25% inclusion of black soldier fly meal showed limited adverse effects, 50% HI dietary inclusion is not recommended in gilthead seabream diet, since possible alteration in lipid deposition, particularly at hepatic level, were highlighted in this fish species.},
}

Animals
*Sea Bream/anatomy & histology/microbiology/physiology
*Gastrointestinal Microbiome
*Animal Feed/analysis
*Liver/anatomy & histology
*Diet/veterinary
Animal Nutritional Physiological Phenomena

@article {pmid40261446,
year = {2025},
author = {Fatima, N and Fatima, H and Ahmad, S and Hashmi, MATS and Sheikh, N},
title = {Understanding the role of Hedgehog signaling pathway and gut dysbiosis in fueling liver cancer.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {411},
pmid = {40261446},
issn = {1573-4978},
mesh = {Humans ; *Hedgehog Proteins/metabolism ; *Dysbiosis/metabolism/complications/microbiology ; *Liver Neoplasms/metabolism/microbiology/pathology ; Signal Transduction ; *Gastrointestinal Microbiome/physiology ; *Carcinoma, Hepatocellular/metabolism/pathology/microbiology ; Animals ; Cell Proliferation ; },
abstract = {Liver cancer is one of the most prevalent types of cancer worldwide with less than 20% of patients surviving in the past half a decade. Several molecular pathways have been uncovered that may lead to the development of liver cancer but more recently the Hedgehog pathway (HH) and its interactions with the gut microbiota has emerged as an underlying cause of the development of liver cancer. Gut-liver axis is vital to maintaining homeostasis. The HH pathway controls cellular differentiation, proliferation, and apoptosis evasions, its abnormal activation can lead to uncontrolled proliferation of liver cancer stem cells. Additionally, the intricate interplay between HH signaling and the gut microbiota introduces a novel dimension. Recent investigations suggest that potential modulation of HH activity by gut microbiota influence HCC progression. This review explores a crosstalk between HH signaling and the gut microbiota, uncovering intricate mechanisms by which it fuels liver cancer development. This interplay provides insights into gut dysbiosis, HCC etiology and potential therapeutic avenues, highlighting the cooperative role of HH signaling and gut microbiota in shaping the overall HCC landscape.},
}

Humans
*Hedgehog Proteins/metabolism
*Dysbiosis/metabolism/complications/microbiology
*Liver Neoplasms/metabolism/microbiology/pathology
Signal Transduction
*Gastrointestinal Microbiome/physiology
*Carcinoma, Hepatocellular/metabolism/pathology/microbiology
Animals
Cell Proliferation

@article {pmid40261397,
year = {2025},
author = {Jiang, J and Zhu, P and Ding, X and Zhou, L and Li, X and Lei, Y and Wang, H and Chen, L and Li, X and Fei, Y and Ouyang, D and Li, X and Zhang, W},
title = {The microbiome-derived metabolite trimethylamine N-oxide is associated with chronic kidney disease risk.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {97},
pmid = {40261397},
issn = {1432-0614},
support = {2022JJ80100//Natural Science Foundation of Hunan Province/ ; 2023TJ-N20//Huxiang Youth Talent Support Program/ ; },
mesh = {Humans ; *Methylamines/metabolism ; *Renal Insufficiency, Chronic/epidemiology/microbiology ; Male ; Female ; Middle Aged ; Cross-Sectional Studies ; Aged ; China/epidemiology ; *Microbiota ; Adult ; Glomerular Filtration Rate ; Risk Factors ; },
abstract = {Previous studies have established a correlation between the microbiome-derived metabolite trimethylamine N-oxide (TMAO) and decreased renal function, but with great heterogeneity. Moreover, population-based evidence remains scarce, particularly in Chinese populations. We designed a meta-analysis and a population-based cross-sectional study in China to examine the associations between TMAO and chronic kidney disease (CKD). In meta-analysis, among 2125 pooled subjects with 1240 controls and 885 CKD patients, a significant association was observed between TMAO and CKD, with a standardized mean difference of - 0.93 (95% confidence interval: - 1.11, - 0.75). Meta-regression analysis identified gender, age, and body mass index (BMI) as significant heterogeneity factors. In our population-based study of 5584 subjects with an estimated glomerular filtration rate (eGFR) ≥ 60 mL/min/1.73 m[2] from Sijing community, 100 developed CKD in 2 years. We matched 195 controls by age and gender from the 5484 non-CKD subjects. Male subjects and alcohol consumers exhibited a lower risk of CKD with adjusted odds ratio (OR) of 0.471 (P < 0.05) and 0.320 (P < 0.05), respectively. When comparing subjects in the lowest tertile of TMAO, adjusted OR reached to 1.243 (P > 0.05) for those in the middle and 2.123 (P < 0.05) in the highest tertile (P for trend < 0.05). TMAO demonstrated a moderate capacity to distinguish CKD from non-CKD subjects (AUC = 0.614, P < 0.01). Our findings indicate TMAO is significantly associated with the risk of CKD, and suggest age, gender, and BMI may confound the relationship between TMAO and CKD. KEY POINTS: • Subjects with elevated TMAO levels have an increased risk of CKD. • TMAO demonstrates a moderate capacity to distinguish CKD from non-CKD cases. • Age, gender and BMI may confound the relationship between TMAO and CKD.},
}

Humans
*Methylamines/metabolism
*Renal Insufficiency, Chronic/epidemiology/microbiology
Male
Female
Middle Aged
Cross-Sectional Studies
Aged
China/epidemiology
*Microbiota
Adult
Glomerular Filtration Rate
Risk Factors

@article {pmid40261385,
year = {2025},
author = {Martin, FP and Poulain, C and Mulier, JH and Motos, A and Gourain, V and Ogan, I and Montassier, E and Launey, Y and Lasocki, S and Cinotti, R and Dahyot Fizelier, C and Ranzani, O and Reyes, LF and Martin-Loeches, I and Derde, L and Torres, A and Cremer, O and Roquilly, A},
title = {Identification and validation of robust hospital-acquired pneumonia subphenotypes associated with all-cause mortality: a multi-cohort derivation and validation.},
journal = {Intensive care medicine},
volume = {},
number = {},
pages = {},
pmid = {40261385},
issn = {1432-1238},
support = {847782 (HAP2 project).//Horizon 2020 Framework Programme/ ; },
abstract = {PURPOSE: Despite optimal antimicrobial therapy, the treatment failure rate of hospital-acquired pneumonia (HAP) routinely reaches 40% in critically ill patients. Subphenotypes have been identified within sepsis and acute respiratory distress syndrome with important predictive and possibly therapeutic implications. We derived prognosis subphenotypes for HAP and explored whether they were associated with biological markers and response to treatment.

METHODS: We separately analysed data from four cohorts of critically ill patients in France (PNEUMOCARE, n = 511, ATLANREA, n = 401), Netherlands (MARS, n = 1351) and Europe-South America (ENIRRI, n = 900) to investigate HAP heterogeneity using unsupervised clustering based on clinical and routine biological variables available at HAP diagnosis. Then, we developed a machine learning-based workflow to create a simplified classification model using discovery data sets. This model was validated by applying it to an independent replication data set from an international randomized clinical trial comparing linezolid and tedizolid for the treatment of HAP (VITAL, n = 726 patients). The primary outcome was the association of subphenotypes with 28-day all-cause mortality. Secondary analyses included subphenotype associations with treatment failure at test-of-cure, respiratory microbiome and cytokine profiles in the ATLANREA subgroup, and treatment response in the VITAL trial.

RESULTS: We tested twelve metrics and determined that a two-cluster model best fits all cohorts. HAP subphenotype 2 had greater disease severity, lower body temperature, and worse PaO2/FiO2 ratio than subphenotype 1 patients. Although the prevalence of subphenotype 2 ranged from 26.9 to 66.9% across the four derivation cohorts, the rates of 28-day mortality and treatment failure at test-of-cure were consistently higher to subphenotype 1 (p < 0.01 for all comparisons). Subphenotype 2 was associated with greater respiratory microbiome dysbiosis and higher levels of proinflammatory cytokines in the ATLANREA cohort, as well as with statistically significant tedizolid effect modification in the VITAL trial (Relative Risk of treatment failure with tedizolid = 1.52; 95% CI 1.12-2.06 in subphenotype 1 vs. = 0.98; 95% CI 0.7-1.38 in subphenotype 2).

CONCLUSIONS: We identified two robust clinical subphenotypes by extensively analyzing HAP data sets. Their associations with respiratory microbiome composition, systemic inflammation, and treatment efficacy in independent data sets highlight their potential for prognostic value and predictive enrichment in future clinical trials aimed at personalized therapies.},
}

@article {pmid40261360,
year = {2025},
author = {Cho, KH and Kwon, Y and Kasani, PH and Lee, SG and Jeong, SJ},
title = {Influence of Maternal Weight Dynamics Prior to and Throughout Gestation on Early Infant Gut Microbiome Colonization.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {32},
pmid = {40261360},
issn = {1432-184X},
support = {HR22C1605//Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea/ ; },
mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Pregnancy ; *Bacteria/classification/genetics/isolation & purification ; Infant, Newborn ; RNA, Ribosomal, 16S/genetics ; Adult ; Body Mass Index ; Feces/microbiology ; *Gestational Weight Gain ; Male ; Meconium/microbiology ; Infant ; *Body Weight ; },
abstract = {This study is aimed at exploring the relationship between maternal weight categories, including pre-pregnancy body mass index (P-BMI) and gestational weight gain (GWG), and the composition of the infant gut microbiome in the early days of life. We recruited 71 mother-infant pairs from Kangwon National University Hospital and Bundang CHA Hospital, collecting meconium samples from the infants within the first 5 days postpartum. Using 16S ribosomal RNA gene sequencing (V3-V4 region), this study assessed microbial diversity and the relative abundance of specific bacterial taxa in these initial stool samples. Participants were categorized into groups based on maternal P-BMI and GWG, enabling a comprehensive comparison of the microbiota composition in the infants' meconium across different maternal weight metrics. Our analysis identified significant variations in the infant gut microbiome correlated with maternal weight categories. Key findings include a differential abundance of genera such as Sphingobacteriaceae, Bacillaceae, Cytophagaceae, and Alteromonadaceae across maternal P-BMI groups, whereas Moraxellaceae and Rhodospirillaceae varied across GWG groups. In the P-BMI category, infants born to overweight mothers demonstrated a higher abundance of Pseudopedobacter, and a lower abundance of Citrobacter and Lachnospira, while infants in the underweight group showed a higher abundance of Lachnospira and Weissella. In the normal weight group, Citrobacter and Pseudopedobacter were more abundant. Within the GWG category, infants in the inadequate group showed a higher abundance of Klebsiella, whereas the normal group showed a higher abundance of Holdemania. The composition of the infant gut microbiome in the early postnatal period is significantly influenced by maternal weight categories. Understanding the role of maternal weight in shaping early microbial colonization may provide insights into developing strategies to optimize infant health outcomes through targeted interventions before and during pregnancy.},
}

Humans
Female
*Gastrointestinal Microbiome
Pregnancy
*Bacteria/classification/genetics/isolation & purification
Infant, Newborn
RNA, Ribosomal, 16S/genetics
Adult
Body Mass Index
Feces/microbiology
*Gestational Weight Gain
Male
Meconium/microbiology
Infant
*Body Weight

@article {pmid40261358,
year = {2025},
author = {Bharadwaj, P and Devi, CJ and Thakur, D},
title = {Unlocking Rhizosphere Dynamics: Exploring Mechanisms of Plant-Microbe Interactions for Enhanced Tea (Camellia sinensis (L.) O. Kuntze) Productivity.},
journal = {Current microbiology},
volume = {82},
number = {6},
pages = {257},
pmid = {40261358},
issn = {1432-0991},
mesh = {*Rhizosphere ; *Camellia sinensis/microbiology/growth & development ; *Soil Microbiology ; Plant Roots/microbiology ; Bacteria/metabolism/genetics ; Mycorrhizae/physiology ; },
abstract = {The rhizosphere, the interface between plant roots and soil, refers to the contact zone where plants and soil microbes engage in beneficial and parasitic interactions. The significant interactions and their importance form a dynamic interface between the roots of plants and the soil. Beneficial ones, especially plant growth-promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF), improve plant development and enhance stress resistance due to microbial secretions, exudates from roots, and edaphic factors. All these are very important in cultivating tea (Camellia sinensis (L.) O Kuntze) plants, boosting growth, yield, and leaf content of amino acids, proteins, caffeine, and polyphenols. Yet, the molecular mechanisms of such interactions necessitate high-end technologies like genome editing and proteomics to fine-tune rhizosphere dynamics for greater plant health and productivity. The root exudates, rich in nutrients, serve as a source of food for the soil microbes while facilitating communication and colonisation by beneficial organisms, such as AMF and bacteria, thus significantly impacting the performance of a tea plant. High nitrogen fertilisers are readily applied in tea farming, although environmental risks include soil acidification and increased emissions of nitrous oxide (N2O), a potent greenhouse gas. Understanding and manipulating plant root-soil microbe interactions are critical for developing sustainable farming systems that enhance productivity without causing environmental damage. This review describes the mechanisms by which beneficial microbes function in the rhizosphere, strategies for modifying root exudates to improve tea production, and the tea microbiome's underexplored potential in contributing towards sustainability. This review thus emerges as one that presents knowledge gaps and possible future directions in tea microbiome science predicated on the amelioration of tea farming by enhancing productivity and ensuring environmental sustainability.},
}

*Rhizosphere
*Camellia sinensis/microbiology/growth & development
*Soil Microbiology
Plant Roots/microbiology
Bacteria/metabolism/genetics
Mycorrhizae/physiology

@article {pmid40261296,
year = {2025},
author = {Almonte, AA and Thomas, S and Zitvogel, L},
title = {Microbiota-centered interventions to boost immune checkpoint blockade therapies.},
journal = {The Journal of experimental medicine},
volume = {222},
number = {7},
pages = {},
doi = {10.1084/jem.20250378},
pmid = {40261296},
issn = {1540-9538},
mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects/immunology ; *Neoplasms/immunology/microbiology/therapy/drug therapy ; Dysbiosis ; Animals ; *Immunotherapy/methods ; },
abstract = {Immune checkpoint blockade therapies have markedly advanced cancer treatment by invigorating antitumor immunity and extending patient survival. However, therapeutic resistance and immune-related toxicities remain major concerns. Emerging evidence indicates that microbial dysbiosis diminishes therapeutic response rates, while a diverse gut ecology and key beneficial taxa correlate with improved treatment outcomes. Therefore, there is a growing understanding that manipulating the gut microbiota could boost therapy efficacy. This review examines burgeoning methods that target the gut microbiome to optimize therapy and innovative diagnostic tools to detect dysbiosis, and highlights challenges that remain to be addressed in the field.},
}

Humans
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Gastrointestinal Microbiome/drug effects/immunology
*Neoplasms/immunology/microbiology/therapy/drug therapy
Dysbiosis
Animals
*Immunotherapy/methods

@article {pmid40261064,
year = {2025},
author = {Žuštra, A and Leonard, VR and Holland, LA and Hu, JC and Mu, T and Holland, SC and Wu, LI and Begnel, ER and Ojee, E and Chohan, BH and Richardson, BA and Kinuthia, J and Wamalwa, D and Slyker, J and Lehman, DA and Gantt, S and Lim, ES},
title = {Longitudinal dynamics of the nasopharyngeal microbiome in response to SARS-CoV-2 Omicron variant and HIV infection in Kenyan women and their children.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0156824},
doi = {10.1128/msystems.01568-24},
pmid = {40261064},
issn = {2379-5077},
abstract = {UNLABELLED: The nasopharynx and its microbiota are implicated in respiratory health and disease. The interplay between viral infection and the nasopharyngeal microbiome is an area of increased interest. The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the coronavirus disease 2019 pandemic, on the nasopharyngeal microbiome among individuals living with HIV is not fully characterized. Here, we describe the nasopharyngeal microbiome before, during, and after SARS-CoV-2 infection in a longitudinal cohort of Kenyan women (21 living with HIV and 14 HIV-uninfected) and their children (18 HIV-exposed, uninfected and 7 HIV-unexposed, uninfected) between September 2021 and March 2022. We show using genomic epidemiology that mother and child dyads were infected with the same strain of the SARS-CoV-2 Omicron variant that spread rapidly across Kenya. We used metagenomic sequencing to characterize the nasopharyngeal microbiome of 20 women and children infected with SARS-CoV-2, six children negative for SARS-CoV-2 but experiencing respiratory symptoms, and 34 timepoint-matched SARS-CoV-2-negative mothers and children. Since individuals were sampled longitudinally before and after SARS-CoV-2 infection, we could characterize the short- (within a week of infection) and longer- (average of 38 days post-infection) term impact of SARS-CoV-2 infection on the nasopharyngeal microbiome. We found that mothers and children had significantly different microbiome composition and bacterial load (P-values < 0.0001). In both mothers and children, the nasopharyngeal microbiome did not differ before and after SARS-CoV-2 infection, regardless of HIV exposure status. Our results indicate that the nasopharyngeal microbiome is resilient to SARS-CoV-2 infection and was not significantly modified by HIV.

IMPORTANCE: The nasopharyngeal microbiome plays an important role in human health. The degree of impact that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has on the nasopharyngeal microbiome varies among studies and may be influenced by diverse SARS-CoV-2 variants and variations in the microbiome between individuals. Our results show that the nasopharyngeal microbiome was not altered substantially by SARS-CoV-2 infection nor by HIV infection in mothers or HIV exposure in children. Our findings highlight the resilience of the nasopharyngeal microbiome after SARS-CoV-2 infection. These findings advance our understanding of the nasopharyngeal microbiome and its interactions with viral infections.},
}

@article {pmid40261045,
year = {2025},
author = {Doing, G and Shanbhag, P and Bell, I and Cassidy, S and Motakis, E and Aiken, E and Oh, J and Adams, MD},
title = {TEAL-Seq: targeted expression analysis sequencing.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0098424},
doi = {10.1128/msphere.00984-24},
pmid = {40261045},
issn = {2379-5042},
abstract = {Metagenome sequencing enables the genetic characterization of complex microbial communities. However, determining the activity of isolates within a community presents several challenges, including the wide range of organismal and gene expression abundances, the presence of host RNA, and low microbial biomass at many sites. To address these limitations, we developed "targeted expression analysis sequencing" or TEAL-seq, enabling sensitive species-specific analyses of gene expression using highly multiplexed custom probe pools. For proof of concept, we targeted about 1,700 core and accessory genes of Staphylococcus aureus and S. epidermidis, two key species of the skin microbiome. Two targeting methods were applied to laboratory cultures and human nasal swab specimens. Both methods showed a high degree of specificity, with >90% reads on target, even in the presence of complex microbial or human background DNA/RNA. Targeting using molecular inversion probes demonstrated excellent correlation in inferred expression levels with bulk RNA-seq. Furthermore, we show that a linear pre-amplification step to increase the number of nucleic acids for analysis yielded consistent and predictable results when applied to complex samples and enabled profiling of expression from as little as 1 ng of total RNA. TEAL-seq is much less expensive than bulk metatranscriptomic profiling, enables detection across a greater dynamic range, and uses a strategy that is readily configurable for determining the transcriptional status of organisms in any microbial community.IMPORTANCEThe gene expression patterns of bacteria in microbial communities reflect their activity and interactions with other community members. Measuring gene expression in complex microbiome contexts is challenging, however, due to the large dynamic range of microbial abundances and transcript levels. Here we describe an approach to assessing gene expression for specific species of interest using highly multiplexed pools of targeting probes. We show that an isothermal amplification step enables the profiling of low biomass samples. TEAL-seq should be widely adaptable to the study of microbial activity in natural environments.},
}

@article {pmid40261032,
year = {2025},
author = {Cho, M-Y and Eom, J-H and Choi, E-M and Yang, S-J and Lee, D and Kim, YY and Kim, H-S and Hwang, I},
title = {Recent advances in therapeutic probiotics: insights from human trials.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0024024},
doi = {10.1128/cmr.00240-24},
pmid = {40261032},
issn = {1098-6618},
abstract = {SUMMARYRecent advances in therapeutic probiotics have shown promising results across various health conditions, reflecting a growing understanding of the human microbiome's role in health and disease. However, comprehensive reviews integrating the diverse therapeutic effects of probiotics in human subjects have been limited. By analyzing randomized controlled trials (RCTs) and meta-analyses, this review provides a comprehensive overview of key developments in probiotic interventions targeting gut, liver, skin, vaginal, mental, and oral health. Emerging evidence supports the efficacy of specific probiotic strains and combinations in treating a wide range of disorders, from gastrointestinal (GI) and liver diseases to dermatological conditions, bacterial vaginosis, mental disorders, and oral diseases. We discuss the expanding understanding of microbiome-organ connections underlying probiotic mechanisms of action. While many clinical trials demonstrate significant benefits, we acknowledge areas requiring further large-scale studies to establish definitive efficacy and optimal treatment protocols. The review addresses challenges in standardizing probiotic research methodologies and emphasizes the importance of considering individual variations in microbiome composition and host genetics. Additionally, we explore emerging concepts such as the oral-gut-brain axis and future directions, including high-resolution microbiome profiling, host-microbe interaction studies, organoid models, and artificial intelligence applications in probiotic research. Overall, this review offers a comprehensive update on the current state of therapeutic probiotics across multiple domains of human health, providing insights into future directions and the potential for probiotics to revolutionize preventive and therapeutic medicine.},
}

@article {pmid40261031,
year = {2025},
author = {Liu, Z and Yang, H and Huang, R and Li, X and Sun, T and Zhu, L},
title = {Vaginal mycobiome characteristics and therapeutic strategies in vulvovaginal candidiasis (VVC): differentiating pathogenic species and microecological features for stratified treatment.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0028424},
doi = {10.1128/cmr.00284-24},
pmid = {40261031},
issn = {1098-6618},
abstract = {SUMMARYVulvovaginal candidiasis (VVC) is a prevalent global health burden, particularly among reproductive-aged women. Recurrent VVC affects a significant proportion of this population, presenting therapeutic challenges. The predominant pathogen, Candida albicans, opportunistically transitions from a commensal organism to a pathogen when microenvironmental conditions become dysregulated. Recently, non-albicans Candida species have gained attention for their reduced antifungal susceptibility and recurrence tendencies. Diagnosis is constrained by the limitations of conventional microbiological techniques, while emerging molecular assays offer enhanced pathogen detection yet lack established thresholds to differentiate between commensal and pathogenic states. Increasing resistance issues are encountered by traditional azole-based antifungals, necessitating innovative approaches that integrate microbiota modulation and precision medicine. Therefore, this review aims to systematically explore the pathogenic diversity, drug resistance mechanisms, and biofilm effects of Candida species. Vaginal microbiota (VMB) alterations associated with VVC were also examined, focusing on the interaction between Lactobacillus spp. and pathogenic fungi, emphasizing the role of microbial dysbiosis in disease progression. Finally, the potential therapeutic approaches for VVC were summarized, with a particular focus on the use of probiotics to modulate the VMB composition and restore a healthy microbial ecosystem as a promising treatment strategy. This review addresses antifungal resistance and adopts a microbiota-centric approach, proposing a comprehensive framework for personalized VVC management to reduce recurrence and improve patient outcomes.},
}

@article {pmid40261026,
year = {2025},
author = {Li, C and Xu, X and Zhao, X and Du, B},
title = {The inconsistent pathogenesis of endometriosis and adenomyosis: insights from endometrial metabolome and microbiome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0020225},
doi = {10.1128/msystems.00202-25},
pmid = {40261026},
issn = {2379-5077},
abstract = {UNLABELLED: Endometriosis (EM) and adenomyosis (AM) are interrelated gynecological disorders characterized by the aberrant presence of endometrial tissue and are frequently linked with chronic pelvic pain and infertility, yet their pathogenetic mechanisms remain largely unclear. In this cross-sectional study, we analyzed endometrial samples from 244 participants, split into 91 EM patients, 56 AM patients, and 97 healthy controls (HC). We conducted untargeted liquid chromatography-mass spectrometry (LC-MS) and 5R 16S rRNA sequencing to examine endometrial metabolome and microbiome profiles. Additionally, we integrated transcriptomic analysis using nine transcriptomic data sets to investigate the biological basis of these conditions. Metabolomic profiling and 16S rRNA sequencing revealed distinct metabolic and microbial signatures. Specific pathways, including linoleic acid and glycerophospholipid metabolism, show significant alterations in both conditions. Notably, four metabolites, including phosphatidylcholine 40:8 [PC(40:8)], exhibited marked changes in both EM and AM, suggesting shared pathological features. Furthermore, taxonomic analysis identified unique bacterial species associated with each condition, particularly those belonging to the phylum Proteobacteria, which correlated with altered metabolic signatures. Machine learning models demonstrated high predictive accuracy for differentiating between AM, EM, and HC based on metabolic and microbial signatures. Integrative analysis with transcriptomic data highlighted distinct pathways related to immune response and signaling transduction for each condition. Our study provides fresh insights into the pathogenesis of AM and EM through a multi-omic approach, suggesting potential inconsistencies in the underlying pathogenetic mechanisms.

IMPORTANCE: Existing research highlighted a connection between endometriosis (EM) and adenomyosis (AM), underscoring their overlapping symptoms and potential shared pathophysiological mechanisms. Although the role of microbiota in inflammatory conditions has been acknowledged, comprehensive investigations into the endometrial microbiota in cases of EM and AM have been limited. Previous studies identified distinct microbial communities associated with these conditions; however, they were constrained by small sample sizes and a lack of integrated analyses of microbiota and metabolomics. Furthermore, the ongoing debate over whether EM and AM should be classified as separate diseases or related phenotypes emphasizes the necessity for further exploration of their molecular interactions. Our study uncovers distinct microbial and metabolic signatures associated with each condition, revealing both shared and unique pathways that may contribute to their pathogenesis. Furthermore, the integration of transcriptomic data offers valuable insights into the complex interactions underlying these disorders.},
}

@article {pmid40261021,
year = {2025},
author = {Su, X and Tian, Z and Fang, Y and Zhou, S and Ma, S},
title = {Effects of high-dose glucocorticoids on gut microbiota in the treatment of Graves' ophthalmopathy.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0246724},
doi = {10.1128/spectrum.02467-24},
pmid = {40261021},
issn = {2165-0497},
abstract = {Many studies indicate the gut microbiome is associated with diseases caused by administering high-dose glucocorticoids (GCs), such as hypertension, hyperglycemia, and osteoporosis. However, the association between intestinal flora and the use of high-dose GCs remains elusive. We aimed to characterize gut microbiome in Graves' ophthalmopathy (GO) patients after administering high-dose GCs. In this study, 20 primary GO patients were recruited. The differences in gut microbiota of GO patients before and after administering high-dose GCs were analyzed by 16S rDNA sequencing technology. Untargeted metabolomic analysis was used to examine the differences in gut metabolites between two groups. There were significant differences in α and β diversities of gut microbiota in GO patients before and after administering high-dose GCs. The random forest analysis indicated that three intestinal bacteria (Faecalibacterium, Streptococcus, and Prevotella) could distinguish the two groups with the highest accuracy, which was proven by receiver operator characteristic curve and linear discriminant analysis effect size analysis. The short-chain fatty acid-producing ability in GO patients' gut after high-dose GC administration was significantly decreased. The 5-hydroxytryptamine levels significantly increased in the gut of GO patients after administering high-dose GCs. Our study suggests that high-dose GC administration causes the changes in gut microbiome and metabolites. Moreover, the altered flora and metabolites are related to hypertension, hyperglycemia, and osteoporosis. These findings can help understand the development of side effects caused by high-dose GCs and can be further used to develop potential probiotics to facilitate the prevention for those side effects.IMPORTANCEFor the first time, we revealed that gut microbiome and metabolome in Graves' ophthalmopathy patients after high-dose glucocorticoid (GC) administration significantly changed, and the altered flora and metabolites are related to hypertension, hyperglycemia, and osteoporosis. These findings can help understand the development of side effects caused by high-dose GCs and can be further used to develop potential probiotics to facilitate the prevention for those side effects.},
}

@article {pmid40261004,
year = {2025},
author = {Zhao, C and Bai, Z and Chen, X and Shang, S and Shen, B and Bai, L and Qu, D and Wu, Y and Wu, Y},
title = {Staphylococcus epidermidis uses the SrrAB regulatory system to modulate oxidative stress and intracellular survival in mouse macrophage cell line Ana-1.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0173724},
doi = {10.1128/msystems.01737-24},
pmid = {40261004},
issn = {2379-5077},
abstract = {UNLABELLED: The two-component system (TCS) SrrAB responds to oxidative stress in Staphylococcus epidermidis. A srrAB deletion mutant (∆srrAB) was constructed using S. epidermidis strain 1457 (SE1457) as the parent strain to study its regulatory function in oxidative stress. Compared to SE1457, the viable cell counts of the ∆srrAB mutant significantly decreased in the post-stationary phase culture, coinciding with a sharp increase in reactive oxidative species (ROS) accumulation. The impaired growth of the ∆srrAB mutant was partially restored by shifting the culture from oxic to microaerobic conditions. Consistently, growth of the ∆srrAB mutant in tryptone soy broth (TSB) medium containing H2O2 was notably inhibited compared to parent strain SE1457, and the mutant showed significantly decreased resistance (100- to 1,000-fold) to H2O2 and cumene hydroperoxide in both oxic and microaerobic conditions, which was fully rescued by the addition of ROS inhibitor 2,2-dipyridyl. Furthermore, the deletion of srrAB resulted in decreased intracellular survival in the Ana-1 macrophages, likely due to intracellular ROS accumulation. The complementation of srrAB in the ∆srrAB mutant restored ROS resistance and intracellular survival to wild-type levels. RNA-seq analysis revealed that srrAB deletion affected the transcription levels of 610 genes, including those involved in oxidative stress, respiratory and energy metabolism, and transition ion homeostasis. These findings were corroborated by quantitative real-time reverse transcription-PCR. In the ∆srrAB mutant, expressions of ROS-scavenging genes katA, ahpC, scdA, serp1797, and serp0483 were downregulated compared to SE1457. Electrophoretic mobility shift assay further demonstrated phosphorylated SrrA bound to the promoter regions of srrAB, katA, ahpC, scdA, serp1797, and serp0483 genes. This study elucidates that in S. epidermidis, SrrAB is the critical TCS to sense and respond to the oxidants, directly regulating transcription levels of the genes involved in ROS scavenging and ion homeostasis, thereby facilitating S. epidermidis detoxification of ROS and adaptation to the commensal environment.

IMPORTANCE: Staphylococcus epidermidis in the human skin and mucous microbiome is a leading cause of hospital-acquired infection, whereas the mechanism by which it inhabits, adapts, and further results in infection is not well known. In this study, we found that the two-component regulatory system SrrAB directly regulates transcription levels of the genes involved in reactive oxidative species (ROS) scavenging and ion homeostasis in S. epidermidis, influencing ROS accumulation during growth, thereby facilitating detoxification of ROS and adaptation to the commensal environment. This work provides new molecular insight into the mechanisms of SrrAB in regulating resistance and intracellular viability against oxidative stress in S. epidermidis.},
}

@article {pmid40260917,
year = {2025},
author = {Wu, L and Kensiski, A and Gavzy, SJ and Lwin, HW and Song, Y and France, MT and Lakhan, R and Kong, D and Li, L and Saxena, V and Piao, W and Shirkey, MW and Mas, VR and Ma, B and Bromberg, JS},
title = {Rapamycin immunomodulation utilizes time-dependent alterations of lymph node architecture, leukocyte trafficking, and gut microbiome.},
journal = {JCI insight},
volume = {10},
number = {8},
pages = {},
doi = {10.1172/jci.insight.186505},
pmid = {40260917},
issn = {2379-3708},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/immunology ; *Lymph Nodes/drug effects/immunology/pathology ; Mice ; *Sirolimus/pharmacology ; *Immunomodulation/drug effects ; Mice, Inbred C57BL ; Male ; Leukocytes/drug effects/immunology ; Female ; *Immunosuppressive Agents/pharmacology ; T-Lymphocytes, Regulatory/immunology/drug effects ; Spleen/immunology/drug effects ; Time Factors ; },
abstract = {Transplant recipients require lifelong, multimodal immunosuppression to prevent rejection by reducing alloreactive immunity. Rapamycin is known to modulate adaptive and innate immunity, but its full mechanism remains incompletely understood. We investigated the understudied effects of rapamycin on lymph node (LN) architecture, leukocyte trafficking, and gut microbiome and metabolism after 3 (early), 7 (intermediate), and 30 (late) days of rapamycin treatment. Rapamycin significantly reduced CD4+ T cells, CD8+ T cells, and Tregs in peripheral LNs, mesenteric LNs, and spleen. Rapamycin induced early proinflammation transition to protolerogenic status by modulating the LN laminin α4/α5 expression ratios (La4/La5) through LN stromal cells, laminin α5 expression, and adjustment of Treg numbers and distribution. Additionally, rapamycin shifted the Bacteroides/Firmicutes ratio and increased amino acid bioavailability in the gut lumen. These effects were evident by 7 days and became most pronounced by 30 days in naive mice, with changes as early as 3 days in allogeneic splenocyte-stimulated mice. These findings reveal what we believe to be a novel mechanism of rapamycin action through time-dependent modulation of LN architecture and gut microbiome, which orchestrates changes in immune cell trafficking, providing a framework for understanding and optimizing immunosuppressive therapies.},
}

Animals
*Gastrointestinal Microbiome/drug effects/immunology
*Lymph Nodes/drug effects/immunology/pathology
Mice
*Sirolimus/pharmacology
*Immunomodulation/drug effects
Mice, Inbred C57BL
Male
Leukocytes/drug effects/immunology
Female
*Immunosuppressive Agents/pharmacology
T-Lymphocytes, Regulatory/immunology/drug effects
Spleen/immunology/drug effects
Time Factors

@article {pmid40260382,
year = {2025},
author = {Hisamatsu, D and Ogata, Y and Suda, W and Mabuchi, Y and Naraoka, Y and Yamato, T and Ikeba, A and Kumagai, K and Hattori, M and Akazawa, C},
title = {Alteration of salivary Streptococcus is associated with statin therapy in older adults: a cohort study.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1455753},
pmid = {40260382},
issn = {1663-9812},
abstract = {BACKGROUND: Salivary microbiome alterations are associated with chronic diseases, such as cardiovascular disease, diabetes, and dementia. These chronic diseases often coexist in older adults, leading to polypharmacy. This situation complicates the relationship between systemic diseases and salivary microbiome dysbiosis. Previous studies have demonstrated the association of the human gut microbiome with common prescription drug use, including polypharmacy. However, a comprehensive analysis of the salivary microbiome and prescription drugs is yet to be conducted in older adults. Therefore, in this study, we performed a multivariate analysis to investigate the relationship between salivary microbiomes and host variables, including prescribed drugs, cognitive function, and oral health, in Japanese older adults with different disease backgrounds.

METHODS: We enrolled non-hospitalised 82 older adults aged ≥70 years from a Japanese village community, and collected metadata, including age, sex, body mass index, cognitive function, oral health, alcohol consumption, smoking, and common prescription drug information. We performed multivariate analyses and functional predictions on the salivary microbiome based on 16S ribosomal RNA gene amplicon sequencing, including the metadata as potential confounders.

RESULTS: We observed a relationship between the human salivary microbiome and prescribed drug use in Japanese older adults with a heterogeneous background of comorbidities. The effects of several prescribed drugs, such as statins, proton pump inhibitors, and transporter/symporter inhibitors, on the salivary microbiome diversity were more prominent than those of host variables, including age, sex, and oral health. Notably, statin use was strongly correlated with a decrease in the Streptococcus abundance. Furthermore, statin intensity and obesity may be associated with altering the salivary microbiome, including functional predictions for vitamin biosynthesis and purine nucleotide degradation pathways in statin users.

CONCLUSION: Our multivariate analysis, adjusted for prescribed drug use and non-use, revealed the drug-specific alteration of salivary microbiome composition in Japanese older adults with comorbidities. To our knowledge, this study is the first to described the association of common prescription drug use with salivary microbiome alterations in older adults. Our findings indicated that prescribed drug use is a key factor in understanding the link between salivary microbiome changes and systemic diseases in older adults.},
}

@article {pmid40260306,
year = {2025},
author = {Voigt, RM and Lowry, CA},
title = {Editorial: The microbiome-gut-brain axis and posttraumatic stress disorder.},
journal = {Frontiers in neuroscience},
volume = {19},
number = {},
pages = {1592604},
doi = {10.3389/fnins.2025.1592604},
pmid = {40260306},
issn = {1662-4548},
}

@article {pmid40260116,
year = {2025},
author = {Wang, J and Wang, Y and Cao, J and Chen, Y and Yu, J and Sun, N},
title = {Identification and characterization of bile microbiota in patients with biliary obstructive diseases using next-generation sequencing of 16S rRNA and ITS.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1575824},
pmid = {40260116},
issn = {2235-2988},
mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *Bile/microbiology ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Male ; Female ; Aged ; *Bacteria/classification/genetics/isolation & purification ; Fungi/classification/genetics/isolation & purification ; *Microbiota/genetics ; Adult ; Aged, 80 and over ; DNA, Ribosomal Spacer/genetics/chemistry ; DNA, Bacterial/genetics/chemistry ; *Cholestasis/microbiology ; },
abstract = {BACKGROUND: Comparative studies of the bile microbiota in different biliary obstructive infections remain limited. This study aims to characterize bile microbiota and investigate differences in microbial profiles across various biliary obstructive diseases.

METHODS: This study included patients with biliary obstructive diseases admitted to Jinling Hospital and Suqian First Hospital. The cohort consisted of individuals with benign biliary disorders, malignant biliary obstruction, and biliary obstruction secondary to severe acute pancreatitis (SAP) or intestinal fistulas. A total of 133 bile samples were collected from 118 patients and analyzed using next-generation sequencing (NGS) targeting the bacterial 16S rRNA gene and the fungal internal transcribed spacer (ITS) gene. Clinical data, including routine culture results, were extracted from electronic medical records.

RESULTS: NGS targeting the 16S rRNA and ITS revealed a positive rate of 68.42% for bile samples, which was higher than the culture positivity rate of 60.15%, indicating a significant difference (Chi-square test, p < 0.05). The predominant bacteria identified in the bile samples through NGS were Klebsiella pneumoniae, Acinetobacter baumannii, and Escherichia coli. Bacterial species varied among benign biliary diseases, malignant obstructive diseases, and biliary obstruction caused by SAP or intestinal fistulas. Fungi were detected in 7.52% (10/133) of the samples, with 4 samples obtained from patients with biliary obstructive diseases due to SAP. Microbial diversity and clustering analysis showed no significant differences among various biliary disorders. Based on the culture results, the sensitivity and specificity of NGS were 81.82% and 69.64%, respectively.

CONCLUSION: The composition of bile microbes may be related to the etiology of biliary obstruction. Klebsiella pneumoniae, Acinetobacter baumannii, and Escherichia coli are the predominant bacteria found in bile. NGS can be effectively applied for the identification and characterization of bile microbes associated with various biliary obstruction diseases.},
}

Humans
*RNA, Ribosomal, 16S/genetics
*Bile/microbiology
Middle Aged
High-Throughput Nucleotide Sequencing
Male
Female
Aged
*Bacteria/classification/genetics/isolation & purification
Fungi/classification/genetics/isolation & purification
*Microbiota/genetics
Adult
Aged, 80 and over
DNA, Ribosomal Spacer/genetics/chemistry
DNA, Bacterial/genetics/chemistry
*Cholestasis/microbiology

@article {pmid40260115,
year = {2025},
author = {Zheng, Z and Jin, W and Guo, W and Jin, Z and Zuo, Y},
title = {Oral Fusobacterium nucleatum exacerbates ulcerative colitis via the oral-gut axis: mechanisms and therapeutic implications.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1564169},
pmid = {40260115},
issn = {2235-2988},
mesh = {Humans ; *Fusobacterium nucleatum/pathogenicity/physiology ; *Colitis, Ulcerative/microbiology/therapy ; *Fusobacterium Infections/microbiology/complications ; *Mouth/microbiology ; Animals ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Fusobacterium nucleatum (F. nucleatum) is an anaerobic bacterium known for its association with periodontal disease and oral infections. It has been implicated in the development of gastrointestinal diseases such as inflammatory bowel disease and colorectal cancer. Ulcerative colitis (UC), which is characterized by chronic inflammation of the colon, is a condition of unknown etiology with a rising incidence rate, significantly affecting the quality of life for patients. The increased intestinal permeability during UC may facilitate the adherence or invasion of F. nucleatum into the damaged intestinal barrier, leading to exacerbated inflammation.

METHODS: This article introduces the concept of the oral-gut axis, reviewing existing literature to analyze the role of F. nucleatum in the pathogenesis of UC and exploring its potential pathogenic mechanisms. It also summarizes the latest advances in treating patients with UC who have F. nucleatum and looks forward to prospective therapeutic strategies and the translational prospects of F. nucleatum within the oral-gut axis.

RESULTS: F. nucleatum may be a key player in the pathogenesis of UC, likely due to its invasiveness during periods of increased intestinal permeability. The paper also discusses innovative approaches for the prevention and management of UC exacerbated by F. nucleatum, paving the way for more effective treatment of UC.

CONCLUSION: The review offers new insights into the complex relationship between the oral microbiome and intestinal diseases, enhancing our understanding of their dynamic interactions. There is a paucity of literature on therapeutic approaches, indicating a need for further clinical research.},
}

Humans
*Fusobacterium nucleatum/pathogenicity/physiology
*Colitis, Ulcerative/microbiology/therapy
*Fusobacterium Infections/microbiology/complications
*Mouth/microbiology
Animals
Gastrointestinal Microbiome

@article {pmid40260113,
year = {2025},
author = {Zhao, Z and Li, J and Liu, J and Zhang, X and Qie, Y and Sun, Y and Liu, N and Liu, Q},
title = {Alcohol exposure alters the diversity and composition of oral microbiome.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1561055},
pmid = {40260113},
issn = {2235-2988},
mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; *Microbiota/drug effects ; Rats ; Male ; *Bacteria/classification/genetics/drug effects/isolation & purification ; DNA, Bacterial/genetics/chemistry ; Aspartate Aminotransferases/blood ; *Ethanol/administration & dosage ; Biodiversity ; Alanine Transaminase/blood ; DNA, Ribosomal/chemistry/genetics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; *Alcohol Drinking/adverse effects ; },
abstract = {INTRODUCTION: Alcohol exposure has been shown to have complex, and sometimes paradoxical, associations with various serious diseases. Currently, there is no knowledge about the effects of alcohol exposure on the dynamics of oral microbial communities.

OBJECTIVE: The study aims to investigate the effects of chronic alcohol consumption on the diversity and composition dynamics of the rat oral microbiota using 16S rRNA gene amplicon sequencing.

METHODS: In our study, there were 2 groups, including a control group (C group) and an alcohol group (A group), with 10 rats in every group. For ten weeks, rats in the A group were treated with alcohol intragastrically every day, whereas rats in the C group got water. After 10 weeks, serum levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were measured. Oral swabs were taken from both groups, and total DNA was extracted for high-throughput sequencing of the 16S rRNA gene.

RESULTS: According to the results obtained from our study, significant differences were observed in the relative abundances of microbial communities. Alpha diversity measures were statistically significantly higher (P < 0.05) in the A group compared to the C group. At the genus level, alcohol exposure altered the relative abundance of several microbes, including increased relative abundance of unidentified_Chloroplast, Acinetobacter, Vibrio, Romboutsia, Pseudoalteromonas, Aeromonas, Ralstonia, Turicibacter, Shewanella, and Bacteroides. Conversely, Haemophilus and Streptococcus were significantly less abundant in the A group.

CONCLUSION: Alcohol exposure was associated with the diversity and composition of the oral microbiome. These findings contribute to our understanding of the potential role of oral bacteria in alcohol-related oral and systemic diseases, providing foundational work for future prevention and intervention studies.},
}

Animals
RNA, Ribosomal, 16S/genetics
*Mouth/microbiology
*Microbiota/drug effects
Rats
Male
*Bacteria/classification/genetics/drug effects/isolation & purification
DNA, Bacterial/genetics/chemistry
Aspartate Aminotransferases/blood
*Ethanol/administration & dosage
Biodiversity
Alanine Transaminase/blood
DNA, Ribosomal/chemistry/genetics
Sequence Analysis, DNA
High-Throughput Nucleotide Sequencing
*Alcohol Drinking/adverse effects

@article {pmid40260089,
year = {2025},
author = {Xu, P and Pan, C and Yuan, M and Zhu, Y and Wei, S and Lu, H and Zhang, W},
title = {Viral metagenomics reveals diverse viruses in the fecal samples of children with acute respiratory infection.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1564755},
pmid = {40260089},
issn = {1664-302X},
abstract = {INTRODUCTION: Changes in the gut microbiome have been associated with the development of acute respiratory infection (ARI). However, due to methodological limitations, our knowledge of the gut virome in patients with ARIs remains limited.

METHODS: In this study, fecal samples from children with ARI were investigated using viral metagenomics.

RESULTS: The fecal virome was analyzed, and several suspected disease-causing viruses were identified. The five viral families with the highest abundance of sequence reads were Podoviridae, Virgaviridae, Siphoviridae, Microviridae, and Myoviridae. Additionally, human adenovirus, human bocavirus, human astrovirus, norovirus, and human rhinovirus were detected. The genome sequences of these viruses were respectively described, and phylogenetic trees were constructed using the gene sequences of the viruses.

DISCUSSION: We characterized the composition of gut virome in children with acute respiratory infections. However, further research is required to elucidate the relationship between acute respiratory infection and gut viruses.},
}

@article {pmid40260086,
year = {2025},
author = {Hu, Y and Yang, LY and Lei, MY and Yang, YX and Sun, Z and Wang, W and Han, ZM and Cheng, L and Lv, ZL and Han, M and Yang, LM},
title = {Bacillus vallismortis acts against ginseng root rot by modifying the composition and microecological functions of ginseng root endophytes.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1561057},
pmid = {40260086},
issn = {1664-302X},
abstract = {INTRODUCTION: The endophytic microbiome serves a crucial function as a secondary line of defense against pathogen invasion in plants. This study aimed to clarify the mechanism of action of the ginseng plant growth-promoting rhizobacteria (PGPR) Bacillus vallismortis SZ-4 synergizing with endophytic microorganisms in the prevention and control of root rot.

METHODS: Ginseng root samples from a susceptible group (CK) with a disease level of 0-2 and a biocontrol group (BIO) treated with strain SZ-4 were collected. We employed high-throughput sequencing to examine the microbial community structure of ginseng roots at different disease levels, explore beneficial endophytic bacteria, and evaluate the efficacy of strain SZ-4 in mitigating root rot through synergistic interactions with ginseng endophytic flora.

RESULTS: The application of the PGPR B. vallismortis SZ-4 biocontrol fungicide has been found to help ginseng resist Fusarium solani by modulating the richness and structure of endophytic microbial populations. The endophytic bacteria HY-43 and HY-46 isolated from ginseng roots treated with B. vallismortis SZ-4 were identified as Bacillus velezensis based on morphological, physiological, and biochemical characteristics, as well as 16S rDNA and gyrB sequencing analyses. The endophytic bacteria HY-43 and HY-46 were combined with strain SZ-4 to generate the bacterial consortia CS4-43 and CS4-46, respectively. Both CS4-43 and CS4-46 significantly enhanced the inhibitory effects of the single strain SZ-4, as well as HY-43 and HY-46, against ginseng root rot, while also promoting plant growth.

DISCUSSION: These findings offers a theoretical foundation for studying the microecological prevention and control of ginseng diseases as well as new insights for conducting research on the efficient and precise management of plant diseases.},
}

@article {pmid40259625,
year = {2025},
author = {Abukhiran, IM and Masaadeh, AH and Byrne, JD and Bosch, DE},
title = {Mucosal microbiome markers of complete pathologic response to neoadjuvant therapy in rectal carcinoma.},
journal = {Cancer research communications},
volume = {},
number = {},
pages = {},
doi = {10.1158/2767-9764.CRC-25-0036},
pmid = {40259625},
issn = {2767-9764},
abstract = {The intestinal microbiome contributes to colorectal carcinogenesis, disease progression, and response to therapy. Pathologic complete response is the therapeutic goal of neoadjuvant chemoradiation in rectal carcinoma. Nonoperative management has become an accepted strategy, and markers of complete treatment response are needed. Intestinal commensal bacteria contribute to treatment response and radiation colitis, and microbiome-targeted therapies have shown promise in clinical trials. We investigated the relationship between mucosa-associated bacteria, neoadjuvant therapy response, and radiation colitis symptoms in 57 patients who received neoadjuvant regimens with no therapy, chemotherapy only, or chemoradiation. The design was a retrospective cohort study. Microbiome profiling was performed by 16S rDNA sequencing of formalin-fixed paraffin-embedded tissue at the proximal margin of resection. Global beta diversity differed according to neoadjuvant therapy modality and was associated with radiation colitis. Taxonomic differences were detectable at phylum and lower classification levels, and radiation-induced colitis was associated with enrichment of the Bacillaceae family. Taxonomic features, including reduced Streptococcus, Lachnospiraceae, and Bacillaceae, were enriched in complete histopathologic responders to neoadjuvant therapy. Taxon-based prediction of metabolic pathways identified enrichment of prokaryotic NAD+ biosynthesis and salvage pathways in complete responders. Mucosal microbiome responses to multimodal neoadjuvant therapy reflect symptomatic radiation colitis, histopathological evidence of radiation injury, and pathologic treatment response. Post-treatment microbiome beta diversity markers of complete pathologic response may be useful in decisions to manage rectal carcinoma non-operatively.},
}

@article {pmid40259344,
year = {2025},
author = {Zhang, Q and Hutchison, ER and Pan, C and Warren, MF and Keller, MP and Attie, AD and Lusis, AJ and Rey, FE},
title = {Systems genetics uncovers associations among host amylase locus, gut microbiome, and metabolic traits in mice.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {101},
pmid = {40259344},
issn = {2049-2618},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Amylases/genetics/metabolism ; Genome-Wide Association Study ; Metagenomics/methods ; Male ; Bacteroidetes/genetics/classification/isolation & purification ; Mendelian Randomization Analysis ; Firmicutes/genetics/classification/isolation & purification ; Cecum/microbiology ; },
abstract = {BACKGROUND: Population studies have revealed associations between host genetic and gut microbiome in humans and mice. However, the molecular bases for how host genetic variation impacts the gut microbial community and bacterial metabolic niches remain largely unknown.

RESULTS: We leveraged 90 inbred hyperlipidemic mouse strains from the hybrid mouse diversity panel (HMDP), previously studied for a variety of cardio-metabolic traits. Metagenomic analysis of cecal DNA followed by genome-wide association analysis identified genomic loci that were associated with microbial enterotypes in the gut. Among these, we detected a genetic locus surrounding multiple amylase genes that were associated with abundances of Firmicutes (Lachnospiraceae family) and Bacteroidetes (Muribaculaceae family) taxa encoding distinct starch and sugar degrading capabilities. The genetic variants at the amylase gene locus were associated with distinct gut microbial communities (enterotypes) with different predicted metabolic capacities for carbohydrate degradation. Mendelian randomization analysis revealed host phenotypes, including liver fibrosis and plasma HDL-cholesterol levels, that were associated with gut microbiome enterotypes.

CONCLUSIONS: This work reveals novel relationships among host genetic variation, gut microbial enterotypes, and host metabolic traits and supports the notion that variation of host amylase may represent a key determinant of gut microbiome in mice. Video Abstract.},
}

Animals
Mice
*Gastrointestinal Microbiome/genetics
*Amylases/genetics/metabolism
Genome-Wide Association Study
Metagenomics/methods
Male
Bacteroidetes/genetics/classification/isolation & purification
Mendelian Randomization Analysis
Firmicutes/genetics/classification/isolation & purification
Cecum/microbiology

@article {pmid40259196,
year = {2025},
author = {Zhang, T and Zhong, H and Yang, M and Shi, X and Yang, L and Yang, J and Liu, H and Luo, Y and Xie, Y and Zhong, Z and Peng, G and Zhang, K and Zheng, C and Zhang, M and Zhou, Z},
title = {Lactobacillus salivary LSbg3 is a Potential Food Probiotic Having Excellent Anti-pathogen Effect That Might Improve Antibiotic-Resistant Diarrhea in Dogs.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40259196},
issn = {1867-1314},
abstract = {Antibiotics may disrupt the intestinal microbiota balance and induce antimicrobial resistance. Although probiotics should be a priority treatment for animal diarrhea, it still has chance to be used as same/or behind as antibiotics in the clinic. Among the probiotics, Lactobacillus (Lact.) was the most frequently utilized in clinical setting since its excellent ability of safety, anti-pathogen, stress resistance, and easy colonization in intestine. In this study, we screened 24 strains of Lact. in the presence of antibiotics from clinical common antibiotic-treated feces, identified L. salivarius LSbg3 exhibiting good stress resistance, potent antibacterial activity, and exceptional intestinal adhesion capability. Its genome showed a good function of regulating intestinal nutrition while lack of transmission antibiotic-resistance genes. Additionally, in a simulated canine diarrhea with failed antibiotic treatment, LSbg3 had a good efficacy in the releasing diarrhea, balancing the microbiome and suppressing typical pathogens, positioning a potential food probiotic have excellent effect on anti-pathogen that can effectively improve antibiotic-resistant diarrhea in dogs.},
}

@article {pmid40259168,
year = {2025},
author = {Al-Juhani, AA and Gaber, AM and Desoky, RM and Binshalhoub, AA and Alzahrani, MJ and Alraythi, MS and Showail, S and Aseeri, AA},
title = {From microbial data to forensic insights: systematic review of machine learning models for PMI estimation.},
journal = {Forensic science, medicine, and pathology},
volume = {},
number = {},
pages = {},
pmid = {40259168},
issn = {1556-2891},
abstract = {BACKGROUND: Estimating post-mortem interval (PMI) is crucial for forensic timelines, yet traditional methods are prone to errors from witness testimony and biological markers sensitive to environmental factors. New molecular and microbial techniques, such as DNA degradation patterns and bacterial community analysis, have shown promise by improving PMI estimation accuracy and reliability over traditional methods. Machine learning further enhances PMI estimation by leveraging complex microbial data. This review addresses the gap by systematically analyzing how microbiome-based PMI predictions compare across organs, environments, and machine learning techniques.

METHODS: We retrieved relevant articles up to September 2024 from PubMed, Scopus, Web of Science, IEEE, and Cochrane Library. Data were extracted from eligible studies by two independent reviewers. This included the number and species of subjects, tissue sample used, PMI range in the study, machine learning algorithms, and model performance.

RESULTS: We gathered 1252 records from five databases after excluding 750 duplicates. After screening titles and abstracts, 43 records were assessed for eligibility, resulting in 28 included articles. Our ranking of machine learning models for PMI estimation identified the top five based on error metrics and explained variance. Wang (2024) achieved a mean absolute error (MAE) of 6.93 h with a random forests (RF) model. Liu (2020) followed with an MAE of 14.483 h using a neural network. Cui (2022) used soil samples for PMI predictions up to 36 days, reaching an MAE of 1.27 days. Yang (2023) employed an RF model using soil samples, achieving an MAE of 1.567 days in summer and an MAE of 2.001 days in winter. Belk (2018) an RF model on spring soil samples with 16S rRNA data, attaining an MAE of 48 accumulated day degrees (ADD) (~ 3-5 days) across a PMI range of 142 days.

CONCLUSION: Machine learning models, particularly RF, have demonstrated effectiveness in PMI estimation when combined with 16S rRNA and soil samples. However, improving model performance requires standardized parameters and validation across diverse forensic environments.},
}

@article {pmid40259094,
year = {2025},
author = {Ofri, M and Kristal, E and Cohen, B and Beigelman, A and Hazan, G},
title = {The impact of neonatal antibiotic exposure on the development of childhood food allergies.},
journal = {European journal of pediatrics},
volume = {184},
number = {5},
pages = {304},
pmid = {40259094},
issn = {1432-1076},
mesh = {Humans ; *Anti-Bacterial Agents/adverse effects/therapeutic use ; Retrospective Studies ; Infant, Newborn ; Female ; Male ; Israel/epidemiology ; Infant ; *Food Hypersensitivity/epidemiology/etiology ; Incidence ; Risk Factors ; Child ; },
abstract = {Food allergies (FAs) in children have become increasingly prevalent. While early life factors such as gut microbiome disruptions have been implicated, the association between neonatal antibiotic exposure and subsequent FAs remains a topic of ongoing debate. This nationwide cohort study aimed to investigate the impact of neonatal antibiotic exposure on the development of childhood FA. This population-based retrospective cohort study analyzed data from Clalit-Healthcare-Services, Israel's largest state-mandated healthcare provider. The cohort included neonates (aged 0-60 days) admitted with fever between 2011 and 2018. Patients with confirmed infectious etiologies were excluded. The cohort was divided into two groups: those who received systemic antibiotics (Antibiotic (+)) and those who did not (Antibiotic (-)). FA cases were identified using ICD-9 codes up to age 6. Multivariate logistic regression and survival analysis models were utilized and adjusted for inflammatory markers, maternal atopy, and socioeconomic status. Among 2780 neonates, 1220 received antibiotics, while 1560 did not. The incidence of FAs was significantly higher in the Antibiotic (+) group compared to the Antibiotic (-) group (2.5% vs. 1.3%, P = 0.02). Adjusted analysis revealed that systemic antibiotic exposure during the neonatal period was associated with a threefold increased risk of FA up to age 6 (OR = 2.89, 95% CI = 1.34-6.92, P = 0.01). Conclusions: This study provides strong evidence linking neonatal antibiotic exposure to an increased risk of childhood FAs, particularly in the first 2 years of life. The findings highlight the importance of judicious antibiotic use in young infants.},
}

Humans
*Anti-Bacterial Agents/adverse effects/therapeutic use
Retrospective Studies
Infant, Newborn
Female
Male
Israel/epidemiology
Infant
*Food Hypersensitivity/epidemiology/etiology
Incidence
Risk Factors
Child

@article {pmid40259019,
year = {2025},
author = {Wang, T and Ahmad, S and Cruz-Lebrón, A and Ernst, SE and Olivos Caicedo, KY and Jeong, Y and Binion, B and Mbuvi, P and Dutta, D and Fernandez-Materan, FV and Breister, AM and Tang, E and Lee, JW and Kang, JD and Harris, SC and Ikegawa, S and Gaskins, HR and Erdman, JW and Yang, G and Cann, I and Daniel, SL and Hylemon, PB and Anantharaman, K and Bernardi, RC and Alves, JMP and Sfanos, KS and Irudayaraj, J and Ridlon, JM},
title = {An expanded metabolic pathway for androgen production by commensal bacteria.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40259019},
issn = {2058-5276},
support = {GM134423//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; CA287126//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; GM145920//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; AI147127//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; GM145965//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; CA287126//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 23CHAL13//Prostate Cancer Foundation (PCF)/ ; 23CHAL13//Prostate Cancer Foundation (PCF)/ ; MCB-2143787//National Science Foundation (NSF)/ ; },
abstract = {Commensal bacteria have been implicated in the modulation of steroid hormones, including circulating androgen levels in the host. However, the microbial genetic pathways involved in androgen production have not been fully characterized. Here we identify a microbial gene encoding an enzyme that catalyses the conversion of androstenedione to epitestosterone in the gut microbiome member Clostridium scindens and named this gene desF. We demonstrate that epitestosterone impacts androgen receptor-dependent prostate cancer cell proliferation in vitro. We also demonstrate that stool desF levels are elevated in patients with prostate cancer who are unresponsive to abiraterone/prednisone therapy. Bacterial isolates from urine or prostatectomy tissue produced androgens, and 17β-hydroxysteroid dehydrogenase activity encoded by the desG gene was detected in strains of the urinary tract bacterium Propionimicrobium lymphophilum. Furthermore, we demonstrate that urinary androgen-producing bacterial strains can promote prostate cancer cell growth through metabolism of cortisol and prednisone. Abiraterone, which targets host desmolase (CYP17A1), a rate-limiting enzyme in adrenal steroidogenesis, does not inhibit bacterial desmolase (DesAB), whereas the conversion of prednisone to androgens by DesAB, DesF and DesG drives androgen-receptor-dependent prostate cancer cell line proliferation in vitro. Our results are a significant advance in steroid microbiology and highlight a potentially important role for gut and urinary tract bacteria in host endocrine function and drug metabolism.},
}

@article {pmid40258876,
year = {2025},
author = {da Silva Morais, E and Grimaud, GM and Warda, A and Stephens, N and Ross, RP and Stanton, C},
title = {Bacteroides maternus sp. nov., a novel species isolated from human faeces.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13808},
pmid = {40258876},
issn = {2045-2322},
support = {12/RC/2273_P2 and 19/ SP/6989/SFI_/Science Foundation Ireland/Ireland ; },
mesh = {Humans ; *Feces/microbiology ; *Bacteroides/genetics/classification/isolation & purification ; Phylogeny ; Female ; Base Composition ; Genome, Bacterial ; RNA, Ribosomal, 16S/genetics ; Fatty Acids ; },
abstract = {A novel bacterial strain, MSB163, was isolated from the stool sample of a healthy mother, 4 weeks after giving birth via vaginal delivery. Taxonomic identification tools revealed that MSB163 belongs to the genus Bacteroides, but it is distinct from any currently known species. The closest related species is Bacteroides cellulosilyticus strain BFG- 250, with an average nucleotide identity (fastANI) of 94.51%. The genome length of MSB163 is 6,440,948 bp and the GC content 42.95%. Two plasmids were identified in the whole genome sequence. MSB163 is a Gram-negative, rod-shaped, non-motile anaerobic bacterium. The optimum growth conditions were at 37 °C, pH 7 and 0% (w/v) NaCl. The respiratory quinones were the menaquinones MK- 10 and MK- 11 and C15:0 ANTEISO was the major fatty acid. The predominant polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phospholipid. According to the taxonomic results and physiological analysis, strain MSB163 represents a novel species of the genus Bacteroides, for which we propose the name Bacteroides maternus, since the type strain was isolated from the stool sample of a mother. B. maternus type strain (MSB163) sequencing can be accessed under the biosample ID SAMN3953129 on NCBI. The strain was deposited on BCCM/LMG Bacteria Collection under the accession number LMG 33,374 and Leibniz Institut DSMZ GMBH under the accession number DSM 117,047.},
}

Humans
*Feces/microbiology
*Bacteroides/genetics/classification/isolation & purification
Phylogeny
Female
Base Composition
Genome, Bacterial
RNA, Ribosomal, 16S/genetics
Fatty Acids

@article {pmid40258837,
year = {2025},
author = {Ghogare, SS and Pathan, EK},
title = {Intratumor fungi specific mechanisms to influence cell death pathways and trigger tumor cell apoptosis.},
journal = {Cell death discovery},
volume = {11},
number = {1},
pages = {188},
pmid = {40258837},
issn = {2058-7716},
abstract = {Cancer, uncontrolled cell growth due to the loss of cell cycle regulation, is often found to be associated with viral infections and, as recent studies show, with bacterial infections as well. Emerging reports also suggest a strong link between fungi and cancer. The crucial virulence trait of fungi, the switch from yeast (Y) to hyphal (H) form, is found to be associated with carcinogenesis. The physicochemical properties and signal transduction pathways involved in the switch to the hyphal form overlap with those of tumor cell formation. Inhibiting differentiation causes apoptosis in fungi, whereas preventing apoptosis leads to cancer in multicellular organisms. Literature on the fungi-cancer linkage, though limited, is increasing rapidly. This review examines cancer-specific fungal communities, the impact of fungal microbiome on cancer cell progression, similarities between fungal differentiation and cells turning cancerous at biochemical and molecular levels, including the overlaps in signal transduction pathways between fungi and cancer. Based on the available evidence, we suggest that molecules inhibiting the yeast-hyphal transition in fungi can be combined with those targeting tumor cell apoptosis for effective cancer treatment. The review points out fertile research areas where mycologists and cancer researchers can collaborate to unravel common molecular mechanisms. Moreover, antibodies targeting fungal-specific chitin and glucan can be used for the selective neutralization of tumor cells. These new combinations of potential therapies are expected to facilitate the development of target-specific, less harmful and commercially feasible anticancer therapies. We bring together available evidence to argue that fungal infections could either trigger cancer or have a significant role in the development and progression of cancer. Hence, cancer-associated fungal populations could be utilized as a target for a combination therapy involving the integration of anticancer and antifungal drugs as well as inhibitors of fungal morphogenesis to develop more effective anticancer therapies.},
}

@article {pmid40258729,
year = {2025},
author = {Lwere, K and Muwonge, H and Sendagire, H and Sajatovic, M and Williams, SM and Gumukiriza-Onoria, JL and Buwembo, D and Buwembo, W and Nassanga, R and Nakimbugwe, R and Nazziwa, A and Munabi, IG and Nakasujja, N and Kaddumukasa, M},
title = {Characterization of the gut microbiome in Alzheimer disease and mild cognitive impairment among older adults in Uganda: A case-control study.},
journal = {Medicine},
volume = {104},
number = {16},
pages = {e42100},
doi = {10.1097/MD.0000000000042100},
pmid = {40258729},
issn = {1536-5964},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Cognitive Dysfunction/microbiology ; Male ; Female ; Aged ; *Alzheimer Disease/microbiology ; Case-Control Studies ; Uganda/epidemiology ; Middle Aged ; Feces/microbiology ; Aged, 80 and over ; },
abstract = {Alzheimer disease (AD) is associated with significant shifts in the gut microbiome and is characterized by reduced microbial diversity and changes in the abundance of specific taxa. These alterations can disrupt the gut-brain axis, leading to increased intestinal permeability ("leaky gut"), systemic inflammation, and oxidative stress. Such microbial changes are thought to contribute to neurodegenerative changes, as observed in AD and cognitive decline, thus emphasizing the role of the microbiome in aging-related neurological health. Our study in urban and rural population in Uganda recruited 104 participants aged 60 years and older, categorized into AD, mild cognitive impairment (MCI), and control groups based on Montreal Cognitive Assessment (MoCA) scores and ICD-11/DSM-V criteria. DNA was extracted from fecal samples using a QIAamp kit and polymerase chain reaction (PCR) products were sequenced using Nanopore. We used diversity indices, principal coordinate analysis (PCoA), permutational multivariate analysis of variance (PERMANOVA), and linear discriminant analysis effect size (LefSe) to identify significant microbial differences among groups. Gut microbiome diversity, as measured by the Chao1 and Shannon indices, was significantly reduced in patients with AD. The AD group had the lowest diversity compared to that of the control group (P < .05). PCoA showed distinct microbial shifts between patients with AD and controls, with MCI showing an intermediate profile. Genera such as Novosphingobium and Staphylococcus were more prevalent in the controls, whereas Hafnia-Obesumbacterium and Dickeya were more common in AD. Age-related changes included increases in Exiguobacterium and Carnobacterium and decreases in Acinetobacter and Klebsiella. Distinct microbial profiles were identified in the AD, MCI, and control groups, suggesting potential microbiome markers of cognitive impairment in the Ugandan population.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Cognitive Dysfunction/microbiology
Male
Female
Aged
*Alzheimer Disease/microbiology
Case-Control Studies
Uganda/epidemiology
Middle Aged
Feces/microbiology
Aged, 80 and over

@article {pmid40258435,
year = {2025},
author = {Ramirez, A and Brelsfoard, CL},
title = {A comparison of the structure and diversity of the microbial communities of Culicoides midges.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107622},
doi = {10.1016/j.actatropica.2025.107622},
pmid = {40258435},
issn = {1873-6254},
abstract = {Culicoides midges (Diptera: Ceratopogonidae) comprise over 1,400 species globally and are vectors for several human and veterinary pathogens. The microbiota of insect vectors plays an essential role in the interactions between the host and pathogen and can impact the ability of the insect to transmit pathogens or parasites. Characterizing the microbiome composition of Culicoides could yield novel approaches to control midge populations and impact disease transmission. This study characterized and compared the bacterial and fungal microbiota of five Culicoides species. Utilizing 16s and ITS amplicon sequencing, we identified diverse bacterial communities, with Proteobacteria as the most abundant phylum. Notably, Rickettsia, Midichloria, and Asaia were the predominant genera across samples. Fungal analysis revealed Ascomycota as the primary taxon, with Cladosporium being the most prevalent genus. Little difference in overall bacterial and fungal diversity was observed between species, suggesting that the five Culicoides species examined share some common members of their microbiota but differ in overall composition. Our findings highlight the potential of exploiting midge-associated microbiota for developing novel biological control strategies to target Culicoides species populations and the pathogens they transmit.},
}

@article {pmid40258420,
year = {2025},
author = {Li, J and Chen, J and Li, J and Hao, M and Ma, W},
title = {Potential causal association between the oral microbiome and bipolar disorder.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jad.2025.04.058},
pmid = {40258420},
issn = {1573-2517},
abstract = {BACKGROUND: The oral microbiome can influence the growth, development, and regulation of the nervous system through various pathways; however, its relationship with bipolar disorder (BD) remains ambiguous. This study aims to investigate the causal relationship between the oral microbiome and BD through Mendelian randomization (MR) analysis.

METHODS: Data regarding single nucleotide polymorphisms (SNPs) in GWAS summary statistics for oral microbiota and BD were obtained from two studies: one reported the association between the oral microbiome and the human genome, encompassing both the dorsum of the tongue and saliva microbiomes. The other study investigated the association between BD and the human genome, categorizing BD into BD I and BD II for separate analyses. Thus, three data components were utilized: BD, BD I, and BD II. In this study, GWAS data for saliva and dorsum of the tongue microbiomes were analyzed separately for BD, BD I, and BD II. The inverse variance weighted (IVW) method was used to assess the causal relationship between the oral microbiome and BD. Analyses were conducted only when the number of instrumental variable SNPs was no less than two. The MR-Egger regression and IVW methods were employed to evaluate heterogeneity, whereas the MR-Egger intercept test was utilized to assess pleiotropy. For MR results exhibiting heterogeneity or pleiotropy, sensitivity analyses were performed using the weighted median, simple mode, weighted mode, MR-Egger test, and leave-one-out methods. Furthermore, funnel plots were employed to evaluate publication bias. Reverse MR analysis was also performed to investigate the potential bidirectional interactions between BD and the oral microbiota.

RESULTS: A causal relationship exists between the oral microbiome and BD. The effects of the microbiome from different regions of the oral cavity on BD are variable, with a more pronounced impact noted on BD I. This study identified two overlapping causal relationships shared between BD I and BD II, both exhibiting the same directional influence: ①Salivary s Prevotella aurantiaca SGB 2854 (Taxonomy ID: 596085, species); ② Tongue s Prevotella sp000467895 SGB 1817 (Taxonomy ID: 838, genus). Additionally, there are two overlapping bacteria with opposing directional effects: ① Salivary g Eggerthia (Taxonomy ID: 1279384, genus); ② Salivary s unclassified SGB 2636. Three differential bacteria that exclusively regulate one subtype were identified: ① Salivary s Lachnoanaerobaculum sp000296385 SGB 3537 (Taxonomy ID: 1164882, genus); ② Tongue s unclassified SGB 689; ③ Tongue s unclassified SGB 572. Among these, the genus g Eggerthia in saliva inhibits BD I while promoting BD II; conversely, salivary s unclassified SGB 2636 inhibits BD II while promoting BD I. The analysis of tongue s unclassified SGB 489 and s unclassified SGB 1215 demonstrated pleiotropy without causal significance. The reverse MR analysis identified that BD I may influence four microbial species, including f Leptotrichiaceae (Taxonomy ID: 1129771, family), f Streptococcaceae (Taxonomy ID: 1300, family), s unclassified SGB 1210, and s unclassified SGB 1950. There may be a bidirectional causal relationship between s unclassified SGB 1950 and BD I. Additionally, Reverse Mendel suggested that there was no significant causal relationship between BD and salivary and dorsal tongue microbes.

CONCLUSION: Our Mendelian randomization results indicate a causal relationship between the oral microbiome and the development of BD. However, the microbial profiles associated with the different subtypes, BD I and BD II, differ significantly; even within the same genus, the direction of influence on BD I and BD II varies, suggesting that the underlying mechanisms for the development of BD I and BD II may differ substantially.},
}

@article {pmid40258415,
year = {2025},
author = {Carballo Quintá, M and Perez Castro, S and Freire Rodriguez, A and Daviña Nuñez, C and Bellas Pereira, A and Cabrera Alvargonzalez, JJ and Perez Schoch, M and Muller Arteaga, CA and Sanchez Garcia, JF and Cespón Outeda, E and Lopez Diez, E},
title = {Gut microbiota and prostate cancer: an analysis of bacterial communities across various clinical scenarios.},
journal = {Actas urologicas espanolas},
volume = {},
number = {},
pages = {501748},
doi = {10.1016/j.acuroe.2025.501748},
pmid = {40258415},
issn = {2173-5786},
abstract = {INTRODUCTION AND OBJECTIVES: Gut microbiota (GM) comprises a diverse community of bacteria associated with a wide range of diseases. Emerging research indicates that GM dysbiosis may affect the progression of prostate cancer (PC) and its response to treatment. This study aimed to describe GM in patients with PC at various disease stages.

MATERIALS AND METHODS: A cross-sectional study was conducted at Complejo Hospitalario Universitario de Vigo between 2023 and 2024. 49 patientes were classified into three groups: active surveillance (AS), disease-free post-treatment (DF) and advanced disease (AD). Faecal samples were obtained for GM analysis and DNA was used for 16S rRNA sequencing. The structure of the microbial community was examined via alpha and beta diversity analysis, and differential abundance was measured using the LinDA model.

RESULTS: Alpha diversity analysis revealed diminished taxon richness in patients under AS and in those treated with androgen receptor pathway in hibitors (ARPI). Beta diversity analysis indicated substantial changes attributable to the treatment group, radiation, hormone therapy, and ARPI. The AD group had a diminished number of potentially advantageous bacteria (Methanobrevibacter, Paraprevotella, Colidextribacter) and an elevated abundance of Terrisporobacter and Streptococcus compared to the DF group. The AS group showed reduction in Intestinibacter, Adlercreutzia, Subdoligranulum, and Methanobrevibacter, along with an increase in Fusicatenibacter, Lachnospiraceae, and Lachnoclostridium.

CONCLUSIONS: Patients who remain disease-free after therapy have restored microbiota abundant in potential beneficial bacteria, in contrast to individuals with severe disease or those under active monitoring. This study indicates that gut microbiome characteristics could assist in risk assessment and act as possible treatment targets for prostate cancer.},
}

@article {pmid40257861,
year = {2025},
author = {Hu, M and Zhu, X and Huang, X and Hua, L and Lin, X and Zhang, H and Hu, Y and Tong, T and Li, L and Xuan, B and Zhao, Y and Zhou, Y and Ding, J and Ma, Y and Jiang, Y and Ning, L and Zhang, Y and Wang, Z and Fang, JY and Zhang, Y and Xiao, X and Hong, J and Chen, H and Li, J and Chen, H},
title = {Optimizing anti-PD-1/PD-L1 therapy efficacy and fecal microbiota transplantation donor selection through gut mycobiome-based enterotype.},
journal = {Cell reports},
volume = {44},
number = {5},
pages = {115589},
doi = {10.1016/j.celrep.2025.115589},
pmid = {40257861},
issn = {2211-1247},
abstract = {Immunotherapy has revolutionized cancer treatment, but response variability remains a challenge. The gut microbiome's role in therapeutic efficacy is well established, but the impact of the gut mycobiome is less understood. Using unsupervised clustering, we identify two gut mycobiome-based enterotypes, favorable type and unfavorable type, characterized by distinct microbial compositions linked to immunotherapy outcomes. Favorable-type enterotypes exhibit higher fungal and bacterial alpha diversity, enriched butyrate-producing bacteria, and metabolic pathways related to butyric acid and sugar/starch metabolism. External validation confirms their predictive value in assessing immunotherapy efficacy. Multi-omics analysis reveals increased CD8[+] T cell infiltration in the tumor microenvironment of favorable-type patients. Fecal microbiota transplantation (FMT) from favorable-type donors enhances anti-PD-1 sensitivity, promotes CD8[+] T cell infiltration, and boosts butyrate production in vivo. These findings highlight the gut mycobiome's role in immunotherapy response and support FMT from favorable-type donors as a potential strategy for improving treatment outcomes and patient stratification.},
}

@article {pmid40257829,
year = {2025},
author = {Mogeni, P and Ochieng, JB and Atlas, HE and Tickell, KD and Rwigi, D and Kariuki, K and Aluoch, LR and Sonye, C and Apondi, E and Ambila, L and Diakhate, MM and Singa, BO and Liu, J and Platts-Mills, JA and Fang, FC and Walson, JL and Houpt, ER and Pavlinac, PB},
title = {Impact of macrolide resistance on azithromycin for prevention of rehospitalization or death among children discharged from hospitals in Western Kenya.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf208},
pmid = {40257829},
issn = {1537-6613},
abstract = {BACKGROUND: The Toto Bora trial tested whether a 5-day course of azithromycin reduced the risk of re-hospitalization or death in the 6 months following hospitalization among Kenyan children and found no overall benefit. We hypothesized that macrolide resistance in gut microbes could modify azithromycin's effect.

METHODS: From June 2016 to November 2019, Kenyan children aged 1-59 months were enrolled at hospital discharge and randomized to azithromycin or placebo. DNA from fecal samples and E. coli isolates was analyzed for common macrolide resistance genes. Cox proportional hazards regression models, including interaction terms between randomization arm and individual macrolide-resistance genes, were used to analyze time to rehospitalization or death, with Bonferroni correction applied to account for multiple comparisons.

RESULTS: Among 1,393 children tested, 94.7% had at least one macrolide-resistance gene in their fecal DNA at hospital discharge; most commonly mph(A) (68.6%; 955/1393), followed by msr(D) (67.3%; (937/1393), and erm(B) (60.7%; 846/1393). Mef(A) (23.7%; 330/1393) was the only macrolide-resistance gene that modified azithromycin's effect on re-hospitalization or death (interaction p-value=0.008). In children without the mef(A) gene, azithromycin reduced the hazard of rehospitalization or death by a third (HR=0.66, 95%CI: 0.45-0.99) whereas among children with the mef(A) gene, there was a higher risk in those randomized to azithromycin (HR=2.72, 95%CI: 1.21-6.09). The effect size of azithromycin's impact on mortality and rehospitalization as separate outcomes in children with and without mef(A) were consistent but underpowered.

INTERPRETATION: Macrolide resistance in the gut microbiome may influence the efficacy of azithromycin in children discharged from the hospital.},
}

@article {pmid40257664,
year = {2025},
author = {Yu, Y and Yang, X and Deng, J and Yin, Y and Wu, Y and Yu, R},
title = {Association of the gut microbiome with diabetic nephropathy and the mediated effect of metabolites: friend or enemy?.},
journal = {International urology and nephrology},
volume = {},
number = {},
pages = {},
pmid = {40257664},
issn = {1573-2584},
support = {(U21A20411)//National Natural Science Foundation of China/ ; (22JBZ002)//Hunan University of Chinese Medicine Disciplinary Construction' Revealing the List and Appointing Leaders' Project/ ; },
abstract = {OBJECTIVE: The effects of gut microbiome and its metabolites on diabetic nephropathy (DN) have been inadequately elucidated. The aim of this study is to assess the causal effect of gut microbiome on DN and the mediated effect of metabolites by a two-step Mendelian randomization (MR).

METHODS: Datasets of gut microbiome, metabolites, and DN were acquired in genome-wide association studies and screened for single nucleotide polymorphisms according to the underlying assumptions of MR. Subsequently, inverse variance weighted was used as the primary method for MR analysis to assess the causal effect of gut microbiome on DN and the mediated effect of metabolites. Finally, MR-Egger intercept, Cochran's Q test, and leave-one-out sensitivity analysis were used to assess the horizontal pleiotropy, heterogeneity, and robustness of the results, respectively.

RESULTS: The MR analysis demonstrated that Parabacteroides merdae increased the genetic susceptibility to DN by reducing acetylcarnitine (C2) to propionylcarnitine (C3) ratio (mediated proportion 8.95%, mediated effect 0.024) and alpha-ketobutyrate to 3-methyl-2-oxovalerate ratio (mediated proportion 19.90%, mediated effect 0.053). MR Egger showed that these results lack horizontal pleiotropy (p ≥ 0.05). Cochran's Q and sensitivity analysis suggested these results had no heterogeneity (p ≥ 0.05) and were robust.

CONCLUSION: Our findings revealed the pathway by which Parabacteroides merdae increased the genetic susceptibility to DN by regulating acetylcarnitine (C2) to propionylcarnitine (C3) ratio and alpha-ketobutyrate to 3-methyl-2-oxovalerate ratio. It provides new genetic insights for understanding the pathogenesis of DN and related drug research.},
}

@article {pmid40257638,
year = {2025},
author = {Ji, M and Xiong, K and Fu, D and Chi, Y and Wang, Y and Yao, L and Yang, X and Yan, Y and Zhu, H and Li, Y and Ren, B and Zou, L},
title = {Correction to: The landscape of the microbiome at different stages of root caries.},
journal = {Clinical oral investigations},
volume = {29},
number = {5},
pages = {255},
doi = {10.1007/s00784-025-06349-7},
pmid = {40257638},
issn = {1436-3771},
}

@article {pmid40257450,
year = {2025},
author = {Wan, J and Yoon, SE and Pamela, R and Kai Jie Wong, I and Vitale, M and Cartier, H and Garson, S and Yi, KH},
title = {Lactobacillus-Derived Exosome Therapy for Active Acne Vulgaris, Post-Inflammatory Hyperpigmentation, and Atrophic Scarring.},
journal = {The Journal of craniofacial surgery},
volume = {},
number = {},
pages = {},
pmid = {40257450},
issn = {1536-3732},
abstract = {BACKGROUND: Acne vulgaris often leads to post-inflammatory hyperpigmentation (PIH) and atrophic scarring, affecting patients' quality of life. Traditional treatments may have side effects and inconsistent efficacy. An imbalance in the skin microbiome, particularly a deficiency in Lactobacillus species, has been implicated in acne pathogenesis. Lactobacillus-derived exosomes (LDE) offer a novel, cell-free therapeutic approach with anti-inflammatory and regenerative properties.

OBJECTIVE: This case series evaluates the efficacy and safety of LDE therapy combined with microneedling in patients with active acne, PIH, and atrophic scarring.

METHODS: Three patients with moderate to severe acne [Investigator's Global Assessment (IGA) scores 2-4], visible PIH, and atrophic scarring underwent biweekly microneedling treatments followed by topical application of LDE (BLESKIN EXXO, Daeyang Medical) over 2 months. Assessments were conducted at baseline and 2-month post-treatment, utilizing the IGA scale for acne severity, the Postinflammatory Hyperpigmentation Area and Severity Index (PIHASI) for PIH, and the Goodman and Baron Scarring Grading System for atrophic scarring. Two independent, blinded dermatologists evaluated clinical photographs and scored all outcomes. Patient satisfaction was recorded on a 10-point Likert scale.

RESULTS: All patients exhibited significant improvements in acne severity, PIH, and atrophic scarring. IGA scores decreased from baseline values of 3 to 4 to 1 to 2 post-treatment. PIHASI scores were reduced by 4 to 6 points, and Goodman and Baron scores improved by one grade level. Patient satisfaction scores ranged from 8 to 9 out of 10. Minimal adverse events were noted, with only one instance of transient erythema observed during the study.

CONCLUSION: LDE therapy combined with microneedling seems to be a promising treatment modality for active acne, PIH, and atrophic scarring, demonstrating significant clinical improvements with high patient satisfaction and minimal adverse effects. Further research with larger cohorts and controlled studies is warranted to validate these findings.},
}

@article {pmid40257025,
year = {2025},
author = {Fakruddin, M and Chowdhury, Z and Suprova, SN and Ul Islam, B and Sultana Jime, J and Bulbul, N and Anam, MB and Bin Mannan, S and Shishir, MA},
title = {Microbial Influences: The Microbiome's Impact on Pancreatic Cancer Development and Progression.},
journal = {Current pharmaceutical biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113892010356542250407143257},
pmid = {40257025},
issn = {1873-4316},
abstract = {Pancreatic ductal adenocarcinoma (PDAC) presents significant challenges due to its dense stromal environment, which impedes treatment efficacy. Recent molecular and phenotypic analyses have enhanced our understanding of PDAC, driving the development of targeted therapies. Emerging research highlights the crucial role of the pancreatic tumor microbiome in PDAC initiation and progression. However, the specific mechanisms influencing the tumor microenvironment (TME) and systemic immunity remain incompletely understood. Studies have elucidated various genetic mutations, signaling pathways, and cellular interactions driving PDAC progression, aiding the development of targeted therapies. Despite these advances, overall survival rates for PDAC patients remain low, necessitating novel therapeutic strategies. Therapeutic strategies targeting the microbiome hold significant potential. Therapeutic strategies aimed at modulating microbiomes demonstrate significant potential for treating diseases and enhancing human well-being. Early research indicates that manipulating the microbiome could alter the TME to enhance the efficacy of existing treatments and lead to new therapeutic modalities. Modulating microbiomes might improve the delivery and effectiveness of chemotherapeutic agents or sensitize the tumor to immunotherapy, potentially revolutionizing PDAC treatment paradigms. Microbes can indirectly contribute to pancreatic cancer by inducing chronic inflammation and immune dysregulation. Microbes create a pro-inflammatory environment conducive to cancer development. This persistent inflammation can lead to genetic mutations and a suppressed immune response, fostering an environment where cancer cells can thrive. This review synthesizes current evidence on how the microbiome influences PDAC development and progression, emphasizing its potential for early disease detection and novel therapeutic strategies. Early detection, particularly in premalignant conditions such as chronic pancreatitis and intraductal papillary mucinous neoplasm (IPMN), is crucial for improving patient outcomes through timely intervention.},
}

@article {pmid40256745,
year = {2025},
author = {Ruiz-Toquica, J and Franco Herrera, A and Medina, M},
title = {Endozoicomonas dominance and Vibrionaceae stability underpin resilience in urban coral Madracis auretenra.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19226},
pmid = {40256745},
issn = {2167-8359},
mesh = {Animals ; *Anthozoa/microbiology/physiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Coral Reefs ; Colombia ; Ecosystem ; Seasons ; },
abstract = {Coral resilience varies across species, with some exhibiting remarkable stability and adaptability, often mediated by their associated microbiomes. Given the species-specific nature of coral-microbiome interactions, investigating the microbiomes of urban-adapted corals provides critical insights into the health, dynamics, and functioning of coral holobionts. In this study, we examined the microbiome of Madracis auretenra, a Caribbean coral from Santa Marta, Colombia, across contrasting environmental conditions. Over two years, we compared the microbiomes of healthy and stressed coral colonies from two distinct reef habitats-urban and protected-using 16S rRNA gene sequencing (V4 region) to assess microbial diversity. Our findings revealed microbial richness and diversity were primarily influenced by seasonal and local factors rather than host-specific traits such as interaction with algae, health status, or microhabitat. These variations were not substantial enough to disrupt the overall microbial community structure, which remained stable across temporal and spatial scales. Dominant taxa included Endozoicomonas, along with Vibrionaceae and Rhodobacteraceae, which form dense ecological interaction networks. Notably, nutrient and oxygen levels emerged as key drivers of microbiome fluctuations, yet Vibrionaceae populations exhibited exceptional temporal stability. These findings highlight the presence of a well-structured and resilient coral microbiome with minimal seasonal variability, even in urban-influenced environments. We propose that the dominance of Endozoicomonas and the stability of Vibrionaceae populations play a pivotal role in maintaining microbiome balance, ultimately contributing to the ecological resilience of M. auretenra in dynamic reef habitats.},
}

Animals
*Anthozoa/microbiology/physiology
*Microbiota
RNA, Ribosomal, 16S/genetics
Coral Reefs
Colombia
Ecosystem
Seasons

@article {pmid40256744,
year = {2025},
author = {Pakpahan, C and Laurus, G and Hartanto, MC and Singh, R and Saharan, A and Darmadi, D and Rezano, A and Wasian, G},
title = {Potential relationship of the gut microbiome with testosterone level in men: a systematic review.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19289},
pmid = {40256744},
issn = {2167-8359},
mesh = {Humans ; *Testosterone/blood/metabolism ; *Gastrointestinal Microbiome/physiology ; Male ; Dysbiosis ; },
abstract = {The gut microbiome influences the metabolism and health of several organs beyond the gut and has recently gained considerable attention. The gut plays a central role in food digestion, absorption, nutrition, and general health. Hence, the gut microbiome has become a research subject for almost all health conditions. Imbalance or dysbiosis in the gut microbiome can cause different health issues in men, including reproductive and sexual health issues associated with testosterone levels. Several studies have investigated the relationship between the gut microbiome and testosterone levels. In this systematic review, we aimed to examine the relationship between the gut microbiome and testosterone levels in men. Literature searches were conducted by scanning PubMed, ProQuest, EBSCO, Taylor & Francis Online, Wiley Online, Springer Link, Web of Science, Google Scholar, and Science Direct databases for relevant keywords following the preferred reporting items for the systematic review guidelines. This review included cross-sectional, case-control, retrospective, and prospective cohort studies. Quality assessment was conducted using the Newcastle-Ottawa Scale. We found a significant positive correlation between the gut microbiome and testosterone levels in men. Several microbes play substantial roles in testosterone production. Mechanisms have been proposed as factors that contribute to testosterone levels, namely the hypothalamus-pituitary-gonad axis modulation, androgen metabolism, and intestinal homeostasis, by balancing the bone morphogenic protein (BMP) and the Wnt diverse microbiome. Ruminococcus showed a stronger correlation with testosterone levels than other microorganisms. The gut microbiome has complex correlations with testosterone metabolism. However, the microbiome with the most significant influence on testosterone levels cannot be easily identified and requires further research.},
}

Humans
*Testosterone/blood/metabolism
*Gastrointestinal Microbiome/physiology
Male
Dysbiosis

@article {pmid40256741,
year = {2025},
author = {Du, Z and Zhao, C and Li, J and Shen, Y and Ren, G and Ding, J and Peng, J and Ye, X and Miao, J},
title = {Ginsenosides and gut microbiota: differential effects on healthy individuals and irritable bowel syndrome subtypes.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19223},
pmid = {40256741},
issn = {2167-8359},
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology/drug therapy ; *Gastrointestinal Microbiome/drug effects ; *Ginsenosides/pharmacology/therapeutic use ; Adult ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Diarrhea/microbiology/drug therapy ; Healthy Volunteers ; Young Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: Irritable bowel syndrome (IBS) is a common gastrointestinal disorder with poorly understood mechanisms. Variations in gut microbiota composition are observed in different IBS subtypes. Ginsenosides have shown potential in alleviating IBS symptoms, but their interactions with gut microbiota in different IBS subtypes are not well studied.

METHODS: In this study, we investigated the effects of ginsenosides on the gut microbiota of both healthy participants and participants suffering from IBS characterized by diarrhea (IBS-D) or constipation (IBS-C), using in vitro fermentation alongside 16S rRNA sequencing and bioinformatics analyses.

RESULTS: The analysis demonstrated that there were no statistically significant alterations in α- or β-diversity between the ginsenosides-treated and control groups across all models. However, the microbial composition assessment revealed the presence of 51 shared genera, with notable variations in composition and a significant enrichment of specific taxa. Specifically, the LEfSe analysis revealed that, following ginsenosides treatment, the healthy model groups exhibited significant enrichment of Stenotrophomonas and Achromobacter, while the IBS-D model groups demonstrated significant enrichment of Pseudomonas and Stenotrophomonas.

CONCLUSIONS: The results elucidate the distinctive microbial signatures associated with ginsenosides treatment across both healthy and IBS-D groups, underscoring the potential therapeutic efficacy of ginsenosides in modulating gut microbiota. This study highlights the necessity for further investigation into targeted microbiome therapies for IBS, which may facilitate the development of more personalized and efficacious treatment strategies for gastrointestinal health.},
}

Humans
*Irritable Bowel Syndrome/microbiology/drug therapy
*Gastrointestinal Microbiome/drug effects
*Ginsenosides/pharmacology/therapeutic use
Adult
Male
Female
RNA, Ribosomal, 16S/genetics
Middle Aged
Diarrhea/microbiology/drug therapy
Healthy Volunteers
Young Adult
Feces/microbiology

@article {pmid40255763,
year = {2025},
author = {Rathore, K and Shukla, N and Naik, S and Sambhav, K and Dange, K and Bhuyan, D and Imranul Haq, QM},
title = {The Bidirectional Relationship Between the Gut Microbiome and Mental Health: A Comprehensive Review.},
journal = {Cureus},
volume = {17},
number = {3},
pages = {e80810},
pmid = {40255763},
issn = {2168-8184},
abstract = {The gut microbiome plays a fundamental role in mental health, influencing mood, cognition, and emotional regulation through the gut-brain axis. This bidirectional communication system connects the gastrointestinal and CNS, facilitated by microbial metabolites, neurotransmitters, and immune interactions. Recent research highlights the association between gut dysbiosis and psychiatric disorders, including anxiety, depression, and stress-related conditions. Key findings indicate that altered microbial diversity, decreased short-chain fatty acid (SCFA) production, and increased neuroinflammation contribute to mental health disturbances. This paper explores the mechanism linking the gut microbiome to brain function, including microbial neurotransmitter synthesis, vagus nerve signaling, and hypothalamic-pituitary-adrenal (HPA) axis modulation. Additionally, it evaluates the potential of microbiome-targeted interventions, such as probiotics, prebiotics, dietary modifications, and fecal microbiota transplantation (FMT), in alleviating psychiatric symptoms. Microbiome sequencing and bioinformatics advances further support the development of personalized microbiome-based mental health interventions. Despite promising evidence, challenges such as inter-individual variability, methodological inconsistencies, and the need for longitudinal studies remain. Future research should focus on standardizing microbiome assessment techniques and optimizing therapeutic applications. Integrating precision psychiatry with microbiome-based diagnostics holds immense potential in transforming mental health treatment.},
}

@article {pmid40255304,
year = {2025},
author = {Alam, MK and Hajeer, MY and Abdulrahim, MAM and Ayman Falah, ZA and Abdulkarim, FAA},
title = {Impact of orthodontic treatment on oral microbiome diversity and composition: A longitudinal study.},
journal = {Bioinformation},
volume = {21},
number = {1},
pages = {62-65},
pmid = {40255304},
issn = {0973-2063},
abstract = {The change in oral microbiome diversity and composition during fixed orthodontic treatment was done using 16S rRNA sequencing. Saliva and plaque samples from 60 participants were analyzed at baseline, 3 months and 6 months. Alpha diversity significantly decreased at 3 months (mean: 2.8 ± 0.4) but partially recovered by 6 months (mean: 3.0 ± 0.3). Beta diversity analysis revealed significant microbial composition shifts (p < 0.01) with an increase in Streptococcus mutans and a decline in Streptococcus sanguinis. Hence, orthodontic treatment alters the oral microbiome, emphasizing the need for enhanced oral hygiene to prevent dysbiosis.},
}

@article {pmid40255291,
year = {2025},
author = {Mikhail, SG and O'Dwyer, DN},
title = {The lung microbiome in interstitial lung disease.},
journal = {Breathe (Sheffield, England)},
volume = {21},
number = {2},
pages = {240167},
pmid = {40255291},
issn = {1810-6838},
abstract = {Interstitial lung disease (ILD) is a heterogeneous chronic form of lung disease. The pathogenesis of ILD is poorly understood and a common form of ILD, idiopathic pulmonary fibrosis (IPF) is associated with poor prognosis. There is evidence for substantial dysregulated immune responses in ILD. The microbiome is a key regulator of the immune response, and the lung microbiome correlates with alveolar immunity and clinical outcomes in ILD. Most observational lung microbiome studies have been conducted in patients with IPF. A consistent observation in these studies is that the bacterial burden of the lung is elevated in patients with IPF and predicts mortality. However, our understanding of the mechanism is incomplete and our understanding of the role of the lung microbiome in other forms of ILD is limited. The microbiomes of the oropharynx and gut may have implications for the lung microbiome and pulmonary immunity in ILD but require substantial further research. Here, we discuss the studies supporting a role for the lung microbiome in the pathogenesis of IPF, and briefly describe the putative role of the oral-lung axis and the gut-lung axis in ILD.},
}

@article {pmid40255248,
year = {2025},
author = {Favale, N and Costa, S and Summa, D and Sabbioni, S and Mamolini, E and Tamburini, E and Scapoli, C},
title = {Comparison of microbiome community structure and dynamics during anaerobic digestion of different renewable solid wastes.},
journal = {Current research in microbial sciences},
volume = {8},
number = {},
pages = {100383},
pmid = {40255248},
issn = {2666-5174},
abstract = {This study analysed the effect of the different lignocellulose composition of two crop substrates on the structure and dynamics of bacterial communities during anaerobic digestion (AD) processes for biogas production. To this end, cereal grains and grape pomace biomasses were analysed in parallel in an experimental AD bench-scale system to define and compare their metagenomic profiles for different experimental time intervals. The bacterial community structure and dynamics during the AD process were detected and characterised using high-resolution whole metagenomic shotgun analyses. Statistical evaluation identified 15 strains as specific to two substrates. Some strains, like Clostridium isatidis, Methanothermobacter wolfeii, and Methanobacter sp. MB1 in cereal grains, and Acetomicrobium hydrogeniformans and Acetomicrobium thermoterrenum in grape pomace, were never before detected in biogas reactors. The presence of bacteria such as Acetomicrobium sp. and Petrimonas mucosa, which degrade lipids and protein-rich substrates, along with Methanosarcina sp. and Peptococcaceae bacterium 1109, which tolerate high hydrogen pressures and ammonia concentrations, suggests a complex syntrophic community in lignin-cellulose-enriched substrates. This finding could help develop new strategies for the production of a tailor-made microbial consortium to be inoculated from the beginning of the digestion process of specific lignocellulosic biomass.},
}

@article {pmid40255244,
year = {2025},
author = {You, Z and Jain, S and Shen, S and Mao, J and Martyn, JAJ},
title = {Pathophysiology and management of burn injury-induced pain.},
journal = {Burns open : an international open access journal for burn injuries},
volume = {10},
number = {},
pages = {},
pmid = {40255244},
issn = {2468-9122},
abstract = {This review examines the pathophysiology and therapeutic management of burn injury-induced pain (BIP). Burn injury, occurring globally in about 11 million people, often induces the most intense pain, but its management remains suboptimal. The pain often persists even after complete wound healing and hospital discharge causing both long-term disability and neurological dysfunction. The fact that BIP persists well beyond the initial hospitalization is not well recognized and should be underscored as the pain involves even non-burned areas. The pathophysiology of the latter problem is poorly understood and needs further study. Opioids, the mainstay for moderate to severe pain relief after major burn injury, with time, have poor analgesic and serious side effects. Accurate assessment pain of BIP and its biology at different stages of treatment helps to provide effective treatments of the different etiological factors that cause BIP and their sequelae. Based on clinical and pre-clinical studies, we discuss the current knowledge on the underlying cellular and molecular mechanisms in the initiation and persistence of BIP during the acute phase and later phases of injury. Opioid receptor-mediated signaling changes per se and immune microglia responses in concert exaggerate nociceptive behavior. Both burn injury and opioids upregulate spinal NMDA receptor expression and microglia changes, which further exaggerate pain. BIP has inflammatory and neuropathic components. Pharmacological and non-pharmacological approaches currently available for management of BIP is discussed. Areas that need further study include the role of other central and peripheral factors in the exaggeration of pain well beyond wound healing. Novel non-opioid methods to rectify BIP is important to develop in view of the potential for opioid use disorder. The role of microbiome in chronic pain syndromes is an unexplored territory and its relevance to BIP needs further examination. Pruritus or itch, though very common and important in the pharmacotherapy of burns, the discussion of this topic is brief. Extensive review of this topic is beyond the scope of this review in view of the vast body of knowledge and varying and multiple treatment options.},
}

@article {pmid40255203,
year = {2025},
author = {Comai, S and Manchia, M and Bosia, M and Miola, A and Poletti, S and Benedetti, F and Nasini, S and Ferri, R and Rujescu, D and Leboyer, M and Licinio, J and Baune, BT and Serretti, A},
title = {Moving towards precision and personalized treatment strategies in psychiatry.},
journal = {The international journal of neuropsychopharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1093/ijnp/pyaf025},
pmid = {40255203},
issn = {1469-5111},
abstract = {Precision psychiatry aims to improve routine clinical practice by integrating biological, clinical, and environmental data. Many studies have been performed in different areas of research on major depressive disorder, bipolar disorder, and schizophrenia. Neuroimaging and EEG findings have identified potential circuit-level abnormalities predictive of treatment response. Protein biomarkers, including IL-2, S100B, and NfL, and the kynurenine pathway illustrate the role of immune and metabolic dysregulation. Circadian rhythm disturbances and the gut microbiome have also emerged as critical transdiagnostic contributors to psychiatric symptomatology and outcomes. Moreover, advances in genomic research and polygenic scores support the perspective of personalized risk stratification and medication selection. While challenges remain, such as data replication issues, prediction model accuracy and scalability, the progress so far achieved underscores the potential of precision psychiatry in improving diagnostic accuracy and treatment effectiveness.},
}