@article {pmid40544520,
year = {2025},
author = {Zhang, E and Gong, GA and Huang, S and Bao, Y and Ji, L and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Zhang, W},
title = {Viral Metagenomics of the Bharal (Pseudois nayaur) within the Qinghai-Tibet Plateau Revealed Diverse Viruses.},
journal = {Polish journal of microbiology},
volume = {74},
number = {2},
pages = {143-152},
doi = {10.33073/pjm-2025-012},
pmid = {40544520},
issn = {2544-4646},
abstract = {The Qinghai-Tibetan Plateau (QTP) provides a home to diverse flora and fauna, and its ecosystems are unique worldwide. The study focused on the bharal, an endemic species found in the QTP and adjacent regions. We applied viral metagenomics technology to extract samples from the feces of 10 wild bharal. Viral nucleic acids were isolated, enriched, and sequenced from these samples, revealing the presence of a novel strain of Astroviridae virus. Phylogenetic analysis and sequence comparison identified this virus as part of the Mamastro-virus, forming a cluster with other Mamastrovirus species. Recombination analysis confirmed a multiple recombination event, suggesting that the new strain may be a potential recombinant. Additionally, nearly complete genome sequences of viruses belonging to the family Circoviridae were characterized, and a phylogenetic tree was constructed based on genotyping and predicted amino acid sequence analysis of the rep protein. Overall, this study helps us better understand the viral communities in the gut microbiome of the rare bharal. Moreover, the new recombinant discovered in this study will provide insights into the origin, genetic diversity, and evolution of bharal from the QTP and play a crucial role in future research on its presence in the intestinal ecology of sheep.},
}

@article {pmid40544519,
year = {2025},
author = {Yu, X and Liang, J and Yang, R and Gai, W and Zheng, Y},
title = {Clinical Features and Value of Tracheal Aspirate Metagenomic Next-Generation Sequencing for Severe Pneumonia in Children in Pediatric Intensive Care Unit.},
journal = {Polish journal of microbiology},
volume = {74},
number = {2},
pages = {192-205},
doi = {10.33073/pjm-2025-016},
pmid = {40544519},
issn = {2544-4646},
abstract = {Pneumonia is a leading cause of mortality in children. While metagenomic next-generation sequencing (mNGS) has the potential to detect all the microorganisms in pneumonia patients, the relationship between these microorganisms and the patients' clinical characteristics remains to be established. Fifty-five children, diagnosed with severe pneumonia and undergoing tracheal aspirate (TA) mNGS for pathogen detection at The Heilongjiang Hospital of Beijing Children's Hospital between July 2021 and November 2022, were included in this study. The clinical characteristics, pathogen distribution, and microbiome features of these children were analyzed. Results showed that the rate of mixed infections was notably high (80%, 44/55), with bacterial-viral infections being the most common. Streptococcus pneumoniae, Mycoplasma pneumoniae (MP), Candida albicans, and Respiratory syncytial virus (RSV) were the most common pathogens in this cohort. Furthermore, RSV and S. pneumoniae were the most prevalent pathogens in children younger than 12 months (infants), while MP and Haemophilus influenzae were more commonly identified in children between 12 and 144 months. Increased richness and diversity of the microbiota were observed in the TA of the older children. Linear discriminant analysis (LDA) effect size (LEfSe) analysis identified that RSV and Streptococcus mitis were the specific species associated with infants. In contrast, Human bocaparvovirus 1 and Prevotella histicola were significantly enriched in the older children. In addition, the top 20 most abundant species exhibited correlations with neutrophil count and C-reactive protein. This study emphasizes the significance of employing mNGS to understand better the clinical characteristics and microbial diversity in pediatric patients with severe pneumonia.},
}

@article {pmid40544517,
year = {2025},
author = {Cen, L and Qin, L and Chen, W and Wei, L and Tang, C and Teng, X and Tian, Z},
title = {Causal Relationship between Gut Microbiota and Pulmonary Embolism: An Analysis Using Mendelian Randomization.},
journal = {Polish journal of microbiology},
volume = {74},
number = {2},
pages = {153-164},
doi = {10.33073/pjm-2025-013},
pmid = {40544517},
issn = {2544-4646},
abstract = {Previous research has demonstrated a connection between an unbalanced gut microbiome (GM) and lung diseases, suggesting that gut bacteria may affect lung health through the "gut-lung" axis. However, the direct connection between GM and pulmonary embolism (PE) is unclear. Mendelian randomization studies were used to investigate GM's genetic relationship with PE. A total of 18,340 independent genewide association studies (GWAS) yielded single nucleotide polymorphisms (SNPs) linked to the GM, which were then used as instrumental variables in a multiple regression analysis (MR) to examine the effect of GM on the risk of PE within the IEU Open GWAS project, which included 2,118 PE cases and 359,076 controls. The principal analytical methodology utilized in this research was inverse variance weighting (IVW), complemented by assessments for pleiotropy and heterogeneity to confirm the results' resilience. The findings of this study are predominantly derived from the IVW method, providing evidence for causal associations between four distinct genera of GM and the risk of PE. Specifically, our analysis suggests that Slackia (p = 0.031), Oscillospira (p = 0.038), Bacteroides (p = 0.032), and Clostridium sensu stricto 1 (p = 0.049) may be linked to a decreased likelihood of developing PE. Importantly, our analysis yielded no evidence of heterogeneity or pleiotropy. In this MR study, we have established through genetic analysis that specific GM are significantly involved in the development of PE, underscoring the connection between the gut-lung axis and suggesting avenues for future research into the impact of GM on PE.},
}

@article {pmid40544514,
year = {2025},
author = {Gao, Y and Ma, J and Wang, K and Ma, K and Zhao, W and Su, J and Ma, L},
title = {Roles of Gut Microbiota and Associated Metabolites in Clostridioides difficile Infection.},
journal = {Polish journal of microbiology},
volume = {74},
number = {2},
pages = {206-217},
doi = {10.33073/pjm-2025-017},
pmid = {40544514},
issn = {2544-4646},
abstract = {Clostridioides difficile infection (CDI), is the most common healthcare problem primarily involving the colon of individuals who's gut microbiota has been disrupted. Proteobacteria (officially updated and recognized as Pseudomonadota), a minor gut-associated microbial community within a healthy host, could serve as a metric for CDI. However, the alterations of specific members of Proteobacteria in the context of CDI are not thoroughly understood. Based on the summary data of microbiome from 7,738 participants in the Dutch cohort, linkage disequilibrium score regression (LDSC) was used to explore the causal effect of 207 gut microbiome on CDI. Secondly, we performed a Mendelian randomization analysis to investigate the causal relationship between 31 microbiota taxa affiliated with Proteobacteria and CDI. Finally, three significant taxa (p < 0.05, OR > 1) were utilized to conduct the mediation analysis of 1,400 metabolites based on a two-step Mendelian randomization study (two-step MR). The inverse-variance weighted method was conducted as a primary analysis to estimate the causal effect, and the robustness of the results was tested via sensitivity analysis using multiple methods. Bivariate LDSC analysis identified a strong correlation between four populations affiliated with Proteobacteria (Pasteurellaceae, Haemophilus, Pasteurellales and Haemophilus parainfluenzae) and CDI. In two-step MR, Burkholderiales order exerted detrimental effects on CDI by decreasing the levels of 3-hydroxylaurate (OR 0.896; 95%CI, 0.803-0.998; p = 0.047), indicating that metabolite did act as mediator between gut microbiota and CDI. We conducted a study to assess the relations between genetically predicted gut microbiota and metabolite levels with CDI. These results highlight the potential of targeting Burkholderiales and 3-hydroxylaurate as a new antimicrobial strategy against CDI.},
}

@article {pmid40544396,
year = {2025},
author = {Li, P and Sun, Z and Chen, X and Shao, Q and Wu, H},
title = {Mapping current research status and emerging frontiers of lipidomics: a comprehensive data-mining-based study.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {21},
number = {4},
pages = {85},
pmid = {40544396},
issn = {1573-3890},
support = {LHGJ20240576, LHGJ20190948)//Union Project of Medical and Technology Research Program of Henan Province/ ; },
abstract = {BACKGROUND: Lipids are crucial biomolecules involved in various biological processes, with changes in lipid profiles closely linked to the development of multiple disorders. Recent advances in lipidomics have transformed our understanding of lipid metabolism, yet challenges remain, highlighting the need for a comprehensive bibliometric study to identify current research status and emerging frontiers in this rapidly evolving field.

METHODS: This study collected publications related to lipidomics from the Web of Science Core Collection database. Bibliometric visualization was conducted using VOSviewer, CiteSpace, and an online analytical platform. A variety of bibliometric methods were employed, including co-authorship analysis, co-occurrence analysis, co-citation analysis, cluster analysis, and burst detection.

RESULTS: A total of 7989 papers including 6961 research articles and 1028 review papers were identified. Over the past two decades, the annual number of publications on lipidomics has shown an overall increasing trend (R[2] = 0.933). In terms of contributors, the United States and China have maintained their prominence, with the highest output and the most financial support. At the institutional and individual levels, the University of California System and professor Han Xianlin produced the largest number of papers related to lipidomics. By analyzing the trends in disciplinary flow, this study reveals the increasingly close relationship between fields such as molecular biology, genetics, and clinical medicine, as well as materials science. Obesity was the most studied disease in this domain, followed by Alzheimer's disease, non-alcoholic fatty liver disease, type 2 diabetes, as well as metabolic syndrome. Keywords analysis reveals that the current research focus in the field centered around omics approaches in lipidomics, inflammation and oxidative stress, biomarkers and diagnostic applications, analytical techniques of lipidomics, and lipid metabolism and disease mechanisms. And in the future, the following topics including lipid metabolism and disease pathology, microbiome and lipid interactions, ferroptosis and lipid peroxidation, emerging therapeutic approaches and technologies, as well as technological advancements in lipidomics, are continuing to receive sustained attention.

CONCLUSIONS: This bibliometric analysis, for the first time, provides a detailed overview of the knowledge structure and highlights the evolving research trends in lipidomics over the past two decades. The systematic summary offers a clear and comprehensive understanding of lipidomics, and also deliver valuable perspectives for future research in this field.},
}

@article {pmid40544319,
year = {2025},
author = {Cao, X and Yuan, Q and Hu, C and Zhang, H and Sun, X and Yan, B and Ma, X and Zhang, L and Huang, L and Li, S and Zhang, Z},
title = {Wild wisdom meets cultivation: comparative rhizomicrobiome analysis unveils the key role of Paraburkholderia in growth promotion and disease suppression in Coptis chinensis.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {150},
pmid = {40544319},
issn = {2049-2618},
support = {2060302-2301-09//Key project at central government level/ ; 2060302-2101-13//Key project at central government level/ ; },
abstract = {BACKGROUND: The sustained monoculture and irregular planting practices rendered the cultivated Coptis chinensis more prone to various diseases compared to its wild counterparts. Rewilding the rhizomicrobiome of cultivated plants has emerged as a promising strategy to promote plant growth, but ancestral microbiota suitable for C. chinensis remain largely uncharted.

RESULTS: The amplicon data analyses revealed that habitat transition strongly influenced the rhizosphere microbial communities. The rhizomicrobiomes of wild C. chinensis encompassed a more diverse array of ecological groups and exhibited a greater functional diversity compared to their cultivated counterparts. A higher proportion of beneficial fungi was observed in the rhizosphere of wild C. chinensis, while the cultivated plants had a higher population of pathogenic fungi. Furthermore, a well-documented plant-growth-promoting rhizobacterium genus, Paraburkholderia, was found to play an essential role in the resistance of the wild C. chinensis to potential disease caused by Ilyonectria. Two strains of Paraburkholderia (Paraburkholderia nemoris and Paraburkholderia phytofirmans) were isolated, and in vitro experiments confirmed that these isolates possess various growth-promoting properties and antagonistic activities against known pathogens for C. chinensis root rot. Both of the Paraburkholderia isolates could markedly promote the plant immune response and enhance the overall health of the cultivated C. chinensis.

CONCLUSIONS: By a comprehensive comparison of the rhizosphere microbiome between wild and cultivated C. chinensis, the promising bacterial genus Paraburkholderia was identified as a beneficial microbe significantly promoting the growth of C. chinensis, providing pivotal insights for future endeavors aimed at engineering the rhizosphere microbiome of C. chinensis, as well as other medicinal herbs. Video Abstract.},
}

@article {pmid40544290,
year = {2025},
author = {Chege, MN and Ferretti, P and Webb, S and Macharia, RW and Obiero, G and Kamau, J and Alberts, SC and Tung, J and Akinyi, MY and Archie, EA},
title = {Eukaryotic composition across seasons and social groups in the gut microbiota of wild baboons.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {70},
pmid = {40544290},
issn = {2524-4671},
support = {R01 AG071684//National Institutes of Health/ ; R01 AG071684//National Institutes of Health/ ; DEB 1840223//National Science Foundation/ ; },
abstract = {BACKGROUND: Animals coexist with complex microbiota, including bacteria, viruses, and eukaryotes (e.g., fungi, protists, and helminths). While high-throughput sequencing is commonly used to characterize bacterial communities in animal microbiota, these methods are less often applied to gut eukaryotic composition. Here we used shotgun metagenomic sequencing to characterize eukaryotic diversity in the microbiomes of wild baboons and tested the degree to which eukaryotic community composition was predicted by host social group membership, sex, age, sequencing depth, and season of sample collection.

RESULTS: We analyzed a total of 75 fecal samples collected in 2012 and 2014 from 73 wild baboons in the Amboseli ecosystem in Kenya. DNA from these samples was subjected to shotgun metagenomic sequencing, revealing members of the kingdoms Protista, Chromista, and Fungi in 90.7%, 46.7%, and 20.3% of all samples, respectively (percentages indicate the percent of samples in which each kingdom was observed). Social group membership explained 11.2% of the global diversity in gut eukaryotic species composition, but we did not detect statistically significant effects of season, host age, or host sex. Across samples, the most prevalent protists were Entamoeba coli (74.66% of samples), Enteromonas hominis (53.33% of samples), and Blastocystis subtype 3 (38.66% of samples), while the most prevalent fungi included Pichia manshurica (14.66% of samples), and Ogataea naganishii (6.66% of samples).

CONCLUSIONS: Protista, Chromista, and Fungi are common members of the gut microbiome of wild baboons. More work on eukaryotic members of primate gut microbiota is important for primate health monitoring and management strategies.},
}

@article {pmid40544285,
year = {2025},
author = {Kilama, J and Islam, S and Amat, S},
title = {Correction: Bovine ocular microbiome: the next frontier in managing pinkeye in cattle.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {69},
pmid = {40544285},
issn = {2524-4671},
}

@article {pmid40544178,
year = {2025},
author = {Qiu, YS and Ye, C and Li, Q and Jiang, LC and Zhou, CC and Fu, H and Li, DJ and Chen, D and Shen, FM},
title = {Improved gut microbiota by selenium-enriched Bifidobacterium longum DD98 alleviates chemotherapy-induced intestinal mucositis via inhibiting the STING pathway.},
journal = {NPJ science of food},
volume = {9},
number = {1},
pages = {107},
pmid = {40544178},
issn = {2396-8370},
support = {82003638//National Natural Science Foundation of China/ ; 82204537//National Natural Science Foundation of China/ ; 24SF1900902//Shanghai Science and Technology Innovation Action Plan/ ; },
abstract = {Intestinal mucositis, a common chemotherapy side effect, lacks effective treatments. This study evaluated the protective effect of selenium-enriched Bifidobacterium longum DD98 (SeDD98) on irinotecan-induced intestinal mucositis. Irinotecan caused intestinal mucositis, characterized by weight loss, severe diarrhea, damaged intestinal structure, reduced tight junction proteins, and gut dysbiosis. These effects could be inhibited by SeDD98. Additionally, fecal microbiota from SeDD98-treated mice protected against intestinal mucositis. Mechanistically, irinotecan activated the stimulator of interferon genes (STING) / nuclear factor kappa-B (NF-κB) pathway, whereas SeDD98 and fecal microbiota from SeDD98-treated mice suppressed this activation. Furthermore, depletion of gut microbiota by a broad-spectrum antibiotic cocktail (ABX) blunted the protective effect of SeDD98 and its inhibition of the STING/NF-κB pathway. These findings suggest that SeDD98 could protect against intestinal mucositis via inhibiting the STING/NF-κB pathway, likely through improving gut microbiota. Overall, SeDD98 may be a potential therapeutic agent for preventing chemotherapy-induced intestinal mucositis via gut microbiome improvement.},
}

@article {pmid40543864,
year = {2025},
author = {Peng, P and Yan, X and Chen, L and Li, X and Yang, H and Miao, Y and Zhao, F},
title = {Electroactive biofilm enhances synergistic degradation of sulfamethoxazole and roxarsone in actual livestock wastewater: extracellular electron transfer drives metabolic network remodeling.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122173},
doi = {10.1016/j.envres.2025.122173},
pmid = {40543864},
issn = {1096-0953},
abstract = {Livestock wastewater is characterized by high concentrations of organic matter and diverse antibiotics. A major challenge in its anaerobic treatment is the effective degradation and thorough removal of coexisting antibiotic contaminants. In this study, an external voltage was applied to establish an electroactive biofilm, thereby enhancing the co-metabolic degradation of sulfamethoxazole and roxarsone. Application of +0.6 V (Ag/AgCl) increased the 72 h TOC removal efficiency to 52.1%. At the same time, sulfamethoxazole and roxarsone removal efficiencies reached 90.8% and 100%, respectively. The results from liquid chromatography-mass spectrometry (HPLC-MS/MS) and density functional theory (DFT) calculations revealed sulfamethoxazole degradation pathways: N-O bond cleavage and hydroxylation. Roxarsone degradation primarily involved nitro group reduction and C-As bond cleavage. The pharmacophore of sulfamethoxazole was effectively removed, and inorganic arsenic from roxarsone degradation was efficiently immobilized. Toxicity analysis confirmed that the electroactive biofilm notably reduced toxic intermediate accumulation. Elevated concentrations of NADH and ATP in the electroactive biofilm indicated enhanced microbial substrate metabolism and generation of more electron donors. The higher absolute abundance of the sulfamethoxazole degradation gene (SadABC) in the electroactive biofilm indicated that sulfamethoxazole degrading enzyme (sadABC) gained more electrons. Microbiome analysis revealed the upregulation of genes linked to extracellular electron transfer (EET), the tricarboxylic acid (TCA) cycle, nitro-reduction, and sulfate reduction pathway, confirming the electroactive biofilm enhances substrate metabolism and co-metabolic antibiotic degradation. Electroactive biofilm offers a viable strategy for antibiotic removal in livestock wastewater.},
}

@article {pmid40543709,
year = {2025},
author = {Brehm, V and Wang, Z and Rocha, L and Jones, B and Jenq, RR and Chang, CC and Cheng, GS and Hsu, J and Sharifi, H and Yanik, G and Luna, L and Waqar, A and Zaveri, J and Dickey, BF and Bashoura, L and Shpall, EJ and Zinter, M and O'Dwyer, D and Champlin, RE and Chen, G and Alousi, A and Paczesny, S and Peterson, CB and Sheshadri, A},
title = {Inflammatory markers and microbiome dysbiosis in hematopoietic cell transplant recipients with lung graft-versus-host disease.},
journal = {Transplantation and cellular therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtct.2025.06.020},
pmid = {40543709},
issn = {2666-6367},
abstract = {Bronchiolitis obliterans (BOS) is a manifestation of pulmonary chronic graft versus host disease (cGVHD) and is a devastating complication of allogenic hematopoietic stem cell transplantation (HCT). Early detection and treatment of BOS may improve outcomes, but biomarkers which accurately identify BOS early are lacking. We aimed to determine whether certain validated cGVHD markers could also accurately diagnose BOS as compared to patients without BOS and with or without extrapulmonary cGVHD. In addition, we sought to determine whether dysbiosis of gut or oral microbiomes was associated with BOS or with inflammatory biomarkers. We enrolled 43 allogenic HCT recipients, of whom 16 had BOS. For each patient, we obtained pulmonary function tests, measured the levels of nine serum biomarkers utilizing enzyme linked immunosorbent assays, and analyzed both the oral and gut microbiome using microbial DNA amplification and sequencing. We compared biomarker levels to lung function, both at baseline and over time, as well as to microbiome diversity. Higher IL1RL1 (p = 0.002) and IL-17 (p = 0.041) at enrollment were negatively correlated with FEV1% lung function over time. Increases in IL1RL1 (p = 0.035), IL-17 (p = 0.009), and WFDC2 (p = 0.045) levels over time were associated with worsened lung function/FEV1% over time. There were minimal correlations between gut microbiome diversity and lung function or serum biomarkers. Oral microbiome alpha diversity was lower in subjects with BOS than without (p = 0.00057), and oral beta diversity was associated with FEV1% and with levels of several biomarkers. Our pilot study suggests that certain serum cGVHD markers may identify allogeneic HCT recipients at higher risk for pulmonary impairment over time, and should be followed with robust, controlled studies.},
}

@article {pmid40543454,
year = {2025},
author = {Kang, M and Jo, J and Shin, H and Kang, HW},
title = {Therapeutic potential of wavelength-dependent photobiomodulation on gut inflammation in an in vitro intestinal model.},
journal = {Journal of photochemistry and photobiology. B, Biology},
volume = {269},
number = {},
pages = {113201},
doi = {10.1016/j.jphotobiol.2025.113201},
pmid = {40543454},
issn = {1873-2682},
abstract = {Recently, photobiomodulation (PBM) has emerged as a novel therapeutic approach for modulating the gut microbiome, offering potential for the regulation of intestinal inflammation. Although PBM has been primarily used for various clinical applications, recent studies suggest that its effects may extend to the regulation of microbial imbalances and chronic inflammation. The biological effects of PBM are wavelength-dependent, as the wavelength of light determines tissue penetration depth and cellular response. The current study aimed to compare the inflammation-modulatory effects of PBM at four different wavelengths (405, 532, 635, and 808 nm) and to elucidate the underlying molecular mechanisms of PBM in intestinal inflammation. An in vitro co-culture model consisting of Caco-2 cells and Lactobacillus was established to simulate the intestinal environment. Cellular inflammation was induced by lipopolysaccharide (LPS) stimulation, followed by wavelength-dependent PBM treatment at a dosage of 10 J/cm[2] (100 mW/cm[2] for 100 s, applied as a single irradiation). Among the wavelengths, 635 nm significantly reduced nitric oxide production and suppressed the expression of pro-inflammatory cytokines (TNF-α, IL-6, IL-1β, and iNOS). Furthermore, western blot and qPCR analyses revealed that 635 nm PBM downregulated key signaling factors in the MAPK/NF-kB pathway, indicating a potential molecular mechanism for its anti-inflammatory effect. These findings suggest that PBM, particularly at 635 nm, may serve as an effective strategy for modulating intestinal inflammation. Further studies will investigate the anti-inflammation and microbiome modulation effects of PBM in an in vivo model of inflammatory bowel disease.},
}

@article {pmid40543238,
year = {2025},
author = {Liu, L and Liu, L and Zhuang, H and Li, A and Liu, Z and Jiao, M and Li, J and Xue, S and Li, J and Ren, Y and Mao, Y},
title = {Intestinal microbiota responses to environmental microbiomes and factors across populations of the Manila clam Ruditapes philippinarum.},
journal = {Marine environmental research},
volume = {210},
number = {},
pages = {107296},
doi = {10.1016/j.marenvres.2025.107296},
pmid = {40543238},
issn = {1879-0291},
abstract = {Intestinal microbiota is essential for the health, immune defense, and environmental adaptability of aquatic animals. Still, the interactions involving the intestinal microbiota of the Manila clam Ruditapes philippinarum, the microbiomes of their habitat, and environmental factors remain unclear. This study analyzed the microbial community structure and functional characteristics in clam intestine, water, and sediment across three distribution areas in Laizhou Bay (LZ), Jiaozhou Bay (JZ), and Sanggou Bay (SG) on the Shandong Peninsula, China. Correlations between microbial communities and water parameters were also examined. The results revealed distinct microbial communities in the intestine and habitats across the three areas, with water parameters serving as key drivers of geographic microbial variation. Intestinal selective pressures overwhelmed environmental factors in shaping intestinal microbiota. Intestinal microbiota closely resembled water microbiomes in richness, diversity, and dominant species abundance, indicating that water microbiomes likely served as the primary source of the clam intestinal microbiota. Microbial networks facilitated environmental adaptation by constructing large networks or boosting network density and modularity. Functional differentiation in the intestinal microbiota, driven by environmental influences, facilitated diverse ecological adaptation strategies. Moreover, low salinity, high dissolved oxygen, and high nutrient contents in the water favored specialized intestinal microbiota with narrower niche breadth, while high salinity, low chlorophyll a, and broader nutrient contents promoted stochastic microbiota with broader niche breadth. These findings provide valuable knowledge on the interactions between clam intestinal microbiota and environmental factors, providing a scientific basis for microbiome management strategies in clam seedling production and aquaculture practices.},
}

@article {pmid40542443,
year = {2025},
author = {Kadharusman, MM and Syahputra, RA and Kurniawan, R and Hadinata, E and Tjandrawinata, RR and Taslim, NA and Romano, R and Santini, A and Nurkolis, F},
title = {Seagrass Enhalus acoroides extract mitigates obesity and diabetes via GLP-1, PPARγ, SREBP-1c modulation and gut microbiome restoration in diabetic zebrafish.},
journal = {Diabetology & metabolic syndrome},
volume = {17},
number = {1},
pages = {235},
pmid = {40542443},
issn = {1758-5996},
abstract = {BACKGROUND: The global rise in obesity and type 2 diabetes highlights the need for safe and effective therapeutic interventions. Enhalus acoroides is a tropical seagrass rich in carotenoids and other bioactives. Its potential for metabolic regulation has been suggested in vitro, but in vivo efficacy and molecular mechanisms remain unexplored. This study aimed to evaluate the anti-obesity and anti-diabetic effects of Enhalus acoroides extract (SEAE) in a zebrafish model of diet- and glucose-induced metabolic dysfunction.

METHODS: Adult zebrafish were subjected to overfeeding and glucose immersion, after overfeeding and 14 days of glucose immersion to induce diabetes, adult zebrafish were randomized into three groups: untreated diabetic, SEAE-treated (5 mg/L), and metformin-treated (3.3 mg/L) for 20 days. Body weight, fasting blood glucose, lipid profile, gene expression (GLP-1, PPARγ, SREBP-1c), and gut microbiota profiles via 16 S rRNA sequencing were assessed.

RESULTS: SEAE significantly reduced body weight and blood glucose in diabetic zebrafish (p < 0.05), with efficacy comparable to or exceeding Metformin. It upregulated GLP-1 and downregulated PPARγ and SREBP-1c. SEAE also reduced total cholesterol, triglycerides, and LDL levels, while increasing HDL levels. Moreover, SEAE restored the Firmicutes/Bacteroidetes ratio, increased alpha diversity, and shifted beta diversity toward healthy controls. SEAE-treated fish showed microbial profiles closer to normal than those treated with Metformin.

CONCLUSIONS: SEAE exhibits strong anti-obesity and anti-hyperglycemic effects by modulating key metabolic pathways and restoring gut microbial homeostasis. These findings highlight SEAE as a promising marine-derived therapeutic candidate for metabolic syndrome and warrant further investigation as a functional food or nutraceutical.

CLINICAL TRIAL: Not applicable.},
}

@article {pmid40542437,
year = {2025},
author = {Duran-Pinedo, A and Solbiati, JO and Teles, F and Yanping, Z and Frias-Lopez, J},
title = {Correction: Longitudinal host-microbiome dynamics of metatranscription identify hallmarks of progression in periodontitis.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {147},
pmid = {40542437},
issn = {2049-2618},
}

@article {pmid40542387,
year = {2025},
author = {Wang, H and Sheng, L and Yazdi, Z and Li, X and Liu, Z and Canakapalli, S and Zhou, Y and Liao, C and Emami, S and Kelly, AM and Roy, LA and Soto, E and Wang, L},
title = {The impact of florfenicol treatment on the microbial populations present in the gill, intestine, and skin of channel catfish (Ictalurus punctatus).},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {68},
pmid = {40542387},
issn = {2524-4671},
support = {National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; },
abstract = {BACKGROUND: Florfenicol is a broad-spectrum antimicrobial approved in many countries for treating bacterial infections in production animals. Although florfenicol has been widely used in the US catfish industry, its impact on the native microbiota within catfish tissues remains largely unknown. Florfenicol treatment is followed by a mandatory withdrawal period to ensure drug residues fall below regulatory limits before harvest. This interval also allows for the potential recovery of the native microbiota. In particular, the skin and gill microbiota have often been overlooked in aquaculture microbiome research. Moreover, the dynamics of microbial communities and resistome profiles following drug withdrawal are still poorly understood, despite their ecological significance.

RESULTS: A significant increase in intestinal microbial diversity was observed at the end of the withdrawal period. The highest alpha diversity (Shannon index) was observed in catfish intestines. This increase indicated the restoration of the normal microbiota in catfish intestine. The predominant bacterial phyla shared among catfish gill, intestine, and skin are Proteobacteria (62%), Bacteroidetes (18%), Actinobacteriota (12%), Firmicutes (3%), Patescibacteria (2%), and Verrucomicrobiota (1%). Florfenicol application can have lasting effects through the withdrawal period, particularly altering the intestinal microbial community.

CONCLUSION: The result of this study underscores the impact of florfenicol treatment on the bacterial landscape and antibiotic resistance in catfish, highlighting significant changes in microbial composition in the catfish intestine and at the end of the withdrawal period. These findings address the need for monitoring and managing antibiotic resistance in fish farming environments.},
}

@article {pmid40542287,
year = {2025},
author = {Fierer, N and Leung, PM and Lappan, R and Eisenhofer, R and Ricci, F and Holland, SI and Dragone, N and Blackall, LL and Dong, X and Dorador, C and Ferrari, BC and Goordial, J and Holmes, SP and Inagaki, F and Korem, T and Li, SS and Makhalanyane, TP and Metcalf, JL and Nagarajan, N and Orsi, WD and Shanahan, ER and Walker, AW and Weyrich, LS and Gilbert, JA and Willis, AD and Callahan, BJ and Shade, A and Parkhill, J and Banfield, JF and Greening, C},
title = {Guidelines for preventing and reporting contamination in low-biomass microbiome studies.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40542287},
issn = {2058-5276},
support = {SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; DE250101210//Department of Education and Training | Australian Research Council (ARC)/ ; DE230100542//Department of Education and Training | Australian Research Council (ARC)/ ; APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; RGY0058/2022//Human Frontier Science Program (HFSP)/ ; RGY0058/2022//Human Frontier Science Program (HFSP)/ ; },
abstract = {Numerous important environments harbour low levels of microbial biomass, including certain human tissues, the atmosphere, plant seeds, treated drinking water, hyper-arid soils and the deep subsurface, with some environments lacking resident microbes altogether. These low microbial biomass environments pose unique challenges for standard DNA-based sequencing approaches, as the inevitability of contamination from external sources becomes a critical concern when working near the limits of detection. Likewise, lower-biomass samples can be disproportionately impacted by cross-contamination and practices suitable for handling higher-biomass samples may produce misleading results when applied to lower microbial biomass samples. This Consensus Statement outlines strategies to reduce contamination and cross-contamination, focusing on marker gene and metagenomic analyses. We also provide minimal standards for reporting contamination information and removal workflows. Considerations must be made at every study stage, from sample collection and handling through data analysis and reporting to reduce and identify contaminants. We urge researchers to adopt these recommendations when designing, implementing and reporting microbiome studies, especially those conducted in low-biomass systems.},
}

@article {pmid40541719,
year = {2025},
author = {Theise, ND and Kohnehshahri, MN and Chiriboga, LA and Fyfe, B and Cao, W and Zee, S and Imam, R and Pichler-Sekulic, S and Wells, RG},
title = {EVIDENCE OF INTERSTITIAL CONTINUITY WITHIN AND BEYOND THE HUMAN PANCREAS.},
journal = {Human pathology},
volume = {},
number = {},
pages = {105855},
doi = {10.1016/j.humpath.2025.105855},
pmid = {40541719},
issn = {1532-8392},
abstract = {Bodies have continuous reticular networks, comprising collagens and other extracellular matrix components, through all tissues and organs. We recently validated fluid flow through human interstitium and demonstrated that they are filled with hyaluronic acid by staining with biotinylated hyaluronic acid binding protein. Their continuity across tissue boundaries (skin and subcutis), and between organs (colon and mesentery) and along vessels (within adventitia) and nerves (within perineurium) has been demonstrated in this manner. We aim to evaluate the continuity of interstitium within human pancreas and beyond into adjoining tissues. Tissue blocks of histologically normal pancreas from nine pancreatectomy specimens were sectioned in parallel for staining with hematoxylin and eosin, Picrosirius red, and biotinylated hyaluronic acid binding protein. Also, specimens of invasive pancreatic cancer were assessed for interstitial tumor invasion. Picrosirius red ensheathes all microscopic units of the endocrine and exocrine pancreas, including acini, islets, and ducts, adventitia of blood vessels and perineurium, and into adjacent duodenum. Interstitial spaces within the fibrous tissue are filled with hyaluronic acid by staining and are also continuous through all microscopic structures of the pancreas, into adjoining duodenum and along vessels (within adventitia) and nerves (within perineurium). Invasive carcinoma is seen spreading through pre-existing interstitial spaces. Interstitium of the human pancreas is continuous within and beyond the pancreas. This continuity suggests the capacity to be a route of molecular, microbiome, and cellular trafficking and communication. In particular, it is a route of cancer spread.},
}

@article {pmid40541587,
year = {2025},
author = {Pletsch, EA and Smith, AD and Ragonese, JS and Narrowe, AB and Cheung, L and Chen, CT and Wang, TTY and Dawson, HD},
title = {Broccoli consumption alters microbial diversity, metatranscriptome and host transcriptome in mice fed a Total Western Diet.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.05.041},
pmid = {40541587},
issn = {1541-6100},
abstract = {BACKGROUND: Cruciferous vegetables (CV) are a source of dietary fiber and phytochemicals that alter the microbiome in animals and humans. Constituent CV compounds, such as glucosinolates, have demonstrated anti-inflammatory properties in animal models, though often using doses and basal diets that are not relevant to humans. The mechanism(s) are unclear, but the gut microbiota may metabolize these compounds into bioactive molecules that influence immune pathways.

OBJECTIVE: We investigated the effects of a broccoli powder-supplemented Total Western Diet (TWD) on changes in the gut microbiome, the host transcriptome and the metatranscriptome at levels relevant to the human diet to understand how these changes affect metabolic and immune functions.

METHODS: C57BL/6 male mice (n = 40) were fed a TWD control diet for six weeks followed by supplementation with 0, 0.5, 1 or 2.5% broccoli powder (BP) (reflecting a human intake from ¼ -1 cup per day) for three weeks. Microbial communities from cecal contents were taxonomically profiled using 16S rRNA amplicon and shotgun metagenomic sequencing, and metatranscriptomics was used to assess functionality of the microbial communities. The host cecal transcriptome was also assessed.

RESULTS: Beta diversity was significantly higher (p = 1.20E-03) for mice fed the 2.5% BP diet compared to the control group at the species level. Lachnospiraceae MD335 was significantly more abundant in mice fed higher levels of broccoli, and analysis of bacterial RNA transcripts indicated a dose-dependent increase in transcription of genes associated with butyrate and acetate production, plant cell wall degradation and carbohydrate utilization. Activation of the aryl hydrocarbon receptor pathway in the cecum was evident.

CONCLUSIONS: Consumption of a broccoli-supplemented TWD induces changes in the gut microbiome, host and microbial gene expression that affect immune health and inflammation in the gut at levels that are achievable in the human diet.},
}

@article {pmid40541131,
year = {2025},
author = {Delcourt, H and Verbrugghe, L and Vandenplas, Y and Huysentruyt, K},
title = {Systematic review and meta-analysis of randomized controlled trials on pre-, pro-, post- and synbiotic supplementation in follow-on formula.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {51},
number = {},
pages = {101-114},
doi = {10.1016/j.clnu.2025.05.022},
pmid = {40541131},
issn = {1532-1983},
abstract = {BACKGROUND & AIM: The remarkable plasticity of the gut microbiome during the first three years of life offers a critical window of opportunity to influence gut health. The aim of this study is to summarize high quality evidence from randomized controlled trials on the health benefits (respiratory tract infections, diarrheal episodes, febrile days, antibiotic use, microbiome modulation and secretory IgA) of prebiotics, probiotics, synbiotics and postbiotics added to follow-on formula.

METHODS: A comprehensive literature search for randomized controlled trials (RCTs) using Medline, Embase, Lilacs, and Cochrane was performed up to February 2025 (PROSPERO CRD42024500457). Only RCTs involving healthy children between six months and three years were considered. Quality assessment was done using the ROBINS II tool. Random effects models were used to obtain odd ratio (OR) and number needed to treat (NNT) via meta-analysis.

RESULTS: Out of 2755 search results, 23 studies were included (n = 6984 children) with an overall low risk of bias (14/23) as assessed by the Robins II tool. The OR for respiratory tract infections in pro-,pre- and synbiotics added to a follow-on formula was 0.22 (95 % CI: 0.05-1.09; NNT = 82; CI 95 %: 67-674), 0.84 (95 % CI: 0.66-1.07; NNT = 28; 95 % CI: 11-75) and 0.75 (95 % CI: 0.54-1.05; NNT = 18; 95 % CI: 9-102), respectively. The OR for diarrheal episodes in pre- and synbiotics added to a follow-on formula 1.40 (95 % CI: 0.71-2.79; NNT = 40, 95 % CI: 10-53) and 1.26 (95 % CI: 0.96-1.66; NNT = 17, 95%CI: 8-94), respectively. For the combination of other interventions with other outcomes insufficient studies were available to perform a meta-analysis.

CONCLUSION: Pre- and synbiotics may help protect against respiratory tract infection, though they do not appear to offer the same benefit for preventing diarrheal episodes. High quality evidence for the effect of biotics added to follow-on formula on health outcomes is sparse. More research is needed to confirm the observed health effects.},
}

@article {pmid40541100,
year = {2025},
author = {Tang, X and Mao, M and Zhang, X and Gao, H and Wang, Z and Fang, R and Cheng, HW and Jiang, S},
title = {Cecal microbiota transplantation enhances calcium retention through modulation of gut microbiota and intestinal calcium transporter gene expression in chicks.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105437},
doi = {10.1016/j.psj.2025.105437},
pmid = {40541100},
issn = {1525-3171},
abstract = {Bone development during early life is crucial for maintaining skeletal health and productivity in laying hens. The aim of this study was to investigate the effects of transferring cecal bacterial material of healthy adult hens on growth performance, gut integrity, microbial development, and bone metabolism of recipient chicks. Cecal contents were collected from 12 healthy Lohmann Pink-shell laying hens aged 47 weeks (donors). A total of 120 1-day-old Lohmann Pink chicks (recipients) were randomly assigned to 2 treatments for a 34-day trial: CONT (0.1 mL saline, Control) and CMT (0.1 mL cecal microbial solution). Each group had 10 replicates and 6 chicks per replicate. The pooled cecal sample as well as saline was administered via oral gavage once daily from day 1 to day 10, and then boosted on days 16, 23, and 30. One bird from each replicate was randomly taken for sample collection at day 34 (n=10). The results showed that CMT chicks had significantly higher Ca and P retention rates than CONT chicks. The mRNA expressions of intestinal Ca transporters, CaBP-D28K and VDR in the ileum and NCX1 in the jejunum, were also upregulated in CMT chicks. Additionally, the mRNA expression of a tight junction protein, ZO-1, was upregulated in the duodenum of CMT chicks. CMT chicks also had higher mRNA expressions of pro-inflammatory cytokines, IL-6, IL-1β, and TNF-α, in the intestinal tract. Furthermore, CMT chicks had a more diverse and mature gut microbial community compared to CONT chicks. The relative abundances of SCFA-produced bacteria (e.g., Bacteroides, Rikenellaceae_RC9_gut_group, and Prevotellaceae_UCG-001) were increased, while the relative abundances of Alistipes, Lactobacillus, and Barnesiella were reduced in CMT chicks. However, there were no CMT effects on body weight, organ indexes, bone morphology, and gene expression-associated with bone metabolism. This study demonstrates that transferring cecal bacteria from adult laying hens enhances calcium absorption and retention in newly hatched chicks by upregulating key calcium transporters and enhancing intestinal barrier integrity via modulating the gut microbiome.},
}

@article {pmid40541049,
year = {2025},
author = {Lazarus, BE and Mueller, RC and Germino, MJ},
title = {Soil-microbial communities respond less than plant communities to synthetic- or bio-herbicides applied to address the exotic grass-fire cycle in rangelands.},
journal = {The Science of the total environment},
volume = {991},
number = {},
pages = {179831},
doi = {10.1016/j.scitotenv.2025.179831},
pmid = {40541049},
issn = {1879-1026},
abstract = {The exotic grass-fire cycle is degrading semiarid rangelands, such as the vast areas of shrub-steppe in North America now invaded by fire-promoting cheatgrass. Chemical- or bio-herbicides are sprayed onto soils to inhibit the invaders, but information on chemical- or bio-herbicide impacts to soil microbial communities is limited. We asked how the soil-microbiome responded to the bioherbicide Pseudomonas fluorescens strain ACK55 in comparison to the separate and combined effects of a conventional pre-emergent chemical herbicide, imazapic, in two cheatgrass-invaded sagebrush-steppe sites. First-year microbial responses were evaluated using targeted sequencing of the 16S and LSU rRNA genes for bacteria+archaea and fungi, respectively, and were related to plant-community responses. A strong cheatgrass reduction with imazapic at one site was accompanied by a small shift in bacteria+archaea (16S) community composition with no effect on microbial alpha diversity, and this shift was small in comparison to natural microbiome variation between sites. ACK55 was not detected in soil a year after application, and it caused only transient and marginally significant reductions in annual grass cover accompanied by small reductions in soil fungi species richness. Full-length sequencing of the ACK55 16S rRNA gene and phylogenetic analyses revealed that ACK55 is more likely P. salmonii than P. fluorescens. Knowledge gaps remain on the duration and consequences of microbial-community shifts with imazapic and why molecular analyses showed ACK55 did not persist in soils. Confusion regarding microbial biopesticides can result where isolation, effectiveness testing, commercial release, and regulation are not guided by molecular taxonomic analyses.},
}

@article {pmid40540864,
year = {2025},
author = {Shi, B and Liu, C and Wang, J and Du, Z and Hou, K and Wang, J and Wang, J and Li, B and Zhu, L},
title = {3,6-dibromocarbazole have a significant effect on diversity, community and function of soil microorganisms.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138962},
doi = {10.1016/j.jhazmat.2025.138962},
pmid = {40540864},
issn = {1873-3336},
abstract = {In recent years, polyhalogenated carbazoles (PHCZs) have been increasingly detected in soil, potentially posing risks to soil health. 3,6-dibromocarbazole (3,6-BCZ), a representative PHCZ, is frequently found in the soil environment. However, the effects of 3,6-BCZ contamination on microbial communities remain largely unexplored. In this study, we investigated the impact of varying concentrations of 3,6-BCZ on the soil microbiome using 16S rDNA gene amplicon sequencing and quantitative PCR techniques at 3, 10, 80 days (pre-, mid-, final-). α-Diversity analysis revealed that bacterial Shannon indices increased with 3,6-BCZ exposure (0.1 mg kg[-1] 1.45 %, 1 mg kg[-1] 4.73 %, 10 mg kg[-1] 4.45 %, 100 mg kg[-1] 5.97 %) at 80 d, compared to solvent soil group (SC). The concentration of 1, 10 and 100 mg kg[-1] 3,6-BCZ significantly increased bacterial diversity and altered community structure, enriching genera such as Bacillus, Adhaeribacter, and Nitrospira genera. Network analysis further demonstrated that bacterial interactions within the soil microbiome became more complex and competitive under 3,6-BCZ exposure. Additionally, functional prediction via FAPROTAX indicated significant alterations in microbial community functional groups, particularly those related to carbon and nitrogen cycling. Specifically, 3,6-BCZ promoted bacterial metabolic functions such as aerobic nitrite oxidation, nitrification, nitrogen fixation, hydrocarbon degradation, and methylotrophy, while inhibiting ureolysis and chitinolysis after 80 days of exposure. Notable changes were also observed in genes associated with nitrogen fixation (nifH), nitrification (AOA-amoA and AOB-amoA), and carbon cycling (cbbLR and cbbLG). Overall, our findings suggest that PHCZs can impact soil health and microbial functionality, highlighting the need for further research to inform risk-based policy development.},
}

@article {pmid40540838,
year = {2025},
author = {Conti Taguali, S and Pöter, R and Aloi, F and Fernández-Trujillo, C and Acedo, A and La Spada, F and Li Destri Nicosia, MG and Pane, A and Schena, L and Cacciola, SO},
title = {Influence of environmental and agronomic variables on soil microbiome in citrus orchards: A comparative analysis of organic and conventional farming system.},
journal = {Microbiological research},
volume = {299},
number = {},
pages = {128260},
doi = {10.1016/j.micres.2025.128260},
pmid = {40540838},
issn = {1618-0623},
abstract = {Crop health and productivity depend on the structure and functionality of soil microbiota associated with the root system of plants. The agricultural policy of the European Union promotes organic farming systems to ensure environmental sustainability and food safety. The objective of this study was to investigate the impact of organic farming on soil microbiome in citrus orchards. The soil microbiota of eight conventionally and seven organically managed commercial citrus orchards across eastern Sicily was characterised using Illumina sequencing and BeCrop® primers for PCR amplification. The structure (diversity and relative abundance) and functionality of soil bacterial and fungal communities depended primarily on the sampling site. Other variables influencing the soil microbiome included soil total carbon content, seasonality, rootstock genotype, soil tillage and irrigation system. The latter three exerted differential effects on either bacterial or fungal communities. Conversely, age and visible health status of the tree had negligible influence on both communities. The differences between organically and conventionally managed citrus orchards accounted for a significant proportion of the variability, indicating a relevant effect of the farming system on soil microbiome. Organically managed orchards compared to those managed conventionally exhibited higher microbial diversity and a unique composition of nutrient-cycling microbes. In particular, organic farming promoted beneficial microbial functions, such as nitrogen fixation and phosphorus solubilization. Findings provide insights into the dynamic and complex interactions between environmental variables and soil microbial communities in citrus orchards, confirming the potential of microbial diversity as an indicator of sustainability in agricultural systems.},
}

@article {pmid40540603,
year = {2025},
author = {Chen, HY and Wu, PS and Li, ZY and Liu, YC and Yeh, SR and Duan, BC and Cheng, KW and Hsu, CC and Chiu, YL and Lee, WT and Fan, SZ and Wang, PY},
title = {Gut microbiome and host TOR pathway interact to regulate predator-induced aversive memory in Drosophila melanogaster.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {25},
pages = {e2422928122},
doi = {10.1073/pnas.2422928122},
pmid = {40540603},
issn = {1091-6490},
support = {111-2320-B-002-018 112-2320-B-002-026 113-2321-B-418-005 113-2320-B-002-021-MY3//National Science and Technology Council (NSTC)/ ; 113-2321-B-418-005//National Science and Technology Council (NSTC)/ ; NHRI-12A1-CG-CO-08-2325-2//National Health Research Institutes (NHRI)/ ; 112L895401//National Taiwan University ()/ ; 113-UN0065//National Taiwan University Hospital (NTUH)/ ; },
abstract = {The gut microbiome has emerged as a key factor influencing a wide range of host physiological processes and behaviors, though the mechanisms behind these effects remain only partially understood. In this study, we explored the role of the gut microbiome in memory regulation using a parasitoid wasp-induced oviposition depression paradigm in Drosophila melanogaster. Our findings show that flies with depleted gut microbiota, either through axenic culture or antibiotic treatment, exhibited significant memory impairments. However, reintroducing the commensal bacterium Lactobacillus plantarum alone was sufficient to restore memory, while coinoculation with Acetobacter pomorum further enhanced memory performance. Hemolymph metabolomic analyses revealed reduced amino acid levels in antibiotic-treated flies, which were linked to impaired Drosophila target of rapamycin (dTOR) signaling. Additionally, genetic manipulation of dTOR or dietary supplementation with branched-chain amino acids either mimicked or rescued the memory deficits caused by antibiotic treatments. These results suggest that the gut microbiome is essential for regulating memory function by maintaining amino acid homeostasis and proper dTOR signaling, with profound implications for advancing knowledge of cognitive regulation.},
}

@article {pmid40540565,
year = {2025},
author = {Chen, N and Cai, P and Lin, X and Song, ZM and He, J and Li, Z and Li, Z and Zhang, D and Song, Y and Li, YX},
title = {Autoinducing peptides regulate antibiotic production to potentially shape root microbiome.},
journal = {Science advances},
volume = {11},
number = {25},
pages = {eadw5076},
pmid = {40540565},
issn = {2375-2548},
abstract = {Microbes use signaling molecules to regulate multiple physiological processes and mediate chemical interactions. Decoding these chemical languages is instrumental in comprehending microbial regulatory mechanisms within complex microbiota. Here, we discover previously unidentified autoinducing peptides (AIPs) derived from the plant probiotic bacterium Paenibacillus polymyxa, identified as Pp-AIPs. Omics analyses coupled with genetic manipulations revealed that Pp-AIP1 could effectively modulate the production of multiple antimicrobial secondary metabolites at nanomolar concentration, expanding known AIP functions. Furthermore, through inoculating P. polymyxa in the natural rhizosphere microbiome and analyzing its antagonistic interactions against root microbes, we suggest that Pp-AIPs may influence the microbial community composition through modulating the antimicrobial spectrum. Global analysis of biosynthetic gene clusters (BGCs) reveal widespread co-occurrence of uncharacterized AIPs with secondary metabolite BGCs. This study underscores the unreported roles of AIPs in antibiotic regulation and the microbiome interactions, advancing knowledge of quorum-sensing mechanisms in microbial ecosystems.},
}

@article {pmid40540444,
year = {2025},
author = {Shi, Y and Yan, F and Wang, W and Li, X},
title = {Letter to the editor - intratumoral fusobacterium nucleatum associates with advanced-stage colorectal cancer and poor prognosis in a Chinese cohor.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000002655},
pmid = {40540444},
issn = {1743-9159},
}

@article {pmid40540409,
year = {2025},
author = {Wang, HB and Liu, XP and Shu, YC and Li, G and Sun, CL and Jones, DL and Zhu, YG and Lin, XY},
title = {Molecular Composition of Exogenous Dissolved Organic Matter Regulates Dissimilatory Iron Reduction and Carbon Emissions in Paddy Soil.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c03323},
pmid = {40540409},
issn = {1520-5851},
abstract = {Soil carbon (C) cycling under anoxic conditions is mechanistically linked to dissimilatory iron (Fe) reduction, potentially influenced by exogenous dissolved organic matter (DOM). However, the impact of complex exogenous DOM on soil microbial activity and C-Fe coupling in paddy soils remains underexplored. With a 100-day microcosm experiment, we found that biochar-DOM significantly promoted Fe reduction and accelerated CH4 and CO2 emissions, and manure-DOM increased soil CO2 emissions. These effects may be caused by the following mechanisms: DOM molecules with high aromaticity and high double bond equivalence (DBE), including lignins-polyphenols, lignins-polycyclic aromatics, and condensed aromatics-polycyclic aromatics, promoted soil Fe reduction and CH4 emissions with enrichment of soil Fe-reducing bacteria, r-strategists, and reduction of methanotrophs at the early stage of incubation. Conversely, DOM with low aromaticity, low DBE, and high H/C enhanced CO2 emissions with the enhancement of recalcitrant C degradation and CH4 oxidation at the late stage of incubation. In conclusion, our study highlights the importance of the molecular composition of organic amendment-derived DOM in regulating soil Fe reduction and greenhouse gas emissions. The findings offer novel insights into the effective utilization of agricultural resources and the potential mitigation of greenhouse gas production and emissions.},
}

@article {pmid40540354,
year = {2025},
author = {Roichman, A and Reyes-Castellanos, G and Chen, Z and Chen, Z and Mitchell, SJ and MacArthur, MR and Sawant, A and Levett, L and Powers, JR and Burgo, V and Gomez-Jenkins, M and Ibrahim, M and Xu, X and Tomlinson, B and Hang, X and Pamer, EG and Wei, Y and Kang, Y and White, EP and Rabinowitz, JD},
title = {Dietary Fiber Lacks a Consistent Effect on Immune Checkpoint Blockade Efficacy Across Diverse Murine Tumor Models.},
journal = {Cancer research},
volume = {},
number = {},
pages = {},
doi = {10.1158/0008-5472.CAN-24-4378},
pmid = {40540354},
issn = {1538-7445},
abstract = {Immune checkpoint blockade (ICB) has transformed cancer treatment, but success rates remain limited. Recent research suggests that dietary fiber enhances ICB efficacy through microbiome-dependent mechanisms. However, prior studies in mice compared grain-based chow (high-fiber) to low-fiber purified diet, but these diets also differed in other dimensions, including phytochemicals. Therefore, further work is needed to establish the robustness of the effect of fiber on ICB across cancer types and dietary contexts. Here, we investigated gut microbiome composition, metabolite levels, and ICB activity in mice fed grain-based chow or purified diets with differing quantities of isolated fibers (cellulose and inulin). Compared to dietary fiber content, consumption of chow versus purified diet had a greater effect on the gut microbiome and a much stronger impact on the metabolome. Studies in multiple tumor models revealed that fiber has a weaker impact on ICB (anti-PD-1) efficacy than previously reported. While diet impacted ICB in some models, the effect was not directionally consistent. None of the models tested displayed the pattern expected if fiber controlled ICB efficacy: strong efficacy in both chow and high-fiber purified diet but low efficacy in low-fiber purified diet. Thus, dietary fiber appears to have limited or inconsistent effects on ICB efficacy in mouse models, and other dietary factors that correlate with fiber intake may underlie clinical correlations between fiber consumption and immunotherapy efficacy.},
}

@article {pmid40540179,
year = {2025},
author = {Agrawal, A and Acharya, AB and Sahu, B and Barik, TK and Patel, AK},
title = {Bacterial community composition and diversity associated with developmental stages of Anopheles subpictus.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40540179},
issn = {1618-1905},
support = {DST/INSPIRE FELLOWSHIP/2020/IF200208//Department of Science and Technology, Ministry of Science and Technology, India/ ; },
abstract = {Malaria remains the deadliest vector-borne disease globally. Among different malaria vectors, Anopheles subpictus has been regarded as the potent vector across many Indian states. Microbiota in mosquitoes are critical determinants for their development, physiology, and vector competence, which differ significantly among mosquito species, life stages, and environmental parameters. Microbial profiles linked with various life stages of the emerging malaria vector, An. subpictus remain unexplored. In this study, 16S rRNA amplicon sequencing (V1-V9 regions) was used to explore and analyze the microbial community dynamics within and between life stages. A total of 287,077 bacterial reads were generated and distributed into 40 phyla, 75 classes, 160 orders, 334 families, 961 genera, and 2398 species. Diversity analyses revealed that bacterial community structure varied significantly across the three life phases (larvae, pupae, adult) of An. subpictus. The larval stage has higher species richness compared to subsequent developmental stages. The sequence-based taxonomic profiling revealed that Methylobacterium, Clostridium, Bradyrhizobium, Cytophaga, Roseateles, Mitsuaria, Sphingomonas and Wolbachia were the dominant bacterial genera across the different life stages. Moreover, Methylobacterium sp. (51.6%) was the most abundant taxa in the adult female stage, whereas the larval stage was mainly dominated by Cytophaga (15.2%). This research advances our understanding of bacterial community composition and dynamics across the developmental succession of An. subpictus. The finding pinpoints dominant bacterial candidates that could be harnessed to develop microbial-based control strategies aimed at limiting mosquito-borne diseases.},
}

@article {pmid40540085,
year = {2025},
author = {Aminurrasyid, AHB and Mohd Ikmal, A and Nadarajah, KK},
title = {The Rice-Microbe Nexus: Unlocking Productivity Through Soil Science.},
journal = {Rice (New York, N.Y.)},
volume = {18},
number = {1},
pages = {56},
pmid = {40540085},
issn = {1939-8425},
support = {Fundamental Research Grant FRGS/1/2023/STG01/UKM/01/1//Ministry of Higher Education, Malaysia/ ; Fundamental Research Grant FRGS/1/2023/STG01/UKM/01/1//Ministry of Higher Education, Malaysia/ ; Fundamental Research Grant FRGS/1/2023/STG01/UKM/01/1//Ministry of Higher Education, Malaysia/ ; },
abstract = {Rice is a staple crop and a primary food source for nearly half of the global population. Its cultivation is heavily dependent on irrigation systems, which is crucial in determining productivity. Beyond irrigation, the genetic characteristic of rice significantly influences its growth, resilience, and yield. These factors are closely connected to the soil microbiome within the rhizosphere, where interactions between plants, soil, and microbes occur, ultimately affecting agricultural outcomes. Different rice genotypes and agricultural practices shape soil microbiomes uniquely, impacting crop resilience and yield. Additionally, the growth stage of rice influences root exudation patterns, which in turn affects the composition and functionality of the rhizospheric microbiome. As the plant matures, the quantity and quality of root exudates evolve alongside its physiological changes, further modifying microbial communities in the surrounding soil. This review explores the complex interplay among irrigation strategies, rice genotypes, and growth phases, examining their collective impact on soil microbial diversity, offering insights into leveraging soil microbiomes for sustainable crop management and enhanced production. In addition it also highlights biotechnological tools and approaches that may be utilized in sustainable rice farming.},
}

@article {pmid40539946,
year = {2025},
author = {Theirlynck, T and Staat, L and Servania, D and Engelen, AH and van Tussenbroek, BI and Muyzer, G and Visser, PM and Amaral-Zettler, L},
title = {Nutrient-driven growth and microbiome shifts in the brown alga Sargassum fluitans III.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70045},
pmid = {40539946},
issn = {1529-8817},
support = {CEECINST/00114/2018//Portuguese national fund, Foundation for Science and Technology/ ; LA/P/0101/2020 (DOI:10.54499/LA/P/0101/2020)//Portuguese national fund, Foundation for Science and Technology/ ; UIDB/04326/2020 (DOI:10.54499/UIDB/04326/2020)//Portuguese national fund, Foundation for Science and Technology/ ; NWOCA.1 of the Sargassum Call2 research program//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
abstract = {Since 2011, holopelagic Sargassum has been accumulating in a region of the tropical Atlantic now referred to as the Great Atlantic Sargassum Belt (GASB). Among the hypothesized contributors to these accumulations are the increased inputs of nitrogen (N) and phosphorus (P) in the tropical Atlantic Ocean. Little is known about the effects of N and P additions on Sargassum physiology and its microbiome. We studied the effects of N, P, and NP additions on the growth, photosynthetic efficiency, and microbiome composition of Sargassum fluitans III in a six-day experiment on the Caribbean Island of Curaçao. Sargassum fluitans III took up most nitrate and phosphate within 3 days with respective uptake rates of 0.343 and 0.0399 μmol · g[-1] DW · h[-1]. Fv/Fm decreased in the control after 6 days but remained constant in nutrient treatments. Growth rates did not differ significantly among treatments, but a trend in higher growth rates in the NP treatment was discerned, suggesting a possible NP co-limitation. The relative abundance of epiphytic Cyanobacteria such as Schizothrix and bacteria such as Lentilitoribacter increased under N and P addition, while heterotrophic Rhodobacteraceae decreased in abundance. Microeukaryotic communities responded with varying changes in alpha diversity, possibly steered by increased photosynthesis and growth of S. fluitans III or bacterial interactions. The physiological response to N and P and rapid change of the microbiome demonstrates that the studied S. fluitans III can quickly benefit from increased nutrient concentrations, which might contribute to its growth success in the GASB.},
}

@article {pmid40539808,
year = {2025},
author = {Sun, H and Chen, Q and Zhang, D and Hu, L and Li, S and Lu, M and Wang, Y and Su, H and Gao, Y and Guo, J and Zhao, Y and Du, J and Liu, C and Xia, H and Xu, Y and Ge, X and Yang, Q},
title = {Integrative study of pulmonary microbiome and clinical diagnosis in pulmonary tuberculosis patients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0156324},
doi = {10.1128/spectrum.01563-24},
pmid = {40539808},
issn = {2165-0497},
abstract = {UNLABELLED: This study investigated the diagnostic potential of mNGS for detecting MTB in pulmonary tuberculosis patients. We analyzed pulmonary microbiome data to assess its impact on mNGS diagnostic accuracy and explored the association between microbiome profiles and clinical diagnosis. Bronchoalveolar lavage fluid samples were collected from 236 patients with pulmonary infections, and the diagnostic performance of mNGS was compared with traditional methods in detecting MTB. Furthermore, the incidence of false negatives and false positives, as well as the characteristics of the lung microbiota in TB patients, was analyzed to improve the diagnostic precision of mNGS. We observed that among all detection methods, mNGS showed the highest sensitivity (73.33%), followed by X-pert (60.00%), culture (53.33%), RT-PCR (53.33%), and sputum smear (23.33%). Notably, mNGS produced 3 false positive results in 236 samples, yielding a specificity of 98.54%. Analysis of the pulmonary microbiome revealed significant differences in both α-diversity and β-diversity between patients with TB and uninfected controls (P<0.05). Shannon index and Chao1 index were identified as significant predictors associated with MTB infection. ROC curve analysis demonstrated an AUC of 0.765, indicating good discriminatory performance. This study suggested that integrating wet-laboratory techniques with bioinformatics analysis can further enhance the diagnostic accuracy of mNGS for TB. Furthermore, microbiome analysis holds significant potential for the diagnosis of MTB infection.

IMPORTANCE: This study focuses on the application of next-generation sequencing (NGS) technology in detecting Mycobacterium tuberculosis in bronchoalveolar lavage fluid and explores the impact of M. tuberculosis infection on the pulmonary microbiome. By optimizing the methods and conducting microbial analyses, the accuracy of metagenomic NGS for detecting M. tuberculosis has been improved.},
}

@article {pmid40539779,
year = {2025},
author = {Monod, V and Hofstetter, V and Viret, O and Zufferey, V and Gindro, K and Croll, D},
title = {Landscape-scale endophytic community analyses in replicated grapevine stands reveal that dieback disease is unlikely to be caused by specific fungal communities.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0078225},
doi = {10.1128/aem.00782-25},
pmid = {40539779},
issn = {1098-5336},
abstract = {Tree diebacks are complex and multifactorial diseases with suspected biotic and abiotic components. Microbiome effects on plant health are challenging to assess due to the complexity of fungal and bacterial communities. Grapevine wood dieback is the main threat to sustainable production worldwide, and no causality with microbial species has been established despite long-standing claims of fungal drivers. Here, we aimed to test the hypothesis that grapevine esca disease progression has reproducible drivers in the fungal species community. For this, we analyzed a set of 21 vineyards planted simultaneously with a single susceptible cultivar to provide unprecedented replication at the landscape scale. We sampled a total of 496 plants at the graft union across vineyards in 2 different years to perform deep amplicon sequencing analyses of the fungal communities inhabiting grapevine trunks. The communities were highly diverse with a total of 4,129 amplified sequence variants assigned to 697 distinct species. We detected trunk fungal community shifts over years of sampling, vineyards and climatic conditions, as well as disease status. However, we detect no specific fungal species driving symptom development across vineyards, contrary to long-standing expectations. The high degree of environmental standardization in the decade-long experimental plots and the well-powered replication provide the clearest evidence yet that grapevine wood dieback is most likely caused by environmental factors rather than specific pathogens. Furthermore, our study shows how landscape-scale replicated field surveys allow for powerful hypothesis testing for complex dieback disease drivers and prioritize future research directions.IMPORTANCETree diebacks are complex diseases suspected to be caused by both biological and environmental drivers. Grapevine wood dieback is a major threat to vineyards worldwide, but no specific microbial species have been experimentally implicated, despite claims that fungi are causing the symptoms. Here, we tested whether the progression of grapevine esca disease is driven by specific fungal species. We analyzed 21 long-established vineyards planted at the same time with the same susceptible grape variety to ensure consistent conditions. Over the years, we observed changes in the fungal communities inhabiting the trunk depending on the vineyard, climate, and disease status. However, contrary to expectations, we did not detect any specific fungal species that consistently could cause symptoms across the vineyards. The high level of environmental control and replication in our study provides strong evidence that grapevine wood dieback is more likely caused by environmental factors rather than specific pathogens.},
}

@article {pmid40539731,
year = {2025},
author = {Lee, S and Kim, G and Seong, SM and Cho, CG and Park, SW and Shin, H and Kim, S and Kim, JY},
title = {Nasal Microbial Community Shifts Following Treatment in Chronic Rhinitis: An Observational Study.},
journal = {The Laryngoscope},
volume = {},
number = {},
pages = {},
doi = {10.1002/lary.32295},
pmid = {40539731},
issn = {1531-4995},
support = {NRF-2021R1I1A1A01056576//National Research Foundation of Korea/ ; RS-2024-00358007//Ministry of Science and ICT, South Korea/ ; //Dongguk University, College of Medicine Research Fund/ ; },
abstract = {OBJECTIVES: Nasal microbiome helps maintain mucosal homeostasis and immune function. Previous studies suggested the pathogenesis of chronic rhinitis and the nasal microbiome were related. This study aimed to evaluate the treatment effect on the nasal microbiome in chronic rhinitis through analyzing microbial diversity and composition in pre- and post-treatment status.

METHODS: In participants diagnosed with chronic rhinitis, nasal microbiome samples were collected before and after treatment. Treatment regimens included intranasal corticosteroid spray, oral antihistamines, and/or oral leukotriene receptor antagonists. The degree of symptom improvement was measured by rhinitis symptom questionnaires assessing four nasal symptoms, two ocular symptoms, and quality of life (QOL). Laboratory tests were performed at baseline, including serum total immunoglobulin E, blood eosinophil percentage, and skin prick test.

RESULTS: A total of 22 patients were enrolled. Total nasal symptom score (TNSS), TNSS eye (TNSS with two ocular symptoms), and QOL questionnaire scores all significantly decreased after treatment (p < 0.001). Alpha diversity showed no significant changes, while intra-group distances were significantly decreased for both unweighted and weighted distances after treatment (p < 0.05). The relative abundance of Staphylococcus increased, while that of Alloprevotella decreased after treatment (p < 0.05). Predominant genera in most subjects were Staphylococcus, Acinetobacter, and Burkholderiaceae, and all significantly correlated to QOL improvement after treatment (p < 0.05).

CONCLUSIONS: This study investigated the impact of chronic rhinitis treatment on the nasal microbiome and its association with symptom improvement. The changes in the nasal microbiome following treatment may enhance our understanding of its role in chronic rhinitis pathophysiology and therapeutic response.},
}

@article {pmid40539526,
year = {2025},
author = {Mu, M and Xu, Q and Hao, Q and Li, X and Wu, Z and Zhang, Q and Liu, S and Man, X and Xiao, L and Zou, Y and Li, S and He, N},
title = {Multiomics Analysis of Bacteroides cellulosilyticus Anticolitis via Gut Microbiota Metabolite-Mediated PI3K-Akt Signaling Pathway.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c00637},
pmid = {40539526},
issn = {1520-5118},
abstract = {Ulcerative colitis (UC) is a chronic inflammatory bowel disease characterized by mucosal inflammation and dysbiosis of the gut microbiota. Bacteroides cellulosilyticus (B. cellulosilyticus) is a multifunctional carbohydrate-degrading bacterium that may serve as a probiotic to enhance gut health by regulating gut microbiota. However, its specific role and mechanisms in UC remain unclear. This study utilized a population cohort and combined microbiome, metabolome, and transcriptome analyses to explore the therapeutic effects and potential mechanisms of B. cellulosilyticus on dextran sulfate sodium (DSS)-induced colitis in mice. After B. cellulosilyticus treatment, mice exhibited a 10.3% increase in body weight recovery (p < 0.01), a 12.9% reduction in disease activity index (DAI) scores (p < 0.05), and significant decreases in pro-inflammatory cytokine levels, including a 21.9% drop in IL-6 and a 24.6% reduction in TNF-α (p < 0.05; p < 0.0001). Notably, B. cellulosilyticus significantly inhibited the PI3K/Akt signaling pathway by effectively reducing the phosphorylation levels of both PI3K and Akt proteins. Additionally, metabolomic analysis revealed that B. cellulosilyticus significantly affected the gut metabolic profile. It led to increased levels of metabolites related to gut health, such as hypoxanthine. These metabolic changes were closely associated with the improvement of the microbial community composition. B. cellulosilyticus effectively restored microbial diversity and abundance in DSS-induced colitis. The integrated analysis of multiple omics approaches indicates that B. cellulosilyticus has the potential to serve as a probiotic therapeutic agent for UC. It offers new dietary and therapeutic strategies for managing UC by regulating the gut microbiota, altering metabolic profiles, and downregulating the PI3K-Akt signaling pathway.},
}

@article {pmid40539103,
year = {2025},
author = {Lin, ZY and He, SS and Mo, ZT and Liao, XT and Feng, ZS and Kong, J and Zhu, L and Li, Y and Tan, HY and Su, ZW and Jia, CH and Wu, F},
title = {Integrated analysis of serum metabolomics and fecal microbiome in infants with necrotizing enterocolitis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1584041},
pmid = {40539103},
issn = {1664-302X},
abstract = {BACKGROUND: Necrotizing enterocolitis (NEC), a lethal gastrointestinal disorder in preterm infants, remains poorly understood in its pathology, and early diagnosis are critically limited. Multi-omics approaches present unprecedented opportunities to elucidate NEC pathogenesis and identify clinically translatable biomarkers.

METHODS: Infants with Bell stage II-III NEC and gestational age-matched controls were enrolled. Serum/stool samples from NEC patients at acute (NEC-D) and recovery (NEC-R) phases, and controls (non-NEC) were collected. Fecal metagenomic sequencing and serum untargeted metabolomic profiling were performed. Clinical parameters were compared.

RESULTS: The study comprised seven NEC and seven non-NEC infants. Baseline neonatal characteristics and maternal perinatal parameters showed no significant differences between NEC-D and non-NEC except for markedly lower leukocyte counts in NEC infants. Fecal metagenomics revealed severely diminished alpha diversity in NEC-D versus both non-NEC controls and NEC-R, characterized with lower Chao1 index. NEC-D exhibited elevated Escherichia coli relative abundance alongside reduced Staphylococcus haemolyticus, Staphylococcus aureus, Staphylococcus epidermidis, and Lactobacillus paracasei. Correspondingly, KEGG functional gene analysis demonstrated impaired metabolism in NEC-D. Serum metabolomics identified significantly decreased ornithine, DL-arginine, L-threonine, leucine, and D-proline in NEC-D versus non-NEC. NEC-D also showed lower taurodeoxycholic acid, glycocholic acid, and chenodeoxycholic acid compared to NEC-R. Integrative analysis revealed a positive correlation between the metabolites D-proline and ornithine and the Lactobacillus paracasei, Staphylococcus epidermidis, and Staphylococcus aureus abundance.

CONCLUSION: NEC is characterized by gut microbiota dysbiosis with reduced diversity, altered functional gene expression, and disrupted host-microbiota metabolic crosstalk. The identified serum metabolite-microbiome correlations provide mechanistic insights into NEC pathogenesis and potential diagnostic biomarkers.},
}

@article {pmid40539101,
year = {2025},
author = {Cui, X and Ding, Z and Ji, Y and Liu, J and Chang, Z and Zhang, J and Wang, X and Liu, K and Liu, Y},
title = {Stir-baked Xanthii fructus ameliorates adjuvant arthritis by regulating gut microbiota, short-chain fatty acids and metabolites.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1599529},
pmid = {40539101},
issn = {1664-302X},
abstract = {INTRODUCTION: Rheumatoid arthritis (RA) is a common and widespread autoimmune disease whose incidence is increasing. Stir-baked Xanthii fructus (XF) is used to treat RA in clinic. However, it's in vivo efficacy and mechanistic pathways remain unclear. This study aimed to explored XF's therapeutic effects and its mechanisms by comprehensive serum metabolomics and gut microbiota analysis.

METHODS: The components in XF were identified using the UPLC-MS technique. A rat model of adjuvant arthritis was established using complete Freund's adjuvant to evaluate the efficacy of XF. The in vivo mechanisms were explored through microbiome, short-chain fatty acid (SCFAs), and metabolomics analysis.

RESULTS: In total, 27 components were identified in XF. The treatment effectively suppressed inflammatory factors and alleviated pannus and cartilage damage. In addition, this article revealed a substantial remodeling of the gut microbiota composition, characterized by a reduced abundance of pro-inflammatory bacteria, increased populations of immunomodulatory bacteria and restored levels of SCFAs. Serum metabolomic profiling identified 17 arthritis-associated metabolites, primarily involved in glycerophospholipid metabolism and bile acid biosynthesis. Then, a strong correlation was found between gut microbiota and serum metabolites, indicating that XF exerts its therapeutic effects through immunomodulation, energy homeostasis regulation, and redox balance maintenance via the gut-joint axis.

DISCUSSION: This study provides new insights for further research into the targeted therapy of XF to ameliorate adjuvant arthritis.},
}

@article {pmid40538825,
year = {2025},
author = {Hofman, J and Brenerova, P and Borilova Linhartova, P},
title = {State-of-the-art approaches in the investigation of human seminal bacteriome using metagenomic methods.},
journal = {Frontiers in reproductive health},
volume = {7},
number = {},
pages = {1557912},
pmid = {40538825},
issn = {2673-3153},
abstract = {Although the understanding of the causes of infertility is the key to its successful treatment, recent studies have shown that as many as 50% of male-caused infertility cases are considered idiopathic. The microbial colonization of the male reproductive system was shown to be associated with reduced male reproductive fitness. Investigation of the seminal microbiome, however, remains challenging. This article aimed to improve this situation by creating the first comprehensive review of literature on the metagenomic methods (including the pre-analytical and analytical approaches) used in the research on human seminal bacteriome (total bacterial DNA in the matrix), published in 2018-2024. A total of 29 studies addressing the analysis of the human seminal bacteriome were identified. The analysis typically involved DNA extraction from the supernatant using commercial kits, amplification of the gene for 16S rRNA, and sequencing of amplicons. Where the separation of seminal plasma was performed, centrifugation was the dominant method used for this purpose. The significant heterogeneity in individual steps of methodological approaches in the analysis of the human seminal bacteriome complicates the comparison of results among studies and the establishment of standard procedures, hindering clinical advancements. For this reason, a protocol for the analysis of the human seminal plasma bacteriome is proposed here, which could lead to improved comparability of results among studies and make future research more efficient. This protocol is founded on rigorous quality control measures, compliance with the WHO laboratory manual for sample collection, extensive pretreatment involving mechanical and enzymatic lysis, DNA extraction using the QIAamp DNA Mini Kit (Qiagen), and short-read sequencing conducted on the MiSeq platform (Illumina).},
}

@article {pmid40538755,
year = {2025},
author = {Krama, T and Krams, R and Popovs, S and Gudrā, D and Ustinova, M and Fridmanis, D and Trakimas, G and Contreras-Garduño, J and Cīrule, D and Rantala, MJ and Adams, CB and Jõers, P and Krams, IA},
title = {Effects of Trichomonas gallinae infection and diet on blood microbiome composition in european greenfinches (Chloris chloris).},
journal = {Frontiers in physiology},
volume = {16},
number = {},
pages = {1576833},
pmid = {40538755},
issn = {1664-042X},
abstract = {Recent research has reported microbial invasion of the bloodstream in various disease-associated conditions. In this study, we investigated the role of trichomonosis outbreak (caused by the Trichomonas gallinae parasite) and food availability in shaping the blood microbiome composition of wintering greenfinches (Chloris chloris). Data were collected during two periods: before the outbreak (December) and during the outbreak (February). No bacterial contamination was observed in pre-epidemic blood samples. All individuals were infected during the outbreak, but greenfinches with irregular food access exhibited lower bacterial contamination in their blood. Individuals with permanent food access had a greater proportional representation of specific microbial taxa and higher alpha diversity in their blood microbiomes. However, beta diversity did not differ between the two groups. We demonstrated that trichomonosis infection and feeding regime play critical roles in mediating septic conditions of peripheral circulation during an outbreak, with food accessibility influencing blood microbial contamination. These findings integrate the impacts of feeding regimes and hematological responses to improve our understanding of the complex interactions between diet, disease, and physiological resilience in wild birds.},
}

@article {pmid40538713,
year = {2025},
author = {Kuang, X and Shen, J and Zheng, L and Duan, Y and Ma, Y and Leung, EL and Dai, L},
title = {Applications of bacteriophages in precision engineering of the human gut microbiome.},
journal = {Engineering microbiology},
volume = {5},
number = {1},
pages = {100189},
pmid = {40538713},
issn = {2667-3703},
abstract = {As our understanding of the role of the gut microbiome in human diseases deepens, precision engineering of the gut microbiome using bacteriophages has gained significant attention. Herein, we review the recent advances in bacteriophage-mediated modulation of the gut microbiome, discuss approaches at the ecological and genetic levels, and summarize the challenges and strategies pertinent to each level of intervention. Drawing on the structural attributes of bacteriophages in the context of precision engineering, we examined the latest developments in the field of phage administration. Gaining a nuanced understanding of microbiome manipulation will yield tailored strategies and technologies. This could revolutionize the prevention and treatment of diseases linked to gut pathogens and offer new avenues for the therapeutic use of bacteriophages.},
}

@article {pmid40538711,
year = {2025},
author = {Lathakumari, RH and Vajravelu, LK and Gopinathan, A and Vimala, PB and Panneerselvam, V and Ravi, SSS and Thulukanam, J},
title = {The gut virome and human health: From diversity to personalized medicine.},
journal = {Engineering microbiology},
volume = {5},
number = {1},
pages = {100191},
pmid = {40538711},
issn = {2667-3703},
abstract = {The human gut virome plays a crucial role in the gut and overall health; its diversity and regulatory functions influence bacterial populations, metabolism, and immune responses. Bacteriophages (phages) and eukaryotic viruses within the gut microbiome contribute to these processes, and recent advancements in sequencing technologies and bioinformatics have greatly expanded our understanding of the gut virome. These advances have led to the development of phage-based therapeutics, diagnostics, and artificial intelligence-driven precision medicine. The emerging field of phageomics shows promise for delivering personalized phage therapies that combat antimicrobial resistance by specifically targeting pathogenic bacteria while preserving beneficial microbes. Moreover, CRISPR-Cas systems delivered via phages have shown success in selectively targeting antibiotic resistance genes and enhancing treatment effectiveness. Phage-based diagnostics are highly sensitive in detecting bacterial pathogens, offering significant benefits for human health and zoonotic disease surveillance. This synthesis of the current knowledge highlights the pivotal role of the gut virome in regulating microbial communities and its transformative potential in personalized medicine, emphasizing its importance in advancing therapeutic and diagnostic strategies for improving health outcomes.},
}

@article {pmid40538528,
year = {2025},
author = {Alqam, ML and Jones, BC and Hitchcock, TM},
title = {Safety Evaluation of Topical Products Containing Live Cultures and Ferment of Cutibacterium Acnes Subspecies Defendens Strain XYCM42 in Individuals Predisposed to Acne Vulgaris.},
journal = {The Journal of clinical and aesthetic dermatology},
volume = {18},
number = {5},
pages = {44-53},
pmid = {40538528},
issn = {1941-2789},
abstract = {BACKGROUND: For individuals with acne-prone skin, identifying a topical regimen that does not lead to progression of their inflammatory issues often poses a challenge. A topical skin probiotic regimen containing a specific strain of Cutibacterium acnes (C. acnes) subspecies defendens, XYCM42, has been shown to be beneficial in improving skin health and appearance in individuals with generally healthy skin, but the use of the skin probiotic has not been sufficiently assessed in individuals with acne-prone skin.

OBJECTIVE: The purpose of this study was to evaluate the safety and efficacy of daily application of a topical skin biome care regimen containing a living C. acnes subsp. defendens derivative strain, XYCM42, its ferment, and adjunct topicals in individuals with acne-prone skin.

METHODS: This eight-week study was conducted at five locations and included 136 total participants. At baseline, Week 1, Week 4, and Week 8, subjects completed product questionnaires and symptom severity surveys. Of the study subjects, 20 were enrolled for clinical efficacy evaluation at all timepoints. Clinical assessments included blemish lesion counts, Investigator's Global Assessment (IGA) of acne lesion severity, and clinical grading of skin cosmetic and safety parameters.

RESULTS: As early as Week 1 of regimen application, clinical observations demonstrated statistically significant improvements in acne severity scores, with no subjects reporting increased or worsened acne during the study. By Week 4, subjects showed significant changes in nearly all skin cosmetic parameters assessed, including skin texture, clarity, tone, fine wrinkling, undereye dark circles, dryness, and erythema. Lesion counts were significantly reduced from baseline at all timepoints, with 100 percent of subjects experiencing fewer non-inflammatory lesions and 70 percent and 30 percent with fewer papule and pustule inflammatory lesions, respectively, by the end of the study. No adverse events were reported.

CONCLUSION: This at-home use study demonstrates that use of the XYCM42-based topical skin biome care regimen is both safe and appropriate for individuals with acne-prone skin. More broadly, the outcomes of this study provide further support toward the beneficial and commensal nature of C. acnes subsp. defendens in promoting skin health.},
}

@article {pmid40538297,
year = {2025},
author = {van Hees, K and van Velzen, R and Thijssen, J and Hofmans, L and Dijkman, R and Ducatelle, R and Molenaar, RJ},
title = {New Method for Early Detection of Gut Health Issues in Broilers.},
journal = {Avian pathology : journal of the W.V.P.A},
volume = {},
number = {},
pages = {1-21},
doi = {10.1080/03079457.2025.2521354},
pmid = {40538297},
issn = {1465-3338},
abstract = {Flocks differ in levels for Lactobacillales, Lachnospiraceae and Ruminococcaceae.Gut Damage Ratio between broilers with or without gut health problems differ.Results of both assays in broilers of 21 days of age relate significantly to SW.},
}

@article {pmid40538224,
year = {2025},
author = {Sun, S and Xin, Q and Ma, Z and Gao, W and Cheng, J and Liu, Y and Huang, Y and Zhang, H and Yang, Y and Lin, X and Zheng, L and Xu, X and Ding, C and Li, J},
title = {Self-Assembled Photothermal Particles Boost Synergistic Biofilm Eradication and Remineralization in Early Dental Caries Treatment.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e2503224},
doi = {10.1002/smll.202503224},
pmid = {40538224},
issn = {1613-6829},
support = {2022YFC2405905//National Key Research and Development Program of China/ ; 52373295//National Natural Science Foundation of China/ ; U22A20158//National Natural Science Foundation of China/ ; 52473311//National Natural Science Foundation of China/ ; RD-03-202409//Interdisciplinary Innovation Project of West China Hospital of Stomatology/ ; sklpme 2023-2-02//State Key Laboratory of Polymer Materials Engineering/ ; 2024NSFSC0241//Sichuan Science and Technology Program/ ; },
abstract = {Dental caries, driven by dietary habits and microbial biofilms, remains a significant global health issue. In situ biomimetic remineralization is considered a promising method, but its low efficiency is a key challenge. Additionally, the interference of cariogenic bacteria further exacerbates the problem. In this study, self-assembled photothermal particles (PAEB) with light-boosted synergistic biofilm eradication and remineralization properties for caries treatment are reported. Composed by polyaspartic acid-stabilized amorphous calcium phosphate (Pasp-ACP) and ε-poly-L-lysine/baicalein (EPL-BC), PAEB enable efficient light-to-heat conversion under near-infrared light exposure due to polymerization and stacking of baicalein. The localized hyperthermia, accompanied with EPL-BC disrupts bacterial membranes and eradicates biofilm by more than 99%, which is seven times higher than the non-radiation group (12.86%) and ≈21 times higher than the fluoride group (4.35%). Meanwhile, the releasing of calcium and phosphate ions is accelerated for rapid remineralization, with highest hardness recovery (1.96 GPa) of all groups, comparable to untreated healthy enamel. Moreover, in vivo microbiome analysis confirms that PAEB selectively reduces the abundance of cariogenic Streptococcus spp. while maintaining overall microbial diversity and oral ecological balance, presenting a promising solution for non-invasive dental caries treatment. This photothermal-enhanced strategy gives a reference for the design of bioactive therapeutic dental materials.},
}

@article {pmid40538021,
year = {2025},
author = {Abs, E and Saleska, SR and Allison, SD and Ciais, P and Song, Y and Weintraub, MN and Ferriere, R},
title = {Microbiome Adaptation Could Amplify Modeled Projections of Global Soil Carbon Loss With Climate Warming.},
journal = {Global change biology},
volume = {31},
number = {6},
pages = {e70301},
doi = {10.1111/gcb.70301},
pmid = {40538021},
issn = {1365-2486},
support = {891576//H2020 Marie Skłodowska-Curie Actions/ ; PIA-10-LBX-54//MemoLife Laboratory of Excellence/ ; //FACE Partner University Fund, CNRS Mission pour l'Interdisciplinarité, PSL University/ ; //Ecole Doctorale 474 - Frontières de l'Innovation en Recherche et Éducation/ ; DE-SC0016440//Basic Energy Sciences/ ; DE-SC0025551//Basic Energy Sciences/ ; //Schmidt Sciences/ ; 2022070//Division of Environmental Biology/ ; DEB-1831493//Division of Environmental Biology/ ; },
abstract = {Warming alters soil microbial traits through ecological and evolutionary processes, directly influencing the decomposition of organic matter, which significantly affects global soil carbon emissions. Yet, soil carbon models largely ignore these processes and their implications for global responses to warming. Here, we incorporate eco-evolutionary theory into a mechanistic model describing microbial soil carbon decomposition to address the question of whether such processes could have consequential effects on climate carbon feedbacks globally. We assume that a key trait of microbes, their resource allocation to production of exoenzymes (which facilitate decomposition of organic matter)-is optimized to environmental temperatures by natural selection. We find that eco-evolutionary optimization results in microbes allocating more resources to enzyme production under warming. When applied at the global scale, eco-evolutionary optimization enhances the biological realism of soil carbon models and significantly amplifies global soil carbon loss by 2100. Our results highlight the significant potential of microbial eco-evolutionary responses to influence carbon cycle feedbacks to climate change, and motivate an urgent need for more comprehensive data to accurately quantify the adaptive potential of microbiomes in response to climate change.},
}

@article {pmid40537904,
year = {2025},
author = {Khongkool, K and Taweechotipatr, M and Payungporn, S and Sawaswong, V and Lertworapreecha, M},
title = {Characterization and Evaluation of Lactobacillus plantarum LC5.2 Isolated from Thai Native Pigs for its Probiotic Potential in Gut Microbiota Modulation and Immune Enhancement.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2503028},
doi = {10.4014/jmb.2503.03028},
pmid = {40537904},
issn = {1738-8872},
abstract = {Probiotic supplementation, particularly with Lactobacillus species, enhances growth performance, maintains gastrointestinal microbial balance, and prevents infections in livestock. This study isolated Lactobacillus strains from the feces of healthy native pigs in southern Thailand and assessed their probiotic properties and safety through both in vitro and in vivo evaluations. Nine Lactobacillus strains showed probiotic potential, with Lactobacillus plantarum LC5.2 demonstrating the best characteristics. This strain tolerated both acid and bile (100% tolerance) and exhibited strong adhesion properties, including high auto-aggregation (69.74%), cell surface hydrophobicity (77.14%), adhesion to Caco-2 cells (9.31%), and biofilm formation. It also exhibited antibacterial activity, inhibiting EHEC, EPEC, and Salmonella Typhimurium through organic acid production. Co-aggregation with these pathogens ranged from 60.83% to 74.09%. Safety evaluations showed no hemolytic activity, susceptibility to antibiotics, and co-existence with other probiotics. In mice, L. plantarum LC5.2 showed no toxicity, with normal food intake, behavior, and weight gain. No abnormalities were found in the small intestine, colon, liver, or spleen. Mice administered the probiotic had significantly higher intestinal IgA levels. Gut microbiome analysis revealed no notable structural alterations but indicated an increase in beneficial bacteria, including Lactobacillus. These results suggest that L. plantarum LC5.2 demonstrates strong probiotic potential, safety, and benefits for gut health, making it a promising candidate for livestock applications.},
}

@article {pmid40537897,
year = {2025},
author = {Jung, W and Son, YM},
title = {Nanoparticle-Driven Modulation of Mucosal Immunity and Interplay with the Microbiome.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2404033},
doi = {10.4014/jmb.2504.04033},
pmid = {40537897},
issn = {1738-8872},
abstract = {Mucosal surfaces are dynamic immunological interfaces that play a critical role in maintaining host defense and microbial homeostasis. Disruptions in the interaction between the mucosal immune system and its commensal microbiota have been associated with the onset of several diseases, including inflammatory bowel disease, asthma, and bacterial vaginosis. This review examines recent advances in nanoparticle (NP)-based strategies aimed at modulating mucosal immunity and restructuring microbial communities. It highlights how organic and inorganic NPs such as polysaccharide-based carriers, lipid NPs, and metallic nanomaterials enhance the delivery and stability of probiotics, prebiotics, and synbiotics, and facilitate targeted immunomodulation across gastrointestinal, respiratory, and female reproductive mucosal tissues. NP-based strategies are particularly emphasized for their ability to penetrate mucus barriers, facilitate microbial colonization, modulate cytokine activity, and enhance the restoration of epithelial barrier function. Disease-specific applications, including NP-based therapies for colitis, respiratory inflammation, and vaginal dysbiosis, are also discussed. In addition, this review outlines current challenges related to biosafety, targeting specificity, and clinical translation, and suggests future directions for research. Altogether, NP platforms offer a promising avenue for the precise modulation of mucosal immunity and microbiota, with significant potential in the prevention and treatment of mucosal-associated diseases.},
}

@article {pmid40537892,
year = {2025},
author = {Kang, J and Choi, Y and Keum, GB and Doo, H and Kwak, J and Kim, H and Chae, Y and Lee, S and Yang, H and Kim, S and Sun, X and Kim, HB and Yoo, SJ},
title = {Effect of Diet and Lifestyle Changes on Gut Microbial Diversity in Healthy Adolescents.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2503018},
doi = {10.4014/jmb.2503.03018},
pmid = {40537892},
issn = {1738-8872},
abstract = {The human gut microbiome is a complex ecosystem shaped by both intrinsic and extrinsic factors, with external elements such as diet and exercise significantly influencing its diversity and composition. In this study, we evaluated gut microbiome shifts in adolescents participating in a four-week camp with controlled diets, lifestyle, and a healthy living environment. Stool samples were collected before and after the camp period and analyzed through 16S rRNA gene sequencing to assess changes in microbial composition and diversity. Post-intervention, gut microbiome diversity increased significantly, with notable changes in the relative abundance of taxa such as Lachnospira, Alistipes, and Barnesiella, which are associated with enhanced immune function and gut health. Additionally, functional prediction using PICRUSt indicated an increase in genes associated with energy production and metabolism, suggesting a broader functional impact of lifestyle modifications on gut microbial functionalities. These findings revealed the potential causal relationships between lifestyle modifications and gut microbiome shifts, providing valuable insights into the interactions between environment, diet, and the gut microbiota.},
}

@article {pmid40537703,
year = {2025},
author = {Tronel, A and Roger-Margueritat, M and Plazy, C and Cunin, V and Mohanty, I and Dorrestein, PC and Soranzo, T and Le Gouellec, A},
title = {Untargeted and semi-targeted metabolomics approach for profiling small intestinal and fecal metabolome using high-resolution mass spectrometry.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {21},
number = {4},
pages = {84},
pmid = {40537703},
issn = {1573-3890},
support = {2021/0931//Association Nationale de la Recherche et de la Technologie/ ; 2021/0931//Association Nationale de la Recherche et de la Technologie/ ; RF20230503289//Association Vaincre la Mucoviscidose/ ; ANR-15-IDEX-02//ANR/ ; },
abstract = {INTRODUCTION: The gut microbiome is a complex ecosystem stratified that varies along different sections of the gut. It comprises a wide array of metabolites originating from both food, host, and microbes. Microbially-derived metabolites, such as bile acids, short-chain fatty acids, and indole derivatives, are of significant interest due to their direct interactions with host physiology and regulating function. Most current studies on the gut microbiome focus on fecal samples, which do not fully represent the upper parts of the gut due to its stratification. To collect microbiome samples from the proximal gut microbiome, endoscopic methods or new non-invasive medical devices can be used.

OBJECTIVES: To enable comprehensive profiling of the gut metabolome and analyze key metabolites, we developed a combined approach combining untargeted and semi-targeted metabolomics using a Q-Exactive Plus Orbitrap mass spectrometer.

METHODS: Initially, we selected 49 metabolites of interest for the gut metabolome based on four distinct criteria. We validated these metabolites through repeatability and linearity tests and created a compound database using the software TraceFinder (ThermoFisher Scientific). For untargeted metabolomics, we established a workflow for the annotation and discovery of molecules.

RESULTS: Finally, 37 metabolites were validated for semi-targeted metabolomics, and we conducted a proof of concept on small intestinal and fecal samples form a clinical trial (NCT05477069).

CONCLUSION: Our combined approach, facilitated by molecular networking, demonstrated the potential to discover new metabolites.},
}

@article {pmid40537586,
year = {2025},
author = {King, A},
title = {Single-celled organisms set for greater role in gut health.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40537586},
issn = {1476-4687},
}

@article {pmid40537478,
year = {2025},
author = {Sommer, AJ and Skarlupka, JH and Teseo, S and Otani, S and Suen, G and Coon, KL and Sapountzis, P},
title = {Genomic evidence for flies as carriers of zoonotic pathogens on dairy farms.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {111},
pmid = {40537478},
issn = {2055-5008},
support = {WIS04039//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; },
abstract = {Dairy farms are major reservoirs of zoonotic bacterial pathogens, which harbor antimicrobial resistance genes (ARGs), and raise critical questions about their dissemination on and off the farm environment. Here, we investigated the role of coprophagous muscid flies (Diptera: Muscidae) as carriers of zoonotic pathogens and antimicrobial resistance. We collected cow manure and flies on a dairy farm and used shotgun metagenomics to identify the presence of clinically relevant bacteria, virulence factors, and ARGs in both environments. Our results reveal that, although the fly microbiome is largely composed of manure-associated taxa, they also harbor specific insect-associated bacteria, which may be involved in nutrient provisioning to the host. Furthermore, we identifed shared ARGs, virulence factors, and zoonotic pathogens enriched within the fly gastrointestinal tract (GIT). Our study illustrates the potential flow of pathogenic microorganisms from manure to coprophagous flies, suggesting that flies may pose an important zoonotic threat on dairy farms.},
}

@article {pmid40537474,
year = {2025},
author = {Bradshaw, CS and Plummer, EL and Muzny, CA and Mitchell, CM and Fredricks, DN and Herbst-Kralovetz, MM and Vodstrcil, LA},
title = {Bacterial vaginosis.},
journal = {Nature reviews. Disease primers},
volume = {11},
number = {1},
pages = {43},
pmid = {40537474},
issn = {2056-676X},
abstract = {Bacterial vaginosis (BV) is a vaginal microbiome disorder that is associated with preterm birth and spontaneous abortion, increased risk of HIV infection and sexually transmitted infections, and has negative effects on quality of life. BV affects one in four women globally, with the highest burden in resource-limited settings. Marked alterations in vaginal microbiome composition, in pro-inflammatory cytokines and chemokines, and in the proteome and metabolome characterize BV and contribute to adverse sequelae. Despite its prevalence, the exact aetiologic agent of BV is unknown and its pathophysiology is poorly understood. These knowledge gaps impede diagnostic and management approaches, with recommended treatment strategies resulting in recurrence that exceeds 50% over 3-6 months. New data on the sexual transmission of BV, including evidence that male-partner treatment improves cure, have improved our understanding of its aetiology and pathogenesis, and provide opportunities for developing optimal diagnostic, treatment and prevention strategies. Other factors probably also contribute to the low efficacy of current treatments, including biofilm and/or antimicrobial resistance, and failure to recolonize a favourable vaginal microbiome after treatment. The complex pathophysiology of BV highlights that individualized and multifaceted management approaches will be required to manage the refractory and adverse sequelae of BV.},
}

@article {pmid40537372,
year = {2025},
author = {Kolodkin-Gal, I and Frenkel-Morgenstern, M},
title = {Liquid biopsy for microbiome profiling through nucleotide analysis.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2025.05.021},
pmid = {40537372},
issn = {1879-3096},
abstract = {Liquid biopsy for microbiome analysis is an emerging field that aims to study the composition and dynamics of microbial communities by analyzing biological fluids such as blood, urine, or saliva. This noninvasive method offers a useful approach to understanding microbiome dynamics. It provides insights into different pathologies, enables unbiased pathogen detection through noninvasive sampling, and offers rapid turnaround times. Clinical applications of liquid biopsy are emerging for microbiome exploration, particularly in areas such as infectious disease management, cancer diagnostics, and personalized medicine for chronic bowel diseases. This review highlights the role of liquid biopsy in infection and microbiome exploration, potentially revolutionizing diagnostics and tailored medicine by enabling the real-time monitoring of microbial shifts.},
}

@article {pmid40537345,
year = {2025},
author = {Zhang, C and Turnbaugh, PJ},
title = {Mining microbial metabolites of GPCR-targeted drugs.},
journal = {Trends in pharmacological sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tips.2025.05.014},
pmid = {40537345},
issn = {1873-3735},
abstract = {G protein-coupled receptors (GPCRs) are a large superfamily of receptors critical for mammalian cell-cell communication and a common drug target. A new study has revealed that the human gut microbiome can metabolize GPCR-targeted drugs into both expected and surprising metabolites, with potentially broad implications for the treatment of disease.},
}

@article {pmid40537117,
year = {2025},
author = {Khouri Chalouhi, D and Bertani, I and Esposito, A and Piazza, S and Bez, C and Venturi, V},
title = {An in Planta Enrichment Route to Identify Bacterial Root Endophytes.},
journal = {Environmental microbiology reports},
volume = {17},
number = {3},
pages = {e70136},
doi = {10.1111/1758-2229.70136},
pmid = {40537117},
issn = {1758-2229},
support = {//Arturo falaschi PhD scholarship/ ; PGR10061//MAE-CI/ ; },
abstract = {Microorganisms live in close association with plants, forming ecological interaction webs and providing beneficial traits such as nutrition, growth, and tolerance to biotic and abiotic stresses. Via the rhizosphere, plants recruit bacteria which colonise internal plant tissues, creating a spatial gradient between the rhizosphere and the endosphere. This study presents a high throughput in planta endophyte enrichment scheme designed for the identification of 'super'-endophytic bacteria which can serially colonise the rice root endosphere. Oryza sativa (rice) plants were grown in bulk soil, and endophytes were then recovered from roots. The recovered endophyte mixture was used as inoculum for the first generation of rice plantlets, which were then grown under no stress or nitrogen (N) depletion. The total endophytic community was then purified and used as a second inoculum for a new set of plants; this procedure was repeated for four generations. Enrichment patterns of root bacterial endophytes were observed, such as Kosakonia in the non-stressed plants and Ferrovibrio in plants grown under nitrogen starvation. This enrichment method proved to be suitable for the identification of endophytes which can efficiently colonise the root endosphere.},
}

@article {pmid40536601,
year = {2025},
author = {Gan, B and Zhang, X and Xin, J and Duan, L and Sun, N and Chen, Y and Zeng, J and Lian, Y and Li, H and Wang, H and Ni, X and Ma, H},
title = {Lactobacillus johnsonii HL79 mitigate plateau environment-induced hippocampal dysfunction in mice.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {96},
pmid = {40536601},
issn = {2191-0855},
support = {U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; },
abstract = {Plateau environment represents a common terrestrial characterized by multistress conditions including hypobaric hypoxia, low temperature, and intense radiation, yet sustain over 100 million permanent or transient inhabitants. While this extreme environment exerts profound impacts on cerebral architecture and gut microbiota homeostasis, precipitating cognitive deficits and microbiome-derived intestinal pathologies, the mechanistic interplay between plateau environment adaptation and microbial dynamics remains contentious. Here, we employ a microbiota-gut-brain axis framework to investigate whether probiotic intervention can ameliorate hippocampal impairments induced by simulated plateau environment exposure (3500-4000 m) in mice. Through simulated plateau environment exposure experiments, we revealed that extreme high-altitude conditions induced hippocampal memory dysfunction in mice, exacerbated oxidative stress damage in hippocampal tissues, and altered synaptic plasticity-related biomarkers including CREB transcription factor, BDNF protein levels, and electrophysiological power spectra. Administration of HL79 alleviated these burdens, including memory dysfunction and tissue damage, though complete reversal was not achieved. Combined hippocampal transcriptomic analyses suggested that HL79's beneficial effects primarily involved modulation of lipid-related gene expression in the hippocampus, consistent with prior reports of plateau environmental impacts on gene expression. Serum metabolomic results further reinforced this inference that differential metabolites regulated by HL79 are mainly enriched in bile secretion, taurine and hypotaurine metabolism, linoleic acid metabolism, and PPAR signaling pathways, though the precise regulatory mechanisms require further elucidation. This research provides a novel microbiota-gut-brain axis-based regulatory strategy for adaptation to extreme plateau environments and offers new evidence for understanding the relationship between gut microbiota and plateau environment adaptation at high elevations.},
}

@article {pmid40536441,
year = {2025},
author = {Xia, K and Jiao, Y and Zhang, L and Gao, R and Wang, F and Pan, Y and Cui, S and Lin, Y and Wu, T and Li, L and Wu, X and Ruan, Y and Sun, J and Yin, L and Chen, C and Lin, M},
title = {Multi-Omics Analysis of Ileal Mucosa and Mesentery Before and After Ileocecal Resection in Crohn's Disease.},
journal = {United European gastroenterology journal},
volume = {},
number = {},
pages = {},
doi = {10.1002/ueg2.70069},
pmid = {40536441},
issn = {2050-6414},
abstract = {Crohn's disease (CD), a type of inflammatory bowel disease (IBD), is a chronic disorder involving any part of the gastrointestinal tract. Ileocecal resection may serve as a more effective treatment option for early CD. However, the potential relationship and mechanisms between the ileocecum and remission induction of CD are still elusive. In this study, we conducted 16S rRNA sequencing and liquid chromatography-tandem mass spectrometry (LC-MS/MS) on 68 terminal ileal mucosa and mesentery samples from 34 patients with CD. The results showed an improvement in the microbial health of the ileal mucosa and mesentery in patients with CD after ileocecal resection. In addition, specific spatial alterations in microbiota and metabolites were observed before and after surgery. Furthermore, differentially expressed metabolites in the ileal mucosa and mesentery were subjected to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. The findings of this study support the therapeutic value of ileocecal resection in CD from a multi-omics perspective and may guide the clinical translation of microbiome-based strategies for precise treatment of CD.},
}

@article {pmid40536191,
year = {2025},
author = {Dietz, M and Gates, TJ and Sikdar, R and Subramanian, S and Elias, MH and Staley, C},
title = {Impeding Quorum Sensing Among the Intestinal Microbiota Impacts the Metastatic Rate of Colorectal Cancer.},
journal = {Cancer medicine},
volume = {14},
number = {12},
pages = {e71009},
pmid = {40536191},
issn = {2045-7634},
support = {//Norm and Pat Wells Grant/ ; //Minnesota Colorectal Cancer Research Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/pathology/microbiology/drug therapy/genetics ; Female ; Male ; Mice ; *Quorum Sensing/drug effects ; Mice, Inbred C57BL ; Neoplasm Metastasis ; Disease Models, Animal ; Feces/microbiology ; Humans ; },
abstract = {BACKGROUND: The gut microbiota is associated with colorectal cancer (CRC) risk and CRC metastatic potential. However, the role of bacteria in CRC progression and metastasis remains unclear.

AIMS: Here, we hypothesized that microbial communication, mediated through quorum sensing (QS), was a critical component regulating microbial functions related to cancer progression and metastasis.

MATERIALS & METHODS: To test this, male and female C57BL/6 mice were injected with organoids modeling aggressive colon cancer (CRC), carrying mutations in Apc, Kras, p53, and Smad4. Two groups of mice were treated with two different quorum quenching (QQ) lactonases (GcL or SsoPox) for 8 weeks (n = 10/group/sex). Fecal samples were collected weekly and characterized by Illumina next-generation sequencing, with tissues collected during necropsy.

RESULTS: Male mice treated with SsoPox had fewer metastases than control mice (χ[2] = 3.206, p = 0.073), with no SsoPox-treated male developing a metastasis. In contrast, female mice treated with SsoPox had more metastases than control mice (χ[2] = 2.554, p = 0.110), and every female, SsoPox-treated mouse that developed a primary tumor also developed metastasis by the experimental endpoint. However, QQ treatment was shown to minimally affect the gut microbiome composition. Similarly, no significant differences were observed in inflammatory response as assessed by immunofluorescent staining or fecal concentrations of immunoglobulin A, calprotectin, or lipocalin-2. Differences in fecal short-chain fatty acid concentrations also did not differ significantly.

DISCUSSION: These results suggest that QQ treatment has a sex-based effect on CRC metastatic rate.

CONCLUSION: Targeting communication among the gut microbiome may be a promising avenue for the development of CRC therapies that minimally impact microbial community composition and host immune response.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Colorectal Neoplasms/pathology/microbiology/drug therapy/genetics
Female
Male
Mice
*Quorum Sensing/drug effects
Mice, Inbred C57BL
Neoplasm Metastasis
Disease Models, Animal
Feces/microbiology
Humans

@article {pmid40535760,
year = {2025},
author = {Yoo, JY and Dutta, M},
title = {Editorial: Microbiome: the modulator of human health.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1625412},
pmid = {40535760},
issn = {1663-9812},
}

@article {pmid40535543,
year = {2025},
author = {Meyers, M and Stoffels, CBA and Frache, G and Letellier, E and Feucherolles, M},
title = {Microbiome in cancer metastasis: biological insights and emerging spatial omics methods.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1559870},
pmid = {40535543},
issn = {2235-2988},
mesh = {Humans ; *Microbiota ; *Neoplasm Metastasis/pathology ; Tumor Microenvironment ; *Neoplasms/microbiology/pathology ; Metabolomics/methods ; Genomics/methods ; Proteomics/methods ; Animals ; },
abstract = {The role of the microbiome in cancer metastasis has emerged as a critical area of research, with growing evidence suggesting that microbial composition and interactions within the tumour microenvironment may significantly influence metastatic progression. This review explores the role of the microbiome in cancer metastasis, as well as potential key bacteria and their mechanisms through which they could impact tumour dissemination, seeding and growth. Biological models used to study metastasis are discussed to provide context for the further investigation of these interactions. In order to answer unresolved questions regarding the microbiome's involvement in metastatic dissemination, recent advancements in spatial biology techniques are examined, including spatial genomics, transcriptomics, proteomics and metabolomics, which enable the spatial mapping of microbial interactions within the tumour microenvironment. Additionally, multimodal-omics imaging approaches are highlighted for their potential to integrate multiple molecular layers, offering comprehensive insights into the microbiome's role in cancer metastasis. The review also addresses the challenges and limitations of these techniques, underscoring the complexity of studying microbiome-tumour interactions and offering directions for future research to better explore and target the microbiological landscape in metastatic cancer.},
}

Humans
*Microbiota
*Neoplasm Metastasis/pathology
Tumor Microenvironment
*Neoplasms/microbiology/pathology
Metabolomics/methods
Genomics/methods
Proteomics/methods
Animals

@article {pmid40535353,
year = {2025},
author = {Huang, L and Meng, J and Lin, S and Peng, Z and Zhang, R and Shen, X and Zheng, W and Zheng, Q and Wu, L and Wang, X and Wang, Y and Mao, R and Sun, C and Li, X and Feng, ST},
title = {Integrating Gut Microbiome and Metabolomics with Magnetic Resonance Enterography to Advance Bowel Damage Prediction in Crohn's Disease.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {7631-7649},
pmid = {40535353},
issn = {1178-7031},
abstract = {PURPOSE: Cumulative bowel damage (BD) critically influences the progression and prognosis of Crohn's disease (CD). Although the Lémann Index (LI) remains the standard for BD assessment, its clinical utility is limited by heavy reliance on extensive clinical data. Multiparametric magnetic resonance enterography (MRE) provides noninvasive macroscopic evaluation of BD severity, however, it fails to characterize microscopic alterations. We therefore integrated MRE with gut microbiome and metabolomic data to uncover mechanistic insights and develop a comprehensive model for better prediction of BD.

METHODS AND RESULTS: In this prospective two-center study, 309 CD patients were stratified into BD and non-BD groups using LI. Patients underwent MRE, fecal 16S rRNA gene sequencing, and fecal/serum metabolomic analysis. Thirty healthy controls were included for comparison. The relationships between microbial/metabolic factors and MRE features were explored using correlation and mediation analyses. Seven machine learning algorithms, each paired with seven distinct combinations of multi-omics features, were evaluated using nested 5-fold cross-validation to construct an optimal prediction model. BD patients exhibited reduced gut microbial diversity (P<0.05), with Erysipelatoclostridium and [Ruminococcus]_gnavus_group as key discriminators. Metabolomics revealed elevated fecal aromatic amino acids and depleted serum glycerophospholipids/sphingolipids (P<0.05) linked to MRE-quantified features through mediation by microbial pathways (eg, 22.8% mediation effect of Prevotella_9 on penetration, P ACME=0.022). The optimal Xtreme Gradient Boosting Classifier (XGBC) model integrating three microbial genera, six fecal metabolites, three serum metabolites, and three MRE features achieved superior performance (AUC 0.857 and 0.829 in the derivation and external validation cohorts, respectively). SHapley Additive exPlanations (SHAP) analysis prioritized perianal diseases, Erysipelatoclostridium, and fecal alanine as key contributors.

CONCLUSION: Our study underscores the interplay between gut microbial dysbiosis, metabolic alterations, and MRE-quantified structural changes in BD patients. The integrated multi-omics model provides a promising tool for BD prediction, enabling precise CD severity stratification and personalized clinical decision-making.},
}

@article {pmid40535324,
year = {2025},
author = {Liu, S and Lin, Z and Zhou, J and Yang, X and You, L and Yang, Q and Li, T and Hu, Z and Zhan, X and Jiang, Y and Sun, B},
title = {Distinct Airway Microbiome and Metabolite Profiles in Eosinophilic and Neutrophilic Asthma.},
journal = {Journal of asthma and allergy},
volume = {18},
number = {},
pages = {1003-1022},
pmid = {40535324},
issn = {1178-6965},
abstract = {BACKGROUND: Asthma is a chronic, heterogeneous disease driven by inflammatory phenotypes, primarily eosinophilic asthma (EA) and neutrophilic asthma (NEA). While allergen triggers are well-known, the role of the airway microbiome and metabolites in asthma exacerbations remains poorly understood.

METHODS: We recruited 64 participants (24 EA, 20 NEA, 20 healthy controls [HC]) for the discovery cohort, with validation in an external cohort (10 EA, 8 NEA, 8 HC). Induced sputum samples were analyzed using 16S rRNA sequencing to profile bacterial composition and non-targeted metabolomics to assess airway metabolites. Random forest models identified diagnostic markers, validated in the external cohort.

RESULTS: Significant shifts in airway microbiota were observed, particularly between NEA and HC, and between EA and NEA. Four bacterial general-Stenotrophomonas, Streptococcus, Achromobacter, and Neisseria-were consistently identified across groups. Veillonella was more abundant in NEA vs HC, while Achromobacter was enriched in NEA vs EA, indicating distinct microbial signatures. Metabolomic profiling revealed distinct pathways: pyrimidine metabolism (EA vs HC), tryptophan metabolism (NEA vs HC), and arachidonic acid metabolism (EA vs NEA). Microbial-metabolite correlations indicated microbiota-driven metabolic activity. Biomarker candidates were validated in the external cohort.

CONCLUSION: The airway microbiota and metabolites are intricately linked to asthma exacerbations, with distinct patterns between EA and NEA. These findings highlight their potential as diagnostic biomarkers and therapeutic targets for personalized asthma management.},
}

@article {pmid39710259,
year = {2025},
author = {Callaway, T and Perez, HG and Corcionivoschi, N and Bu, D and Fluharty, FL},
title = {International Symposium on Ruminant Physiology: The holobiont concept in ruminant physiology-More of the same, or something new and meaningful to food quality, food security, and animal health?.},
journal = {Journal of dairy science},
volume = {108},
number = {7},
pages = {7567-7575},
doi = {10.3168/jds.2024-25847},
pmid = {39710259},
issn = {1525-3198},
abstract = {The holobiont concept has emerged as an attempt to recognize and describe the myriad interactions and physiological signatures inherent to a host organism, as affected by the microbial communities that colonize and co-inhabit the environment within which the host resides. The field acknowledges and draws upon principles from evolution, ecology, genetics, and biology, and in many respects has been pushed by the advent of high throughput DNA sequencing and, to a lesser extent, other omics-based technologies. Despite the explosion in data generation and analyses, much of our current understanding of the human and ruminant holobiont is based on compositional forms of data and thereby, restricted to describing host phenotypes via associative or correlative studies. So, where to from here? We will discuss some past findings arising from ruminant and human gut microbiota research and seek to evaluate the rationale, progress, and opportunities that might arise from the holobiont approach to the ruminant and human host. In particular, we will consider what is a "good" or "bad" host gastrointestinal microbiome in different scenarios, as well as potential avenues to sustain or alter the holobiont. Although the holobiont approach might improve food quality, food security, and animal health, these benefits will most likely be achieved via a judicious and pragmatic compromise in data generation, both in terms of its scale as well as its generation, in context with the forgotten knowledge of ruminant and human physiology.},
}

@article {pmid40535110,
year = {2025},
author = {Raimi, A and Adeleke, R},
title = {High-throughput sequencing analysis of community diversity and functional structure of endophytic bacteria in edible vegetable crops: potential implication on plant microbiological quality.},
journal = {3 Biotech},
volume = {15},
number = {7},
pages = {216},
pmid = {40535110},
issn = {2190-572X},
abstract = {UNLABELLED: This study evaluated the diversity and functional structure of endophytic bacterial communities residing within four common leafy vegetables: Brassica oleracea, Lactuca sativa, Allium cepa, and Spinacia oleracea, cultivated under organic (OF) and conventional (CF) farming systems. Utilizing high-throughput 16S rRNA gene sequencing and the PICRUSt2 pipeline, the research assessed the influence of plant species, organ (leaf/root), and fertilizer type on these microbial communities. Findings revealed that plant species and organ type significantly shaped endophytic bacterial community composition and diversity. Onion communities were distinct, and roots exhibited higher diversity and richness compared to leaves. Fertilizer type significantly impacted overall bacterial diversity, with CF farms showing higher diversity than OF. Microbial network analysis identified keystone taxa, including network hubs like Serratia and Streptomyces, and module hubs like Solirubrobacter, Corynebacterium, and Mycobacterium. Functional predictions indicated diverse metabolic capabilities, with organ type significantly affecting pathway abundance (leaves enriched in carbohydrate degradation, roots in nutrient metabolism/degradation). OF farms showed higher predicted abundance of some potential virulence pathways, while CF farms had higher abundance of certain biotechnological pathways. Vegetable nutrient content significantly correlated with both bacterial community composition and predicted metabolic pathways. This study highlights the complex interplay between farming practices, plant factors, endophytic microbiomes, and their functional potential, underscoring implications for vegetable microbiological quality and potential human health.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04380-9.},
}

@article {pmid40535082,
year = {2025},
author = {Wang, C and Hu, B and Liang, Q and Jiang, H and Yuan, L and Li, S},
title = {Oral microbiome and risk of lung cancer: results from a two-sample mendelian randomization analysis.},
journal = {Translational lung cancer research},
volume = {14},
number = {5},
pages = {1715-1723},
pmid = {40535082},
issn = {2218-6751},
abstract = {BACKGROUND: Numerous studies have suggested that the oral microbiome may function as a biomarker for lung cancer screening. However, the relationship between oral microbiome and lung cancer has not been thoroughly investigated. Consequently, investigating the causal relationship between oral microbiome and lung cancer was the primary goal of this study.

METHODS: We conducted a two-sample Mendelian randomization (MR) analysis to investigate the causal relationship between the oral microbiome and lung cancer. Summary statistics for the oral microbiomes were obtained from large-scale metagenome-genome-wide association studies (mgGWAS), while genome-wide association study (GWAS) summary statistics for lung cancer were sourced from the IEU-OpenGWAS online platform. We employed inverse variance weighted (IVW) analysis and Wald ratio methods to evaluate the causal associations between the oral microbiome and lung cancer. Finally, we performed MR Steiger's test to strengthen the validity of the causal associations.

RESULTS: Three oral microbiomes were causally associated with lung cancer. Gemella haemolysans (pheno.388) from saliva and an unclassified species (pheno.844) of Clostridia from saliva were protective factors for lung cancer, and an unclassified species (pheno.1354) of Prevotella from tongue was a risk factor for lung cancer. And there is no bidirectional association of causality between oral microbiomes and lung cancer.

CONCLUSIONS: The oral microbiomes, Gemella haemolysans (pheno.388) from saliva, an unclassified species (pheno.844) of Clostridia from saliva and an unclassified species (pheno.1354) of Prevotella from tongue, were causally associated with lung cancer. Oral microbiology holds significant potential for clinical applications in etiologic exploration, early screening, prevention, and enhancing survival in lung cancer. Regarding treatment, personalized therapy based on oral flora may provide novel therapeutic strategies for lung cancer.},
}

@article {pmid40535022,
year = {2025},
author = {Blaustein, RA and Smith, JE and Toro, M and Pachepsky, Y and Stocker, MD},
title = {Water metagenomes reflect physicochemical water quality throughout a model agricultural pond.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1535096},
pmid = {40535022},
issn = {1664-302X},
abstract = {Agricultural ponds are essential irrigation resources, though may also serve as reservoirs for pathogens and antimicrobial resistance (AMR) genes. While monitoring microbiological water quality is critical for food safety, the influence of sampling factors (e.g., when and where to collect samples) in making risk assessments and potential applications for using environmental covariates as indicators remain unclear. Here, we explored the hypothesis that metagenomes of agricultural waters change with spatiotemporal shifts in physicochemical water quality, i.e., across water depths over time. Water samples and underlying sediments were collected at a model pond at the surface and within the water column (0, 1, 2 m depths) throughout one day (i.e., 9:00, 12:00, 15:00). All samples were processed for shotgun metagenomic sequencing analysis and enumeration of various water quality parameters (e.g., temperature, nutrient concentrations, turbidity, pH, culturable Escherichia coli). At the pond surface, Microcystis aeruginosa and members of Cyanobacteria, along with genes encoding pathways related to photosynthesis and nucleotide biosynthesis, were enriched throughout the day. In contrast, within the water column (1-2 m depths) and sediments, diverse members of Proteobacteria and Actinobacteria were more dominant, along with encoded pathways related to respiration and amino acid biosynthesis. Various aspects of water quality (i.e., chlorophyll dissolved organic matter, ammonia, E. coli concentrations) correlated with water metagenome diversity, albeit not with any specific AMR genes or virulence factors. Nevertheless, de novo assembly of sequenced reads uncovered 22 unique strains encoding several AMR, virulence, or stress response genetic elements, thus linking metagenome functional potential to key taxa. Overall, our findings highlight distinctions in agricultural pond water metagenomes at the surface and in the water column and demonstrate the potential for metagenomic surveillance in water quality monitoring to support food safety.},
}

@article {pmid40535009,
year = {2025},
author = {He, S and Qi, Y},
title = {The microbiota, the malarial parasite, and the mice-a three-sided relationship.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1615846},
pmid = {40535009},
issn = {1664-302X},
abstract = {In recent years, the role of gut microbiota in modulating malaria susceptibility and infection progression has emerged as a pivotal focus in interdisciplinary research. While existing reviews have delineated mechanisms by which mosquito-associated gut microbiota regulate Plasmodium development, a systematic synthesis of the tripartite interplay among host gut microbiota, Plasmodium and host immunometabolic networks remains absent. Compared with previous studies predominantly focusing on single species or unitary mechanisms, this review fills the gap in cross-species integrated analysis of host-microbiota-pathogen interactions. By consolidating metagenomic, metabolomic, and immunological data, this review transitions from unitary mechanistic explanations to multi-omics-driven systematic analyses, demonstrating that murine microbiota suppresses Plasmodium proliferation through adaptive immune activation and metabolic product regulation. Meanwhile, Plasmodium infection induces decreased microbial diversity and functional pathway deviation in murine microbiota, exacerbating host immunometabolic imbalance. These advancements not only elucidate core biological principles governing "microbiota-host-pathogen" interactions but also transcend traditional pathogen-centric perspectives by pioneering precise intervention strategies based on microbiota homeostasis restoration. This provides theoretical foundation for developing microbiome-targeted precision prevention approaches, which will continue to make substantial contributions to malaria research.},
}

@article {pmid40534981,
year = {2025},
author = {Hodgson, RJ and Cando-Dumancela, C and Liddicoat, C and Ramesh, SA and Edwards, RA and Breed, MF},
title = {Strong Host Modulation of Rhizosphere-to-Endosphere Microbial Colonisation in Natural Populations of the Pan-Palaeotropical Keystone Grass Species, Themeda triandra.},
journal = {Ecology and evolution},
volume = {15},
number = {6},
pages = {e71595},
pmid = {40534981},
issn = {2045-7758},
abstract = {Soil microbiota can colonise plant roots through a two-step selection process, involving recruitment of microbiota first from bulk soil into plant rhizospheres, then into root endospheres. This process is poorly understood in all but a few model species (e.g., Arabidopsis), which is surprising given its fundamental role in plant and soil ecology. Here, we examined the microbial community assembly processes across the rhizospheres and root endospheres in eight natural populations of the pan-palaeotropical C4 grass, Themeda triandra, in southern Australia. Using a space-for-time substitution approach, we assessed whether bacterial root colonisation patterns conformed to the two-step model and tested whether community assembly was driven more by deterministic or stochastic processes. Our results show that the two-step selection process shaped bacterial recruitment dynamics across these natural T. triandra populations, and we provide clear evidence that host plants influence microbial assembly via deterministic pressures that produce strong community convergence within endospheres. These findings highlight the central role of host filtering in shaping a conserved 'core' endosphere microbiome. However, limited understanding of these endosphere communities constrains efforts to harness these important relationships to, for example, improve plant propagation and revegetation practices.},
}

@article {pmid40534416,
year = {2025},
author = {Wang, Z and Wei, M and Wan, J and He, W and Zhou, J and Zhang, Y and Liu, Y and Liu, Y and Liu, D and Zhu, Q and Wang, X and Wu, K},
title = {Oral Microbiota Dysbiosis Initiated by Chronic Colitis and the Possible Role in Oral Mucosa Changes.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.15344},
pmid = {40534416},
issn = {1601-0825},
support = {LCA202206//National Clinical Research Center for Oral Diseases of China/ ; LX2023408//New Technologies of School of Stomatology, Air Force Medical University Fund/ ; 82341223//National Natural Science Foundation of China/ ; 2023-YBSF-171//Key Program of Science Technology in Shaanxi Province/ ; 22JK0547//Special Scientific Research Project of Shaanxi Provincial Education Department/ ; 2019JZ33//Key Program of Natural Science Basic Research Plan in Shaanxi Province/ ; },
abstract = {OBJECTIVE: To investigate oral microbiota dysbiosis and cytopathological changes in oral mucosa of murine chronic colitis model and the correlation between them.

METHODS: Dextran sodium sulfate (DSS) induced chronic colitis was established in SPF C57BL/6 male mice, oral microbiome characterization was performed using 16S rRNA gene sequencing, and cytopathological and immunohistochemistry assessment was performed in oral mucosa.

RESULTS: When chronic colitis was induced, the overall microbial composition of the oral microbiome was altered with increased abundance in phylum Proteobacteria (82.2%), Actinobacteria (2.6%) and decreased abundance in Firmicutes (12.7%), Bacteroidetes (1.1%). Among the top 10 most abundance genera, Streptococcus was the only genera significantly decreased in colitis mice oral cavity. Meanwhile, oral epithelial hyperplasia was identified in the murine chronic colitis model, and the ki67 expression was significantly upregulated in oral epithelium (p < 0.05). The chronic course of colitis did not lead to obvious inflammatory infiltration in the oral mucosa. Spearman analysis indicated a strong inverse correlation (r = -0.52, p = 0.03) between oral Streptococcus and epithelium thickness.

CONCLUSIONS: The chronic colitis mice displayed epithelial hyperplasia in the oral mucosa without obvious inflammatory infiltration, which might be associated with oral dysbiosis, especially a decreased abundance of Streptococcus.},
}

@article {pmid40534245,
year = {2025},
author = {Sierra-Cruz, M and Vilalta, A and Miguéns-Gómez, A and Park, H and Rodríguez-Gallego, E and Blay, MT and Ardévol, A and Pinent, M and Behmoaras, J and Beltrán-Debón, R and Terra, X},
title = {Grape Seed Proanthocyanidins: A Potential Microbiome-Targeted Intervention for Healthy Aging in Rats.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70150},
doi = {10.1002/mnfr.70150},
pmid = {40534245},
issn = {1613-4133},
support = {945413//H2020 Marie Skłodowska-Curie Actions/ ; PID2021-122636OB-I00//Agencia Estatal de Investigación/ ; 2021SGR00201//Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR) del Departament de Recerca i Universitats de la Generalitat de Catalunya/ ; },
abstract = {Aging and age-related metabolic complications are global health issues that pose a serious threat to public health. Gut dysfunction and dysbiosis contribute to age-related health decline. Grape seed-derived procyanidins (GSPE) have shown efficacy in mitigating adaptive homeostasis decline in young animal models, but their impact on intestinal health and the gut microbiome in aged animals remains unexplored. Twenty-one-month-old female rats were treated with 500 mg GSPE/kg of body weight for 10 days. After 11 weeks, GSPE anti-aging potential was evaluated by measuring plasma lipopolysaccharide, gut integrity gene expression, ex vivo gut barrier function, myeloperoxidase activity, and fecal microbiome composition. GSPE shifted the microbiota toward a younger profile, even restoring lost strains in aged rats. Despite the presence of metabolic aging markers, there was minimal deterioration in gut barrier function. Neither ex vivo permeability tests, transcriptional analysis of barrier function, nor gut histology showed significant impairment in gut. Only jejunal myeloperoxidase activity was increased in aged rats and reduced by GSPE. Intestinal barrier function showed mild deterioration in this model of aged rats. GSPE improved the aging process by modulating the gut microbiome, suggesting its potential as a microbiome-targeted intervention for promoting healthy aging.},
}

@article {pmid40534235,
year = {2025},
author = {Renaldi, R and Wiguna, T and Persico, AM and Tanra, AJ},
title = {p-Cresol and p-Cresyl Sulphate Boost Oxidative Stress: A Systematic Review of Recent Evidence.},
journal = {Basic & clinical pharmacology & toxicology},
volume = {137},
number = {1},
pages = {e70065},
doi = {10.1111/bcpt.70065},
pmid = {40534235},
issn = {1742-7843},
support = {//Center for Higher Education Funding and Assessment/ ; //Ministry of Higher Education/ ; //Science, and Technology of the Republic of Indonesia/ ; },
mesh = {*Cresols/toxicity/metabolism ; Humans ; *Oxidative Stress/drug effects ; *Sulfuric Acid Esters/toxicity/metabolism ; Animals ; Reactive Oxygen Species/metabolism ; Renal Insufficiency, Chronic/metabolism ; Biomarkers/metabolism ; Uremic Toxins/metabolism/toxicity ; Neurodegenerative Diseases/metabolism ; },
abstract = {Recent studies have emphasized the significant role of p-cresol and its conjugated form, p-cresyl sulphate (PCS), in enhancing oxidative stress, leading to potential detrimental effects on various biological systems. Both p-cresol and PCS contribute to increased production of reactive oxygen species (ROS), which can result in tissue damage, inflammation and a cascade of physiological abnormalities. Elevated p-cresol levels have been associated with greater clinical severity in autism spectrum disorder, correlating with more severe behavioural manifestations and a history of regression. This systematic review explores the recent evidence on how these compounds promote oxidative stress and their impact on different health conditions. This review also addresses the involvement of p-cresol and PCS in conditions such as chronic kidney disease, Parkinson's disease and other neurodegenerative disorders, where oxidative damage contributes to disease progression. Furthermore, this review highlights the need for further research to understand the precise mechanisms by which p-cresol and PCS modulate oxidative stress and their potential as biomarkers for clinical diagnosis and disease management. SUMMARY: This focused review systematically summarizes recent evidence that oxidative stress plays an important role in the damage of biological systems produced by two uremic toxins, p-cresol and its conjugated form, p-cresyl sulphate (PCS). p-cresol coming from environmental sources or produced by some gut bacterial strains, modulates various conditions, like chronic kidney disease, Parkinson's disease and autism spectrum disorder, among others. Oxidative damage and inflammation seemingly contribute to disease onset, progression and/or severity. The exact mechanism by which p-cresol and PCS promote oxidative stress, their influence on disease trajectory and their potential role as biomarkers merit further investigation.},
}

*Cresols/toxicity/metabolism
Humans
*Oxidative Stress/drug effects
*Sulfuric Acid Esters/toxicity/metabolism
Animals
Reactive Oxygen Species/metabolism
Renal Insufficiency, Chronic/metabolism
Biomarkers/metabolism
Uremic Toxins/metabolism/toxicity
Neurodegenerative Diseases/metabolism

@article {pmid40533873,
year = {2025},
author = {Härer, A and Kurstjens, E and Rennison, DJ},
title = {Host traits and environmental variation shape gut microbiota diversity in wild threespine stickleback.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {67},
pmid = {40533873},
issn = {2524-4671},
support = {458274593//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Despite the growing recognition of the importance of gut microbiota in host ecology and evolution, our understanding of the relative contributions of host-associated and environmental factors shaping gut microbiota composition within and across wild populations remains limited. Here, we investigate how host morphology, sex, genetic divergence, and environmental characteristics influence the gut microbiota of threespine stickleback fish populations from 20 lakes on Vancouver Island, Canada.

RESULTS: Our findings reveal substantial variation in gut microbiota composition and diversity among populations, with host traits exerting a relatively stronger influence on bacterial alpha diversity than environmental characteristics. Previous studies have suggested a link between stickleback body shape and niche specialization, and our results indicate that aspects of host morphology may be associated with gut microbiota divergence among populations, though whether this is related to trophic ecology remains to be explored. Within and across populations, we only observed a weakly defined core microbiota and limited sharing of amplicon sequence variants (ASVs) among hosts, indicating that gut microbiota composition is individualized. Additionally, we detected sex-dependent differences in microbial diversity, opening avenues for future research into the mechanisms driving this variation.

CONCLUSIONS: In sum, our study emphasizes the need to consider both host-associated and environmental factors in shaping gut microbiota dynamics and highlights the complex interplay between host organisms, their associated microbial communities, and the environment in natural settings. Ultimately, these insights add to our understanding of the eco-evolutionary implications of host-microbiota interactions while underscoring the need for further investigation into the underlying mechanisms.},
}

@article {pmid40533851,
year = {2025},
author = {Rahman, N and McCullough, T and Orozco, DF and Walkowiak, S and Farzan, A and Shekarriz, S and Surette, MG and Cicek, N and Derakhshani, H},
title = {Genomic characterization of antimicrobial resistance and mobile genetic elements in swine gut bacteria isolated from a Canadian research farm.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {66},
pmid = {40533851},
issn = {2524-4671},
support = {(RGPIN-2023-04359)//NSERC Discovery Grant/ ; },
abstract = {INTRODUCTION: The widespread use of antimicrobials in the livestock industry has raised global concerns regarding the emergence and spread of antimicrobial resistance genes (ARGs). Comprehensive databases of ARGs specific to different farm animal species can greatly improve the surveillance of ARGs within the agri-food sector and beyond. In particular, defining the association of ARGs with mobile genetic elements (MGEs)-the primary agents responsible for the spread and acquisition of resistant phenotypes among bacterial populations-could help assess the transmissibility potential of clinically relevant ARGs. Recognizing the gut microbiota as a vast reservoir of ARGs, we aimed to generate a representative isolate collection and genome database of the swine gut microbiome, enabling high-resolution characterization of ARGs in relation to bacterial host range and their association with MGEs.

RESULTS: We generated a biobank of bacteria from different sections of the gastrointestinal tracts of four clinically healthy pigs housed at a research farm in Ontario, Canada. The culturing was performed under anaerobic conditions using both selective and general enrichment media to ensure the capture of a diverse range of bacterial families within the swine gut microbiota. We sequenced the genomes of 129 unique isolates encompassing 44 genera and 25 distinct families of the swine gut microbiome. Approximately 85.3% (110 isolates) contained one or more ARGs, with a total of 246 ARGs identified across 38 resistance gene families. Tetracycline and macrolide resistance genes were the most prevalent across different lineages of the swine gut microbiota. Additionally, we observed a wide range of MGEs, including integrative conjugative elements, plasmids, and phages, frequently associated with ARGs, indicating that the swine gut ecosystem is conducive to the horizontal transfer of ARGs. High-throughput alignment of the identified ARG-MGE complexes to large-scale metagenomics datasets of the swine gut microbiome suggests the presence of highly prevalent and conserved resistome sequences across diverse pig populations.

CONCLUSION: Our findings reveal a highly diverse and relatively conserved reservoir of ARGs and MGEs within the gut microbiome of pigs. A deeper understanding of the microbial host range and potential transmissibility of prevalent ARGs in the swine microbiome can inform development of targeted antimicrobial resistance surveillance and disease control programs.},
}

@article {pmid40533779,
year = {2025},
author = {Liu, YC and Tang, XY and Lang, JX and Qiu, Y and Chen, Y and Li, XY and Cao, Y and Zhang, CD},
title = {Effects of antibiotic exposure on risks of colorectal tumors: a systematic review and meta-analysis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {682},
pmid = {40533779},
issn = {1479-5876},
support = {JYTMS20230108//the Scientific Study Project for Institutes of Higher Learning, Ministry of Education, Liaoning Province/ ; RXXM202302//the Young Backbone Talents of China Medical University/ ; LTKMZ20221139//the Scientific Study Project for Institutes of Higher Learning, Ministry of Education, Liaoning Province/ ; },
mesh = {Humans ; *Colorectal Neoplasms/chemically induced/epidemiology/microbiology ; *Anti-Bacterial Agents/adverse effects/therapeutic use ; Risk Factors ; Publication Bias ; Odds Ratio ; Gastrointestinal Microbiome/drug effects ; },
abstract = {BACKGROUND: Increasing evidence suggests that the gut microbiome may play an important role in the development of colorectal tumors. Antibiotic use can affect the gut microbiome and may increase the risks of benign and malignant colorectal tumors.

METHODS: Eligible studies assessing the relationship between antibiotic exposure and the risk of developing benign or malignant colorectal tumors were identified. Odds ratios (ORs) were pooled for antibiotic use versus no use using a random-effects model. Further subgroup and sensitivity analyses were conducted to confirm the consistence and robustness of the main findings. The study protocol was registered with PROSPERO.

RESULTS: Twenty-three studies including 1,145,853 participants were finally included in the analysis. People who had used antibiotics had a 13% increased risk of colorectal tumors compared with those who had never used antibiotics [OR: 1.13; 95% confidence interval (CI) 1.04-1.22; P < 0.01]. Subgroup analysis showed that antibiotic exposure was associated with increased risks of both benign (OR: 1.13; 95% CI 1.00-1.27; P < 0.01) and malignant colorectal tumors (OR: 1.13; 95% CI 1.03-1.23; P < 0.01). In addition, colorectal tumor risk was significantly increased by antibiotic exposure, especially the use of combined antibiotics and a longer period after antibiotic exposure. The main findings were consistent and robust across most subgroups and sensitivity analyses.

CONCLUSIONS: The current findings suggested that antibiotic use increased the risk of developing benign or malignant colorectal tumors. These results highlighted the need for clinicians to prescribe antibiotics cautiously, to reduce colorectal cancer risk.},
}

Humans
*Colorectal Neoplasms/chemically induced/epidemiology/microbiology
*Anti-Bacterial Agents/adverse effects/therapeutic use
Risk Factors
Publication Bias
Odds Ratio
Gastrointestinal Microbiome/drug effects

@article {pmid40533562,
year = {2025},
author = {White, Z and Cabrera, I and Mei, L and Clevenger, M and Ochoa-Raya, A and Kapustka, I and Dominguez, JR and Zhou, J and Koster, KP and Anwar, S and Wang, Q and Ng, C and Sagoshi, S and Matsuo, T and Jayawardena, D and Kim, SH and Kageyama, T and Mitchell, BJ and Rivera, D and Dudeja, PK and Lutz, SE and Kim, KW and Yoshii, A and Chevrier, N and Inoue, M and Sano, T},
title = {Gut inflammation promotes microbiota-specific CD4 T cell-mediated neuroinflammation.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40533562},
issn = {1476-4687},
abstract = {The microbiota has been recognized as a critical contributor to various diseases[1], with multiple reports of changes in the composition of the gut microbiome in contexts such as inflammatory bowel disease[2,3] and neurodegenerative diseases[4]. These microbial shifts can exert systemic effects by altering the release of specific metabolites into the bloodstream[5,6], and the gastrointestinal microbiota has also been reported to exhibit immunomodulatory activity through the activation of innate and adaptive immunity[7,8]. However, it remains unclear how the microbiota contributes to inflammation in the central nervous system (CNS), where these microorganisms are typically absent. Here we report that T cells that recognize gut-colonizing segmented filamentous bacteria can induce inflammation in the mouse intestine and CNS in the absence of functional regulatory T cells. Gut commensal-specific CD4 T cells (Tcomm cells) that are dysregulated in the inflamed gut can become licensed to infiltrate into the CNS regardless of their antigen specificity and have the potential to be re-stimulated by host protein-derived antigens in the CNS via molecular mimicry, whereupon they produce high levels of GM-CSF, IFNγ and IL-17A, triggering neurological damage. These infiltrated Tcomm cells initiate CNS inflammation by activating microglia through their IL-23R-dependent encephalitogenic programme and their IL-23R-independent GM-CSF production. Together, our findings reveal potential mechanisms whereby perturbation of Tcomm cells can contribute to extraintestinal inflammation.},
}

@article {pmid40533471,
year = {2025},
author = {Eggers, S and Hoggarth, ZE and Nagdeo, K and Banas, MJ and Lane, JM and Rechtman, E and Gennings, C and O'Neal, E and Peppard, PE and Sethi, AK and Safdar, N and Malecki, KM and Schultz, AA and Midya, V},
title = {Food insecurity modifies the association between the gut microbiome and the risk of cognitive impairment in adults.},
journal = {npj aging},
volume = {11},
number = {1},
pages = {47},
pmid = {40533471},
issn = {2731-6068},
support = {R00ES032884/ES/NIEHS NIH HHS/United States ; P30ES005605/ES/NIEHS NIH HHS/United States ; P30ES023515/ES/NIEHS NIH HHS/United States ; P30ES023515/ES/NIEHS NIH HHS/United States ; },
abstract = {This study investigated the role of food insecurity as an effect modifier between the gut microbiome, including groups of microbes (cliques), and risk of cognitive impairment (RCI). The analytical sample (n = 360) included adult participants of the Survey of the Health of Wisconsin with complete data on food insecurity, RCI, and 16S rRNA sequencing from stool samples. Microbial cliques associated with RCI were identified using an interpretable machine-learning-based algorithm. All analyses were stratified by food insecurity level, and adjusted for relevant confounders. We identified two cliques whose associations with RCI were modified by food insecurity status. The presence of the clique with either Eisenbergiella or Eubacterium was more strongly associated with RCI for the food-insecure group (β = 0.29, p < 0.0001). A clique representing the presence of Ruminococcus torques, Bacteroides, CAG-352F, and/or Eubacterium had a stronger association with RCI for the food-secure group (β = 0.1, p < 0.0001). Findings suggest food security be considered in RCI etiology.},
}

@article {pmid40533417,
year = {2025},
author = {Li, Z and He, Q and He, X and Xing, X and Fu, S and Sun, X and Ma, M and Wang, D and Mi, N and Zhao, J and Yuan, J and Yang, K},
title = {Long-Term or Recurrent Antibiotic Use in Early Life and the Risk of Type 2 Diabetes: A Population-Based Prospective Cohort and a Case-Control Study.},
journal = {Journal of diabetes},
volume = {17},
number = {6},
pages = {e70113},
doi = {10.1111/1753-0407.70113},
pmid = {40533417},
issn = {1753-0407},
support = {20JR10FA667//Gansu Province Endocrine Disease Clinical Medical Research Center/ ; 19ZDA142//the Major Project of the National Social Science Fund of China: Research on the Theoretical System, International Experience and Chinese Path of Evidence-based Social Science/ ; },
mesh = {Humans ; Case-Control Studies ; *Diabetes Mellitus, Type 2/epidemiology/chemically induced ; Male ; Female ; *Anti-Bacterial Agents/adverse effects ; Prospective Studies ; Risk Factors ; Middle Aged ; Adult ; United Kingdom/epidemiology ; Child ; Gastrointestinal Microbiome/drug effects ; Follow-Up Studies ; Adolescent ; },
abstract = {BACKGROUND: Antibiotics in childhood are commonly used and have been linked to gut microbiome dysbiosis and metabolic disorders. However, direct evidence regarding the association between long-term or recurrent antibiotic use (LRAU) during early life and diabetes was scarce. We performed this study to investigate this association in two population-based studies.

METHODS: We undertook a prospective analysis encompassing 147 010 participants from the UK Biobank. Cox proportional hazard regression was used to calculate hazard ratios (HRs) and 95% confidence intervals (CIs) of self-reported LRAU during early life on diabetes risk. We also conducted a case-control study within the Chinese population, in which 263 diabetes cases and 526 controls were matched for age and living location. Odds ratios (ORs) and 95% CI were was calculated using logistic regression models.

RESULTS: We identified 4314 incident cases of type 2 diabetes over 1 840 944 person-years of follow-up in the UK Biobank. LRAU during early life was associated with a 26% higher risk of diabetes after accounting for putative risk factors (HR, 1.26; 95% CI, 1.16-1.37) in the UK biobank. We observed a more evident association between LRAU and an elevated risk of diabetes in the case-control study (OR, 3.32; 95% CI, 2.06-5.38). The primary finding was robust to several subgroup analyses and sensitivity analyses.

CONCLUSIONS: LRAU during early life may increase the risk of type 2 diabetes. Caution should be exercised when prescribing long-term or recurrent antibiotics to children and adolescents.},
}

Humans
Case-Control Studies
*Diabetes Mellitus, Type 2/epidemiology/chemically induced
Male
Female
*Anti-Bacterial Agents/adverse effects
Prospective Studies
Risk Factors
Middle Aged
Adult
United Kingdom/epidemiology
Child
Gastrointestinal Microbiome/drug effects
Follow-Up Studies
Adolescent

@article {pmid40533342,
year = {2025},
author = {Pedroso, I and Kumbhare, SV and Johnson, S and Muthukumar, KM and Saravanan, SK and Irudayanathan, C and Sharma, G and Tabone, L and Sinha, R and Almonacid, DE and Szoka, N},
title = {Microbiome and genetic predictors of weight loss 12 months postsleeve gastrectomy: insights from a pilot retrospective cohort study.},
journal = {Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.soard.2025.05.008},
pmid = {40533342},
issn = {1878-7533},
abstract = {BACKGROUND: Gut microbiome and genetic biomarkers are increasingly guiding obesity treatment. Bariatric surgery leads to shifts in gut microbial composition and function, while genome-wide association studies reveal genetic underpinnings of polygenic obesity, informing risk, therapeutic outcomes, and nutrigenomics-based interventions.

OBJECTIVES: This pilot study aimed to identify gut microbiome and genetic biomarkers associated with weight loss 12 months after sleeve gastrectomy (SG).

SETTING: Single academic institution university clinic.

METHODS: Sixty-seven patients 12 months post-SG were enrolled: 34 had successful excess weight loss (EWL ≥50%), while 33 had unsuccessful EWL (EWL <50%). Microbiome and genetic profiles were collected and analyzed using ANOVA and regression methods.

RESULTS: The genus Akkermansia was significantly associated with EWL (P = 9.9 × 10[-6]). Several microbial pathways, including propionate synthesis and menaquinone (vitamin K2) production, showed nominally significant (P < .05) associations with greater weight loss. No differences emerged in the Firmicutes/Bacteroidetes ratio. Genetic analyses revealed significant correlations between EWL and polygenic scores for dietary needs and metabolic responses, including distinct vitamin D and K requirements, as well as higher LDL cholesterol levels and predisposition for major depression.

CONCLUSIONS: These findings suggest that both the gut microbiome and genetics may modulate weight loss following bariatric surgery. Integrating microbiome and genetic profiling into bariatric care pathways could enhance personalized obesity treatment. While this pilot, exploratory, and proof-of-concept study has limitations, it supports prior work linking gut microbial pathways to weight loss and suggests new associations. Follow-up studies are warranted to validate these results and further inform precision obesity interventions.},
}

@article {pmid40533327,
year = {2025},
author = {Sullivan, O and Sie, C and Ng, KM and Cotton, S and Rosete, C and Hamden, JE and Singh, AP and Lee, K and Choudhary, J and Kim, J and Yu, H and Clayton, CA and Carranza Garcia, NA and Voznyuk, K and Deng, BD and Plett, N and Arora, S and Ghezzi, H and Huan, T and Soma, KK and Yu, JJ and Tropini, C and Ciernia, AV},
title = {Corrigendum to "Early-life gut inflammation drives sex-dependent shifts in the microbiome-endocrine-brain axis" [Brain Behav. Immun. 125 (2025) 117-139].},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2025.06.007},
pmid = {40533327},
issn = {1090-2139},
}

@article {pmid40533309,
year = {2025},
author = {Xie, QY and Danska, JS},
title = {Large-scale microbiome data initiatives call for diversity.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.06.001},
pmid = {40533309},
issn = {1878-4380},
abstract = {High variability in human gut microbiota is a challenge in the identification of consistent microbe-disease associations. Two Cell papers by Nishijima et al. and Abdill, Graham, et al. addressed this by curating large public microbiome datasets. They highlight long overlooked drivers of gut microbiome variance, such as fecal microbial biomass and geographical locations of study participants, necessitating diverse population representation in microbiome research.},
}

@article {pmid40533209,
year = {2025},
author = {Stolberg-Mathieu, G and Mikkelsen, LS and Gottlieb, AD and Mølgaard, C and Roager, HM},
title = {The MOTILITY Mother-Child Cohort: a Danish prospective longitudinal cohort study of the infant gut microbiome, nutrition and bowel habits - a study protocol.},
journal = {BMJ open},
volume = {15},
number = {6},
pages = {e094965},
doi = {10.1136/bmjopen-2024-094965},
pmid = {40533209},
issn = {2044-6055},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Infant ; Denmark ; Longitudinal Studies ; Prospective Studies ; Female ; Infant, Newborn ; *Defecation/physiology ; Milk, Human ; *Nutritional Status ; Male ; Child Development ; Mothers ; Feces/microbiology ; },
abstract = {INTRODUCTION: Concurrent with infants' progression in dietary complexity and gut microbiome diversity, infants gradually change their defecation patterns during the first year of life. However, the links between bowel habits, the gut microbiota and early life nutrition remain unclear. The primary outcome is to characterise the gut microbiome development from birth to 1 year of age. Second, to investigate how bowel habits and nutrition in early life relate to the gut microbiome and metabolome during this period of life, and to explore how the development of the gut microbiome associates with host development.

METHODS AND ANALYSIS: The MOTILITY Mother-Child Cohort (MOTILITY) is a Danish prospective longitudinal cohort study enrolling up to 125 mother-infant dyads. Assessments occur at 36 weeks gestation (visit 1), birth (screening of infant) and 3, 6, 9 and 12 months (±2 weeks) post partum (visits 2-5). At visit 1, maternal anthropometrics, self-collected faecal and urine samples, and questionnaires on bowel habits and lifestyle are obtained. Between visits, infant faecal (biweekly), urine (monthly) and maternal breast milk (monthly until 6 months of age) samples are collected at home, and bowel habits and dietary intake are assessed biweekly by self-reported questionnaires. At visits 2-5, infant blood and saliva samples are collected, and anthropometric measurements are obtained. In addition, dietary intake is recorded thrice throughout the study period for mother and infant, respectively, and infant whole-gut transit time is estimated by sweet corn tests at 9 and 12 months of age. Birth, growth, motor development, sleep patterns, tooth development, overall health and well-being are assessed using questionnaires. Univariate and multivariate statistics will be applied to identify associations between the gut microbiome, early life nutrition and host physiology including bowel habits during the first year of life.

ETHICS AND DISSEMINATION: The MOTILITY study has been approved by the Research Ethics Committee for the Capital Region of Denmark (reference number: H-21063016). Selected results will be made available to the participants in the form of a summary document. Results will be published in peer-review journals and by means of national and international conferences.

TRIAL REGISTRATION NUMBER: NCT05491161.},
}

Humans
*Gastrointestinal Microbiome/physiology
Infant
Denmark
Longitudinal Studies
Prospective Studies
Female
Infant, Newborn
*Defecation/physiology
Milk, Human
*Nutritional Status
Male
Child Development
Mothers
Feces/microbiology

@article {pmid40533202,
year = {2025},
author = {Andrews, C and Vodapally, S and Foster, LP and Lawandy, I and Murphy, M and Castellanos, M and Moncada, D and Mourao, ML and Bhushan, B and Berger, PK and Fichorova, R and Monthé-Drèze, C and Freedman, SD and Angelidou, A and Martin, CR and Sen, S},
title = {Cohort profile: Mother and Infant Metabolome and Microbiome (MIMM) study, a prospective cohort study of mothers and infants in Boston, Massachusetts.},
journal = {BMJ open},
volume = {15},
number = {6},
pages = {e096957},
doi = {10.1136/bmjopen-2024-096957},
pmid = {40533202},
issn = {2044-6055},
mesh = {Humans ; Female ; Prospective Studies ; *Breast Feeding/statistics & numerical data ; Infant ; *Milk, Human/chemistry/microbiology/metabolism ; Adult ; Infant, Newborn ; Boston ; *Metabolome ; *Microbiota ; Male ; Mothers ; Pregnancy ; },
abstract = {PURPOSE: Breastfeeding is beneficial to the health of both the mother and infant. Despite recommendations to breastfeed by organisations including the WHO and the American Academy of Pediatrics, rates of breastfeeding remain below public health goals. The Mother and Infant Metabolome and Microbiome (MIMM) study is a prospective cohort study of healthy mother-term infant dyads designed to comprehensively assess the perinatal, maternal, neonatal and infant factors that are associated with breastfeeding outcomes and human milk composition.

PARTICIPANTS: MIMM participants were recruited from two medical centres in Boston, Massachusetts, from 2019 to 2023 and are followed for 2 years. Dyads were included if the mother delivered a singleton infant at ≥37 weeks' gestation, was discharged home <72 hours after vaginal delivery or <6 days after caesarean delivery, spoke English, planned to breastfeed (either exclusively or with formula supplementation) and was willing and able to conduct follow-up through 2 years. Dyads were excluded from the study if the infant was admitted to the neonatal intensive care unit for longer than 72 hours. A total of 156 dyads were enroled in the study; however, eight participants dropped out prior to hospital discharge and will be excluded from all analyses (ie, no data was collected), resulting in a final cohort sample size of 148 mother-infant dyads. Approximately 62% of participants were White, 20% were Black or African American, 11% were Asian and 7% were more than one or unknown race. The cohort was highly educated, with 87% of participants having at least a college degree. Median maternal pre-pregnancy body mass index was 24.8 kg/m[2] and infant gestational age was 39.3 weeks. Approximately 43% of infants were born via caesarean delivery, and 45.5% were female.

FINDINGS TO DATE: MIMM study procedures include longitudinal (1) collections of maternal blood, vaginal swab, stool and milk and infant blood and stool samples and (2) assessments of breastfeeding status, child neurodevelopment and growth and maternal health at birth, 6 weeks and 6, 12, 18 and 24 months. Data collection through 18 months is complete. The overall objective of the MIMM study is to identify potential targets to improve breastfeeding outcomes, human milk composition and ultimately, maternal and child health. Preliminary analyses, reported in conference presentations (with ongoing analyses and results manuscripts pending), have found that (1) mothers with higher levels of stress were less likely to be exclusively breastfeeding their infants at 6 weeks; (2) higher breastfeeding intensity was associated with greater postpartum weight loss at 6 weeks; (3) feeding type was a more relevant predictor of feeding frequency and volume compared with feeding mode; (4) infants who received exclusive human milk had higher food enjoyment compared with those who received any formula; and (5) infants of mothers with obesity had higher average feeding volume per feed.

FUTURE PLANS: Data collection for the final 24-month visit is expected to be completed by August 2025. We expect that all sample assays will be completed by December 2025. Findings will continue to be submitted for presentation at scientific conferences, and we expect to publish the first findings from this cohort in manuscript format in 2025.},
}

Humans
Female
Prospective Studies
*Breast Feeding/statistics & numerical data
Infant
*Milk, Human/chemistry/microbiology/metabolism
Adult
Infant, Newborn
Boston
*Metabolome
*Microbiota
Male
Mothers
Pregnancy

@article {pmid40533070,
year = {2025},
author = {Russell, M and Cain, E and Bazzano, L and De Anda, I and Woo, JG and Urbina, EM},
title = {Collecting at-Home Biometric Measures for Longitudinal Research From the i3C: Feasibility and Acceptability Study.},
journal = {JMIR human factors},
volume = {12},
number = {},
pages = {e71103},
doi = {10.2196/71103},
pmid = {40533070},
issn = {2292-9495},
mesh = {Humans ; Female ; Male ; Middle Aged ; Feasibility Studies ; Longitudinal Studies ; Adult ; Aged ; Wearable Electronic Devices ; },
abstract = {BACKGROUND: The use of individual wearable devices or internet-based applications to collect biometric data from research participants is popular, but several devices may be needed to replace a full set of research measurements.

OBJECTIVE: In this study, we assessed the feasibility of a "Virtual Home Clinic" within the context of long-term epidemiologic studies.

METHODS: Participants from 3 study cohorts were recruited. Devices were sent to the home to measure anthropometrics, resting metabolic rate, blood pressure (BP), heart rate (HR), heart rhythm, oxygen saturation, glucose, total cholesterol, physical activity, diet, sleep duration or quality, and arterial stiffness over the course of 1 week. Stool and saliva were also self-collected for microbiome, DNA, and cotinine. Feasibility and acceptability of collecting measurements using home devices were assessed.

RESULTS: A total of 134 participants were enrolled (87% female, 31% Black; mean age 54.2, SD 8.4 years). Furthermore, 91% (N=122) performed at least one of the home tests. At least two-thirds of participants were able to complete all of the requested readings for glucose, electrocardiogram, BP, diet record, and resting metabolic rate. The scale that measured weight, body composition, and pulse wave velocity (PWV) was more difficult to use (113/134, 84% participants recorded at least one weight and 84/134, 63% recorded a PWV). The device to measure total cholesterol was least successful (32/134, 24% participants completed all readings, 72/134, 54% provided at least one result). Return of biospecimens was highly successful (115/134, 86% returned saliva and 113/134, 84% returned stool). Of 95 who responded to the user acceptability survey, 38 (40%) participants preferred home assessment, 36 (38%) preferred clinic, and 21 (22%) did not have a preference. The mean user acceptability score across devices for ease of use was 4.3 (SD 1.0), for instructions was 4.5 (SD 0.7), and for time to use was 3.9 (SD 1.1; scale of 1-5, with higher scores indicating greater acceptability). The study team documented several regulatory or IT, connectivity or account, data retrieval, and logistical issues encountered during the study.

CONCLUSIONS: Despite several complications involved with managing multiple devices and applications, most of the components of the virtual home clinic were reasonably feasible and acceptable to participants.},
}

Humans
Female
Male
Middle Aged
Feasibility Studies
Longitudinal Studies
Adult
Aged
Wearable Electronic Devices

@article {pmid40532960,
year = {2025},
author = {Johnstone, N and Kadosh, KC},
title = {A randomised controlled trial of the effects of Galacto-Oligosaccharides on the gut brain-axis of young females.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2025.06.020},
pmid = {40532960},
issn = {1090-2139},
abstract = {Galacto-oligosaccharides (GOS) are prebiotics that modulate gut microbiota and are implicated in the gut-brain axis (GBA), with preclinical models reporting effects on neurochemistry, brain function, and cognition. Here we report the results of a randomised, double-blind, placebo-controlled trial in 83 healthy females (17-25 years), who received GOS or placebo for 28 days. Assessments occurred at baseline, endline, and 28 days post-supplementation. The primary outcome was trait anxiety, secondary outcomes were brain-based levels of GABA and glutamate in the dorsolateral prefrontal cortex (dlPFC), anterior cingulate cortex, and inferior occipital gyrus (IOG) (measured with [1]H-MRS), and gut microbiome composition. Tertiary outcomes included social anxiety, depression, emotion behaviour, reaction times, and nutritional intake. Analyses included intention-to-treat, per-protocol, and sensitivity approaches. Trait anxiety did not differ between groups at endline (p = 0.443), though trends favoured lower anxiety in the GOS group at follow-up (p = 0.069). GOS reduced GABA at trend significance in the IOG (p = 0.053) in the Intention to Treat (ITT) population and dlPFC (p = 0.088) in high-anxious participants, with effects persisting at follow-up. GOS transiently increased Bifidobacterium abundance (p = 0.001) but did not affect microbiome diversity. Tertiary outcomes showed no significant changes in social anxiety or depression but faster reaction rates in high-anxious participants for simple (p = 0.036) and choice tasks (p < 0.001). Nutritional intake was unaffected. While GOS supplementation did not significantly reduce trait anxiety, it produced neurochemical changes and transient modulations of the gut microbiome in Bifidobacterium abundance, indicating GOS-induced changes can be traced along the GBA.},
}

@article {pmid40532868,
year = {2025},
author = {Krishnapriya, and Kishanchand, DK and Rishikesh, and Venkatachalam, S and Alikunju, AP and Deepti, A and Sivan, U and Sasidharan, BCP},
title = {Remodelling the Gut Ecosystem: A Dysbiosis Model to Elucidate Gut-Organ Axis Dynamics in Mice.},
journal = {Physiology & behavior},
volume = {},
number = {},
pages = {115000},
doi = {10.1016/j.physbeh.2025.115000},
pmid = {40532868},
issn = {1873-507X},
abstract = {Gut dysbiosis, an imbalance in intestinal microbiota composition, influences various physiological and pathological processes. We present a refined method to induce gut dysbiosis in mice, offering a valuable tool for investigating the gut-organ axis. Using an antibiotic cocktail, we induced dysbiosis and characterised its effects on host physiology and gut microbiota. Our analysis revealed significant alterations in bacterial diversity and composition, with the test group showing an increased abundance of potentially pathogenic genera like Clostridia_vadinBB60_group_ge and Escherichia-Shigella and decreased presence of beneficial microbes such as Prevotellaceae_UCG-001 and Muribaculaceae_ge. These changes were accompanied by shifts in predicted metabolic pathways, suggesting widespread functional alterations in the gut ecosystem. Notably, our dysbiosis model exhibited a 'subclinical' state, meaning that despite significant microbial shifts and physiological changes - including increased faecal water content, prolonged gastrointestinal transit time, elevated ileal acetylcholinesterase activity, and enlarged cecum - it was characterized by the absence of overt inflammation, alongside increased glutathione levels in the colon and an intact gut barrier. This unique model allows for exploring subtle, long-term effects of microbiome disruption on distant organ systems, providing a valuable platform for investigating the gut-organ axis in various diseases. Our findings offer promising avenues for research into therapeutic interventions targeting the gut microbiome and its extensive physiological impacts.},
}

@article {pmid40532867,
year = {2025},
author = {Graf, M and Murgueitio, N and Sheridan, MA and Quinn, RA and Carlson, AL and Vogel, SC and Styner, MA and Alex, AM and Stephens, RL and Roach, J and Sagarnaga, N and Mills-Koonce, WR and Azcarate-Peril, MA and Short, SJ and Knickmeyer, RC and Propper, CB},
title = {Gut microbiome is associated with insula structure in neonates.},
journal = {Physiology & behavior},
volume = {},
number = {},
pages = {115001},
doi = {10.1016/j.physbeh.2025.115001},
pmid = {40532867},
issn = {1873-507X},
abstract = {The infant brain and gut microbiome both develop rapidly in early infancy. Growing evidence indicates that the gut microbiome plays a critical role in shaping neurodevelopment early in life, possibly through effects on brain regions involved in affective, interoceptive, and sensory processes. This study used brain magnetic resonance imaging (MRI) and whole genome sequencing of fecal samples to examine associations between the gut microbiome and brain structures in infants at 2 weeks of age. We identified significant relationships between specific gut microbiome characteristics and brain volumes in key regions involved in affective, sensory, and interoceptive processing. Our most consistent findings were associations between gut microbiome composition and insula volume, suggesting that the insula may be particularly sensitive to gut microbiome influences during the neonatal period. Specifically, a significant negative association between insula volume and the abundance of Veillonella was observed. Alpha diversity (Shannon) and functional pathways were also related to insula structure. Enterobacter was negatively associated with thalamus volume. These findings contribute to the growing evidence of a developing gut-brain axis, highlighting links between the gut and brain as early as 2 weeks of age. Future research should investigate the mechanisms by which specific microbial taxa and diversity patterns impact neurodevelopment by way of the insula, as well as explore the potential long-term implications of these early relationships on sensory, interoceptive, and affective processing, and behavioral outcomes.},
}

@article {pmid40532861,
year = {2025},
author = {Biswas, I and Mitra, D and Mallik, C and Das Mohapatra, PK},
title = {Characterization and toxicity assessment of metabiotic produced through natural tannin fermentation by newly isolated probiotic Lactiplantibacillus plantarum PKI15 and study of its effect on gut microbiome through metagenomics approach.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107815},
doi = {10.1016/j.micpath.2025.107815},
pmid = {40532861},
issn = {1096-1208},
abstract = {Metabiotic fabrication has been done by mixed plant fermentation of Terminalia bellirica and Phyllanthus emblica fruit extract with probiotic bacteria Lactiplantibacillus plantarum PKI15 and showed considerable tannase (0.36 U/ml), gallic caid and pyrogallol production. Fermentative end-product analysis through FTIR, LC-MS and GC-MS analysis result indicates the presence of several bioactive compounds confirming the presence of gallic acid and pyrogallol respectively. Molecular docking analysis of the identified bioactive compounds with the protein myeloperoxidase denotes quercetin-3β-D-glucoside as the best ligand showing a binding score of -9.5 Kcal/mol. The formulated metabiotic revealed potential antibacterial and antioxidant properties activities. In-vivo toxicity assessment was done on the laboratory rats. Results revealed reduced body weight, urea content and creatinine level. Increase in superoxide dismutase, catalase activity and reduced content of conjugated diene, glutamate pyruvate transaminase and glutamic-oxaloacetic transaminase further supports the antioxidative potential of the metabiotic. Further study through histological sectioning of liver, kidney and spleen showed no structural abnormalities. Finally, metagenomics analysis of the gut microbiome of the experimental rats was done to check the influence of the formulated metabiotic on the gut commensals and it was found that species of Bifidobacterium and Pseudomonas are the most prevalent members of the examined groups, while, the relative proportion of other bacterial genera, such as Lactobacillus, Lactococcus, and Bacillus, were found to vary among the groups. Thus, both the in vivo and in silico studies proved that the formulated metabiotic is non-toxic and safe in use.},
}

@article {pmid40532696,
year = {2025},
author = {Er, YX and Lee, SC and Aneke, C and Conlan, S and Muslim, A and Deming, C and Che, Y and Yap, NJ and Tee, MZ and Abdull-Majid, N and Shahrizal, S and Leong, KF and Han, J and Shen, Z and Than, LTL and Park, M and Mohd Sayed, I and , and Seyedmousavi, A and Kong, HH and Loke, P and Segre, JA and Lim, YAL},
title = {Trichophyton concentricum fungal infections and skin microbiomes of Indigenous Peninsular Malaysians.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.05.034},
pmid = {40532696},
issn = {1097-4172},
abstract = {Recent outbreaks of multidrug-resistant fungi infecting human skin emphasize the importance of understanding fungal pathophysiology and spread. In efforts to address health concerns with various Indigenous Peninsular Malaysians (Orang Asli [OA]), tinea imbricata-a Trichophyton concentricum fungal skin infection-emerged as a particular concern. We investigated the etiology and transmission of tinea imbricata by culturing, testing antifungal sensitivities, and sequencing T. concentricum isolates in remote OA villages. Among regionally conserved isolates, we identified the emergence of terbinafine-resistant T. concentricum microbiologically and genomically. Investigating the skin microbiomes of 82 Indigenous OA, we found unique microbiota and lower relative abundances of bacterial commensals (Cutibacterium acnes, Staphylococcus epidermidis) among OA versus Malaysian and US urban populations, emphasizing how understudied populations provide unprecedented knowledge on host-microbiome co-evolution. These findings provide valuable insights into clinical, microbiological, and genomic features of chronic fungal skin infections, offering the potential to inform strategies to address drug resistance and effective therapy.},
}

@article {pmid40532695,
year = {2025},
author = {Sepela, RJ and Jiang, H and Shin, YH and Hautala, TL and Clardy, J and Hibbs, RE and Bellono, NW},
title = {Environmental microbiomes drive chemotactile sensation in octopus.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.05.033},
pmid = {40532695},
issn = {1097-4172},
abstract = {Microbial communities coat nearly every surface in the environment and have co-existed with animals throughout evolution. Whether animals exploit omnipresent microbial cues to navigate their surroundings is not well understood. Octopuses use "taste-by-touch" chemotactile receptors (CRs) to explore the seafloor, but how they distinguish meaningful surfaces from the rocks and crevices they encounter is unknown. Here, we report that secreted signals from microbiomes of ecologically relevant surfaces activate CRs to guide octopus behavior. Distinct molecules isolated from individual bacterial strains located on prey or eggs bind single CRs in subtly different structural conformations to elicit specific mechanisms of receptor activation, ion permeation and signal transduction, and maternal care and predation behavior. Thus, microbiomes on ecological surfaces act at the level of primary sensory receptors to inform behavior. Our study demonstrates that uncovering interkingdom interactions is essential to understanding how animal sensory systems evolved in a microbe-rich world.},
}

@article {pmid40532682,
year = {2025},
author = {Lu, N and Yao, Y and Gao, M and Liu, Z and Xie, H and Liu, J and Jiao, Q},
title = {Investigating the Impact of the Gut Microbiota on Nasal Polyp Development: Insights from Mendelian Randomization.},
journal = {International archives of allergy and immunology},
volume = {},
number = {},
pages = {1-24},
doi = {10.1159/000546793},
pmid = {40532682},
issn = {1423-0097},
abstract = {BACKGROUND: Chronic rhinosinusitis with nasal polyps has a high post-surgery recurrence, suggesting complex pathology. However, research into underlying mechanisms and contributing factors, such as gut microbiota, is lacking.

OBJECTIVE: We investigated the cause-and-effect relationship between nasal polyps and the gut microbiota and determined the influence of metabolic pathways as possible mediators.   Methods: This study utilized genetic data from genome-wide association studies. The datasets included nasal polyp data from FinnGen (6,841 cases and 308,457 control samples), microbial metabolic pathway data from the Dutch Microbiome Project (7,738 samples), and single nucleotide polymorphisms of the gut microbiota from MiBioGen (18,340 samples). First, two-sample Mendelian randomization (MR) analyses were conducted on the gut microbiota, nasal polyps, and metabolic pathways. Next, a two-step MR was employed for mediation analysis to investigate whether metabolic pathways serve as mediators between the gut microbiota and nasal polyps and to estimate the proportion of the effect of metabolism-mediated gut microbiota on nasal polyps.

RESULTS: MR analysis revealed that Alcaligenaceae was associated with a higher risk of nasal polyps by inhibiting enopyranuronate degradation, whereas Desulfovibrionales had the opposite effect by promoting l-isoleucine biosynthesis. In addition, Actinomyces reduced the risk of nasal polyps by inhibiting L-glutamate degradation but also increased the risk by inhibiting sulfate reduction.

CONCLUSION: This study identified a causal relationship between the gut microbiota and nasal polyps, with metabolic pathways as mediators. Our study provides new perspectives and possibilities for the study and treatment of chronic rhinosinusitis with nasal polyps.},
}

@article {pmid40532622,
year = {2025},
author = {Rio-Aige, K and Selma-Royo, M and Massot-Cladera, M and Everard, A and Castell, M and Rodríguez-Lagunas, MJ and Collado, MC and Pérez-Cano, FJ},
title = {A diet rich in fibre and vegetable protein during gestation and lactation shapes maternal immunity, intestinal microbiota and lipid metabolism.},
journal = {EBioMedicine},
volume = {117},
number = {},
pages = {105784},
doi = {10.1016/j.ebiom.2025.105784},
pmid = {40532622},
issn = {2352-3964},
abstract = {BACKGROUND: Establishing optimal maternal nutritional habits during pregnancy, breastfeeding, and early life is crucial for the health and welfare of both the mother and the child. However, research is lacking to understand the associated mechanisms linking maternal diet to health outcomes. The objective of this study was to assess the potential influence of two distinct diets, consumed during gestation and lactation, on the microbiota composition, immunity and lipid metabolism of Lewis dams.

METHODS: Diet 1 (D1, Mediterranean diet-like) was characterized by a high fibre content, vegetable protein, and fish oil; whereas Diet 2 (D2, slightly Western diet-like) was enriched with animal protein and lard. Fecal samples were collected weekly throughout the nutritional intervention. Blood, tissue samples (adipose tissue, intestine, mammary gland, spleen and liver) and cecal content were collected from the mother at the end of lactation (day 21) to examine the effects on the epithelial barrier, lipid metabolism, microbiota composition and metabolites, as well as the mucosal immunity.

FINDINGS: According to our findings, consumption of the D1 diet had a beneficial impact on the mothers compared to the D2 diet. D1 increased the intestinal surface area and enhanced the mucosal immunity, as evidenced by a rise in fecal immunoglobulin (Ig) A and Ig-coated bacteria levels, along with an increase in total IgG in the mesenteric lymph nodes, as well as elevated levels of T helper (Th)1-associated IgG2c isotype. Furthermore, D1 influenced the adiposity and exerted an anti-obesogenic effect on brown adipose tissue by up-regulating the expression of the genes Ucp-1, Cidea, Prdm16 and Gpr43. D1 also influenced the cecal microbiota composition, impacting its functions such as the production of short-chain fatty acids in the caecum. D1 reduced microbiota diversity by increasing beneficial taxa, such as Ruminococcaceae family and Turicibacter genus, among others. These genera showed correlations with the analysed immune and lipid metabolism parameters suggesting that microbiome modulation serves as a link between the observed systemic effects and the dietary intervention.

INTERPRETATION: The study highlights that a diet rich in fibre, vegetable protein, and fish oil, consumed during gestation and lactation, enhances maternal health by improving intestinal function, mucosal immunity, and exerting anti-obesogenic effects on lipid metabolism, likely mediated by modifications in the cecal microbiota composition and function.

FUNDING: The study was supported by LaMarató-TV3 (DIM-2-ELI, ref. 2018-27/30-31).},
}

@article {pmid40532561,
year = {2025},
author = {Oh, S and Byeon, H and Wijaya, J},
title = {Digital health framework for the predictive surveillance and diagnosis of atopic dermatitis.},
journal = {Water research},
volume = {284},
number = {},
pages = {124012},
doi = {10.1016/j.watres.2025.124012},
pmid = {40532561},
issn = {1879-2448},
abstract = {Atopic dermatitis (AD) is an inflammatory skin disease with immunological and environmental triggers that reduces the quality of life and increases the burden on health services. It is thus important to establish effective surveillance and diagnosis methods for the development of preventive and therapeutic interventions. In line with this, the present study established a digital health framework combining urban big data analytics, machine learning modeling, and environmental bioinformatics for the predictive surveillance and diagnosis of the nationwide AD prevalence in Korea. In this process, urban big data from environmental (e.g., immune response inducers), crowdsourced (web search keywords related to AD symptoms), and municipal microbiome sources (AD-associated bacteria detectable in wastewater) were combined and employed as input variables. Data preprocessing (i.e., feature selection, scaling, and normalization), model testing and selection, and hyperparameter tuning were then used to improve the prediction accuracy for AD prevalence. By applying explainable artificial intelligence methods, highly explanatory predictors, such as specific skin disease keywords associated with AD patients and environmental and inflammatory factors, were identified. Environmental genomics revealed that Streptococcus strains were dominant in human-derived wastewater, with operational taxonomic units that were strongly associated with inflammation-inducing bacteria originating from AD patients. Bioinformatic analysis subsequently revealed the pathogenotype and resistotype of these inflammation-related bacteria. Overall, our digital health framework holds great promise as an alternative to conventional complex and costly surveillance systems for the proactive guidance of the decision-making of health professionals regarding the surveillance, diagnosis, and therapeutic treatment of environmental diseases.},
}

@article {pmid40532026,
year = {2025},
author = {Matsumoto, Y and Hitaka, Y and Hirata, H and Yamamoto, Y and Kobayashi, K and Isoyama, N and Matsubara, T and Watanabe, K and Mizukami, Y and Nakagawa, S and Mishima, K and Harada, K and Shiraishi, K},
title = {Exploration of predictive factors based on oral and intestinal bacterial flora for treating patients with urothelial carcinoma.},
journal = {PloS one},
volume = {20},
number = {6},
pages = {e0324814},
doi = {10.1371/journal.pone.0324814},
pmid = {40532026},
issn = {1932-6203},
mesh = {Humans ; Male ; Female ; *Gastrointestinal Microbiome ; Saliva/microbiology ; Middle Aged ; Aged ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Immune Checkpoint Inhibitors/therapeutic use ; *Mouth/microbiology ; Phylogeny ; Case-Control Studies ; Adult ; *Urologic Neoplasms/microbiology/drug therapy ; },
abstract = {PURPOSE: The role of intestinal flora in carcinogenesis and chemotherapy efficacy has been increasingly studied; however, comparisons between oral and intestinal flora remain limited. Given the oral microbiome's role in systemic inflammation and immune modulation, it may significantly influence cancer progression and response to immunotherapy. This study aimed to identify the microbial changes in urothelial carcinoma (UC) by analyzing oral saliva and stool samples from healthy individuals and UC patients. We also examined the association between microbial composition and immune checkpoint inhibitor (ICI) response.

METHODS: A total of 20 healthy individuals and 38 patients with UC were analyzed. Among them, 27 patients with UC underwent ICI treatment. Oral saliva and stool samples were analyzed for 16S rRNA sequences to assess bacterial composition. Operational taxonomic units were generated, and phylogenetic analysis was performed using the Illumina BaseSpace.

RESULTS: Patients with UC showed higher Veillonellaceae and Prevotellaceae levels in saliva and stool, with lower levels of these bacteria associated with more prolonged overall survival and progression-free survival, particularly Veillonellaceae in stool. A higher neutrophil-to-lymphocyte ratio correlated with increased levels of these bacteria.

CONCLUSION: Veillonellaceae and Prevotellaceae are potential microbial biomarkers of survival outcomes and ICI efficacy in patients with UC. Non-invasive oral microbial sampling may facilitate personalized cancer treatment strategies.},
}

Humans
Male
Female
*Gastrointestinal Microbiome
Saliva/microbiology
Middle Aged
Aged
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Immune Checkpoint Inhibitors/therapeutic use
*Mouth/microbiology
Phylogeny
Case-Control Studies
Adult
*Urologic Neoplasms/microbiology/drug therapy

@article {pmid40531585,
year = {2025},
author = {Gevelinger, MM and Khemmani, M and Joyce, C and John, J and Sohail, S and Nasse, A and Fontes Noronha, M and Acevedo-Alvarez, M and Pham, T and Wolfe, AJ and Mueller, ER},
title = {Resilience of the Urogenital Microbiota Following Urogynecologic Surgery.},
journal = {Urogynecology (Philadelphia, Pa.)},
volume = {31},
number = {7},
pages = {650-659},
pmid = {40531585},
issn = {2771-1897},
mesh = {Humans ; Female ; *Microbiota ; Longitudinal Studies ; Middle Aged ; Adult ; Postmenopause ; *Vagina/microbiology ; Premenopause ; Aged ; RNA, Ribosomal, 16S ; *Urogenital System/microbiology ; *Pelvic Floor Disorders/surgery ; Postoperative Period ; Urinary Bladder/microbiology ; *Gynecologic Surgical Procedures ; },
abstract = {IMPORTANCE: Little is known about the resilience of the urogenital microbiota in response to urogynecologic surgery.

OBJECTIVES: The aim of this study was to determine if the urogenital microbiota are disrupted after surgery and if the postoperative composition returns to a preoperative baseline. We also sought to determine if the process of recovery differs in premenopausal women versus postmenopausal women.

STUDY DESIGN: Women undergoing surgery for pelvic floor disorders were invited to participate in this longitudinal descriptive study. Catheterized urine specimens and vaginal swabs were obtained at 4 timepoints: (1) day of surgery prior to antibiotic administration and surgical preparation; (2) immediately postoperatively; (3) 3-week postoperative visit; and (4) 12-week postoperative visit. Bacterial DNA was extracted, sequenced by 16S rRNA gene sequencing and classified taxonomically. Longitudinal data analyses were performed using linear mixed-effects models evaluating Jensen-Shannon divergence and α diversity measures.

RESULTS: Forty women, 50% of whom were postmenopausal, were included. There were significant alterations in α diversity over time (P time ≤0.05 for all comparisons), except richness in the bladder. There was perturbation immediately postoperatively, with a return to preoperative baseline at 3 and 12 weeks postoperatively. At each timepoint, premenopausal participant microbiota were not diverse, whereas postmenopausal women had diverse compositions. Jensen-Shannon divergence indices were stable in both the bladder (P = 0.95) and vagina (P = 0.88) over time in premenopausal women but showed divergence from the preoperative vagina for postmenopausal women (P = 0.004).

CONCLUSIONS: The urogenital microbiome is altered after urogynecologic surgery. In premenopausal versus postmenopausal women, the composition, stability, and process of recovery differ.},
}

Humans
Female
*Microbiota
Longitudinal Studies
Middle Aged
Adult
Postmenopause
*Vagina/microbiology
Premenopause
Aged
RNA, Ribosomal, 16S
*Urogenital System/microbiology
*Pelvic Floor Disorders/surgery
Postoperative Period
Urinary Bladder/microbiology
*Gynecologic Surgical Procedures

@article {pmid40531331,
year = {2025},
author = {Yu, Y and Park, S and Jeon, J and Lee, SH and Kim, H and Seo, D and Park, M and Park, E and Kim, JY and Cho, SJ and Jo, S and Park, G and Yang, JY},
title = {The radioprotective role of human Alistipes onderdonkii identified by multi-omic analysis in patients with prostate cancer.},
journal = {Discover oncology},
volume = {16},
number = {1},
pages = {1142},
pmid = {40531331},
issn = {2730-6011},
support = {2018R1A5A2023879//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; 2018R1A5A2023879//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; 2018R1A5A2023879//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; 2018R1A5A2023879//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; 2018R1A5A2023879//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; 2018R1A5A2023879//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; RS-2024-00460591//Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education/ ; A21IP13//Korea Hydro & Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro & Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro & Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro & Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro & Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro & Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro & Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro & Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro & Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro & Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro & Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro & Nuclear Power CO., LTD/ ; RS-2023-00301938//Learning & Academic research institution for Master's·PhD students, and Postdocs (LAMP) Program of the National Research Foundation of Korea (NRF) grant funded by the Ministry of Education/ ; RS-2023-00301938//Learning & Academic research institution for Master's·PhD students, and Postdocs (LAMP) Program of the National Research Foundation of Korea (NRF) grant funded by the Ministry of Education/ ; RS-2023-00301938//Learning & Academic research institution for Master's·PhD students, and Postdocs (LAMP) Program of the National Research Foundation of Korea (NRF) grant funded by the Ministry of Education/ ; RS-2023-00301938//Learning & Academic research institution for Master's·PhD students, and Postdocs (LAMP) Program of the National Research Foundation of Korea (NRF) grant funded by the Ministry of Education/ ; RS-2023-00301938//Learning & Academic research institution for Master's·PhD students, and Postdocs (LAMP) Program of the National Research Foundation of Korea (NRF) grant funded by the Ministry of Education/ ; },
abstract = {BACKGROUND: Advances in medical science improved cancer treatment outcomes, and radiotherapy became a common modality used by 50% of cancer patients. However, radiotherapy induces gastrointestinal distress, and it can severely impair patients' quality of life. During irradiation, the gut microbiome is critical in maintaining intestinal health and influences the body's response. This study examines the alterations in the gut microbiome and serum metabolites of prostate cancer patients undergoing radiotherapy. We investigate the potential radioprotective effects of Alistipes (A.) onderdonkii.

METHODS: Ten patients with prostate cancer receiving radiotherapy were included in this study. Fecal and serum samples were collected, and diarrhea symptoms were monitored along with each radiotherapy section.

RESULTS: After radiotherapy, nine microbiomes and 129 serum metabolites displayed significant changes associated with irradiation-induced gastrointestinal toxicity. Dehydroascorbic acid and A. onderdonkii found a correlation in the analysis between metabolites and the microbiome. Administration of A. onderdonkii significantly improved survival and reduced intestinal damage in mice after radiation exposure, suggesting A. onderdonkii as a protective agent in radiotherapy.

CONCLUSIONS: This result highlights A. onderdonkii as a potential microbial candidate for mitigating irradiation-induced damage in the gastrointestinal tract. It appears to alleviate oxidative stress and support mucosal integrity, thereby promoting resistance to radiation-induced injury.

IMPACT: This finding establishes the foundation for developing microbiome-based therapeutics for the gut health of cancer patients undergoing radiotherapy.},
}

@article {pmid40530883,
year = {2025},
author = {Ganote, CL and Caesar, L and Rice, DW and Whitaker, RJ and Newton, ILG},
title = {Evolutionary trends in Bombella apis CRISPR-Cas systems.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0016625},
doi = {10.1128/msystems.00166-25},
pmid = {40530883},
issn = {2379-5077},
abstract = {UNLABELLED: Bacteria and archaea employ a rudimentary immune system, CRISPR-Cas, to protect against foreign genetic elements such as bacteriophage. CRISPR-Cas systems are found in Bombella apis. B. apis is an important honey bee symbiont, found primarily in larvae, queens, and hive compartments. B. apis is found in the worker bee gut but is not considered a core member of the bee microbiome and has therefore been understudied with regard to its importance in the honey bee colony. However, B. apis appears to play beneficial roles in the colony, by protecting developing brood from fungal pathogens and by bolstering their development under nutritional stress. Previously, we identified CRISPR-Cas systems as being acquired by B. apis in its transition to bee association, as they are absent in a sister clade. Here, we assess the variation and distribution of CRISPR-Cas types across B. apis strains. We found multiple CRISPR-Cas types, some of which have multiple arrays, within the same B. apis genomes and also in the honey bee queen gut metagenomes. We analyzed the spacers between strains to identify the history of mobile element interaction for each B. apis strain. Finally, we predict interactions between viral sequences and CRISPR systems from different honey bee microbiome members. Our analyses show that the B. apis CRISPR-Cas systems are dynamic; that microbes in the same niche have unique spacers, which supports the functionality of these CRISPR-Cas systems; and that acquisition of new spacers may be occurring in multiple locations in the genome, allowing for a flexible antiviral arsenal for the microbe.

IMPORTANCE: Honey bee worker gut microbes have been implicated in everything from protection from pathogens to breakdown of complex polysaccharides in the diet. However, there are multiple niches within a honey bee colony that host different groups of microbes, including the acetic acid bacterium Bombella apis. B. apis is found in the colony food stores, in association with brood, in worker hypopharyngeal glands, and in the queen's digestive tract. The roles that B. apis may serve in these environments are just beginning to be discovered and include the production of a potent antifungal that protects developing bees and supplementation of dietary lysine to young larvae, bolstering their nutrition. Niche specificity in B. apis may be affected by the pressures of bacteriophage and other mobile elements, which may target different strains in each specific bee environment. Studying the interplay between B. apis and its mobile genetic elements (MGEs) may help us better understand microbial community dynamics within the colony and the potential ramifications for the honey bee host.},
}

@article {pmid40530879,
year = {2025},
author = {Ke, Z and Ma, Q and Ye, X and Jin, Y and Wang, Y and Zhao, X and Su, Z},
title = {Oral delivery of GLP-1 peptide using recombinant Lactobacillus gasseri for the treatment of type 2 diabetes mellitus.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0282824},
doi = {10.1128/spectrum.02828-24},
pmid = {40530879},
issn = {2165-0497},
abstract = {Glucagon-like peptide-1 (GLP-1) is an effective therapeutic peptide for the treatment of type 2 diabetes mellitus (T2DM). Here, we constructed an effective probiotic-based oral GLP-1 delivery system by engineering the probiotic strain of Lactobacillus gasseri (Lgs[GPA]) to secrete GLP-1 fusion peptide, which combines GLP-1 with protein transduction domain (PTD) and a serum albumin binding peptide (ABP), GLP-1-PTD-ABP (GPA). The supernatants of Lgs[GPA] cultures significantly upregulated the expression of PDX-1 and stimulated insulin release in Min6 cells. Daily oral administration of Lgs[GPA] in db/db mice significantly alleviated insulin resistance, hyperglycemia, and dyslipidemia. Simultaneously, the abundance of unclassified_f_Erysipelotrichaceae and Intestinimonas was significantly reduced in db/db mice, while the average abundance of Akkermansia increased in the SD rats. These findings demonstrate that the probiotic-based delivery system represents a versatile and effective strategy for the oral administration of therapeutic peptides. Collectively, our results highlight the potential of this probiotic-based approach as a promising therapeutic and preventive intervention for T2DM.IMPORTANCEIt is important to develop the oral delivery strategy for therapeutic peptides. Due to issues with patient adherence and the low oral bioavailability of current administration methods, researchers have been exploring oral delivery strategies for GLP-1 analogs for many years, including the use of advanced microbiome therapeutics (AMTs). AMTs offer the potential to use engineered microbes for innovative therapeutic applications, such as the oral delivery of GLP-1 analogs. Our approaches offer a general oral delivery strategy for therapeutic peptides. The probiotic-based approach represents a promising method for treating and preventing T2DM.},
}

@article {pmid40530826,
year = {2025},
author = {Carolak, E and Czajkowska, J and Stypułkowska, A and Waszczuk, W and Dutkiewicz, A and Grzymajlo, K},
title = {Being a better version of yourself: genetically engineered probiotic bacteria as host defense enhancers in the control of intestinal pathogens.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2519696},
doi = {10.1080/19490976.2025.2519696},
pmid = {40530826},
issn = {1949-0984},
mesh = {*Probiotics ; Humans ; *Gastrointestinal Microbiome ; Genetic Engineering ; Animals ; *Microorganisms, Genetically-Modified/genetics ; *Bacteria/genetics ; },
abstract = {Intestinal pathogens pose a significant global health burden, and traditional antibiotic treatments often disrupt the beneficial gut microbiota that plays a crucial role in maintaining host health through pathogen prevention and immune regulation. Although probiotics have emerged as promising therapeutic agents, their efficacy is limited by strain-dependent variations, survival challenges in the gastrointestinal tract, and inconsistent immune responses. Recent advances in genetic engineering, particularly CRISPR-Cas systems and their combinations with complementary technologies, such as Cre-lox and RecE/T, have enabled the precise modification of probiotic strains to enhance their therapeutic potential. These enhanced probiotics demonstrate improved functionality through multiple mechanisms, including increased adhesion via the expression of specific proteins (InlA, FnBPA, and LAP), targeted antimicrobial activity through engineered sensing systems (Lactococcus lactis detecting Vibrio cholerae CAI-1), and enhanced immunomodulation through cytokine production. Results have demonstrated the potential of genetically modified probiotics in preventing and treating gastrointestinal infections through mechanisms that include competitive exclusion, bacteriocin production, intestinal barrier reinforcement, and immune modulation. However, challenges remain in ensuring genetic stability and preventing horizontal gene transfer. Future research should focus on optimizing probiotic strains for targeted applications while addressing biosafety concerns. By understanding the complex interplay between probiotics, pathogens, and host immunity, innovative strategies can be developed to harness the full therapeutic potential of probiotic interventions in maintaining gut health.},
}

*Probiotics
Humans
*Gastrointestinal Microbiome
Genetic Engineering
Animals
*Microorganisms, Genetically-Modified/genetics
*Bacteria/genetics

@article {pmid40530746,
year = {2025},
author = {Lee, E and Yang, SI and Suh, DI and Kim, HB and Lee, SY and Kwon, SO and Hong, SJ},
title = {Environmental factors shaping atopic dermatitis: Lessons from longitudinal cohort studies.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {36},
number = {6},
pages = {e70130},
doi = {10.1111/pai.70130},
pmid = {40530746},
issn = {1399-3038},
support = {//Korea Environment Industry & Technology Institute (KEITI)/ ; RS-2022-KE002048//Ministry of Environment (Republic of Korea)/ ; 2008-E33030-00//Korea National Institute of Health/ ; 2009-E33033-00//Korea National Institute of Health/ ; 2011-E33021-00//Korea National Institute of Health/ ; 2012-E33012-00//Korea National Institute of Health/ ; 2013-E51003-00//Korea National Institute of Health/ ; 2014-E51004-00//Korea National Institute of Health/ ; 2014-E51004-01//Korea National Institute of Health/ ; 2014-E51004-02//Korea National Institute of Health/ ; 2017-E67002-00//Korea National Institute of Health/ ; 2017-E67002-01//Korea National Institute of Health/ ; 2017-E67002-02//Korea National Institute of Health/ ; 2020E670200//Korea National Institute of Health/ ; 2020E670201//Korea National Institute of Health/ ; 2020E670202//Korea National Institute of Health/ ; 2023E120300//Korea National Institute of Health/ ; 2023E120301//Korea National Institute of Health/ ; 2023E120302//Korea National Institute of Health/ ; BCRI-25076//Chonnam National University Hospital Biomedical Research Institute/ ; },
mesh = {Humans ; *Dermatitis, Atopic/etiology/epidemiology/immunology ; *Environmental Exposure/adverse effects ; Longitudinal Studies ; Female ; Pregnancy ; Infant ; Exposome ; Gastrointestinal Microbiome ; },
abstract = {Atopic dermatitis (AD) is a prevalent chronic inflammatory skin disease arising from a multifaceted interplay between genetic susceptibility and environmental exposures. Longitudinal cohort studies have been instrumental in elucidating the contribution of environmental factors to both the onset and persistence of AD. This review synthesizes evidence from such studies to delineate key environmental determinants across various domains. Early-life exposures, including delivery mode and antibiotic exposure, modulate microbial composition and function, thereby influencing immune development and predisposing individuals to AD. Both outdoor and indoor air pollutants, such as particulate matter and volatile organic compounds, have been shown to impair skin barrier integrity and dysregulate immune responses, facilitating the initiation and progression of AD. Nutritional factors, encompassing maternal and infant dietary patterns, shape gut microbiota and metabolite profiles and systemic immune activity, further modulating AD risk. Moreover, psychological stress during the prenatal and postnatal periods has been associated with alterations in immune function and epigenetic programming, which may heighten susceptibility to AD. Environmental influences also appear to vary by AD phenotype and trajectory, underscoring the need for individualized prevention strategies. Advances in exposome research, encompassing both external and internal environmental components, have enhanced mechanistic understanding and facilitated the identification of candidate biomarkers. Collectively, current evidence supports the notion that early-life environmental exposures act not as isolated determinants but in concert with genetic, microbial, and immunologic factors to shape AD pathogenesis. A comprehensive framework integrating exposomics and multiomics may ultimately inform the development of targeted preventive and therapeutic strategies for children with AD.},
}

Humans
*Dermatitis, Atopic/etiology/epidemiology/immunology
*Environmental Exposure/adverse effects
Longitudinal Studies
Female
Pregnancy
Infant
Exposome
Gastrointestinal Microbiome