@article {pmid40447085,
year = {2025},
author = {Maughan, L and Koolman, L and Macori, G and Killian, C and Fanning, S and Whyte, P and Bolton, D},
title = {Characterization of bacterial and fungal populations in retail kefirs in Ireland.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-26587},
pmid = {40447085},
issn = {1525-3198},
abstract = {Kefir is an increasingly popular dairy- or sugar-based fermented food product. The aim of our study was to investigate the bacterial and fungal communities in 28 retail kefirs including 21 milk kefirs, including 3 thick kefir yogurt and 4 water kefir products. Full-length amplicon nanopore sequencing of both 16S rRNA (for bacteria) and intergenic spacer (for fungi) was undertaken. The diversity within and between groups was analyzed (α and β diversity) and linear discriminant analysis effect size analysis was undertaken to identify biomarkers that differentially characterize the microbial communities associated with different kefir types. The pH, lactic acid concentration, total viable counts (TVC), lactic acid bacteria (LAB), total coliform counts (TCC), and yeast counts were also investigated. The main bacterial genera (and species) were Lactococcus (cremoris) and Streptococcus (thermophilus), and other bacteria such as Lactobacillus (delbrueckii) and Lentilactobacillus (kefiri) were also detected. The fungal populations were mainly composed of Brettanomyces (anomalus), Zygotorulaspora (florentina) and Kazachstania (unispora), but with many different fungal genera/species detected. The pH ranged from 3.1 to 4.7 with a mean of 4.2 ± 0.07 and the lactic acid content ranged from 0.1 to 9 g/L with a mean of 5.6 ± 0.53. In milk kefirs the TVC, LAB, TCC, and yeast counts ranged from 3.1 to 9.1, 3.4 to 9.0, not detected (ND) to 1.6 and ND to 6.5 log10 cfu/mL or cfu/g, respectively. The corresponding counts in water kefirs were 4.1 to 7.3 (TVC), 4.1 to 7.0 (LAB), ND to 1.1 (TCC), and 3.9 to 7.0 (yeast) log10 cfu/mL or cfu/g, respectively. It was concluded that although the 28 retail kefirs analyzed had a rich diversity of bacteria and fungi the bacteriome was dominated by bacteria belonging to the Lactococcus and Streptococcus genera and the main bacterial species were Lactococcus cremoris, Streptococcus thermophiles, Streptococcus suis, Lactobacillus delbrueckii, and Streptococcus sp. HSISS1. The fungal microbiome was dominated by Zygotorulaspora and the most abundant fungal species included Zygotorulaspora florentina, Brettanomyces anomalus, and Kazachstania unispora. To the best of our knowledge, this is the first study in Ireland to use full-length nanopore sequencing to characterize both bacterial and fungal communities in retail kefirs.},
}

@article {pmid40446899,
year = {2025},
author = {Fang, P and Ye, S and Luo, Z and Guo, R and Jiang, Y and Liu, L and Li, S and Xiao, F},
title = {Nanoplastics under the charge effect: Unveiling the potential threats to amphibian (Rana nigromaculata) growth, intestinal damage, and microbial ecology.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126566},
doi = {10.1016/j.envpol.2025.126566},
pmid = {40446899},
issn = {1873-6424},
abstract = {Nanoplastics (NPs) are a contaminant that may be found in charged forms in the environment, capable of accumulating in aquatic organisms and affecting their health. This study compared the effects of positively charged NPs (PS-NH2, 30nm) and negatively charged NPs (PS-COOH, 30nm) at 6 and 60 mg/L on the growth and development of black-spotted frog tadpoles (Rana nigromaculata), as well as on intestinal damage, and microbial ecology. The results indicated that exposure to both types of NPs significantly reduced the survival rate of tadpoles, while significantly increasing their body weight and body length (p <0.05). Compared to PS-COOH, exposure to PS-NH2 resulted in more adverse intestinal tissue damage and induced more severe intestinal oxidative stress. Furthermore, exposure to PS-NH2 significantly reduced the abundance and diversity of the microbiome associated with gut function and nutrient absorption, indirectly leading to more severe intestinal damage and growth changes. In addition, functional prediction and gene transcription analysis showed that exposure to charged PS-NPs caused changes in genes associated with glycolysis and lipid metabolism, indicating that the glucose-lipid metabolism of tadpoles is impacted. This study demonstrated the growth differences and intestinal toxicity of NPs exposure in tadpoles, explores the potential connections between gut microbiota and glucose-lipid metabolism, and provides new perspectives on the health risks of NPs in amphibians.},
}

@article {pmid40446807,
year = {2025},
author = {Ding, X and Ting, NL and Wong, CC and Huang, P and Jiang, L and Liu, C and Lin, Y and Li, S and Liu, Y and Xie, M and Liu, W and Yuan, K and Wang, L and Zhang, X and Ding, Y and Li, Q and Sun, Y and Miao, Y and Ma, L and Gao, X and Li, W and Wu, WKK and Sung, JJY and Wong, SH and Yu, J},
title = {Bacteroides fragilis promotes chemoresistance in colorectal cancer, and its elimination by phage VA7 restores chemosensitivity.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.05.004},
pmid = {40446807},
issn = {1934-6069},
abstract = {Chemoresistance is a main cause of colorectal cancer (CRC) treatment failure. We identified that Bacteroides fragilis is enriched in patients with CRC resistant to chemotherapy in two independent cohorts, and its abundance is associated with poor survival. Consistently, administration of B. fragilis to CRC xenografts and Apc[Min/+]- and AOM/DSS-induced CRC mice all significantly attenuated the antitumor efficacy of 5-FU and OXA. Mechanistically, B. fragilis colonized colon tumors and mediated its effect via its surface protein SusD/RagB binding to the Notch1 receptor in CRC cells, leading to activation of the Notch1 signaling pathway and the induction of epithelial-to-mesenchymal transition (EMT)/stemness to suppress chemotherapy-induced apoptosis. Either deletion of SusD/RagB or blockade of Notch1 signaling abrogated B. fragilis-mediated chemoresistance. Finally, B. fragilis-targeting phage VA7 selectively suppressed B. fragilis and restored chemosensitivity in preclinical CRC mouse models. Our findings have offered insights into the potential of precise gut microbiota manipulation for the clinical management of CRC.},
}

@article {pmid40446806,
year = {2025},
author = {Li, J and Liu, H and Wang, J and Macdonald, CA and Singh, P and Cong, VT and Klein, M and Delgado-Baquerizo, M and Singh, BK},
title = {Drought-induced plant microbiome and metabolic enrichments improve drought resistance.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.05.002},
pmid = {40446806},
issn = {1934-6069},
abstract = {Plant-microbiome interactions are crucial in maintaining plant health and productivity under stress; however, little is known about these interactions under drought. Here, using wheat as a model, we combine genomics and culture-dependent methods to investigate the interactions between the soil, root, and rhizosphere microbiomes with rhizosphere metabolomes and plant phenotypes. We find that drought conditions promote microbial colonization in plant microbiomes, enriching Streptomyces coeruleorubidus and Leifsonia shinshuensis, while also increasing 4-oxoproline levels in the rhizosphere, potentially attracting S. coeruleorubidus. Consistently, genes facilitating microbial responses to drought, including the N-terminal acetyltransferase rimJ, are enriched, while S. coeruleorubidus and L. shinshuensis reintroduction promotes host drought resistance. Drought-legacy-effect experiments further support these benefits, with increased plant biomass and yield in the subsequent growth cycle under drought. Collectively, this study informs how drought-induced microbial and metabolite enrichments improve plant adaptation to abiotic stresses, potentially informing development of bio-based tools to mitigate drought effects. VIDEO ABSTRACT.},
}

@article {pmid40446645,
year = {2025},
author = {Toporcerová, S and Badovská, Z and Kriváková, E and Mikulová, V and Mareková, M and Altmäe, S and Rabajdová, M},
title = {Embryo secretome in predicting embryo quality and IVF treatment outcome.},
journal = {Reproductive biomedicine online},
volume = {51},
number = {1},
pages = {104825},
doi = {10.1016/j.rbmo.2025.104825},
pmid = {40446645},
issn = {1472-6491},
abstract = {In IVF treatment, accurate prediction of embryo quality and successful embryo implantation are critical challenges. Recent research has highlighted the importance of the embryo secretome, the collection of molecules secreted by the embryo into the culture medium, in assessing embryo quality as a non-invasive preimplantation testing platform. The secretome plays a role in many essential processes, from gamete maturation to embryonic development. Molecules such as cell-free DNA, mitochondrial DNA and small non-coding RNA, including microRNA and PIWI-interacting RNA, together with the proteome, metabolome, microbiome and extracellular vesicles, have emerged as important players in predicting IVF outcomes. These molecules, present in the culture medium, have shown correlations with embryo viability, ploidy and implantation potential. Nevertheless, extensive validation in larger cohorts and an assessment of the applicability of the identified biomarkers in clinical settings is warranted. This article summarizes the molecular markers analysed in spent embryo culture medium and their potential for assessing embryo quality and predicting success in IVF outcomes.},
}

@article {pmid40446472,
year = {2025},
author = {Chen, L and Ahmad, M and Li, J and Li, J and Yang, Z and Hu, C},
title = {Gut microbiota manipulation to mitigate the toxicities of environmental pollutants.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {285},
number = {},
pages = {107425},
doi = {10.1016/j.aquatox.2025.107425},
pmid = {40446472},
issn = {1879-1514},
abstract = {The gut microbiome, commonly termed as a "super organ", plays a crucial role in the modulation of various biological functions associated with metabolism, endocrinology, immunology, and neurology. However, gut microbiome is extremely susceptible to the risks of environmental pollutants, which will drive gut microbial community to dysbiosis. Simultaneously, restoring healthy gut microbiome can protect the hosts from the health hazards of pollutants. It is increasingly verified that probiotics, prebiotics, and fecal microbiota transplantation (FMT) are efficacious measures to manipulate and remediate gut microecosystem. Among various probiotic strains, lactic acid bacteria are the most extensively applied in toxicity mitigation, which is characterized by shaping gut microbiota structure and metabolism, increasing gut epithelial barrier integrity, promoting fecal elimination of pollutants, suppressing inflammation symptoms, and then improving host systemic physiology. Prebiotics are dietary fibers that cannot be digested by the host, but can be fermented by specific gut bacteria to produce short chain fatty acids, which are identified as the key effect molecules in the manifestation of prebiotic toxicity mitigation actions. In addition, by transplanting the entire community of healthy gut microbiota, FMT also shows effective performances in counteracting the adverse effects of environmental pollutants and recovering host animal health. Intriguingly, FMT from young donors is even found to inhibit the toxic disturbances in healthy aging progression. Based on current evidence, this review summarized the findings about using probiotics, prebiotics, and FMT to manipulate gut microbiota and alleviate the health impairment of environmental pollutants. Key mechanistic insights into the interactive behaviors were underlined. Furthermore, the challenges and future directions in harnessing gut microbiota manipulation as a novel therapeutic approach to mitigate pollutant-induced toxicities were postulated. This review is expected to advocate comprehensive scientific research and literally favor the application of health intervention strategies.},
}

@article {pmid40446444,
year = {2025},
author = {Eveleens Maarse, BC and Hofstede, AD and Jansen, MAA and Moerland, M},
title = {A systematic review of pharmaceutical targets in the mucosal immune system for treatment of non-intestinal auto-immune diseases.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {188},
number = {},
pages = {118205},
doi = {10.1016/j.biopha.2025.118205},
pmid = {40446444},
issn = {1950-6007},
abstract = {The mucosal immune system entails the immune cells located in the body's mucosal surfaces and their mediators. Its function is to balance immune responses to pathogens and tolerance to harmless antigens. Treatment of autoimmune diseases is complicated by adverse events caused by suppression of systemic immunity by immunosuppressive medication. Targeting the mucosal immune system specifically in treating autoimmune diseases could circumvent systemic immune suppression and thereby reduce infection risk. This systematic review aims to provide an overview of pharmaceutical targets in the mucosal immune system, as a starting point in the search for new treatments for extra-intestinal auto-immune diseases. Preclinical and clinical studies were included and categorized into eight target categories: 'immune cells', 'signal transduction', 'inflammatory mediators', 'antibodies', 'microbiome', 'tolerance and mucosal vaccination', 'intestinal barrier' and 'other'. Studies investigating the most promising targets, namely mucosal-associated invariant T cells (MAIT cells) and tolerance induction by mucosal vaccination, are described in more detail. MAIT cells have been shown to play a role in the pathophysiology of various auto-immune diseases, particularly in multiple sclerosis (MS). Although the role of these cells has not yet been established fully, mouse studies show that the antagonism of MAIT cells has the potential to be used in the treatment of auto-immune diseases. Mucosal vaccination has demonstrable effects on the immune system, but treatment regimens and antigens must be improved to demonstrate clinical effects more extensively. This systematic review was registered in PROSPERO under number CRD42023421093.},
}

@article {pmid40446379,
year = {2025},
author = {Jiang, G and Ruan, Z and Yin, Y and Hu, C and Tian, L and Lu, JN and Wang, S and Tang, YT and Qiu, R and Chao, Y},
title = {Keystone species in microbial communities: From discovery to soil heavy metal-remediation.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138753},
doi = {10.1016/j.jhazmat.2025.138753},
pmid = {40446379},
issn = {1873-3336},
abstract = {Keystone species have significant impacts on community structure and function regardless of their abundance in space and time, whether individually or collectively. They play a unique and crucial role, and their removal can lead to substantial changes in the microbiome. It is one of the necessary processes to explore key microbial functions and interactions by studying keystone species. The term "keystone species" has been proposed and developed for nearly 60 years, but in microbiology, it is often used interchangeably with similar terms, which hinders the integration and advancement of research. Here, we review similar terms for keystone species in the microbial field and suggest using "keystone species" instead of "keystone taxa". We also summarize and analyze identification approaches for keystone species, highlighting the advantages and disadvantages of each while providing recommendations for selecting appropriate approaches in the environmental field. Based on the serious soil environment problem, this review also takes the research in the field of heavy metal-contaminated soils as case studies, and summarizes and analyzes the research situation of keystone species. Finally, we discuss the current limitations in research on keystone species, offering insights into their future development and application in the microbial field, particularly in remediation for heavy metal-contaminated soils. This review aims to summarize existing research on microbial keystone species and connect the findings to the field of environmental remediation, providing a reference for developing more effective remediation strategies and enhancing our understanding of ecosystem health.},
}

@article {pmid40446358,
year = {2025},
author = {Porcari, S and Ng, SC and Zitvogel, L and Sokol, H and Weersma, RK and Elinav, E and Gasbarrini, A and Cammarota, G and Tilg, H and Ianiro, G},
title = {The microbiome for clinicians.},
journal = {Cell},
volume = {188},
number = {11},
pages = {2836-2844},
doi = {10.1016/j.cell.2025.04.016},
pmid = {40446358},
issn = {1097-4172},
mesh = {Humans ; *Microbiota ; Clinical Trials as Topic ; },
abstract = {Despite promising evidence in diagnostics and therapeutics, microbiome research is not yet implemented into clinical medicine. Several initiatives, including the standardization of microbiome research, the refinement of microbiome clinical trial design, and the development of communication between microbiome researchers and clinicians, are crucial to move microbiome science toward clinical practice.},
}

Humans
*Microbiota
Clinical Trials as Topic

@article {pmid40446105,
year = {2025},
author = {Saxena, V and Datla, A and Pradhan, P and Deheriya, M and Tiwari, N and Shoukath, S},
title = {Impact of smokeless and smoking tobacco on subgingival microbial composition: A comparative study.},
journal = {Przeglad epidemiologiczny},
volume = {79},
number = {1},
pages = {95-103},
doi = {10.32394/pe/203721},
pmid = {40446105},
issn = {0033-2100},
mesh = {Humans ; Female ; Male ; Adult ; *Tobacco, Smokeless/adverse effects ; Cross-Sectional Studies ; India/epidemiology ; Middle Aged ; *Gingiva/microbiology ; *Microbiota ; *Smoking ; },
abstract = {BACKGROUND: Environmental perturbations such as tobacco use causes increased bacterial diversity in the subgingival microbiome. Despite the recognized impact of tobacco on oral health, there is a notable gap in the literature regarding the specific characteristics of the subgingival microbiome among Indian tobacco users.

OBJECTIVE: This study seeks to provide a comparative analysis of subgingival microbial profile of smokeless tobacco users and smokers with an otherwise healthy periodontal environment.

MATERIAL AND METHODS: This cross-sectional study at a Tertiary Dental Hospital in India recruited 118 participants: 52 non-tobacco users (Group 1), 36 smokeless tobacco users (Group 2), and 30 smokers (Group 3). Subgingival samples were collected from mesial surfaces of teeth (16, 46) using sterile paper points and analysed via the streak plate method for bacterial profiling. Clinical examinations assessed oral hygiene, gingival, and periodontal health using indices: Bleeding on Probing (BoP), Pocket Depth (PD), and Approximate Plaque Index (API). Categorical variables were analysed using the Chi-square test, and odds ratios were calculated.

RESULTS: Gender distribution was 76.3% male and 23.7% female (p < 0.05). Group 2 had a significantly higher prevalence of gram-positive cocci (100%) and gram-negative coccobacilli (94.4%) compared to Group 1, with a 12.4 times increased risk for gram-negative coccobacilli (p < 0.05). Group 2 also showed a higher occurrence of Aggregatibacter (88.9%) and a 3.5 times increased risk (p < 0.05). Group 3 exhibited significantly more gram-positive cocci and gram-negative coccobacilli than Group 1, with 3.8 times and 4.7 times increased risks, respectively (p < 0.05). Rothia species were significantly more common in smokers (13.3%) than non-tobacco users (0%) (p < 0.05).

CONCLUSIONS: Despite the absence of periodontal disease, the elevated presence of Aggregatibacter, Enterococcus, Klebsiella, and Rothia species indicates a shift towards increased bacterial diversity and a higher risk of future periodontitis.},
}

Humans
Female
Male
Adult
*Tobacco, Smokeless/adverse effects
Cross-Sectional Studies
India/epidemiology
Middle Aged
*Gingiva/microbiology
*Microbiota
*Smoking

@article {pmid40445957,
year = {2025},
author = {Mhanna, MA and Gauthier, DT and Shollenberger, LM},
title = {Schistosoma mansoni infection causes consistent changes to the fecal bacterial microbiota of mice across and within sites.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0324638},
doi = {10.1371/journal.pone.0324638},
pmid = {40445957},
issn = {1932-6203},
mesh = {Animals ; *Feces/microbiology ; *Schistosomiasis mansoni/microbiology/parasitology ; Mice ; *Schistosoma mansoni ; Female ; *Gastrointestinal Microbiome ; Male ; },
abstract = {Eggs of Schistosoma mansoni are produced by adult female worms in mesenteries of infected hosts. Eggs can cross the intestinal barrier and form granulomas in the tissue or breach and exit the host through fecal excretion. These interactions may affect the host microbiome assemblages. Given the potential for schistosomal alteration of host gut microbiome and subsequent effects on the fecal bacterial composition, it is important to conduct controlled microbiome studies on model animals. While pursuing these studies, it is important to take into account the different conditions in which microbiome studies are conducted and their consequent impacts on variability and reproducibility of results. In particular, we are interested in inter-institutional effects on controlled microbiome studies, in which the study location itself may impact study outcomes. In this work, we report global changes caused by acute and chronic schistosomiasis on the fecal microbiome of mice at two different institutions and three timepoints.},
}

Animals
*Feces/microbiology
*Schistosomiasis mansoni/microbiology/parasitology
Mice
*Schistosoma mansoni
Female
*Gastrointestinal Microbiome
Male

@article {pmid40445867,
year = {2025},
author = {Cai, X and Zhong, L},
title = {Gut microbiome and host interactions in catfish: hybridization structures bacterial communities along catfish intestinal tract.},
journal = {Physiological genomics},
volume = {},
number = {},
pages = {},
doi = {10.1152/physiolgenomics.00058.2025},
pmid = {40445867},
issn = {1531-2267},
support = {CARS-46//China Agriculture Research System of MOF and MARA/ ; },
}

@article {pmid40445430,
year = {2025},
author = {Chen, F and Zhou, Y and Mao, X and Lin, R and Huang, H},
title = {A systematic Mendelian randomized study of the effects of the gut microbiome and immune cells on pancreatic neuroendocrine tumors.},
journal = {Discover oncology},
volume = {16},
number = {1},
pages = {961},
pmid = {40445430},
issn = {2730-6011},
support = {No. 2020J011013//Natural Science Foundation of Fujian Province, China/ ; No. 2023Y9149//Joint Funds for the Innovation of Science and Technology, Fujian province, China/ ; No. 2021-76//Medical Minimally Invasive Center Program of Fujian Province and National Key Clinical Specialty Discipline Construction Program, China/ ; },
abstract = {Pancreatic neuroendocrine tumors (pNETs) are a rare subset of pancreatic cancers often diagnosed late and characterized by complex behaviors. Recent evidence suggests the gut microbiome (GM) significantly influences various diseases by modulating the immune system. This study utilized a Mendelian randomization (MR) approach to investigate the causal relationship between GM and pNETs, using single nucleotide polymorphism data as instrumental variables. Two-sample MR analysis identified significant correlations between GM and immune cell types. The study found eight specific GMs affecting pNETs risk: the family Sutterellaceae (OR: 1.52, 95% CI 1.10-2.10, p = 0.01), the genus Paraprevotella (OR: 1.34, 95% CI 1.05-1.72, p = 0.02), the species Paraprevotella unclassified (OR: 1.40, 95% CI 1.08-1.81, p = 0.01), and the species Ruminococcus torques (OR: 1.45, 95% CI 1.12-1.89, p = 0.01) increased risk, while the class Gammaproteobacteria (OR: 0.75, 95% CI 0.57-0.98, p = 0.04), the family Acidaminococcaceae (OR: 0.70, 95% CI 0.52-0.94, p = 0.02), the species Paraprevotella xylaniphila (OR: 0.72, 95% CI 0.54-0.96, p = 0.03), and the species Bacteroides finegoldii (OR: 0.68, 95% CI 0.51-0.91, p = 0.01) decreased it. Mediation analysis indicated the species Ruminococcus torques mediated the effect of CD25 on CD45RA+ CD4 non-regulatory T cells on pNETs, accounting for 3.6% of the total effect. This study provides evidence suggestive of a potential causal role of specific GM compositions in pNETs progression and their mediation through immune cell signatures. However, mechanistic studies are required to further validate this relationship.},
}

@article {pmid40445204,
year = {2025},
author = {Schaible, GA and Cliff, JB and Crandall, JA and Bougoure, JJ and Mathuri, MN and Sessions, AL and Atwood, J and Hatzenpichler, R},
title = {Comparing Raman and NanoSIMS for heavy water labeling of single cells.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0165924},
doi = {10.1128/spectrum.01659-24},
pmid = {40445204},
issn = {2165-0497},
abstract = {Stable isotope probing (SIP) experiments in conjunction with Raman microspectroscopy (Raman) or nano-scale secondary ion mass spectrometry (NanoSIMS) are frequently used to explore single cell metabolic activity in pure cultures as well as complex microbiomes. Despite the increasing popularity of these techniques, the comparability of isotope incorporation measurements using both Raman and NanoSIMS directly on the same cell remains largely unexplored. This knowledge gap creates uncertainty about the consistency of single-cell SIP data obtained independently from each method. Here, we conducted a comparative analysis of 543 Escherichia coli cells grown in M9 minimal medium in the absence or presence of heavy water ([2]H2O) using correlative Raman and NanoSIMS measurements to quantify the results between the two approaches. We demonstrate that Raman and NanoSIMS yield highly comparable measurements of [2]H incorporation, with varying degrees of similarity based on the mass ratios analyzed using NanoSIMS. The [12]C[2]H/[12]C[1]H and [12]C2[2]H/[12]C2[1]H mass ratios provide targeted measurements of C-H bonds but may suffer from biases and background interference, while the [2]H/[1]H ratio captures all hydrogen with lower detection limits, making it suitable for applications requiring comprehensive [2]H quantification. Importantly, despite its higher mass resolution requirements, the use of C2[2]H/C2[1]H may be a viable alternative to the use of C[2]H/C[1]H due to lower background and higher overall count rates. Furthermore, using an empirical approach in determining Raman wavenumber ranges via the second derivative improved the data equivalency of [2]H quantification between Raman and NanoSIMS, highlighting its potential for enhancing cross-technique comparability. These findings provide a robust framework for leveraging both techniques, enabling informed experimental design and data interpretation. By enhancing cross-technique comparability, this work advances SIP methodologies for investigating microbial metabolism and interactions in diverse systems.IMPORTANCEAccurate and reliable measurements of cellular properties are fundamental to understand the function and activity of microbes. This study addresses to what extent Raman microspectroscopy and nano-scale secondary ion mass spectrometry (NanoSIMS) measurements of single cell anabolic activity can be compared. Here, we study the relationship of the incorporation of a stable isotope ([2]H through incorporation of [2]H2O) as determined by the two techniques and calculate a correlation coefficient to support the use of either technique when analyzing cells incubated with [2]H2O. The ability to discern between the comparative strengths and limitations of these techniques is invaluable in refining experimental protocols, enhancing data comparability between studies, data interpretation, and ultimately advancing the quality and reliability of outcomes in microbiome research.},
}

@article {pmid40445192,
year = {2025},
author = {Mullinax, SR and Darby, AM and Gupta, A and Chan, P and Smith, BR and Unckless, RL},
title = {A suite of selective pressures supports the maintenance of alleles of a Drosophila immune peptide.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
doi = {10.7554/eLife.90638},
pmid = {40445192},
issn = {2050-084X},
support = {AI139154/NH/NIH HHS/United States ; 2330095//National Science Foundation/ ; CMADP COBRE P20-GM103638/NH/NIH HHS/United States ; },
mesh = {Animals ; *Alleles ; Female ; Male ; *Drosophila Proteins/genetics/immunology ; *Selection, Genetic ; Providencia/immunology ; *Drosophila/genetics/immunology/microbiology ; Gastrointestinal Microbiome ; *Drosophila melanogaster/genetics/immunology/microbiology ; *Antimicrobial Peptides/genetics/immunology ; },
abstract = {The innate immune system provides hosts with a crucial first line of defense against pathogens. While immune genes are often among the fastest evolving genes in the genome, in Drosophila, antimicrobial peptides (AMPs) are notable exceptions. Instead, AMPs may be under balancing selection, such that over evolutionary timescales, multiple alleles are maintained in populations. In this study, we focus on the Drosophila AMP Diptericin A, which has a segregating amino acid polymorphism associated with differential survival after infection with the Gram-negative bacteria Providencia rettgeri. Diptericin A also helps control opportunistic gut infections by common Drosophila gut microbes, especially those of Lactobacillus plantarum. In addition to genotypic effects on gut immunity, we also see strong sex-specific effects that are most prominent in flies without functional diptericin A. To further characterize differences in microbiomes between different diptericin genotypes, we used 16S metagenomics to look at the microbiome composition. We used both lab-reared and wild-caught flies for our sequencing and looked at overall composition as well as the differential abundance of individual bacterial families. Overall, we find flies that are homozygous for one allele of diptericin A are better equipped to survive a systemic infection from P. rettgeri, but in general have a shorter lifespans after being fed common gut commensals. Our results suggest a possible mechanism for the maintenance of genetic variation of diptericin A through the complex interactions of sex, systemic immunity, and the maintenance of the gut microbiome.},
}

Animals
*Alleles
Female
Male
*Drosophila Proteins/genetics/immunology
*Selection, Genetic
Providencia/immunology
*Drosophila/genetics/immunology/microbiology
Gastrointestinal Microbiome
*Drosophila melanogaster/genetics/immunology/microbiology
*Antimicrobial Peptides/genetics/immunology

@article {pmid40444979,
year = {2025},
author = {Axelsson-Olsson, D and Gubonin, N and Israelsson, S and Pinhassi, J},
title = {Experimental assessment of interactions between marine bacteria and model protists: from predator-prey relationships to bacterial-mediated lysis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0092925},
doi = {10.1128/aem.00929-25},
pmid = {40444979},
issn = {1098-5336},
abstract = {Bacteria in aquatic environments are a principal food source for predatory protists. Whereas interactions between bacteria and protists are recognized to determine the pathogenesis and epidemiology of several human pathogens, few studies have systematically characterized the interactions between specific aquatic bacteria and protists beyond the prey-predator relation. We, therefore, surveyed individual co-cultures between 18 different genome-sequenced marine bacteria with known virulence gene repertoires and three model protist species widely used for assessing bacteria-protist interactions. Strikingly, 10, 5, and 3 bacterial isolates were capable of lysing the protists Acanthamoeba polyphaga, Tetrahymena pyriformis, and Euglena gracilis, respectively. A majority of the bacteria were able to grow and/or maintain viable populations in the presence of viable protists. Some bacteria survived longer with viable protists but not heat-killed protists and were observed in protist vacuoles. In this respect, marine bacteria are similar to several protist-dependent human pathogens, including Legionella. Analyses of growth patterns in low-nutrient media showed that co-cultivation with A. polyphaga allowed one bacterial strain to overcome nutritional stress and obtain active growth. Five isolates depended on viable amoebae to grow, notwithstanding nutrient media status. The remarkable capability of these marine bacteria to survive encounters with, and even actively kill, model predatory protists under laboratory conditions suggests that diverse bacterial defense strategies and virulence mechanisms to access nutrients may be important in shaping microbial interactions. If verified with native marine and freshwater populations, the diversity of interactions uncovered here has implications for understanding ecological and evolutionary consequences of population dynamics in bacteria and protists.IMPORTANCEThe microbiome constitutes the base of food webs in aquatic environments. Its composition partly reflects biotic interactions, where bacteria primarily are considered prey of predatory protists. However, studies that focus on one or a few species have shown that some bacteria have abilities to escape grazing and may even be capable of lysing their protist predators. In this study, we substantially extend these findings by systematically investigating interactions among multiple taxa of both bacteria and protists. Our results show that marine bacteria display a wider and more complex range of interactions with their predators than generally recognized-from growth dependency to protist lysis. Given that such interactions play key roles in the pathogenesis and epidemiology of several human pathogens, our findings imply that bacterial virulence traits can contribute to defining the structure and ecology of aquatic microbiomes.},
}

@article {pmid40444969,
year = {2025},
author = {Xie, J and Kim, T and Liu, Z and Panier, H and Bokoliya, S and Xu, M and Zhou, Y},
title = {Young gut microbiota transplantation improves the metabolic health of old mice.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0160124},
doi = {10.1128/msystems.01601-24},
pmid = {40444969},
issn = {2379-5077},
abstract = {UNLABELLED: The gut microbiota evolves over a lifetime and significantly impacts the aging process. Targeting the gut microbiota represents a novel avenue to delay aging and aging-related physical and mental decline. However, the underlying mechanism by which the microbiota modulates the aging process, particularly age-related physical and behavioral changes is not completely understood. We conducted fecal microbiota transplantation (FMT) from young or old male donor mice to the old male recipients. Old recipients with young microbiota had a higher alpha diversity than the old recipients with old microbiota. Compared to FMT with old microbiota, FMT with young microbiota reduced body weight and prevented fat accumulation in the old recipients. FMT with young microbiota also lowered frailty, increased grip strength, and alleviated depression and anxiety-like behavior in the old recipients. Consistent with observed physical changes, untargeted metabolomic analysis of serum and stools revealed that FMT with young microbiota lowered age-related long-chain fatty acid levels and increased amino acid levels in the old recipients. Bulk RNAseq analysis of the amygdala of the brain showed that FMT with young microbiota downregulated inflammatory pathways and upregulated oxidative phosphorylation in the old recipients. Our results demonstrate that FMT with young microbiota has substantial positive influences on age-related body composition, frailty, and psychological behaviors. These effects are associated with changes in host lipid and amino acid metabolism in the periphery and transcriptional regulation of neuroinflammation and energy utilization in the brain.

IMPORTANCE: The gut microbiome is a key hallmark of aging. Fecal microbiota transplantation (FMT) using young microbiota represents a novel rejuvenation strategy to delay aging. Our study provides compelling evidence that transplanting microbiota from young mice significantly improved grip strength, frailty, and body composition in aged recipient mice. At the molecular level, FMT improved aging-related metabolic markers in the gut and circulation. Additionally, FMT from young microbiota rejuvenated the amygdala of the aged brain by downregulating inflammatory pathways. This study highlights the importance of metabolic reprogramming via young microbiota FMT in improving physical and metabolic health in elderly recipients.},
}

@article {pmid40444942,
year = {2025},
author = {McClure, R and Rivas-Ubach, A and Hixson, KK and Farris, Y and Garcia, M and Danczak, R and Davison, M and Paurus, VL and Jansson, JK},
title = {Multi-omics of a model bacterial consortium deciphers details of chitin decomposition in soil.},
journal = {mBio},
volume = {},
number = {},
pages = {e0040425},
doi = {10.1128/mbio.00404-25},
pmid = {40444942},
issn = {2150-7511},
abstract = {UNLABELLED: Soil microorganisms interact to carry out decomposition of complex organic carbon and nitrogen compounds, such as chitin, but the high diversity and complexity of the soil microbiome and habitat have posed a challenge to elucidating such interactions. Here, we sought to address this challenge by analysis of a model soil consortium (MSC-2) consisting of eight soil bacterial species. Our aim was to elucidate the specific roles of the member species during chitin metabolism. Samples were collected from MSC-2 incubated in chitin-enriched soil over 3 months. Multi-omics was used to understand how the community composition, transcripts, proteins, and chitin decomposition shifted over time. The data clearly and consistently revealed a temporal shift during chitin decomposition with defined contributions by individual species. A Streptomyces genus member (sp001905665) was a key player in early steps of chitin decomposition, with other MSC-2 members being central in carrying out later steps. These results illustrate how multi-omics applied to a defined consortium untangles the interactions between soil microorganisms.

IMPORTANCE: Although soil microorganisms carry out decomposition of organic matter in soil, the details are unclear due to the complexity of the soil microbiome and the heterogeneity of the soil habitat. Understanding carbon decomposition is of vital importance to determine how the soil carbon cycle functions. This is especially important with regard to understanding the fertility of soils and their ability to support plant growth. To overcome these challenges, we investigated in considerable detail a model soil community during its decomposition of a typical soil organic molecule-chitin. By using a multi-omics approach, we were able to decipher community interactions during chitin breakdown. This information provides a basis for understanding how more complex soil microbial communities interact in nature.},
}

@article {pmid40444793,
year = {2025},
author = {Seo, B and Lim, MY},
title = {Balancing harm and harmony: Evolutionary dynamics between gut microbiota-derived flagellin and TLR5-mediated host immunity and metabolism.},
journal = {Virulence},
volume = {16},
number = {1},
pages = {2512035},
doi = {10.1080/21505594.2025.2512035},
pmid = {40444793},
issn = {2150-5608},
mesh = {*Flagellin/immunology/genetics/metabolism/chemistry ; *Toll-Like Receptor 5/immunology/metabolism ; *Gastrointestinal Microbiome/immunology ; Humans ; Animals ; Immunity, Innate ; Adaptive Immunity ; Host Microbial Interactions/immunology ; Evolution, Molecular ; Bacteria/immunology/genetics ; },
abstract = {The gut microbiota maintains host health and shapes immune responses through intricate host-microbe interactions. Bacterial flagellin, a key microbe-associated molecular pattern, is recognized by Toll-like receptor 5 (TLR5) and NOD-like receptor family caspase activation and recruitment domain-containing 4 inflammasome. This dual recognition maintains the delicate balance between immune tolerance and activation, thereby influencing health and disease outcomes. Therefore, we explored the structural and functional evolution of bacterial flagellin to elucidate its role in innate and adaptive immune responses, along with its impact on metabolic processes, particularly via TLR5. In this review, we highlight the diagnostic and therapeutic potential of flagellin, including its application in vaccine development, cancer immunotherapy, and microbiome-based therapies. We integrated perspectives from structural biology, immunology, and microbiome research to elucidate the co-evolutionary dynamics between gut microbiota-derived flagellin and host immunity. Our interpretations provide a basis for the development of innovative strategies to improve health and disease management.},
}

*Flagellin/immunology/genetics/metabolism/chemistry
*Toll-Like Receptor 5/immunology/metabolism
*Gastrointestinal Microbiome/immunology
Humans
Animals
Immunity, Innate
Adaptive Immunity
Host Microbial Interactions/immunology
Evolution, Molecular
Bacteria/immunology/genetics

@article {pmid40444642,
year = {2025},
author = {Unger, K and Agler, MT},
title = {Beyond defense: microbial modifications of plant specialized metabolites alter and expand their ecological functions.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70254},
pmid = {40444642},
issn = {1469-8137},
support = {//Carl-Zeiss-Stiftung/ ; 458884166//Deutsche Forschungsgemeinschaft/ ; EXC 2051, project number 390713860//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Plant specialized metabolites (PSMs) are compounds that are not involved in primary metabolism but instead confer other roles for the plant host, often related to ecological interactions. In the field of plant-microbe interactions, many PSMs have traditionally been considered for their roles in shaping interactions with pathogens. However, it is increasingly clear that 'defensive' PSMs have broader functions in regulating assembly and functions of plant-associated microbes, a phenomenon that is best studied in the rhizosphere. PSMs, however, are secreted throughout plants to mediate interactions with the environment. In this Tansley insight, we argue that these molecules also play outsize roles in shaping microbial community assembly and functions in the phyllosphere. Additionally, we argue that it is important to consider how microbial activity transforms PSMs, because this may shape how plants interact with the environment. Increased attention to these effects and improved strategies to understand them across scales will lead to insights into how microbial responses to PSMs shape broader plant interactions in the environment.},
}

@article {pmid40444400,
year = {2025},
author = {Burdon, I and Bouras, G and Fenix, K and Yeo, K and Connell, J and Cooksley, C and Barry, E and Vreugde, S and Wormald, PJ and Psaltis, AJ},
title = {Metagenomics or Metataxonomics: Best Practice Methods to Uncover the Sinus Microbiome.},
journal = {International forum of allergy & rhinology},
volume = {},
number = {},
pages = {e23617},
doi = {10.1002/alr.23617},
pmid = {40444400},
issn = {2042-6984},
support = {//Garnett Passe and Rodney Williams Memorial Foundation/ ; APP1196832//National Health and Medical Research Council/ ; },
}

@article {pmid40444264,
year = {2025},
author = {Dalton, KR and Chang, VC and Lee, M and Maki, K and Saint-Maurice, P and Purandare, V and Hua, X and Wan, Y and Dagnall, CL and Jones, K and Hicks, BD and Hutchinson, A and Liao, LM and Gail, MH and Shi, J and Sinha, R and Abnet, CC and London, SJ and Vogtmann, E},
title = {Sleep duration associated with altered oral microbiome diversity and composition in the NIH AARP cohort.},
journal = {Sleep advances : a journal of the Sleep Research Society},
volume = {6},
number = {2},
pages = {zpaf023},
pmid = {40444264},
issn = {2632-5012},
abstract = {STUDY OBJECTIVES: The microbiome is proposed as a contributor to the adverse health impacts from altered sleep. The oral microbiome is a multifaceted microbial community that influences many health functions. However, data on the relationship between sleep and the oral microbiome are limited, and no studies have incorporated lifestyle and environmental exposures.

METHODS: Within a subset (N=1,139) of the NIH-AARP cohort, we examined the association between self-reported sleep duration and the oral microbiome via 16S rRNA gene amplicon sequencing. Statistical models were adjusted for demographic characteristics. Additional models examined the role of various lifestyle and neighborhood exposures on the sleep-oral microbiome association.

RESULTS: Compared to participants reporting the recommended 7-8 hours average sleep duration (n=702), those reporting short sleep (6 or fewer hours, n=284) had consistently decreased within-sample oral microbial diversity [e.g. number of observed amplicon sequence variants difference -8.681, p-value=0.009]. Several bacterial genera were more likely to be absent in the short sleep group. We found a higher relative abundance of Streptococcus and Rothia, and lower abundance of Fusobacterium, Atopobium, and Campylobacter in the short compared to the recommended sleep duration group. Results were consistent when controlling for lifestyle and neighborhood factors.

CONCLUSIONS: Our findings provide evidence for an association of short sleep duration with oral microbial diversity and composition. This suggests that oral bacteria may play a possible mechanistic role related to sleep health. Improved understanding of physiological pathways can aid in the design of interventions that may beneficially improve overall sleep health.},
}

@article {pmid40444051,
year = {2025},
author = {Yang, SF and Chen, XC and Pan, YJ},
title = {Microbiota-derived metabolites in tumorigenesis: mechanistic insights and therapeutic implications.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1598009},
pmid = {40444051},
issn = {1663-9812},
abstract = {Intestinal microbiota is a complex ecosystem of microorganisms that perform diverse metabolic activities to maintain gastrointestinal homeostasis. These microorganisms provide energy and nutrients for growth and reproduction while producing numerous metabolites including lipopolysaccharides (LPS), Bacteroides fragilis toxin (BFT), bile acids (BAs), polyamines (PAs), and short-chain fatty acids (SCFAs). These metabolites are linked to inflammation and various metabolic diseases, such as obesity, type-2 diabetes, non-alcoholic fatty liver disease, cardiometabolic disease, and malnutrition. In addition, they may contribute to tumorigenesis. Evidence suggests that these microbes can increase the susceptibility to certain cancers and affect treatment responses. In this review, we discuss the current knowledge on how the gut microbiome and its metabolites influence tumorigenesis, highlighting the potential molecular mechanisms and prospects for basic and translational research in this emerging field.},
}

@article {pmid40444006,
year = {2025},
author = {Yuan, H and Zhou, J and Wu, X and Wang, S and Park, S},
title = {Enterotype-stratified gut microbial signatures in MASLD and cirrhosis based on integrated microbiome data.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1568672},
pmid = {40444006},
issn = {1664-302X},
abstract = {INTRODUCTION: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a growing global health challenge, characterized by significant variability in progression and clinical outcomes. While the gut microbiome is increasingly recognized as a key factor in liver disease development, its role in disease progression and associated mechanisms remains unclear. This study systematically investigated the gut microbiota's role in MASLD and liver cirrhosis progression, focusing on individual bacterial strains, microbial community dynamics, and functional characteristics across different enterotypes.

METHODS: Publicly available next-generation sequencing(NGS) datasets from healthy individuals and patients with MASLD and cirrhosis were analyzed. Enterotype classification was performed using principal component analysis, with advanced bioinformatics tools, including Linear Discriminant Analysis Effect Size (LEfSe), eXtreme Gradient Boosting (XGBoost), and Deep Cross-Fusion Networks for Genome-Scale Identification of Pathogens (DCiPatho), to identify differentially abundant microbes and potential pathogens. Microbial co-occurrence networks and functional predictions via PICRUSt2 revealed distinct patterns across enterotypes.

RESULTS AND DISCUSSION: The Prevotella-dominated(ET-P) group exhibited a 33% higher cirrhosis rate than the Bacteroides-dominated(ET-B) group. Unique microbial signatures were identified: Escherichia albertii and Veillonella nakazawae were associated with cirrhosis in ET-B, while Prevotella copri was linked to MASLD. In ET-P, Prevotella hominis and Clostridium saudiense were significantly associated with cirrhosis. Functional analysis revealed reduced biosynthesis of fatty acids, proteins, and short-chain fatty acids (SCFAs), coupled with increased lipopolysaccharide(LPS) production and altered secondary bile acid metabolism in MASLD and cirrhosis patients. There were significant microbial and functional differences across enterotypes in MASLD and cirrhosis progression, providing critical insights for developing personalized microbiome-targeted interventions to mitigate liver disease progression.},
}

@article {pmid40444003,
year = {2025},
author = {Guo, Y and Sun, S and Wang, Y and Chen, S and Kou, Z and Yuan, P and Han, W and Yu, X},
title = {Microbial dysbiosis in obstructive sleep apnea: a systematic review and meta-analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1572637},
pmid = {40444003},
issn = {1664-302X},
abstract = {BACKGROUND: The association between the microbiota and obstructive sleep apnea (OSA) remains understudied. In this study, we conducted a comprehensive systematic review and meta-analysis of studies investigating the diversity and relative abundance of microbiota in the gut, respiratory tracts and oral cavity of patients with OSA, aiming to provide an in-depth characterization of the microbial communities associated with OSA.

METHODS: A comprehensive literature search across PubMed, the Cochrane Library, Web of Science, and Embase databases were conducted to include studies published prior to Dec 2024 that compared the gut, respiratory and oral microbiota between individuals with and without OSA. The findings regarding alpha-diversity, beta-diversity, and relative abundance of microbiota extracted from the included studies were summarized. This meta-analysis was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, and the study protocol was registered with PROSPERO (CRD42024525114).

RESULTS: We identified a total of 753 articles, out of which 27 studies were ultimately included in the systematic review, involving 1,381 patients with OSA and 692 non-OSA populations, including 1,215 OSA patients and 537 non-OSA populations in adults and 166 OSA patients and 155 non-OSA populations in children. The results of alpha diversity revealed a reduction in the Chao1 index (SMD = -0.40, 95% CI = -0.76 to -0.05), Observed species (SMD = -0.50, 95% CI = -0.89 to -0.12) and Shannon index (SMD = -0.27, 95% CI = -0.47 to -0.08) of the gut microbiota in patients with OSA. Beta diversity analysis indicated significant differences in the gut, respiratory and oral microbial community structure between individuals with OSA and those without in more than half of the included studies. Furthermore, in comparison to the non-OSA individuals, the gut environment of patients with OSA exhibited an increased relative abundance of phylum Firmicutes, along with elevated levels of genera Lachnospira; conversely, there was a decreased relative abundance of phylum Bacteroidetes and genus Ruminococcus and Faecalibacterium. Similarly, within the oral environment of OSA patients, there was an elevated relative abundance of phylum Actinobacteria and genera Neisseria, Rothia, and Actinomyces.

CONCLUSION: Patients with OSA exhibit reduced diversity, changes in bacterial abundance, and altered structure in the microbiota, especially in the gut microbiota. The results of this study provide basic evidence for further exploration of microbiome diagnostic markers and potential intervention strategies for OSA.},
}

@article {pmid40444002,
year = {2025},
author = {Shao, Q and Zhou, S and Li, Y and Jin, L and Fu, X and Liu, T and Wang, J and Du, S and Chen, C},
title = {The effects of a semen cuscutae flavonoids-based antidepressant treatment on microbiome and metabolome in mice.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1558833},
pmid = {40444002},
issn = {1664-302X},
abstract = {BACKGROUND: Depression is a prevalent psychiatric disorder and one of the leading causes of disability worldwide. Previous studies have shown that Semen Cuscutae flavonoids (SCFs) exert antidepressant effects by modulating the microbiota-neuroinflammation axis and ameliorating hippocampal metabolic disturbances. However, the impact of SCFs on gut microbiota and related metabolomics remains largely undefined. Given that the gut microbiota has been proven to play a significant role in the etiology of depression and serves as a promising target for its treatment in humans, this study aims to elucidate the antidepressant effects of SCFs and to investigate how they modulate microbial and metabolic pathways to alleviate depressive symptoms.

MATERIALS AND METHODS: Chronic unpredictable mild stress (CUMS)-induced mice were used as a depression model. The normal mice and CUMS-induced mice were treated with either vehicle or with SCFs. A range of standardized behavioral assays and physiological indicators were employed to evaluate the antidepressant effects of SCFs. Upon the confirmation of the effectiveness of the SCFs treatment, the composition, richness, and diversity of the fecal microbiota were assessed using 16S rRNA gene sequencing. Additionally, fecal metabolic profiling was analyzed using UHPLC-MS/MS-based metabolomics. Multivariate data analysis was subsequently performed to identify differential metabolites and characterize alterations in fecal metabolites. Furthermore, a correlation analysis between differential metabolites and key microbiota was conducted.

RESULTS: SCFs significantly ameliorated depressive behaviors and the dysregulated diversity of fecal microbiota induced by CUMS. SCFs enhanced the gut microbiota structure in the CUMS group by increasing the Firmicutes/Bacteroidota ratio, significantly elevating the abundance of Firmicutes, Lactobacillus, Limosilactobacillus, and Actinobacteria while reducing the abundance of Bacteroidota and Bacteroides in CUMS-treated mice. Fecal metabolomics analyses revealed that SCFs could modulate metabolic pathways, including aldosterone synthesis and secretion, arachidonic acid metabolism, and primary bile acid biosynthesis.

CONCLUSIONS: Mice with depression induced by CUMS exhibited disturbances in both their gut microbiota and fecal metabolism. However, SCFs restored the balance of the microbial community and corrected metabolic disturbances in feces, exerting antidepressant effects through a multifaceted mechanism.},
}

@article {pmid40443994,
year = {2025},
author = {Kidangathazhe, A and Amponsah, T and Maji, A and Adams, S and Chettoor, M and Wang, X and Scaria, J},
title = {Synthetic vs. non-synthetic sweeteners: their differential effects on gut microbiome diversity and function.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1531131},
pmid = {40443994},
issn = {1664-302X},
abstract = {The rising use of artificial sweeteners, favored for their zero-calorie content and superior sweetness, necessitates understanding their impact on the gut microbiome. This study examines the effects of five common artificial sweeteners-Acesulfame K, Rebaudioside A, Saccharin, Sucralose, and Xylitol-on gut microbiome diversity using minibioreactor arrays. Fecal samples from three healthy individuals were used to inoculate bioreactors that were subsequently supplemented with each sweetener. Over 35 days, microbial diversity and network composition were analyzed. Results revealed synthetic sweeteners like Sucralose and Saccharin significantly reduced microbial diversity, while non-synthetic sweeteners, particularly Rebaudioside A and Xylitol, were less disruptive. Acesulfame K increased diversity but disrupted network structure, suggesting potential long-term negative impacts on microbiome resilience. Sucralose enriched pathogenic families such as Enterobacteriaceae, whereas natural sweeteners promoted beneficial taxa like Lachnospiraceae. Random Matrix Theory (RMT) based analysis highlighted distinct microbial interaction patterns, with Acesulfame K causing persistent structural changes. Findings suggest non-synthetic sweeteners may be more favorable for gut health than synthetic ones, emphasizing cautious use, particularly for those with gut health concerns. This study enhances our understanding of artificial sweeteners' effects on the gut microbiome, highlighting the need for further research into their long-term health implications.},
}

@article {pmid40443829,
year = {2025},
author = {Bacaloni, S and Agrawal, DK},
title = {Nutrition, Gut Microbiota, and Epigenetics in the Modulation of Immune Response and Metabolic Health.},
journal = {Cardiology and cardiovascular medicine},
volume = {9},
number = {3},
pages = {111-124},
pmid = {40443829},
issn = {2572-9292},
abstract = {Immune system function is intricately shaped by nutritional status, dietary patterns, and gut microbiota composition. Micronutrients such as vitamins A, C, D, E, B-complex, zinc, selenium, iron, and magnesium are critical for maintaining physical barriers, supporting immune cell proliferation, and regulating inflammation. Macronutrients-including proteins, fats, and carbohydrates-also modulate immune responses through their impact on immune metabolism and the gut-immune axis. Epigenetic mechanisms, including DNA methylation, histone modifications, and microRNA expression, mediate the long-term effects of diet on immune function and tolerance. Diet-induced alterations in gut microbiota further influence immune homeostasis via microbial metabolites like short-chain fatty acids. Imbalanced diets, particularly the Western diet, contribute to immune dysregulation, chronic inflammation, and the development of metabolic disorders such as obesity and type 2 diabetes. While plant-based and Mediterranean dietary patterns have shown anti-inflammatory and immunoregulatory benefits, gaps remain in understanding the long-term epigenetic impacts of these diets. This review integrates current knowledge on how nutrition and the microbiome regulate immunity, highlighting future directions for personalized dietary strategies in preventing chronic immune-related conditions.},
}

@article {pmid40443663,
year = {2025},
author = {Teuscher, JL and Lupatsii, M and Graspeuntner, S and Jonassen, S and Bringewatt, A and Herting, E and Stichtenoth, G and Bossung, V and Rupp, J and Härtel, C and Demmert, M},
title = {Persistent reduction of Bifidobacterium longum in the infant gut microbiome in the first year of age following intrapartum penicillin prophylaxis for maternal GBS colonization.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1540979},
pmid = {40443663},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Female ; Infant ; *Antibiotic Prophylaxis ; *Streptococcal Infections/prevention & control/microbiology/immunology ; Infant, Newborn ; Pregnancy ; *Streptococcus agalactiae/drug effects ; *Bifidobacterium longum ; *Penicillins/therapeutic use/administration & dosage ; Feces/microbiology ; Male ; *Anti-Bacterial Agents/therapeutic use ; Infectious Disease Transmission, Vertical/prevention & control ; RNA, Ribosomal, 16S/genetics ; },
abstract = {INTRODUCTION: Group B Streptococcus is a significant cause of early-onset disease in term newborns, with a global incidence of 0.41/1000 live births. Intrapartum antibiotic prophylaxis (IAP) has reduced EOD incidence by over 80%, but concerns exist about its impact on the neonatal gut microbiome and potential long-term health effects.

METHODS: This single center study examines the effects of IAP on the fecal infant microbiome in the first year of age and on the T cell phenotype in the first days after birth among 22 infants receiving IAP with penicillin due to maternal GBS colonization and 26 infants not exposed to IAP. The fecal microbiome was analyzed at birth, one month and one year of age through 16S rRNA gene sequencing. Additionally, a T cell phenotyping of peripheral blood was performed between the second and fifth day of age.

RESULTS: At one month, IAP exposed infants had a significantly lower relative abundance of Bifidobacterium longum in fecal samples, an effect which was sustained at one year. In IAP exposed infants we found a proinflammatory T-helper cell profile, characterized by higher IL-17A, RORgt, and TGF-b expression.

DISCUSSION: This study proposes a sustained impact of IAP on the neonatal microbiome and T cell repertoire.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Female
Infant
*Antibiotic Prophylaxis
*Streptococcal Infections/prevention & control/microbiology/immunology
Infant, Newborn
Pregnancy
*Streptococcus agalactiae/drug effects
*Bifidobacterium longum
*Penicillins/therapeutic use/administration & dosage
Feces/microbiology
Male
*Anti-Bacterial Agents/therapeutic use
Infectious Disease Transmission, Vertical/prevention & control
RNA, Ribosomal, 16S/genetics

@article {pmid40443528,
year = {2025},
author = {Zhang, Y and Zhu, H and Fan, J and Zhao, J and Xia, Y and Zhang, N and Xu, H},
title = {A glutamine metabolism gene signature with prognostic and predictive value for colorectal cancer survival and immunotherapy response.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1599141},
pmid = {40443528},
issn = {2296-889X},
abstract = {BACKGROUND: Colorectal cancer (CRC) remains a major cause of cancer mortality, and dysregulated glutamine metabolism has emerged as a potential therapeutic target. However, the precise role of glutamine in CRC progression and treatment response remains debated.

METHODS: The authors collected transcriptome and microbiome information, from multiple sources to construct the GLMscore, a prognostic signature in CRC. To comprehensively characterize the biological features of GLMscore groups, the integration of transcriptomic profiling, KEGG pathway enrichment analysis, immune infiltration analysis, tumor immune microenvironment characterization, microbiome analysis, and tissue imaging were applied. Furthermore, CRC patients were stratified into GLMscore high and GLMscore low groups. The robustness of GLMscore was validated in both training and validation cohorts, and the predictive value for immunotherapy response was assessed. Finally, single-cell RNA sequencing (scRNA-seq) analysis was conducted to delineate the differences between GLMscore high and GLMscore low groups.

RESULTS: High GLMscore was associated with elevated expression of pathways related to tumorigenesis, epithelial-mesenchymal transition (EMT), and angiogenesis. Furthermore, high GLMscore patients exhibited an immunosuppressive TME characterized by increased infiltration of M0 and M2 macrophages, reduced overall immune infiltration (supported by ESTIMATE and TIDE scores), and increased expression of immune exclusion and suppression pathways. Analysis of pathological whole-slide images (WSIs) revealed a lack of intratumoral tertiary lymphoid structures (TLSs) in high GLMscore patients. The GLMscore also predicted resistance to common chemotherapeutic agents (using GDSC data) and, importantly, predicted poor response to immunotherapy in the IMvigor210 cohort. Analysis of 16S rRNA gene sequencing data revealed an enrichment of potentially oncogenic microbiota, including Hungatella and Selenomonas, in high GLMscore group. Single-cell analysis further confirmed the immunosuppressive TME and identified increased cell-cell communication between inflammatory macrophages and tumor cells in high GLMscore group.

CONCLUSION: The authors innovatively constructed GLMscore, a robust scoring system in quantifying CRC patients, exploring the distinct biological features, tumor immune microenvironment and microbiome ecology, exhibiting high validity in predicting survival prognosis and clinical treatment efficacy.},
}

@article {pmid40443227,
year = {2025},
author = {Green, GBH and Cox-Holmes, AN and Marlow, GH and Potier, ACE and Wang, Y and Zhou, L and Chen, D and Morrow, CD and McFarland, BC},
title = {Human microbiota influence the immune cell composition and gene expression in the tumor environment of a murine model of glioma.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2508432},
doi = {10.1080/19490976.2025.2508432},
pmid = {40443227},
issn = {1949-0984},
mesh = {Animals ; *Glioma/immunology/microbiology/genetics ; Mice ; Humans ; *Gastrointestinal Microbiome/immunology ; Disease Models, Animal ; *Tumor Microenvironment/immunology/genetics ; *Brain Neoplasms/immunology/microbiology/genetics ; Cell Line, Tumor ; Feces/microbiology ; Programmed Cell Death 1 Receptor/antagonists & inhibitors/immunology ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Immunotherapy has shown success against other cancers but not glioblastoma. Previous data has revealed that microbiota influences anti-PD-1 efficacy. We have previously found that, when using gnotobiotic mice transplanted with human fecal microbiota, the gut microbial composition influenced the response to anti-PD-1 in a mouse model of glioma. However, the role of the human microbiota in influencing the mouse immune cells in the glioma microenvironment and anti-PD-1 response was largely unknown. Using two distinct humanized microbiome (HuM) lines, we used single-cell RNA sequencing (scRNA-seq) to determine how gut microbiota affect immune infiltration and gene expression in a murine glioma model.

METHODS: 16S rRNA sequencing was performed on fecal samples from HuM1 (H1) and HuM2 (H2) mice. Mice were intracranially injected with murine glioma cells (GL261), and on day 13 treated with one dose of isotype control or anti-PD1. Mice were euthanized on day 14 for analysis of all immune cells in the tumors by scRNA-seq.

RESULTS: HuM1 and HuM2 mice had different microbial populations, with HuM1 being primarily dominated via Alistipes, and HuM2 being primarily composed of Odoribacter. Sc-RNA-seq of the tumor immune cells revealed 21 clusters with significant differences between H1 and H2 samples with a larger population of M1 type macrophages in H1 samples. Gene expression analysis revealed higher expression of inflammatory markers in the M1 population in H2 mice treated with anti-PD-1.

CONCLUSIONS: Microbial gut communities influence the presence and gene activation patterns of immune cells in the brain tumors of mice both under control (isotype) and following anti-PD-1 treatment.},
}

Animals
*Glioma/immunology/microbiology/genetics
Mice
Humans
*Gastrointestinal Microbiome/immunology
Disease Models, Animal
*Tumor Microenvironment/immunology/genetics
*Brain Neoplasms/immunology/microbiology/genetics
Cell Line, Tumor
Feces/microbiology
Programmed Cell Death 1 Receptor/antagonists & inhibitors/immunology
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics/isolation & purification
Mice, Inbred C57BL

@article {pmid40443224,
year = {2025},
author = {Kim, DR and Ko, YM and Lee, D and Kwak, YS},
title = {Root Rot Disease Biocontrol and Microbiome Community Modulation by Streptomyces Strains in Soybean.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2502010},
doi = {10.4014/jmb.2502.02010},
pmid = {40443224},
issn = {1738-8872},
mesh = {*Glycine max/microbiology ; *Streptomyces/physiology/isolation & purification/classification ; *Plant Diseases/microbiology/prevention & control ; *Microbiota ; *Plant Roots/microbiology ; Fusarium ; Rhizosphere ; Antibiosis ; Soil Microbiology ; Antifungal Agents/pharmacology ; Biological Control Agents ; },
abstract = {Traditionally, phytopathogenic fungi control strategies rely primarily upon chemical fungicides, but fungicide resistance pathogen strains have appeared in the fields. Therefore, biocontrol approaches highlighted with sustainable agriculture aspects, especially the genus Streptomyces, are known to suppress numerous plant diseases. Streptomyces bacillaris S8 was isolated from turfgrass rhizosphere, and Streptomyces globisporus SP6C4 was obtained from strawberry pollen. Both strains showed excellent antifungal and antibacterial activities and suppressed various plant diseases in vitro. However, beneficial microorganisms are rarely studied and introduced to another effect on microbial communities when incompatible with the host. The present study aims to assess the potential of effective control of plant diseases by both strains in new crops and to assess the impact of endogenous microbiota. Various diseases pose significant concerns in soybean production, leading to substantial grain yield and quality losses. Root rot caused by Fusarium spp. is known to be the most problematic disease in the soybean cropping system. In the results, S. globisporus SP6C4 and S. bacillaris S8 showed antifungal activity against soybean root rot pathogen, but strain S8 had less than SP6C4. The strain SP6C4 played a role as hub-taxa in the early stage, and the strain S8 was a modulator in microbial communities. Our results demonstrate the antifungal activity of S. globisporus SP6C4 and S. bacillaris S8, which can be expected to grow and reduce the disease of soybeans. The S8 and SP6C4 can also modify the plant microbiota which may open a new dimension of crop microbiome research.},
}

*Glycine max/microbiology
*Streptomyces/physiology/isolation & purification/classification
*Plant Diseases/microbiology/prevention & control
*Microbiota
*Plant Roots/microbiology
Fusarium
Rhizosphere
Antibiosis
Soil Microbiology
Antifungal Agents/pharmacology
Biological Control Agents

@article {pmid40443219,
year = {2025},
author = {Kim, J and Ha, J and Kim, S and Kim, G and Shin, H},
title = {Impact of Ginger on Gut Microbiota Composition and Function in a Bacteroides-Dominant Enterotype.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2503032},
doi = {10.4014/jmb.2503.03032},
pmid = {40443219},
issn = {1738-8872},
mesh = {*Zingiber officinale/chemistry ; *Gastrointestinal Microbiome/drug effects ; Humans ; Feces/microbiology ; *Bacteroides/classification/isolation & purification/genetics/drug effects ; Bacteria/classification/genetics/isolation & purification ; Male ; Adult ; RNA, Ribosomal, 16S/genetics ; Proteobacteria/classification/isolation & purification/genetics ; Female ; Plant Extracts/pharmacology ; },
abstract = {Ginger (Zingiber officinale) has been used worldwide for centuries, valued for both its culinary applications and potential therapeutic properties. Its bioactive compounds exhibit antioxidant, anti-inflammatory, and metabolic regulatory effects, providing physiological benefits to the human body. However, its influence on the gut microbiota remains poorly understood. In this study, we investigated the impact of ginger on gut microbiota using an in vitro fecal incubation model. To minimize interindividual variability, we classified participants into enterotypes based on gut microbial composition, focusing on the Bacteroides-dominant enterotype. While ginger treatment did not significantly affect microbial alpha diversity, it induced distinct shifts in bacterial structure, suggesting compositional changes in the microbiota. At the phylum level, taxonomic analysis revealed a lower relative abundance of Bacteroidota and a higher relative abundance of Proteobacteria in the ginger-treated group compared to the control. Consistently, genus-level analysis showed an increased relative abundance of Acinetobacter and Enterobacteriaceae, both belonging to Proteobacteria, in the ginger-treated group. Predicted functional pathway analysis further revealed that ginger treatment enriched pathways related to linoleic acid metabolism, beta-alanine metabolism, geraniol degradation, and tetracycline biosynthesis. These findings suggest that ginger modulates gut microbiota composition, particularly by increasing the abundance of Proteobacteria-associated genera. This enterotype-based study provides a structured framework for evaluating dietary effects and may support the development of personalized dietary strategies targeting gut microbiome modulation.},
}

*Zingiber officinale/chemistry
*Gastrointestinal Microbiome/drug effects
Humans
Feces/microbiology
*Bacteroides/classification/isolation & purification/genetics/drug effects
Bacteria/classification/genetics/isolation & purification
Male
Adult
RNA, Ribosomal, 16S/genetics
Proteobacteria/classification/isolation & purification/genetics
Female
Plant Extracts/pharmacology

@article {pmid40442920,
year = {2025},
author = {Ordner, J and Narula, N and Chiriboga, L and Zeck, B and Majd, M and Gupta, K and Gaglia, R and Zhou, F and Moreira, A and Iman, R and Ko, JP and Le, L and Wells, RG and Theise, ND},
title = {Continuity of interstitial spaces within and outside the human lung.},
journal = {Journal of anatomy},
volume = {},
number = {},
pages = {},
doi = {10.1111/joa.14280},
pmid = {40442920},
issn = {1469-7580},
abstract = {There is a body-wide network of interstitial spaces that includes three components: a large-scale fascial network made up of fluid-filled spaces containing collagens and other extracellular matrix components like hyaluronic acid (HA), the peri-vascular/capillary interstitium, and intercellular interstitial spaces. Staining for HA within the colon, skin, and liver has demonstrated spatial continuity of the fascial interstitium across tissue layers and between organs, while continuity of HA staining between perineurial and adventitial sheathes beyond organ boundaries confirmed that they also participate in this body-wide network. We asked whether the pulmonary interstitium comprises a continuous organ-wide network that also connects to the body-wide interstitium via routes along nerves and the vasculature. We studied archival lung lobectomy specimens containing normal tissues inclusive of all lung anatomical units from six females and three males (mean age 53+/- 16.5 years). For comparison, we also studied normal mouse lung. Multiplex immunohistochemical cocktails were used to identify: (1) HA, CD34, and vimentin - highlighting interstitium; (2) HA, CD34, and podoplanin (D2-40) - highlighting relationships between the interstitium, vasculature, and lymphatics. Sizes of extracellular APP were measured. Tissues from nine patients (six females, three males, mean age 53+/- 16.5 years) were studied. HA staining was continuous throughout the five major anatomic compartments of the lung: alveolar walls, subpleural connective tissue, centrilobular peribronchovascular compartment, interlobular septal compartment, and axial peribronchovascular of the hilum, with similar findings in murine lung tissue. Continuity with interstitial spaces of the perineurium and adventitia was confirmed. The distribution of APP corresponded to known routes of lymphatic drainage, superficial and deep. APP within perineurium and perivascular adventitia further demonstrated continuity between intra- and extrapulmonary interstitium. To conclude, all segments of the lung interstitium are connected and are linked along nerves and the vascular tree to a body-wide communication network. These findings have significant implications for understanding lung physiology and pathobiology, suggesting routes of passage for inflammatory cells and mediators, malignant cells, and infectious agents. Interstitial spaces may be important in microbiome signaling within and beyond the lung and may be a component of the lung-brain axis.},
}

@article {pmid40442917,
year = {2025},
author = {Fakruddin, M and Amin, T and Shishir, MA and Jameel, RM and Bari, MM and Shameem, NF and Hossain, A and Jerin, N and Bin Mannan, S and Sultana Jime, J and Bulbul, N},
title = {Early-Life Microbiome and Neurodevelopmental Disorders: A Systematic Review and Meta-Analysis.},
journal = {Current neuropharmacology},
volume = {},
number = {},
pages = {},
doi = {10.2174/011570159X360129250508113618},
pmid = {40442917},
issn = {1875-6190},
abstract = {BACKGROUND AND OBJECTIVES: This systematic review intends to find out how neurodevelopmental disorders, including Attention Deficit Hyperactivity Disorder (ADHD) and Autism Spectrum Disorder (ASD), are influenced by the gut microbiota throughout early childhood. The study looks at the variety and types of microbes that a child is exposed to, the particular microbiome profiles associated with neurodevelopmental outcomes, and the molecular processes that underlie these relationships.

METHODS: We performed a thorough search of PubMed, Scopus, the WHO Global Health Library (GHL), and ISI Web of Science. After screening 2,744 original studies based on predetermined eligibility criteria, 19 studies were included. Microbial groupings, presence (high/low), and related neurodevelopmental disorders were among the primary areas of data extraction. The methodological quality of the studies was assessed using the Newcastle-Ottawa Quality Assessment Scale (NOS).

RESULTS: The investigated literature repeatedly showed a strong correlation between dysbiosis of the gut microbiota and neurodevelopmental disorders. Cases of ASD were associated with both a high number of Clostridium species and a low number of Bifidobacterium species. On the other hand, a Low number of E. coli and a high number of the class Clostridia, phylum Firmicute, genus Bifidobacterium, and Akkermansia, as well as the species Listeria monocytogenes, Toxoplasma gondii, Streptococcus mutans, and Mycobacterium tuberculosis have been linked to ADHD. The NOS evaluation showed variation in the quality of the methodology; some studies had high scores, suggesting sound technique, while other studies had lower scores, indicating serious methodological flaws.

CONCLUSION: The results highlight the potential impact of the gut microbiome throughout early life on neurodevelopmental outcomes, indicating that microbial imbalances may play a role in the onset of disorders like ASD and ADHD. However, to improve the quality of data, larger-scale longitudinal studies would be required.},
}

@article {pmid40442807,
year = {2025},
author = {Deng, J and Dai, S and Liu, S and Tu, L and Cui, J and Hu, X and Qiu, X and Lu, H and Jiang, T and Xu, J},
title = {Clinical study of intelligent tongue diagnosis and oral microbiome for classifying TCM syndromes in MASLD.},
journal = {Chinese medicine},
volume = {20},
number = {1},
pages = {78},
pmid = {40442807},
issn = {1749-8546},
support = {82104738//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 2023M732337//China Postdoctoral Science Foundation/ ; ZYYZDXK-2023069//State Administration of Traditional Chinese Medicine of the People's Republic of China/ ; 20244Y0129//Shanghai Municipal Health Commission/ ; 2022509//Intelligence Community Postdoctoral Research Fellowship Program/ ; },
abstract = {BACKGROUND: This study aimed to analyze the tongue image features and oral microbial markers in different TCM syndromes related to metabolic dysfunction-associated steatotic liver disease (MASLD).

METHODS: This study involved 34 healthy volunteers and 66 MASLD patients [36 with Dampness-Heat (DH) and 30 with Qi-Deficiency (QD) syndrome]. Oral microbiome analysis was conducted through 16S rRNA sequencing. Tongue image feature extraction used the Uncertainty Augmented Context Attention Network (UACANet), while syndrome classification was performed using five different machine learning methods based on tongue features and oral microbiota.

RESULTS: Significant differences in tongue color, coating, and oral microbiota were noted between DH band QD syndromes in MASLD patients. DH patients exhibited a red-crimson tongue color with a greasy coating and enriched Streptococcus and Rothia on the tongue. In contrast, QD patients displayed a pale tongue with higher abundances of Neisseria, Fusobacterium, Porphyromonas and Haemophilus. Combining tongue image characteristics with oral microbiota differentiated DH and QD syndromes with an AUC of 0.939 and an accuracy of 85%.

CONCLUSION: This study suggests that tongue characteristics are related to microbial metabolism, and different MASLD syndromes possess distinct biomarkers, supporting syndrome classification.},
}

@article {pmid40442718,
year = {2025},
author = {Pivrncova, E and Bohm, J and Barton, V and Klanova, J and Borilova Linhartova, P},
title = {Viable bacterial communities in freshly pumped human milk and their changes during cold storage conditions.},
journal = {International breastfeeding journal},
volume = {20},
number = {1},
pages = {44},
pmid = {40442718},
issn = {1746-4358},
support = {LM2023069//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; 857560//Horizon 2020 Framework Programme/ ; },
mesh = {Humans ; *Milk, Human/microbiology ; Female ; *Bacteria/isolation & purification/genetics/classification ; *Food Storage/methods ; Adult ; RNA, Ribosomal, 16S ; *Microbiota ; Freezing ; Refrigeration ; Azides ; Propidium/analogs & derivatives ; },
abstract = {BACKGROUND: Human milk harbors diverse bacterial communities that contribute to infant health. Although pumping and storing milk is a common practice, the viable bacterial composition of pumped milk and the impact of storage practice on these bacteria remains under-explored. This metagenomic observational study aimed to characterize viable bacterial communities in freshly pumped human milk and its changes under different storage conditions.

METHODS: In 2023, twelve lactating mothers from the CELSPAC: TNG cohort (Czech Republic) provided freshly pumped milk samples. These samples were stored under various conditions (refrigeration for 24 h, 48 h, or freezing for six weeks) and treated with propidium monoazide (PMA) to selectively identify viable cells. The DNA extracted from individual samples was subsequently analyzed using 16S rRNA amplicon sequencing on the Illumina platform.

RESULTS: The genera Streptococcus, Staphylococcus, Diaphorobacter, Cutibacterium, and Corynebacterium were the most common viable bacteria in fresh human milk. The median sequencing depth and Shannon index of fresh human milk samples treated with PMA (+ PMA) were significantly lower than in untreated (-PMA) samples (p < 0.05 for all), which was true also for each time point. Also, significant changes in these parameters were observed between fresh human milk samples and their paired frozen samples (p < 0.05), while no differences were found between fresh human milk samples and those refrigerated for up to 48 h (p > 0.05). Of specific genera, only + PMA frozen human milk samples showed a significant decrease in the central log-ratio transformed relative abundances of the genera Diaphorobacter and Cutibacterium (p < 0.05) in comparison to + PMA fresh human milk samples.

CONCLUSIONS: The study demonstrated that the bacterial profiles significantly differed between human milk samples treated with PMA, which represent only viable bacteria, and those untreated. While storage at 4 °C for up to 48 h did not significantly alter the overall diversity and composition of viable bacteria in human milk, freezing notably affected both the viability and relative abundances of some bacterial genera.},
}

Humans
*Milk, Human/microbiology
Female
*Bacteria/isolation & purification/genetics/classification
*Food Storage/methods
Adult
RNA, Ribosomal, 16S
*Microbiota
Freezing
Refrigeration
Azides
Propidium/analogs & derivatives

@article {pmid40442715,
year = {2025},
author = {Millar, CL and Wolfe, A and Baldyga, K and Dufour, AB and Lipsitz, LA},
title = {Berries and Steps: a protocol of a randomized, placebo-controlled pilot study testing freeze-dried blueberry powder in sedentary older adults with mild depressive symptoms.},
journal = {Nutrition journal},
volume = {24},
number = {1},
pages = {87},
pmid = {40442715},
issn = {1475-2891},
support = {P30AG048785//NIA and Boston Roybal Center/ ; P30AG048785//NIA and Boston Roybal Center/ ; P30AG048785//NIA and Boston Roybal Center/ ; 2022-09412//USDA NIFA/ ; 2022-09412//USDA NIFA/ ; 2022-09412//USDA NIFA/ ; },
mesh = {Humans ; *Blueberry Plants/chemistry ; Pilot Projects ; Aged ; *Sedentary Behavior ; Freeze Drying ; Male ; Female ; Double-Blind Method ; *Fruit/chemistry ; *Depression/diet therapy ; Dietary Supplements ; Powders ; Anthocyanins/administration & dosage ; Dietary Fiber/administration & dosage ; Inflammation ; Motivation ; Middle Aged ; },
abstract = {BACKGROUND: Older adults spend the majority of their day engaging in sedentary behavior, which increases risk of mortality by 22%. Despite the well-established health benefits of physical activity, a large portion of older adults remain sedentary. Recent evidence suggests that inflammation contributes to lack of motivation, which is a critical barrier to overcoming sedentary behavior in older adults. Given that inflammation is highly modifiable by diet, an anti-inflammatory dietary strategy may be a viable way to improve inflammation-driven lack of motivation and ultimately increase physical activity in sedentary older adults. However, interventions targeting such a pathway are scarce. We propose a study intervention protocol, which aims to determine the feasibility and preliminary efficacy of daily supplementation of freeze-dried blueberries. Supplementation with blueberries provides 2 anti-inflammatory nutrients (fiber and anthocyanins) to theoretically reduce inflammation-driven lack of motivation and thereby enhance physical activity in older adults with sedentary behavior and mild depressive symptoms.

METHODS: The current study is planned as a single-site, randomized, double-blind, parallel pilot study in 40 older adults with sedentary behavior and mild depressive symptoms. Individuals with depressive symptoms often lack motivation and have increased levels of inflammatory cytokines, representing an ideal population for an anti-inflammatory dietary intervention to improve motivation. Participants will be randomized to consume either 48 g of freeze-dried blueberry powder (~ 600 mg of anthocyanins and ~ 8 g of fiber) or a nutritionally matched placebo powder (without any known amounts of anthocyanins and fiber) each day for a total of 12 weeks.

DISCUSSION: Identification of a dietary intervention to target the inflammatory pathways may offer a novel and feasible approach to increase motivation and engagement of physical activity in older adults. If feasible and effective, such a strategy would help avoid the plethora of health consequences associated with sedentary behavior and physical inactivity.

TRIAL REGISTRATION: The current study is approved by the Advarra IRB (#Pro00064749) and registered at Clinicaltrials.gov (Identifier: NCT05735587).},
}

Humans
*Blueberry Plants/chemistry
Pilot Projects
Aged
*Sedentary Behavior
Freeze Drying
Male
Female
Double-Blind Method
*Fruit/chemistry
*Depression/diet therapy
Dietary Supplements
Powders
Anthocyanins/administration & dosage
Dietary Fiber/administration & dosage
Inflammation
Motivation
Middle Aged

@article {pmid40442493,
year = {2025},
author = {Madhan Kumar, S and Natarajan, S and Ks, S and Sundarajan, SK and Natarajan, P and Arockiam, AS},
title = {Dentures and the oral microbiome: Unraveling the hidden impact on edentulous and partially edentulous patients - a systematic review and meta-analysis.},
journal = {Evidence-based dentistry},
volume = {},
number = {},
pages = {},
pmid = {40442493},
issn = {1476-5446},
abstract = {OBJECTIVE: This systematic review and meta-analysis evaluate the impact of edentulism and denture use on the oral microbiome, focusing on microbial diversity, colonization and biofilm formation in completely and partially edentulous patients.

METHODS: A comprehensive search was conducted across five databases (PubMed-Medline, Scopus, Embase, Lilacs, and Google Scholar) until June 1, 2024. Randomized and non-randomized clinical trials, observational studies, and cohort studies were included. Data extraction and risk of bias assessment followed PRISMA guidelines. Meta-analysis was performed using STATA and R software with a random effects maximum likelihood model. Microbial co-occurrence networks, heatmaps, and longitudinal trends were analyzed, with heterogeneity assessed using Higgin's I² (substantial heterogeneity defined as I² > 50%).

RESULTS: Thirty-two studies met the inclusion criteria. The oral microbiome in edentulous patients differed significantly from dentate individuals, influenced by denture materials, design, and time. Veillonella abundance in acrylic complete dentures was 13.63% (95% CI = -0.04, 27.29), I² = 90.98%, compared to 49.10% (95% CI = -29.62, 115.81), I² = 99.47% in dentate patients. Candida albicans increased over time in acrylic dentures, from 63.13% (95% CI = 48.93, 77.33), I² = 99.84% after insertion to 344.72 CFU/ml × 10² (95% CI = 139.19, 550.24), I² = 98.30% at nine months. Streptococcus mutans in CAD/CAM dentures increased from 45.54 CFU/ml × 10² (95% CI = 33.82, 57.25), I² = 87.26% at three months to 125.22 CFU/ml × 10² (95% CI = 38.25, 212.18), I² = 97.89% at nine months. Co-occurrence networks revealed strong Candida albicans-Streptococcus mutans synergy, while Fusobacterium nucleatum showed antagonistic interactions. Heatmaps demonstrated microbial dysbiosis in denture stomatitis cases, with increased Porphyromonas gingivalis and Candida albicans and reduced commensals. Longitudinal analyses highlighted the progressive dominance of opportunistic pathogens, emphasizing the need for early and consistent hygiene interventions.

CONCLUSION: Denture wearers exhibit distinct microbial communities influenced by biofilm formation, denture materials, and hygiene practices. Findings highlight the importance of antimicrobial denture materials and effective cleaning protocols in managing microbial colonization. Given high heterogeneity, standardized methodologies are essential for future research. Frequent professional cleaning and individualized hygiene strategies are necessary to prevent denture-associated infections and maintain oral health.},
}

@article {pmid40442386,
year = {2025},
author = {O'Riordan, KJ and Aburto, MR and Nagpal, J and Clarke, G and Cryan, JF},
title = {Microbiome: A Key Regulator of Body-Brain Interactions.},
journal = {Advances in experimental medicine and biology},
volume = {1477},
number = {},
pages = {139-203},
pmid = {40442386},
issn = {0065-2598},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Brain/physiology/microbiology ; Animals ; *Brain-Gut Axis/physiology ; },
abstract = {The gut microbiota, consisting of trillions of microorganisms, plays a critical role in regulating host physiology, including metabolism, immune responses, and brain function. This chapter examines the microbiota-gut-brain axis, a multifaceted bidirectional communication system connecting gut microbial activity with central nervous system processes through immune pathways, metabolic byproducts, and neural circuits like the vagus nerve. The evolution of the gut microbiota throughout an individual's life-from early developmental influences like birth mode and antibiotic use to changes associated with aging and neurodegenerative conditions-highlights its dynamic nature. The chapter reviews experimental approaches and microbiome-based interventions to demonstrate the influence of gut microbiota on neurological conditions such as autism spectrum disorder, anxiety, and Alzheimer's disease. Finally, it emphasises the importance of advancing microbiome-targeted therapies, integrating emerging technologies, and clinical trials to develop personalised strategies for enhancing brain health through gut microbiome modulation.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Brain/physiology/microbiology
Animals
*Brain-Gut Axis/physiology

@article {pmid40442236,
year = {2025},
author = {Jeng, TM and Hsieh, YC and Chang, PY and Li, YL and Tang, SC and Jeng, JS and Hu, CJ and Chiou, HY},
title = {Association between post-stroke cognitive impairment and gut microbiota in patients with ischemic stroke.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18849},
pmid = {40442236},
issn = {2045-2322},
support = {NSTC107-2314-B-038-070-MY3//National Science and Technology Council/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Cognitive Dysfunction/microbiology/etiology ; *Ischemic Stroke/complications/microbiology ; Aged ; Cross-Sectional Studies ; Biomarkers ; Inflammation ; *Stroke/complications/microbiology ; },
abstract = {More than half of stroke survivors have post-stroke cognitive impairment (PSCI). The role of gut microbiota, which can communicate with the brain through the gut-brain axis and affect inflammation, has been receiving increased attention. This cross-sectional study aimed to investigate the association of PSCI, gut microbiota, and inflammatory markers. Patients with first ischemic stroke and complete 3-month and 1-year follow-up data were included and divided into PSCI and non-PSCI groups according to the Montreal Cognitive Assessment (MoCA) score at the above time points. PSCI was defined as having a MoCA less than 23 at either 3 months or 1 year, or a decrease of more than 2 points at both time points. Gut microbiota was assessed by 16 S rRNA gene sequencing and Next Generation Sequencing analysis. The inflammatory markers included interleukins (ILs), eotaxin, G-CSF, TNF-α, IFNγ, sCD40L, and MCP-1. There were 95 ischemic stroke patients (mean age, 60.5 ± 12.1 years; male, 68.4%), including 30 with PSCI and 65 with non-PSCI. In gut microbiota analysis, the PSCI group had a higher abundance of Bacteroidaceae and Clostridiaceae, and the non-PSCI group had a higher abundance of Prevotellaceae, Ruminococcaceae, Oscillibacter, and Faecalibacterium. Ruminococcaceae family under the Oscillospirales order remains significantly different in the two groups in logistic regression model adjusting confounding variables (p = 0.044). In an analysis of inflammatory markers, the plasma levels of eotaxin (p = 0.041) and IL-12p40 (p = 0.031) were significantly higher in the PSCI group than those in the non-PSCI group, and the plasma level of eotaxin was significantly positively correlated with the amount of Clostridiaceae (rho = 0.389, p = 0.045). The study found that PSCI was associated with certain gut microbiota, and these gut microbiotas correlated with the pro-inflammatory marker eotaxin. This suggests that gut microbiota might play a role in the development of cognitive impairment after ischemic stroke.},
}

Humans
*Gastrointestinal Microbiome
Male
Female
Middle Aged
*Cognitive Dysfunction/microbiology/etiology
*Ischemic Stroke/complications/microbiology
Aged
Cross-Sectional Studies
Biomarkers
Inflammation
*Stroke/complications/microbiology

@article {pmid40442154,
year = {2025},
author = {Seong, HJ and Park, YM and Kim, BS and Yoo, HJ and Kim, T and Yoon, SM and Kim, JH and Lee, SY and Lee, YK and Lee, DW and Nam, MH and Hong, SJ},
title = {Integrated multi-omics reveals different host crosstalk of atopic dermatitis-enriched Bifidobacterium longum Strains.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {91},
pmid = {40442154},
issn = {2055-5008},
mesh = {Humans ; *Dermatitis, Atopic/microbiology ; *Gastrointestinal Microbiome ; Infant ; *Bifidobacterium longum/genetics/isolation & purification/classification/metabolism ; Female ; Male ; Metabolomics ; Metagenomics/methods ; Feces/microbiology ; *Host Microbial Interactions ; Clostridium/genetics/isolation & purification ; Transcriptome ; Multiomics ; },
abstract = {The infant gut microbiome is essential for long-term health and is linked to atopic dermatitis (AD), although the underlying mechanisms are not fully understood. This study investigated gut microbiome-host interactions in 31 infants with AD and 29 healthy controls using multi-omics approaches, including metagenomic, host transcriptomic, and metabolomic analyses. Microbial diversity was significantly altered in AD, with Bifidobacterium longum and Clostridium innocuum associated with these changes. At the strain-level, only B. longum differed significantly between groups, with pangenome analyses identifying genetic variations potentially affecting amino acid and lipid metabolites. Notably, B. longum subclade I, which was more prevalent in healthy controls, correlated with host transcriptomic pathways involved in phosphatidylinositol 3-kinase-AKT signaling and neuroactive ligand-receptor pathways, as well as specific metabolites, including tetrahydrocortisol and ornithine. These findings highlight the role of B. longum strain-level variation in infants, offering new insights into microbiome-host interactions related to AD.},
}

Humans
*Dermatitis, Atopic/microbiology
*Gastrointestinal Microbiome
Infant
*Bifidobacterium longum/genetics/isolation & purification/classification/metabolism
Female
Male
Metabolomics
Metagenomics/methods
Feces/microbiology
*Host Microbial Interactions
Clostridium/genetics/isolation & purification
Transcriptome
Multiomics

@article {pmid40442038,
year = {2025},
author = {Turjeman, S and Koren, O},
title = {Bridging the bench-to-bedside divide in microbiome research.},
journal = {Clinical and translational medicine},
volume = {15},
number = {5},
pages = {e70358},
doi = {10.1002/ctm2.70358},
pmid = {40442038},
issn = {2001-1326},
support = {ERC-2020-COG no. 101001355//HORIZON EUROPE European Research Council/ ; 1527/21//Israel Science Foundation/ ; },
}

@article {pmid40441709,
year = {2025},
author = {Dang, T and Fuji, Y and Kumaishi, K and Usui, E and Kobori, S and Sato, T and Narukawa, M and Toda, Y and Sakurai, K and Yamasaki, Y and Tsujimoto, H and Hirai, MY and Ichihashi, Y and Iwata, H},
title = {I-SVVS: integrative stochastic variational variable selection to explore joint patterns of multi-omics microbiome data.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {3},
pages = {},
doi = {10.1093/bib/bbaf132},
pmid = {40441709},
issn = {1477-4054},
support = {JP21J21850//JSPS KAKENHI/ ; JPMJCR1602//JST-CREST Program/ ; JPMJMI120C7//JST-Mirai Program/ ; JPMJAN23D1//JST ALCA-Next Program/ ; },
mesh = {*Microbiota ; Mice ; Animals ; Humans ; Stochastic Processes ; Bayes Theorem ; Glycine max/microbiology ; *Metabolomics/methods ; Algorithms ; *Computational Biology/methods ; Metabolome ; Cluster Analysis ; Multiomics ; },
abstract = {High-dimensional multi-omics microbiome data play an important role in elucidating microbial community interactions with their hosts and environment in critical diseases and ecological changes. Although Bayesian clustering methods have recently been used for the integrated analysis of multi-omics data, no method designed to analyze multi-omics microbiome data has been proposed. In this study, we propose a novel framework called integrative stochastic variational variable selection (I-SVVS), which is an extension of stochastic variational variable selection for high-dimensional microbiome data. The I-SVVS approach addresses a specific Bayesian mixture model for each type of omics data, such as an infinite Dirichlet multinomial mixture model for microbiome data and an infinite Gaussian mixture model for metabolomic data. This approach is expected to reduce the computational time of the clustering process and improve the accuracy of the clustering results. Additionally, I-SVVS identifies a critical set of representative variables in multi-omics microbiome data. Three datasets from soybean, mice, and humans (each set integrated microbiome and metabolome) were used to demonstrate the potential of I-SVVS. The results indicate that I-SVVS achieved improved accuracy and faster computation compared to existing methods across all test datasets. It effectively identified key microbiome species and metabolites characterizing each cluster. For instance, the computational analysis of the soybean dataset, including 377 samples with 16 943 microbiome species and 265 metabolome features, was completed in 2.18 hours using I-SVVS, compared to 2.35 days with Clusternomics and 1.12 days with iClusterPlus. The software for this analysis, written in Python, is freely available at https://github.com/tungtokyo1108/I-SVVS.},
}

*Microbiota
Mice
Animals
Humans
Stochastic Processes
Bayes Theorem
Glycine max/microbiology
*Metabolomics/methods
Algorithms
*Computational Biology/methods
Metabolome
Cluster Analysis
Multiomics

@article {pmid40441385,
year = {2025},
author = {Wirkus, J and Ead, AS and Krga, I and Wang, Y and Pontifex, MG and Muller, M and Vauzour, D and Matsukuma, KE and Zhang, G and Mackenzie, GG},
title = {Normalizing body weight with a dietary strategy mitigates obesity-accelerated pancreatic carcinogenesis in mice.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.05.039},
pmid = {40441385},
issn = {1541-6100},
abstract = {BACKGROUND: Obesity is a modifiable risk factor for pancreatic cancer, but the impact of dietary changes leading to weight loss in pancreatic carcinogenesis remains unknown.

OBJECTIVE: To determine the effects of weight normalization via dietary switch on pancreatic carcinogenesis and associated mechanisms.

METHODS: Five-week-old male and female LSL-Kras[G12D/+]; p48[Cre/+] (KC) mice (8-12/diet group/sex) were fed a high-fat, diet-induced obesity diet (DIO; 60% kcal from fat) or a low-fat, control diet (CD; 11% kcal from fat) for 21 weeks. A subset of mice was fed the DIO for 8 weeks, then switched to CD for 13 additional weeks (DIO→CD). Cancer incidence was evaluated by histology. Lipidomics and RNAseq followed by bioinformatic analysis identified potential mechanisms. The gut microbiome was characterized using 16s rRNA amplicon sequencing. Data were analyzed using one-way analysis of variance.

RESULTS: After 21 weeks, DIO-fed mice had 1.7-fold higher body weight gain, and 60% increase (p<0.05 DIO vs. CD) in pancreatic acinar-to-ductal metaplasia, compared to the other 2 groups. None of the 21 mice fed a CD developed cancer, while 2 out of 21 DIO-fed male mice did. Switching from a DIO to a CD normalized body weight and composition to CD levels, slowed acinar-to-ductal metaplasia and prevented cancer incidence, with no mice developing cancer. Mechanistically, DIO affected gene expression related to cellular metabolism, pancreatic secretions, immune function, and cell-signaling, while CD and DIO→CD had similar global gene expression. Moreover, DIO increased epoxy metabolites of linoleic acid, which were mitigated by the dietary switch. Finally, compared to a CD, DIO altered the gut microbiome and switching from a DIO to a CD restored the gut microbiome profile to resemble that of CD-fed mice.

CONCLUSIONS: Body weight normalization slowed obesity-accelerated pancreatic carcinogenesis, in part, by affecting inflammatory and cell signaling pathways, reducing epoxy metabolites, and modulating the gut microbiome.},
}

@article {pmid40441298,
year = {2025},
author = {Piché, ME and Poirier, P and Wong, JA},
title = {Impact of metabolic surgery on cardiovascular disease outcomes.},
journal = {The Canadian journal of cardiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cjca.2025.05.013},
pmid = {40441298},
issn = {1916-7075},
abstract = {Obesity is strongly associated with a range of cardiovascular conditions, including coronary artery disease, heart failure, atrial fibrillation, and stroke. Metabolic surgery has emerged as one of the most effective interventions for individuals with severe obesity, not only by promoting substantial and durable weight loss but also by improving cardiovascular risk factors and outcomes. Cardiovascular benefits may also be mediated via weight independent mechanisms involving insulin sensitivity, gastrointestinal hormones, bile acid dynamics, and gut microbiome. Long-term cohort studies have documented that metabolic surgery is associated with a reduction in all-cause mortality and major adverse cardiovascular events in this population. This narrative review examines the role of metabolic surgery in the prevention and management of cardiovascular disease associated with severe obesity. It provides an overview of the most common metabolic surgery procedures, including sleeve gastrectomy, Roux-en-Y gastric bypass and biliopancreatic diversion with duodenal switch as well as newer procedures like single-anastomosis duodenal switch. This review also evaluates the impact of these interventions on key cardiovascular risk factors such as type 2 diabetes, hypertension, dyslipidemia, and obstructive sleep apnea, as well as their effects on cardiac structure and function. Metabolic surgery is associated with reductions in all-cause mortality and cardiovascular events, including myocardial infarction and heart failure, especially in individuals with obesity and pre-existing cardiovascular disease. The current evidence supporting the link between metabolic surgery and cardiovascular outcomes is reviewed. Notably, randomized trials specifically focusing on cardiovascular outcomes after metabolic surgery are lacking highlighting an important knowledge gap and their crucial need. Addressing this gap is essential for guiding future clinical practice and optimizing patient care.},
}

@article {pmid40441277,
year = {2025},
author = {Chapron, L and Meistertzheim, AL and Ghiglione, JF and Peru, E and Galand, PE and Lartaud, F},
title = {Beyond plastisphere transfer, deep corals are subject to dysbiosis when exposed to plastics.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126554},
doi = {10.1016/j.envpol.2025.126554},
pmid = {40441277},
issn = {1873-6424},
abstract = {Plastic pollution has been identified as a major threat to marine life and ecosystems, but their biological impacts are still largely unknown. Coral reefs, which are one of the most biodiverse ecosystems on earth that provide essential ecological and economical services, are now recognized to be impacted by plastic pollution from the surface to the deep. Here, we investigated the impact of colonized macro- and microplastics on the microbiome of the most emblematic cold-water coral, Lophelia pertusa. Studies at the associated bacterial level help better understand the early biological pathways that may lead to coral physiological alterations. Both macro- and microplastics induced early (7 days) microbial shifts for L. pertusa polyps, with specific exacerbated effects between plastic sizes observed after 47 days. In the case of stressed corals, we observed an increase of opportunistic and/or pathogenic bacteria that may be induced by different processes whether corals are exposed to macro- (barrier effect) or microplastics (ingestion). Our results however confirm that very few specific bacteria can be directly transferred from plastisphere to coral microbiome. We suggest that shift in coral microbiome was due to general dysbiosis from stress, and poorly from a transfer of microorganisms from the plastisphere. Considering the widespray distribution of macroplastics in the ocean that are continuously fragmented into microplastics, our conclusions suggest that plastics could seriously endangered the cold-water coral reefs.},
}

@article {pmid40441229,
year = {2025},
author = {Wei, F and Zhao, M and Sun, X and Ma, H and Yin, H and Shen, X},
title = {Causal associations between gut microbiota and rheumatoid arthritis: A two-sample Mendelian randomization study.},
journal = {Medicine},
volume = {104},
number = {22},
pages = {e42596},
doi = {10.1097/MD.0000000000042596},
pmid = {40441229},
issn = {1536-5964},
mesh = {*Arthritis, Rheumatoid/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Mendelian Randomization Analysis ; Genome-Wide Association Study ; },
abstract = {The gut microbiota has been implicated in the development of rheumatoid arthritis (RA), but whether these associations reflect causal relationships remains unclear. We conducted a two-sample Mendelian randomization analysis to investigate the potential causal effects of gut microbial taxa on RA risk. Summary-level data from the MiBioGen consortium (n = 13,266) and a large RA genome-wide association study (n = 97,173) were used. Multiple Mendelian randomization methods and sensitivity analyses were applied to ensure robustness. Four microbial taxa showed nominal associations with RA. Increased abundance of Catenibacterium, Desulfovibrio, and Ruminiclostridium 6 was associated with a higher risk of RA, while Lachnospiraceae (UCG008) appeared to have a protective effect. Although these associations did not meet Bonferroni-corrected significance, results were consistent across analytical methods with no evidence of pleiotropy or heterogeneity. This study provides genetic evidence supporting a potential causal link between specific gut microbes and RA risk. The findings highlight host immune modulation as a possible pathway connecting the gut microbiome to RA and identify candidate taxa for future mechanistic and therapeutic research.},
}

*Arthritis, Rheumatoid/microbiology/genetics
*Gastrointestinal Microbiome/genetics
Humans
Mendelian Randomization Analysis
Genome-Wide Association Study

@article {pmid40441205,
year = {2025},
author = {Zhou, J and Xu, Y and Wang, H and Wang, K and Chen, C},
title = {Investigating the causal links among gut microbiome features, inflammation-related proteins, and diverticular disease: Insights from a mediation Mendelian randomization study.},
journal = {Medicine},
volume = {104},
number = {22},
pages = {e42676},
doi = {10.1097/MD.0000000000042676},
pmid = {40441205},
issn = {1536-5964},
support = {No. JDY2023018//Jiangsu University Medical Education Collaborative Innovation Fund Project/ ; No. Z2021010//Medical Research Project of Jiangsu Health Commission/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Mendelian Randomization Analysis ; *Diverticular Diseases/microbiology/genetics ; *Inflammation/genetics ; Genome-Wide Association Study ; Mediation Analysis ; },
abstract = {The pathophysiological mechanisms underlying diverticular disease (DD) remain incompletely understood, and there is considerable debate regarding the roles of gut microbiome features and inflammation-related proteins in the development of the disease. In this study, we employed mediation Mendelian randomization (MR) analysis to investigate the causal relationships among these 3 factors. In this study, we conducted a MR analysis on the genome-wide association studies data of 412 gut microbiome features (207 microbial taxa and 205 pathways), 91 inflammation-related proteins, and DD. We employed the inverse-variance weighted (IVW) method as our primary screening approach, followed by a mediation MR analysis to explore potential causal relationships among these 3 aspects. Our findings were further reinforced by comprehensive heterogeneity analyses, horizontal pleiotropy testing, outlier detection, and "leave-one-out" sensitivity analysis. Through our screening process, we identified potential causal relationships between DD and 18 gut microbiome features, as well as 6 inflammation-related proteins. These include s_Oscillibacter_unclassified (IVW odds ratio (OR): 1.139; 95% confidence interval (CI): 1.044-1.241, P = .003), g_Bilophila (IVW OR: 1.107, 95% CI: 1.016-1.206, P = .020), T-cell surface glycoprotein CD5 levels (IVW OR: 1.065, 95% CI: 1.011-1.123, P = .019), and inosine 5'-phosphate biosynthesis I (IVW OR: 0.882, 95% CI: 0.800-0.973, P = .012), etc. In the mediation MR analysis, we found that the genetic predictors of g_Bilophila and inosine 5'-phosphate biosynthesis I could explain 23.956% and 24.630% of the variation in T-cell surface glycoprotein CD5 levels, respectively. This study detailed analysis of the links between gut microbiome features, inflammation-related proteins, and DD offers key insights into DD pathogenesis and prevention.},
}

Humans
*Gastrointestinal Microbiome/genetics
Mendelian Randomization Analysis
*Diverticular Diseases/microbiology/genetics
*Inflammation/genetics
Genome-Wide Association Study
Mediation Analysis

@article {pmid40441146,
year = {2025},
author = {Yang, Y and Duan, Y and Lang, S and Fondevila, MF and Schöler, D and Harberts, A and Cabré, N and Chen, S and Shao, Y and Vervier, K and Miyamoto, Y and Zhang, X and Chu, H and Yang, L and Tan, C and Eckmann, L and Bosques-Padilla, F and Verna, EC and Abraldes, JG and Brown, RS and Vargas, V and Altamirano, J and Caballería, J and Shawcross, DL and Louvet, A and Lucey, MR and Mathurin, P and Garcia-Tsao, G and Bataller, R and Stärkel, P and Lawley, TD and Schnabl, B},
title = {Targeted inhibition of pathobiont virulence factor mitigates alcohol-associated liver disease.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.05.003},
pmid = {40441146},
issn = {1934-6069},
abstract = {Alcohol-associated liver disease poses a global health burden with high mortality. Imbalances in the gut microbiota are important for disease progression. Using metagenomic sequencing of fecal samples from a multicenter, international cohort of patients with alcohol-associated hepatitis, we found that the presence of virulence factor KpsM, encoded in the genome of Escherichia coli (E. coli), correlated with patient mortality. Functional studies using gnotobiotic mouse models and genetic manipulation of bacteria demonstrated that kpsM-positive E. coli exacerbate ethanol-induced liver disease. The kpsM gene mediates the translocation of capsular polysaccharides to the cell surface. This enables kpsM-positive E. coli to evade phagocytosis by the scavenger receptor Marco on Kupffer cells in the liver, leading to bacterial spread. Importantly, inhibiting kpsM-dependent capsules with the small molecule 2-(4-phenylphenyl)benzo[g]quinoline-4-carboxylic acid (C7) attenuated ethanol-induced liver disease in mice. We show that precision targeting of the virulence factor KpsM is a promising approach to improve outcomes of patients with alcohol-associated hepatitis.},
}

@article {pmid40441086,
year = {2025},
author = {Sharma, P and Das, S and Rituraj, R and Bhagyashree, B},
title = {Understanding oncobiosis in ovarian cancer: Emerging concepts in tumor progression.},
journal = {Pathology, research and practice},
volume = {271},
number = {},
pages = {156026},
doi = {10.1016/j.prp.2025.156026},
pmid = {40441086},
issn = {1618-0631},
abstract = {Ovarian cancer is a leading cause of gynecologic cancer mortality and has recently been linked to microbial dysbiosis or oncobiosis. Tumorigenesis is a highly complex process, and recent research has revealed numerous new mechanisms showing how tumors interact with their surrounding microenvironment. The inclusion of microbiome studies has significantly advanced this field revealing the important role microbes play, not only in maintaining normal physiological functions of the human body but also in influencing oncogenic pathways. This expanding knowledge is deepening our understanding of tumor pathophysiology and is helping to create new diagnostic, prognostic, therapeutic and preventive strategies for specific cancers. This review explores the role of the microbiome in ovarian carcinogenesis, focusing on its interaction with the tumor microenvironment (TME) and its influence on inflammation, immune regulation and metabolic signaling. This review studied dysbiosis in several anatomical compartments such as the gut, oral cavity, lower and upper genital tracts and ovarian tissues, in relation to ovarian oncobiosis. Emerging clinical implications of these studies include the use of microbial profiles as diagnostic or prognostic biomarkers. Therapeutic strategies such as fecal microbiota transplantation and probiotics are also discussed for their ability to restore microbial balance and enhance treatment efficacy. This review highlights the importance of continued research to explore causal relationships between the microbiome and tumorigenesis, positioning microbiome studies as promising tools in ovarian cancer management and improving patient care.},
}

@article {pmid40440906,
year = {2025},
author = {Zhan, Z and Zhang, J and Huang, W and Huang, J},
title = {Transcriptomic strategy provides molecular insights into the growth and ginsenosides accumulation of Panax ginseng.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {143},
number = {},
pages = {156834},
doi = {10.1016/j.phymed.2025.156834},
pmid = {40440906},
issn = {1618-095X},
abstract = {BACKGROUND: Panax ginseng C. A. Meyer, a well-known phytomedicine has been widely used in traditional medicine for centuries. However, its quality and yield are heavily influenced by environmental conditions and cultivation years. For example, ginsenosides as the primary active component of ginseng, the concentration increased with the age of the roots and unevenly distributed across different tissues. Recently, transcriptomic technologies have provided powerful tools for revealing the relationship between gene expression and ginsenoside accumulation during ginseng growth, and researches in this field is continuously expanding, influencing the quality and sustainability of ginseng cultivation.

PURPOSE: Investigating the relationship between ginseng growth and the accumulation of active components may provide new insights for improving ginseng performance and medicinal value. This requires a systematic review and in-depth discussion of relevant research.

STUDY DESIGN AND METHODS: This article reviews the application of transcriptomic strategies in studying the molecular mechanisms of ginseng growth and ginsenoside accumulation. A literature search and analysis were conducted using keywords such as "Panax ginseng" and "transcriptomics/transcriptome," along with terms including "ginsenoside biosynthesis," "microbe/microorganism," "RNA-seq," "cultivation years," "rhizosphere," and "stress."

RESULT: Our study focuses on the transcriptome strategy provides molecular insights into the growth and ginsenosides accumulation of Panax ginseng, we summarized and discussed the dynamic changes in gene expression across cultivation years, specific-tissue, environmental stress, and imbalance of rhizosphere microbes during the ginseng growth and ginsenosides accumulation process. In addition, we also highlight future directions.

CONCLUSION: The cultivation years, specific-tissue, environmental stress, and rhizosphere microbiome imbalance of Panax ginseng are indirectly or directly involved in plant health, biomass production, and the synthesis of ginsenosides. Harnessing these factors to improve the quality and yield of ginseng holds great promise.},
}

@article {pmid40440849,
year = {2025},
author = {Ramadoss, R and Nishad, AK and Moovarkumudalvan, B and Shomar, B},
title = {Bacterial composition of dust deposited in Qatar: A seasonal study.},
journal = {The Science of the total environment},
volume = {985},
number = {},
pages = {179766},
doi = {10.1016/j.scitotenv.2025.179766},
pmid = {40440849},
issn = {1879-1026},
abstract = {Dust storms in the Middle East threaten public health by deteriorating air quality and transporting microorganisms over vast distances. This study analyzes seasonal variations in dust-borne bacterial diversity on photovoltaic (PV) panels using 16S rRNA gene sequencing and bioinformatics to assess community composition and metabolic potential. Our findings suggest that seasonal ecological factors have potential effects on the composition of the airborne bacterial community. In Qatar, the high atmospheric CO2 levels associated with hydrocarbon refining had promoted the growth of hydrocarbon-degrading bacteria belonging to the phyla Campilobacterota, Proteobacteria, and Bacteroidota. High temperatures and photothermal reactions of summer conditions have favored sulfur-metabolizing bacteria. Conversely, milder temperatures, increased humidity, reduced wind speed, and a decline in summer-favoring bacteria had contributed to the increased abundance of the phyla Patescibacteria, Firmicutes, and Actinobacteriota during other seasons. This study had also identified dust borne pathogenic bacteria associated with human and plant diseases, highlighting the need for environmental surveillance to monitor microbial diversity and its shifts driven by ecological factors. This knowledge is crucial for public health, environmental protection, sustainable farming and advancing our understanding of microbial ecology.},
}

@article {pmid40440748,
year = {2025},
author = {Cimmino, F and Silvestri, C and Trinchese, G and Petrella, L and Cavaliere, G and Fogliano, C and Piscitelli, F and Cristino, L and Avallone, B and Banni, S and Sihag, J and Di Marzo, V and Mollica, MP},
title = {Anti-obesity effects of Oleoylethanolamide: Modulation of mitochondrial bioenergetics, endocannabinoidome and gut microbiome.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {188},
number = {},
pages = {118201},
doi = {10.1016/j.biopha.2025.118201},
pmid = {40440748},
issn = {1950-6007},
abstract = {The endocannabinoidome (eCBome) and gut microbiome play key roles in metabolism and obesity, and oleoylethanolamide (OEA), a lipid mediator within the eCBome, is known to reduce food intake and promote fat oxidation. This study investigated the effects of OEA administration on mice with diet-induced obesity, focusing on hepatic inflammation and mitochondrial function, the endocannabinoidome (eCBome), and the gut microbiome. Mice fed standard (STD) or high-fat (HFD) diets for 18 weeks were treated with either vehicle or OEA. Metabolic, inflammatory, oxidative stress and mitochondrial parameters were assessed, along with intestinal and hepatic levels of eCBome lipids and fecal microbiota and short chain fatty acid composition. In HFD-fed mice, OEA decreased body weight, food intake, and serum and liver inflammatory markers, limiting hepatic and body fat accumulation. OEA improved liver mitochondrial oxidative capacity, lipid metabolism and oxidative stress. It reduced intestinal levels of the endocannabinoid 2-arachidonoylglycerol. Effects on microbiota composition were mostly found in the STD-fed group. However, OEA increased the relative abundance of Akkermansia muciniphila more strongly in HFD-fed mice. These findings suggest that OEA may help counteract obesity-related metabolic dysfunction and inflammation, and gut microbiota unbalance, thus representing a promising candidate for future therapeutic strategies.},
}

@article {pmid40440482,
year = {2025},
author = {Zhao, L},
title = {Guild-Level Response of the Gut Microbiome to Nutritional Signals: Advancing Precision Nutrition for Metabolic Health.},
journal = {Annual review of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-nutr-122424-022254},
pmid = {40440482},
issn = {1545-4312},
abstract = {The gut microbiome functions as a hidden organ, providing essential ecosystem services to sustain human health. By identifying stably connected bacteria, we reveal two competing guilds (TCG) as the resilient core of the microbiome: the health-promoting foundation guild (FG) and the proinflammatory pathobiont guild (PG). FG members produce short-chain fatty acids (SCFAs), enhancing gut barrier integrity and systemic resilience, while PG members disrupt metabolism through endotoxins, indoles, and hydrogen sulfide. Together, the FG and PG mediate ∼85% of ecological interactions in a dynamic, seesaw-like relationship. As evolved nutrient sensors for coping with feast-famine cycles, these guilds align host metabolism with dietary patterns. Fiber-rich diets bolster FG activity, maintaining microbial balance and metabolic health, whereas fiber-deficient diets in modern-day society favor chronic PG dominance, driving inflammation and disease. Synthesizing clinical and experimental evidence, this review positions the TCG model as a transformative framework for precision nutrition, guiding strategies to restore microbial balance and address metabolic disorders.},
}

@article {pmid40439988,
year = {2025},
author = {Davidson, IM and Nikbakht, E and Haupt, LM and Dunn, PJ},
title = {Toward accurate vaginal microbiome profiling: protocol, bioinformatics, and core microbiota characterisation.},
journal = {Journal of assisted reproduction and genetics},
volume = {},
number = {},
pages = {},
pmid = {40439988},
issn = {1573-7330},
abstract = {PURPOSE: Rising demand for assisted reproductive technologies (ART) with limited improvements in success rates has driven interest in the impact of the vaginal microbiome on fertility outcomes. In order to fully examine the relationship between the vaginal microbiome and fertility outcomes, methodologies and technological developments must be standardised and benchmarked to provide the most accurate assessment of microbial population representation.

METHODS: This study sought to investigate the utility of 16S sequencing and bioinformatic approaches using nanopore sequencing to characterize core vaginal microbiota in a healthy Australian cohort of reproductive-age women.

RESULTS: Optimisation and comparison of different PCR strategies for whole 16S amplification was undertaken, along with the generation of bioinformatic analysis strategies. Initial qPCR identified the 27F-YM (MIX) primer as the most sensitive for C. trachomatis. However, nanopore sequencing revealed no detectable C. trachomatis across all six samples. Among the bioinformatic tools, Porechop with NanoCLUST most accurately identified microbial presence. Community state type (CST) I-characterised by Lactobacillus crispatus dominance-was identified as the most common CST (66%), aligning with patterns of a healthy vaginal microbiome.

CONCLUSION: The findings highlight a Lactobacillus-rich microbiome as the most common among healthy females; however, further refinement-potentially through a metagenomics approach-is recommended to address 16S rRNA primer limitations to enable improved accuracy of microbial detection for the vaginal microbiome.},
}

@article {pmid40439987,
year = {2025},
author = {Wang, X and Sun, C and Yang, X and Xu, G and Pei, L and Tang, L and Xu, S and Xie, C},
title = {Exploring the potential mechanism of tofacitinib therapy for ankylosing spondylitis through gut microbiome and plasma metabolomics.},
journal = {Clinical rheumatology},
volume = {},
number = {},
pages = {},
pmid = {40439987},
issn = {1434-9949},
abstract = {OBJECTIVE: To explore the role of gut microbiota and plasma metabolites in the therapeutic mechanism of tofacitinib in ankylosing spondylitis (AS).

METHOD: Ten AS patients and ten matched healthy controls (HC) were enrolled in this study. 16S rRNA sequencing and LC-MS profiling was conducted to investigate the gut microbiota and plasma metabolite before and after tofacitinib therapy. An AS mouse model was established to validate the effect of tofacitinib in vivo via H&E staining, western blot, and ELISA.

RESULTS: Tofacitinib improved clinical symptoms in AS patients. Microbiota analysis revealed Microbiota analysis revealed reduced α-diversity (ACE, Chao1) and altered community structure in AS patients compared to HC, which partially normalized post-treatment. LEfSe identified 84 taxa biomarkers; Barnesiella, Coprobacter, Lachnospira, and Lactobacillus tended to return to normal after tofacitinib treatment. Plasma metabolomics uncovered 3 key metabolies, including choline metabolism, glycerophospholipid metabolism, and phenylalanine metabolism. Spearman analysis revealed that the gut microbiota were closely related to the changes in differential plasma metabolites. Combinated tofacitinib and trichostatin therapy attenuated inflammation, restored metabolism caused by AS in mice in vivo.

CONCLUSION: AS patients suffer from dysbiosis of gut microbiota, and the mechanism of tofacitinib treatment of AS may be related to the modulation of gut microbiota and alteration of plasma metabolites. Key Points • Tofacitinib improves clinical symptoms in patients with AS. • Tofacitinib regulates gut microbiota in AS patients. • Tofacitinib regulates plasma metabolites in patients with AS. • Tofacitinib regulates the choline metabolism.},
}

@article {pmid40439700,
year = {2025},
author = {Zaghloul, HAH and Xiao, Z and Tang, J and Xiao, T and Gao, J and Hu, J and Huang, GH},
title = {An aegerolysin-like protein from Heliothis virescens ascovirus 3h (HvAV-3h) shows immune suppression and antibacterial activity.},
journal = {The Journal of general virology},
volume = {106},
number = {5},
pages = {},
doi = {10.1099/jgv.0.002107},
pmid = {40439700},
issn = {1465-2099},
mesh = {Animals ; *Ascoviridae/genetics/immunology ; *Viral Proteins/genetics/immunology/metabolism ; *Moths/virology/immunology ; *Anti-Bacterial Agents/pharmacology ; Immunity, Innate ; Larva/virology ; Host-Pathogen Interactions ; Virus Replication ; Fungal Proteins ; Hemolysin Proteins ; },
abstract = {Aegerolysins are lipid-binding proteins associated with multiple functions, including membrane pore-formation, insecticidal toxicity and defence against predators. Whilst distributed over the kingdoms of the Tree of Life, ascoviruses are the only representative viruses that encode an aegerolysin-like protein. Ascoviruses are entomopathogenic and possess a large dsDNA genome. The present study aimed to functionally characterize the aegerolysin-like protein of Heliothis virescens ascovirus 3h (HvAV-3h), encoded by ORF85, and to explore its potential roles in the interaction between the ascovirus and its host. Our results demonstrate the importance of this species-specific protein to HvAV-3h replication in host cells. In vivo, silencing of this gene for 12-72 h significantly increased the expression of some innate immunity-associated genes, including Toll (114-fold), IMD (44.7-fold) and Hopscotch (22.9-fold). In parallel, we detected significant gradual increases in MyD88 and Relish and decreases in PIAS. Moreover, histopathological analyses of infected larval tissues indicated reduced tissue damage after 72 h of ORF85 gene silencing. The prokaryotic expression of the HvAV-3h aegerolysin, followed by feeding to third-instar Spodoptera exigua larvae for 24 or 48 h led to significant reductions in larval weight. Moreover, the in vitro treatment demonstrated a bactericidal action against Lysinibacillus xylanilyticus, a bacterial resident of some insect guts. Overall, our findings suggest that the protein encoded by ORF85 is associated with the pathogenicity of HvAV-3h and its ability to replicate in host cells. Additionally, aegerolysin may inhibit or kill specific bacterial species in the host microbiome during infection, potentially modulating the host immune response.},
}

Animals
*Ascoviridae/genetics/immunology
*Viral Proteins/genetics/immunology/metabolism
*Moths/virology/immunology
*Anti-Bacterial Agents/pharmacology
Immunity, Innate
Larva/virology
Host-Pathogen Interactions
Virus Replication
Fungal Proteins
Hemolysin Proteins

@article {pmid40439571,
year = {2025},
author = {Hadjigeorgiou, AG and Harkos, C and Mishra, AK and Morad, G and Johnson, SB and Ajami, NJ and Wargo, JA and Munn, LL and Stylianopoulos, T and Jain, RK},
title = {Mathematical Modeling and Association Analysis Deciphers the Impact of the Gut Microbiome on Cancer Immunotherapy.},
journal = {Cancer research},
volume = {},
number = {},
pages = {},
doi = {10.1158/0008-5472.CAN-24-2232},
pmid = {40439571},
issn = {1538-7445},
abstract = {The gut microbiome has emerged as a key regulator of response to cancer immunotherapy. However, a better understanding of the underlying mechanisms by which the microbiome influences immunotherapy is needed to identify strategies to optimize outcomes. To this end, we developed a mathematical model to obtain insights into the effect of the microbiome on the immune system and immunotherapy response. This model was based on i) gut microbiome data derived from preclinical studies, ii) mathematical modeling of the antitumor immune response, iii) association analysis of microbiome profiles with model-predicted immune profiles, and iv) statistical models that correlate model parameters with the microbiome. The model was used to investigate the complexity of murine and human studies on microbiome modulation. Comparison of model predictions with experimental observation of tumor response in the training and test datasets supported the hypothesis that two model parameters, the activation and killing rate constants of immune cells, are the most influential in tumor progression and are potentially affected by microbiome composition. Evaluation of the associations between the gut microbiome and immune profile indicated that the components and structure of the gut microbiome affect the activation and killing rate of adaptive and innate immune cells. Overall, this study contributes to a deeper understanding of microbiome-cancer interactions and offers a framework for understanding how microbiome interactions influence cancer treatment outcomes.},
}

@article {pmid40439440,
year = {2025},
author = {Su, X and Li, X and He, X and Zhou, S and Lyu, A and Cai, Z},
title = {A biotin-free diet attenuates the incidence of collagen-induced arthritis and alleviates microbial dysbiosis.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo01457c},
pmid = {40439440},
issn = {2042-650X},
abstract = {Emerging evidence has shown that the gut microbiota and its products are important triggers in the pathogenesis of rheumatoid arthritis (RA). Biotin is a diet- and microbiome-dependent metabolite and an immune regulator; however, the role of biotin in RA remains unknown. In this study, we observed abnormal fecal biotin excretion in RA patients, which correlated with microbial alterations. Specifically, biotin content was inversely associated with gut microbial genera enriched in healthy controls, including Roseburia and Dorea. Meanwhile, it positively correlated with Oscillospira, which was highly enriched in RA individuals. Moreover, collagen-induced arthritis (CIA) mice fed a biotin-free diet had attenuated arthritis incidence with depressed differentiation of splenic CD3[+] T cells and restored microbial diversities. The biotin-free diet also increased bone mass and protected against inflammation-induced bone loss in CIA mice. Additionally, the biotin-free diet reshaped the host metabolic phenotype of amino acids and microbial composition. Notably, biotin deficiency ameliorated the augmentation of Oscillospira in CIA mice. Collectively, our results suggested a potential link between biotin deficiency, gut microbiota dysbiosis and CIA progression.},
}

@article {pmid40439420,
year = {2025},
author = {Park, J and Kohn, E and Schenk, S and Davis, KM and Clark, JS and Parfrey, LW},
title = {An experimental test of the influence of microbial manipulation on sugar kelp (Saccharina latissima) supports the core influences host function hypothesis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0030125},
doi = {10.1128/aem.00301-25},
pmid = {40439420},
issn = {1098-5336},
abstract = {UNLABELLED: Kelp are valued for a wide range of commercial products and their role in kelp forest ecosystems, making kelp cultivation a rapidly expanding economic sector. Microbes associated with kelp and other macroalgae play a critical role in processes such as nutrient exchange, chemical signaling, and defense against pathogens. Thus, manipulating the microbiome to enhance macroalgal growth and resilience is a promising yet underexplored approach for sustainable kelp cultivation. The core microbiome hypothesis suggests that the bacteria that are consistently found on a host (the core microbes) are likely to have a disproportionate impact on host biology, making them an attractive target for microbiome manipulation. In this study, we surveyed wild Saccharina latissima and their surrounding environment to identify core bacterial taxa, compared them to cultivated kelp, and experimentally tested how cultured bacterial isolates affect kelp development. We found that core bacteria are nearly absent in cultivated juvenile sporophytes in nurseries, but eventually colonize them after outplanting to ocean farm sites. Bacterial inoculants had both positive and negative effects on kelp development. Notably, the strength of association of a bacterial genus with kelp in the wild positively correlated with its impact on gametophyte settlement and sporophyte development in kelp co-culture experiments, aligning with predictions from the core microbiome influences host function hypothesis. These findings affirm the feasibility of using microbial manipulations to improve current kelp aquaculture practices and provide a framework for developing these techniques.

IMPORTANCE: Microorganisms consistently associated with hosts are widely thought to be more likely to impact host biology and health. However, this intuitive concept has not been experimentally evaluated. This study formalizes this concept as the Core Microbiome Influences Host Function hypothesis and experimentally tests this hypothesis in sugar kelp (Saccharina). The distribution of bacteria on wild kelp and core microbes was first identified by compiling a broad dataset of the kelp microbiome sampled across space and time. Bacterial cultures were isolated from the surface of sugar kelp and individually grown in laboratory co-culture with sugar kelp spores to assess the ability of bacterial isolates to influence kelp growth and development. In support of the core influences host function hypothesis, isolates belonging to bacterial genera that are more strongly associated with wild sugar kelp are more likely to influence development in laboratory experiments.},
}

@article {pmid40439402,
year = {2025},
author = {Gill, DS and Ram, S and Rice, PA},
title = {Biologic drug development for treatment and prevention of sexually transmitted infections.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0010724},
doi = {10.1128/cmr.00107-24},
pmid = {40439402},
issn = {1098-6618},
abstract = {SUMMARYSexually transmitted infections (STIs) represent a significant global health burden, with over one million new infections occurring daily. In some instances, the prevalence of antibiotic-resistant pathogens is rising, which exacerbates the challenge. STIs cause severe complications, including infertility, ectopic pregnancies, pre-term births, and heightened risks of HIV acquisition. These outcomes underscore the need for innovative therapeutic and prophylactic strategies. In this review, we provide a comprehensive analysis of the current state of biologic drug development targeting key STIs, focusing on Chlamydia trachomatis, Neisseria gonorrhoeae, herpes simplex virus type 2 (HSV-2), and Treponema pallidum. We examine the complexity of host-pathogen interactions that inform biologic drug design, such as multiple mechanisms of infection, immune evasion strategies, and pathogenic latency. We also explore the role of mucosal immunity, highlighting advances in resident memory T cells and cytokine-driven responses that guide therapeutic targeting, concentrating on Chlamydia trachomatis and Neisseria gonorrhoeae, where recent advances in vaccine development appear promising. We conduct a comprehensive survey of platforms, including vaccines, and explore modalities such as monoclonal antibodies and protein therapeutics. Additionally, we examine emerging technologies like nucleic acid-based therapies, microbiome modulation, and phage-based interventions, highlighting their potential against challenging pathogens like HSV-2 and Treponema pallidum. By examining these established and emerging approaches, this review prioritizes critical opportunities for innovation in biologic therapeutics, addressing unmet needs in STI management. It advocates for integrated strategies leveraging antigenic conservation, host immunity modulation, and novel delivery platforms to achieve durable prophylaxis and effective treatment for high-burden infections globally.},
}

@article {pmid40439232,
year = {2025},
author = {McGivern, BB and Ellenbogen, JB and Hoyt, DW and Bouranis, JA and Stemple, BP and Daly, RA and Bosman, SH and Sullivan, MB and Hagerman, AE and Chanton, JP and Tfaily, MM and Wrighton, KC},
title = {Polyphenol rewiring of the microbiome reduces methane emissions.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf108},
pmid = {40439232},
issn = {1751-7370},
abstract = {Methane mitigation is regarded as a critical strategy to combat the scale of global warming. Currently, about 40% of methane emissions originate from microbial sources, which is causing strategies to suppress methanogens-either through direct toxic effects or by diverting their substrates and energy-to gain traction. Problematically, current microbial methane mitigation knowledge lacks detailed microbiome-centered insights, limiting translation across conditions and ecosystems. Here we utilize genome-resolved metatranscriptomes and metabolomes to assess the impact of a proposed methane inhibitor, catechin, on greenhouse gas emissions for high-methane-emitting peatlands. In microcosms, catechin drastically reduced methane emissions by 72-84% compared to controls. Longitudinal sampling allowed for reconstruction of a catechin degradation pathway involving Actinomycetota and Clostridium, which break down catechin into smaller phenolic compounds within the first 21 days, followed by degradation of phenolic compounds by Pseudomonas_E from days 21 to 35. These genomes co-expressed hydrogen-uptake genes, suggesting hydrogenases may act as a hydrogen sink during catechin degradation and consequently reduce hydrogen availability to methanogens. In support of this idea, there was decreased gene expression by hydrogenotrophic and hydrogen-dependent methylotrophic methanogens under catechin treatment. There was also reduced gene expression from genomes inferred to be functioning syntrophically with hydrogen-utilizing methanogens. We propose that catechin metabolic redirection effectively starves hydrogen-utilizing methanogens, offering a potent avenue for curbing methane emissions across diverse environments including ruminants, landfills, and constructed or managed wetlands.},
}

@article {pmid40439217,
year = {2025},
author = {Ma, H and Dong, Z and Zhang, X and Li, N and Liu, C and Zhou, X and He, J and Ma, J and Zhang, S and Kan, H and Liu, S},
title = {Microbial Dysbiosis in the Lung and Gut in Response to Inhalable Particulate Matters in Pneumoconiosis Patients and Animals.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c00798},
pmid = {40439217},
issn = {1520-5851},
abstract = {Pneumoconiosis is a progressive and life-threatening fibrotic lung disorder caused by the prolonged deposition of inhaled particulate matters (PMs); thus far, no cure is available. Emerging evidence has suggested that the resulting disordered respiratory microbiome is caused by disturbed lung architecture and homeostasis responding to inhalable PMs. Lung microbiome dysbiosis also contributes to injury to the lung and distant organs, such as the intestine, through the lung-gut axis. Current studies on the microbiome-disease interplay are still in their infancy, and sufficient understanding of microbial heterogeneity in pathological processes is lacking. Here we investigated the microbiome in the lung and gut of patients with pneumoconiosis in comparison to healthy individuals. Our findings indicated reciprocal causation between lung injuries and microbial dysbiosis under particle exposure; pulmonary Streptococcus and Stenotrophomonas, along with intestinal Ligilactobacillus and Blautia, may represent key microbial communities influencing pneumoconiosis progression. We defined close microbiota crosstalk between the lung and gut, as evidenced by their interaction networks, implying considerable effects on the gut microenvironment through either direct microbial translocation or other mechanisms such as inflammation-driven alterations. Animal experiments further corroborated the findings in humans. Collectively, our results highlight the potential involvement of the lung-gut axis microbial dysbiosis in pneumoconiosis pathogenesis and open a new avenue to develop microbiome-targeted diagnosis and treatment strategies.},
}

@article {pmid40439157,
year = {2025},
author = {Wang, Z and Cheng, X and Xu, Y and Wang, Z and Ma, L and Li, C and Jiang, S and Li, Y and Guo, S and Du, W},
title = {Unveiling Neonatal Pneumonia Microbiome by High-Throughput Sequencing and Droplet Culturomics.},
journal = {Genomics, proteomics & bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/gpbjnl/qzaf047},
pmid = {40439157},
issn = {2210-3244},
abstract = {Neonatal pneumonia is a leading cause of infant mortality worldwide; however, a lack of microbial profiling, especially of low-abundance species, makes accurate diagnosis challenging. Traditional methods can fail to capture the complexity of the neonatal respiratory microbiota, thereby obscuring its role in disease progression. We describe a novel approach that combines high-throughput sequencing with droplet-based microfluidic cultivation to investigate microbiome shifts in neonates with pneumonia. Using 16S ribosomal RNA (rRNA) gene sequencing of 71 pneumonia cases and 49 controls, we identified 1009 genera, including 930 low-abundance taxa, which showed significant compositional differences between groups. Linear Discriminant Analysis Effect Size analysis identified key pneumonia-associated genera, such as Streptococcus, Rothia, and Corynebacterium. Droplet-based cultivation recovered 299 strains from 94 taxa, including rare species and ESKAPE pathogens, thereby supporting targeted antimicrobial management. Host-pathogen interaction assays showed that Rothia and Corynebacterium induced inflammation in lung epithelial cells, likely via dysregulation of the PI3K-Akt pathway. Integrating these marker taxa with clinical factors, such as gestational age and delivery type, offers the potential for precise diagnosis and treatment. The recovery of diverse species can support the construction of a biobank of neonatal respiratory microbiota to advance mechanistic studies and therapeutic strategies.},
}

@article {pmid40439013,
year = {2025},
author = {Alsergani, M and Zaini, RH and Al Kholaif, N and Al Admawi, M and Savo, MT and Cozac, DA and Tansella, D and Aladani, BA and Di Michele, S and Pergola, V},
title = {Infective endocarditis and oral health: a long-known threat, still a challenge.},
journal = {Monaldi archives for chest disease = Archivio Monaldi per le malattie del torace},
volume = {},
number = {},
pages = {},
doi = {10.4081/monaldi.2025.3497},
pmid = {40439013},
issn = {2532-5264},
abstract = {Infective endocarditis (IE) remains a life-threatening condition associated with high morbidity and mortality, often influenced by the complex interplay between systemic and oral health. The increasing recognition of oral health as a risk modifier has led to greater focus on the oral microbiome, dental procedures, and periodontal disease as potential contributors to bacteremia and IE. This review critically examines the relationship between oral health and IE, exploring pathophysiological mechanisms, risk factors, and the evolving epidemiology of the disease. The discussion includes diagnostic challenges, particularly in culture-negative cases, and the emerging role of advanced imaging and molecular diagnostics in improving early detection. A central focus is placed on preventive strategies, highlighting the debate surrounding antibiotic prophylaxis (AP) in high-risk individuals and the potential role of periodontal therapy in reducing systemic inflammation and transient bacteremia. The review also addresses the growing concern of antimicrobial resistance and the necessity of balancing AP recommendations with antimicrobial stewardship. Additionally, this review identifies critical research gaps, including the need for longitudinal studies on the impact of oral health interventions on IE incidence and the importance of interdisciplinary collaboration between dental and medical professionals in optimizing patient care. By synthesizing current guidelines and emerging evidence, this review underscores the necessity of an integrated, multidisciplinary approach to mitigate the burden of IE and establish oral health as a key pillar of infection prevention.},
}

@article {pmid40438840,
year = {2025},
author = {Saleem, MM and Masood, S and Rahmatullah, MM and Ayesha Imdad, I and Mohammed Aslam Sange, A and Nasr, D},
title = {Gut Microbiota Dysbiosis and Its Role in the Development of Irritable Bowel Syndrome.},
journal = {Cureus},
volume = {17},
number = {4},
pages = {e83084},
pmid = {40438840},
issn = {2168-8184},
abstract = {The gut microbiota refers to the diverse community of symbiotic and pathogenic microorganisms inhabiting the host digestive tract. This microbiome plays a vital role in maintaining the integrity of the digestive system. Irritable bowel syndrome (IBS) is a functional gastrointestinal disorder (FGID) characterized by chronic abdominal pain and altered bowel habits. Although the pathophysiology of IBS remains unclear, recent studies suggest that the disruption of the gut microbiota (dysbiosis) may play a significant role. This study aims to examine the role of the gut microbiota in the development of IBS, analyze factors influencing the gut microbiome, and explore the potential for microbiota-targeted therapies. Relevant literature published from 2014 until 2024 was sourced from Google Scholar, PubMed, and Scopus using the keywords "microbiome", "irritable bowel syndrome", "dysbiosis", "faecal transplantation", and "probiotics". This review revealed consistent evidence of gut microbiota dysbiosis in individuals with IBS, characterized by altered microbial diversity, composition, and metabolic function. Contributing factors included a reduced abundance of beneficial commensals, overgrowth of potentially pathogenic species, and disrupted host-microbiota interactions. This dysbiosis was also frequently associated with symptom severity and specific IBS subtypes. Emerging evidence further highlights the role of diet, stress, and genetic factors in modulating gut microbiota and influencing IBS development. The growing body of research supports a strong link between dysbiosis and the pathogenesis and symptomatology of IBS. Understanding the microbial underpinnings of IBS opens avenues for potential diagnostic biomarkers and innovative therapeutic interventions aimed at restoring a balanced gut microbiota. However, further research is needed to elucidate the underlying mechanisms and translate these insights into effective clinical strategies for the management of IBS. This review underscores the significance of gut microbiota in IBS and its potential as a target for future therapeutic interventions.},
}

@article {pmid40438776,
year = {2025},
author = {Lomelí-Valdez, R and Orozco-Covarrubias, L and Sáez-de-Ocariz, M},
title = {Skin and systemic infections in children with atopic dermatitis: review of the current evidence.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1513969},
pmid = {40438776},
issn = {2296-2360},
abstract = {Atopic dermatitis is a chronic, pruritic inflammatory skin disorder that affects approximately 2%-42% of children worldwide. Its course is frequently complicated by secondary bacterial, viral, and fungal infections, which can exacerbate disease severity and hinder treatment outcomes. These infections are thought to arise due to a disrupted skin barrier, reduced antimicrobial peptide production, alterations in the skin microbiome, and Th2-dominant inflammatory response. Identifying the most prevalent and pathogenic microorganisms in patients with AD is critical for early diagnosis, effective management, and prevention of complications. This review provides an updated synthesis of current knowledge on the infectious agents implicated in AD pathogenesis, summarizing recent findings on the epidemiology, microbial interactions, and immune mechanisms involved. Furthermore, it provides an overview of the latest therapeutic strategies for managing AD and its associated infections. By integrating recent insights into pathogenesis and treatment, this study offers a comprehensive perspective on the evolving landscape of AD management in children.},
}

@article {pmid40438731,
year = {2025},
author = {Gyriki, D and Nikolaidis, CG and Bezirtzoglou, E and Voidarou, C and Stavropoulou, E and Tsigalou, C},
title = {The gut microbiota and aging: interactions, implications, and interventions.},
journal = {Frontiers in aging},
volume = {6},
number = {},
pages = {1452917},
pmid = {40438731},
issn = {2673-6217},
abstract = {The human microbiota, a complex ecosystem of microorganisms inhabiting various body sites, particularly the gut, plays a crucial role in maintaining health and influencing disease susceptibility. Dysbiosis, characterized by alterations in microbial composition and diversity, has been implicated in numerous diseases, including those associated with aging. This review examines the complex relationship between gut microbiota and aging, highlighting the age-associated gut microbiota alterations, the factors contributing to these changes, the links between microbiota and age-related diseases, and the potential of interventions targeting the microbiome to extend lifespan and improve health outcomes in the elderly. Further research is needed to unravel the intricate mechanisms underlying the interplay between the microbiome and aging, paving the way for innovative strategies to promote healthy aging.},
}

@article {pmid40438491,
year = {2025},
author = {Pongsupasamit, P and Thonusin, C and Luewan, S and Chattipakorn, N and Chattipakorn, SC},
title = {Beyond hormones: 3PM approach to vaginal microbiota dynamics in postmenopausal women.},
journal = {The EPMA journal},
volume = {16},
number = {2},
pages = {299-350},
pmid = {40438491},
issn = {1878-5077},
abstract = {Menopause marks a critical transition characterized by ceased ovarian function and declining estrogen levels, affecting multiple systems with vasomotor symptoms and genitourinary syndrome of menopause (GSM). Recent evidence shows vaginal microbiota undergoes significant alterations during menopause, influencing GSM severity. This comprehensive review examined vaginal microbiota dynamics in postmenopausal women through Predictive, Preventive, and Personalized Medicine (3PM/PPPM), revealing characteristic shifts-increased alpha diversity, reduced Lactobacillus dominance, and transitions toward non-Lactobacillus species-that serve as potential predictive biomarkers for the menopausal state, premature ovarian insufficiency, and GSM symptoms. The analysis evaluated microbiota-based risk stratification strategies for vaginal dysbiosis and demonstrated the effectiveness of both hormonal interventions (systemic/local estrogen, tibolone, ospemifene) and non-hormonal alternatives (probiotics, energy-based devices, pessary) in normalizing microbiota composition and improving vaginal health. The application of PPPM/3PM transformed menopausal healthcare from reactive to proactive precision-based care by establishing microbiota-based biomarkers that predict health risks, enable early targeted interventions tailored to specific microbiota profiles, and guide personalized treatment approaches based on individual microbial compositions. While this paradigm shift significantly advances gynecological medicine, research gaps remain in validating baseline microbiota signatures as predictive biomarkers and establishing standardized screening protocols. Further studies are needed to validate interventions such as probiotics and prebiotics, optimizing strain selection for personalized, evidence-based preventive and therapeutic strategies. Developing standardized yet personalized protocols to restore a balanced vaginal microbiome could help alleviate menopause-related symptoms. Advancing microbiota-based personalized therapeutic approaches is crucial to enhancing the quality of life for postmenopausal women through targeted and individualized vaginal health management.},
}

@article {pmid40438350,
year = {2025},
author = {Peng, H and Fu, J},
title = {Unveiling horizontal gene transfer in the gut microbiome: bioinformatic strategies and challenges in metagenomics analysis.},
journal = {National science review},
volume = {12},
number = {6},
pages = {nwaf128},
pmid = {40438350},
issn = {2053-714X},
}

@article {pmid40438348,
year = {2025},
author = {Cao, J and Zhang, Y and Zhang, W and Zhang, F and Wang, J},
title = {Deep-learning of Nanopore sequences reveals the 6mA distribution and dynamics in human gut microbiome.},
journal = {National science review},
volume = {12},
number = {6},
pages = {nwaf120},
pmid = {40438348},
issn = {2053-714X},
}

@article {pmid40438215,
year = {2025},
author = {Hanna, A and Abbas, H and Yassine, F and AlBush, A and Bilen, M},
title = {Systematic review of gut microbiota composition, metabolic alterations, and the effects of treatments on PCOS and gut microbiota across human and animal studies.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1549499},
pmid = {40438215},
issn = {1664-302X},
abstract = {INTRODUCTION: Polycystic ovary syndrome (PCOS) is an endocrine disorder affecting around 12% of women globally, associated with infertility and various comorbidities. Emerging evidence suggests a crucial role of gut microbiota in PCOS pathophysiology, prompting research to investigate alterations in gut microbial composition in patients with PCOS.

METHODS: This systematic review aims to analyze human and animal studies that compare gut microbiota composition, gut-derived metabolites, and treatment interventions in PCOS patients versus healthy controls. A comprehensive literature search was conducted using PubMed, Scopus, and Web of Science, yielding studies examining gut microbiota, metabolomic shifts, and treatment responses in PCOS models and human populations.

RESULTS: Our analysis revealed decreases in alpha diversity in PCOS patients, with more pronounced changes in beta diversity in animal models. Specific bacterial taxa, such as Bacteroides vulgatus, Escherichia-Shigella and Lactobacillus, showed implication in PCOS pathogenesis, suggesting potential microbial markers. Furthermore, discrepancies between human and animal studies show the need for humanized mouse models to bridge this gap. Interventions like probiotics and fecal microbiota transplantation (FMT) showed varying levels of efficacy, with FMT emerging as a more promising but invasive option, offering live bacteriotherapy as a potential therapeutic alternative. Alterations in gut-derived metabolites, including short-chain fatty acids and bile acids, highlighted the multifaceted nature of PCOS, with implications extending to metabolic, hormonal, and gut-brain axis disruptions.

DISCUSSION: In conclusion, PCOS exhibits complex interactions between gut microbiota and metabolic pathways, necessitating further research with standardized methods and larger sample sizes to elucidate the microbiome's role in PCOS.},
}

@article {pmid40438213,
year = {2025},
author = {Ignatyeva, O and Daniel, V and Zelenova, E and Cherdakli, A and Bolashova, E and Matkava, L and Shegurova, A and Volkov, M and Zagainova, A and Kashtanova, D and Ivanov, M and Bembeeva, B and Zubkov, V and Gordeev, A and Priputnevich, T and Yudin, V and Makarov, V and Keskinov, A and Kraevoy, S and Yudin, S and Skvortsova, V},
title = {The "crossover effect" of COVID-19 in pregnancy on the infant microbiome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1569279},
pmid = {40438213},
issn = {1664-302X},
abstract = {BACKGROUND: The COVID-19 pandemic has had a significant impact on public health. However, the impact of COVID-19 infection during pregnancy on the microbiome of the mother and her newborn child still remains poorly understood.

METHODS: This study involved 94 mother-child pairs whose mothers had COVID-19 during pregnancy and 44 newborns as a control group recruited in 2018. Stool samples were collected from women before delivery and from infants at 5-7 days after birth and used for 16S rRNA sequencing.

RESULTS: We found that the microbiomes of infants exposed in utero to COVID-19 showed decreased microbial diversity and richness. Moreover, we observed a higher inter-sample variability between infant samples in the case group, which might suggest destabilization of their microbiomes. Neither alpha- nor beta-diversity metrics differed significantly between the groups depending on the trimester when the mother contracted COVID-19. Thus, the timing of prenatal COVID-19 exposure had no effect on the infant gut microbiome.

CONCLUSION: COVID-19 during pregnancy can significantly compromise the establishment of the infant gut microbiome presumably by disrupting the mother's microbiome.},
}

@article {pmid40438189,
year = {2025},
author = {Temmermans, J and Legein, M and Checchia, I and Felis, GE and Smets, W and Karise, R and Lebeer, S},
title = {Agricultural practices and pollinators modulate the anthosphere microbiome.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf026},
pmid = {40438189},
issn = {2730-6151},
abstract = {The flower microbiome is pivotal in plant health, influencing reproductive success, fruit quality, and pathogen vulnerability. However, the impact of intensified agricultural practices on these microbial communities remains to be understood. This study examines how specific agricultural practices influence the bacterial composition of the strawberry anthosphere, focusing on cultivation intensification. Intensified systems were defined by practices such as indoor glasshouse substrate-based cultivation, increased use of plant protection products, larger cultivation areas, and reliance on managed pollinators. Using citizen science and V4 16S rRNA gene sequencing, we found that flowers in these more intensively managed systems had lower bacterial diversity, more variable microbiomes, and loss of core taxa such as Sphingomonas and Pseudomonas. To determine if pollinators could help mitigate these effects, we conducted exclusion experiments. In a tunnel system, we observed that foraging pollinators facilitated the dispersal of specific bacteria, such as Staphylococcus and Pseudomonas, and increased flower bacterial richness. However, in an open field, foraging pollinators had no significant impact. Our findings highlight the significant impact of cultivation intensification on the anthosphere microbiome and suggest that pollinators may play a role in restoring microbiome diversity. This research fills a critical gap in understanding how agricultural practices shape plant microbiomes and underscores the potential for microbe-based strategies to improve plant health in intensively managed systems.},
}

@article {pmid40438118,
year = {2025},
author = {Diallo, D and Sun, S and Somboro, AM and Baya, B and Koné, A and Diarra, B and Nantoumé, M and Koloma, I and Diakite, M and Holl, J and Maiga, AI and Seydi, M and Theron, G and Hou, L and Fodor, A and Maiga, M},
title = {Metabolic and immune consequences of antibiotic related microbiome alterations during first-line tuberculosis treatment in Bamako, Mali.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1561459},
pmid = {40438118},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; Male ; Female ; Adult ; Mali ; *Dysbiosis/chemically induced/immunology ; Middle Aged ; *Tuberculosis/drug therapy/microbiology/immunology/metabolism ; Cytokines/blood ; Longitudinal Studies ; *Antitubercular Agents/therapeutic use/adverse effects ; Young Adult ; Metabolomics ; },
abstract = {BACKGROUND: Individuals with a history of tuberculosis (TB) treatment are at a higher risk of experiencing a recurrent episode of the disease. Previous cross-sectional studies identified a connection between dysbiosis (alterations) in the gut microbiota composition and the administration of first-line TB antibiotics. However, these studies have not successfully elucidated this dysbiosis's resulting metabolic and immune consequences.

METHODS: In a longitudinal assessment, we studied the antituberculosis drug-related changes in the gut microbiota's composition and the resulting functional consequences. Sputum for TB culture, peripheral blood for metabolomics and cytokines analysis, and stool for shotgun metagenomics were collected from TB participants at Month-0, Month-2, Month-6 of treatment, and 9 Months after treatment (Month-15). Healthy controls were sampled at Month-0 and Month-6.

FINDINGS: We found notable differences in gut microbiota between individuals with TB and healthy controls. While gut microbiota tended to resemble healthy controls at the end of TB treatment, significant differences for many taxa persisted up to Month-15. Concurrently, disturbances in plasma metabolites, including tryptophan, tricarboxylic acids, and cytokine levels were observed. Certain fatty acids associated with inflammation pathways negatively correlated with the abundance of several taxa.

CONCLUSION: We observed alterations in the gut microbiota composition and function during treatment and at Month-15. Numerous changes in bacterial taxa abundances and inflammation-linked metabolites did not reverse at Month-15. This study suggests potential influences of anti-TB drugs and the gut microbiome on the disease outcome, response to treatment, and resistance to future TB infections.},
}

Humans
*Gastrointestinal Microbiome/drug effects/immunology
Male
Female
Adult
Mali
*Dysbiosis/chemically induced/immunology
Middle Aged
*Tuberculosis/drug therapy/microbiology/immunology/metabolism
Cytokines/blood
Longitudinal Studies
*Antitubercular Agents/therapeutic use/adverse effects
Young Adult
Metabolomics

@article {pmid40438084,
year = {2025},
author = {Intini, R and Balsells, S and Bagan, L and Fortuna, G and Sroussi, H and Bagan, J},
title = {Comparative analysis of oral microbiome in saliva samples of oral leukoplakia, proliferative leukoplakia and oral squamous cell carcinoma.},
journal = {Frontiers in oral health},
volume = {6},
number = {},
pages = {1600090},
pmid = {40438084},
issn = {2673-4842},
abstract = {BACKGROUND: Oral potentially malignant disorders (OPMDs), including conventional leukoplakia (OL) and proliferative verrucous leukoplakia (PVL), have distinct risks of progression to oral squamous cell carcinoma (OSCC). A role of the oral microbiome in this transformation is increasingly recognized, but its contribution remains unclear.

OBJECTIVE: This study aimed to analyze and compare the oral microbiota in patients with OL, PVL, and OSCC using 16S rRNA gene sequencing of saliva samples to identify microbial signatures associated with disease progression and to uncover potential biomarkers that would justify an aggressive treatment of OPMDs.

METHODS: Sixty-six subjects with OPMDs were enrolled, comprising OL (n = 10), PVL (n = 28), and OSCC (n = 28). Saliva samples were collected, and DNA was extracted. The V3-V4 regions of the 16S rRNA gene were sequenced using the Illumina MiSeq platform. Bioinformatic analyses, including diversity assessments and taxonomic classification with the SILVA v138 database, were performed using QIIME2. Alpha diversity was evaluated with Chao1, Shannon, and Simpson indices, while beta diversity was assessed using Bray-Curtis and Jaccard distances.

RESULTS: PVL exhibited the highest species richness, followed by OL, with OSCC showing the lowest diversity. While alpha diversity differences among the groups were not statistically significant (p > 0.05), beta diversity revealed distinct microbial community structures between OL and both PVL and OSCC (p < 0.05), but not between PVL and OSCC. At the phylum level, Firmicutes predominated across all groups, with significantly higher Actinobacteriota levels in OL (p = 0.002).

CONCLUSION: Distinct microbial patterns differentiate OL from PVL and OSCC, with OL being different from PVL and OSCC, suggesting progressive microbial dysbiosis in malignant transformation. These findings support the potential of oral microbiome profiling as a non-invasive diagnostic and prognostic tool in oral oncology and highlight the need for longitudinal studies to establish causal relationships.},
}

@article {pmid40437865,
year = {2025},
author = {},
title = {Correction to "Effects of a ketogenic and low-fat diet on the human metabolome, microbiome, and foodome in adults at risk for Alzheimer's disease".},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21},
number = {5},
pages = {e14281},
doi = {10.1002/alz.14281},
pmid = {40437865},
issn = {1552-5279},
}

@article {pmid40437630,
year = {2025},
author = {Almarmouri, C and El-Gamal, MI and Haider, M and Hamad, M and Qumar, S and Sebastian, M and Ghemrawi, R and Muhammad, JS and Burucoa, C and Khoder, G},
title = {Anti-urease therapy: a targeted approach to mitigating antibiotic resistance in Helicobacter pylori while preserving the gut microflora.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {37},
pmid = {40437630},
issn = {1757-4749},
support = {2201110266//University of Sharjah/ ; 24011102102//University of Sharjah/ ; },
abstract = {The global rise in antibiotic resistance has posed significant challenges to the effective management of Helicobacter pylori (H. pylori), a gastric pathogen linked to chronic gastritis, peptic ulcers, and gastric cancer. Conventional antibiotic therapies, while effective, face significant challenges, such as increasing antibiotic resistance, high recurrence rates, and adverse effects such as gut microflora dysbiosis. These limitations have driven the exploration of alternative antibiotic-free therapies, including the use of plant-based compounds, probiotics, nanoparticles, phage therapy, antimicrobial peptides, and H. pylori vaccines. Among these, urease-targeted therapy has shown particular promise. Urease enables the survival and colonization of H. pylori by neutralizing stomach acidity. Targeting this urease without disrupting beneficial gut microflora offers a selective mechanism to impair H. pylori, due to the absence of this enzyme in most of the human gut microbiome. In this review, we highlight advancements and limitations in the field of antibiotic-free therapies, with a particular focus on anti-urease strategies. We explore the structural and functional characteristics of urease, its role in H. pylori pathogenesis, and its potential as a therapeutic target. For the first time, we provide a comprehensive analysis of natural, semisynthetic, and synthetic anti-urease compounds, emphasizing their mechanisms of action, efficacy, and safety profiles. Advances in silico, in vitro, and in vivo studies have identified several promising anti-urease compounds with high specificity and minimal toxicity. By focusing on urease inhibition as a targeted strategy, this review underscores its potential to overcome antibiotic resistance while minimizing gut dysbiosis and improving the outcomes of H. pylori infection treatment.},
}

@article {pmid40437450,
year = {2025},
author = {Yang, S and Zhang, S and Cao, Q and Zhu, G and Liu, J and Li, G and Zhu, M},
title = {Association between oral microbial diversity (only bacteria) and diabetes in U.S. adults: analysis of NHANES 2009-2012 data.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {837},
pmid = {40437450},
issn = {1472-6831},
support = {JSYGY-3-2024-123//Jiangsu Hospital Association's Hospital Management Innovation Research Program/ ; KX-24-C039//Wuxi Association for Science and Technology's Key Soft Science Project/ ; T202325//Wuxi Municipal Health Commission's Science and Technology Achievements and Appropriate Technology Promotion Project/ ; },
mesh = {Humans ; Male ; Cross-Sectional Studies ; Female ; United States/epidemiology ; *Diabetes Mellitus/microbiology/epidemiology ; Adult ; Middle Aged ; *Mouth/microbiology ; Nutrition Surveys ; Microbiota ; Body Mass Index ; RNA, Ribosomal, 16S ; },
abstract = {OBJECTIVE: Studies on the relationship between oral microbial diversity and diabetes were limited. This study analyzed the oral microbial composition and diversity using NHANES data to explore its potential role in diabetes pathogenesis; Methods: A cross-sectional design was employed, utilizing NHANES data (2009-2012), including oral microbiota samples and diabetes-related indicators. Oral samples were collected via mouthwash and analyzed using 16 S rRNA gene sequencing. The Shannon-Wiener Index represented microbial diversity (Only bacteria). Multivariate logistic regression, restricted cubic splines, and subgroup analyses were employed to evaluate associations.

RESULTS: A significant association was found between oral microbial diversity and diabetes. According to the completely adjusted model, a one-unit increment in the Shannon-Wiener Index was associated with a 12.1% increase in the likelihood of developing diabetes (OR = 1.121, 95%CI: 1.120 ~ 1.122). Subgroup analyses showed divergent findings. In subgroups with lower body weight and BMI, increased microbial diversity correlated with a decreased likelihood of developing diabetes (OR = 0.68 (0.68-0.68)); Conclusions: Oral microbial diversity exhibits a complex relationship with diabetes risk. The increase and subsequent decrease of oral microbiota diversity in relation to diabetes risk. This suggests that certain specific microbes or interactions between microbes may influence the development of diabetes. However, due to the many limitations of this study, it cannot prove the causal relationship between oral microbial richness and diabetes. Further longitudinal and mechanistic studies are essential to elucidate the causal links and dynamic alterations between the oral microbiome and the progression of diabetes.},
}

Humans
Male
Cross-Sectional Studies
Female
United States/epidemiology
*Diabetes Mellitus/microbiology/epidemiology
Adult
Middle Aged
*Mouth/microbiology
Nutrition Surveys
Microbiota
Body Mass Index
RNA, Ribosomal, 16S

@article {pmid40437375,
year = {2025},
author = {Qin, S and Yang, Z and Lei, J and Xie, Q and Jiang, L and Fan, Y and Luo, Y and Wei, K and Luo, W and Yu, B},
title = {Comparative efficacy of preventive vs. therapeutic resveratrol in modulating gut microbiota and alleviating inflammation in DSS-induced colitis.},
journal = {BMC immunology},
volume = {26},
number = {1},
pages = {42},
doi = {10.1186/s12865-025-00718-3},
pmid = {40437375},
issn = {1471-2172},
support = {No. 2023GXNSFAA026166//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; No. 2024GXNSFAA010132//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; GXZYA20230264//Guangxi Zhuang Autonomous Region Administration of Traditional Chinese Medicine/ ; No. 82260109//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Resveratrol/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Colitis/chemically induced/drug therapy/microbiology/prevention & control/immunology ; Dextran Sulfate ; Disease Models, Animal ; Mice, Inbred C57BL ; Cytokines/metabolism ; Inflammation/drug therapy ; Toll-Like Receptor 4/metabolism ; Macrophages/immunology ; Male ; Intestinal Mucosa/drug effects/pathology ; Humans ; *Anti-Inflammatory Agents/pharmacology/therapeutic use ; NF-kappa B/metabolism ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) management remains challenging due to limited preventive strategies and the low bioavailability of therapeutic agents like resveratrol (RSV). While RSV exhibits anti-inflammatory properties, its preventive potential via gut microbiome modulation remains unexplored.

METHODS: A murine colitis model was established using 2.5% DSS, with mice randomized into control (CON), DSS, therapeutic RSV treatment (RSV), and preventive RSV treatment (PRE) groups. Clinical outcomes, intestinal barrier integrity, inflammatory cytokines, macrophage polarization, TLR4/NF-κB signaling, and gut microbiota (16S rRNA sequencing) were systematically evaluated.

RESULTS: Preventive RSV (PRE) outperformed therapeutic RSV across all metrics. PRE attenuated colitis severity by 51.4% (weight loss, P < 0.001 vs. RSV) and restored mucosal architecture (P = 0.048 vs. DSS). Mechanistically, PRE normalized barrier function via transcriptional (ZO-1: 56.7% of CON; Occludin: 14-fold induction vs. DSS) and protein-level recovery (ZO-1: 96.5% of CON, P = 0.02), suppressed pro-inflammatory cytokines (TNF-α: 80.8%; IL-6: 69.9%; IL-18: >96%, P < 0.001 vs. DSS), and promoted M2 macrophage polarization (CD206: 1.7-fold vs. CON, P = 0.02) through TLR4/NF-κB inhibition (53% TLR4 reduction vs. 15% with RSV, P < 0.001). Despite comparable α-diversity between RSV and PRE, PRE uniquely enriched barrier-protective taxa (Lactococcus, Muribaculum) and restored microbial amino acid biosynthesis. Crucially, PRE's efficacy despite low systemic bioavailability implicated microbiome-mediated "luminal priming" as its primary mechanism.

CONCLUSIONS: This study redefines preventive RSV as a microbial ecosystem engineer that preemptively fortifies the gut against inflammation via microbiome-immune-metabolic crosstalk. By prioritizing ecological prevention over symptom suppression, our findings offer a transformative "food as medicine" strategy for IBD, highlighting RSV's potential as a chronotherapeutic agent to reshape clinical paradigms.},
}

Animals
*Resveratrol/therapeutic use/pharmacology
*Gastrointestinal Microbiome/drug effects
Mice
*Colitis/chemically induced/drug therapy/microbiology/prevention & control/immunology
Dextran Sulfate
Disease Models, Animal
Mice, Inbred C57BL
Cytokines/metabolism
Inflammation/drug therapy
Toll-Like Receptor 4/metabolism
Macrophages/immunology
Male
Intestinal Mucosa/drug effects/pathology
Humans
*Anti-Inflammatory Agents/pharmacology/therapeutic use
NF-kappa B/metabolism

@article {pmid40437354,
year = {2025},
author = {Mekadim, C and Mrazek, J and Fliegerová, KO and Sechovcová, H and Mahayri, TM and Jarošíková, R and Husáková, J and Wosková, V and Tůma, P and Polák, J and Sojáková, D and Němcová, A and Dubský, M and Fejfarová, V},
title = {The effect of the administration form of antibiotic therapy on the gut microbiome in patients with infected diabetic foot ulcers - DFIATIM trial.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {339},
pmid = {40437354},
issn = {1471-2180},
support = {LX22NPO5104//the European Union- Next Generation EU/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Diabetic Foot/drug therapy/microbiology ; *Anti-Bacterial Agents/administration & dosage/therapeutic use ; Male ; Middle Aged ; Female ; Aged ; Feces/microbiology ; Bacteria/classification/genetics/drug effects/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; Ceftazidime/administration & dosage/therapeutic use ; Amoxicillin-Potassium Clavulanate Combination/administration & dosage ; },
abstract = {BACKGROUND: Diabetic foot infections (DFIs) contribute to the global disability burden. Beta-lactams are the most commonly used antibiotics for treating DFIs. However, the use of antibiotics may lead to disruption of the healthy balance of the gut microbiota, causing dysbiosis.

METHODS: Patients with infected diabetic foot ulcers (iDFUs) were treated with two kinds of beta-lactams (amoxicillin/clavulanic acid or ceftazidime) according to microbial sensitivity of causative agents via bolus or continuous administration modes. Changes in the gut microbiome of patients were analyzed. Diabetic patients without iDFUs were used as a control group. 16 S ribosomal RNA gene amplicon sequencing was performed on stool samples collected from participants.

RESULTS: Alpha diversity and beta diversity of gut microbiota of treated patients did not show significant differences between bolus and continuous modes. However, significant differences were observed between gut microbiota diversity of treated patients and control group. PCoA plots showed individualized responses of the patient's gut microbiota to antibiotics at different times using both administration forms associated with the pre-treatment state of microbiota composition. Enterococcus, Sellimonas, and Lachnoclostridium were the common bacterial markers differentially abundant in the gut microbiota of antibiotic-treated patients with iDFUs while Roseburia, Dorea, and Monoglobus were mainly abundant in the gut microbiota of patients without iDFUs. Predicted pathways like "Transporters", "ABC transporters" and "Phosphotranspherase system (PTS)" were upregulated in the gut microbiome of patients treated with bolus regime which may lead to increased intestinal barrier permeability.

CONCLUSION: The present study reported alterations in gut microbiota composition and functionality and provided the bacterial markers as well as potential metabolic signatures associated with each administration mode in patients with iDFUs, which may be used as a reference set for future studies of the effect of antibiotics administration on the gut microbiome of patients with iDFUs. This study shed light on the importance of understanding the effect of antibiotic administration form on gut microbiome in patients with iDFUs.

TRIAL REGISTRATION: The DFIATIM Clinical Trial (Full title: "Rationalisation of ATB therapy in diabetic foot infection and its impact on the intestinal microbiota") is submitted to the European Union Clinical Trials Database under the EudraCT Number: 2019-001997-27. The date of registration is July 17th, 2020.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Diabetic Foot/drug therapy/microbiology
*Anti-Bacterial Agents/administration & dosage/therapeutic use
Male
Middle Aged
Female
Aged
Feces/microbiology
Bacteria/classification/genetics/drug effects/isolation & purification
RNA, Ribosomal, 16S/genetics
Dysbiosis/microbiology
Ceftazidime/administration & dosage/therapeutic use
Amoxicillin-Potassium Clavulanate Combination/administration & dosage

@article {pmid40437350,
year = {2025},
author = {Benning, S and Mahmoud, FM and Espindola-Hernandez, P and Liu, B and Pritsch, K and Radl, V and Winkler, JB and Winkelmann, T and Beerhues, L and Schloter, M},
title = {Inoculation of apple plantlets with Rhodococcus pseudokoreensis R79[T] enhances diversity and modulates the structure of bacterial rhizosphere communities in soil affected by apple replant disease.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {715},
pmid = {40437350},
issn = {1471-2229},
mesh = {*Malus/microbiology ; *Rhizosphere ; *Soil Microbiology ; *Rhodococcus/physiology ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology ; *Plant Diseases/microbiology ; Biodiversity ; },
abstract = {BACKGROUND: Apple replant disease (ARD) represents a dysbiotic rhizosphere condition potentially driven by root exudates including phytoalexins at the root-soil interface. A promising mitigation strategy could be the application of bioinoculants that reduce these compounds and foster a diverse microbiome. This study investigated the effects of Rhodococcus pseudokoreensis R79[T], a strain with benzoate-degrading capabilities and genetic potential to degrade biphenyls, on the rhizosphere microbiome of apple plantlets grown in ARD-affected soil in a greenhouse experiment.

RESULTS: We applied R79[T] at 10⁶ to 10⁹ CFU/ml, assessing its impact on bacterial 16S rRNA diversity and abundance, as well as the abundance of biphenyl dioxygenase (bphd) genes. Eight weeks post-inoculation reads of strain R79[T] persisted in the rhizosphere, particularly at higher inoculation levels. Inoculation enhanced bacterial diversity and bphd gene abundance, with significant shifts in community composition. Key responders included members of Gaiellales, which increased, and Streptomyces, which decreased. Co-occurrence network analysis revealed that inoculation promoted positive interactions, more homogeneous connectivity, and a higher degree of connections. Effects on bacterial community structure varied significantly with inoculation concentration.

CONCLUSIONS: The fact that R79[T] enhanced rhizosphere bacterial diversity and modulated community composition in ARD-affected soil highlights the potential of R79[T] to reshape microbial interactions. Further research is needed to elucidate the mechanisms underlying these effects, including studies on in situ degradation of phytoalexins and inoculation of R79[T] alongside bacteria for plant growth promotion (PGP) in synthetic communities for elevated efficiency against ARD.},
}

*Malus/microbiology
*Rhizosphere
*Soil Microbiology
*Rhodococcus/physiology
RNA, Ribosomal, 16S/genetics
Plant Roots/microbiology
*Plant Diseases/microbiology
Biodiversity

@article {pmid40437096,
year = {2025},
author = {Yoshida, TM and Nguyen, M and Zhang, L and Lu, BY and Zhu, B and Murray, KN and Mineur, YS and Zhang, C and Xu, D and Lin, E and Luchsinger, J and Bhatta, S and Waizman, DA and Coden, ME and Ma, Y and Israni-Winger, K and Russo, A and Wang, H and Song, W and Al Souz, J and Zhao, H and Craft, JE and Picciotto, MR and Grutzendler, J and Distasio, M and Palm, NW and Hafler, DA and Wang, A},
title = {The subfornical organ is a nucleus for gut-derived T cells that regulate behaviour.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40437096},
issn = {1476-4687},
abstract = {Specialized immune cells that reside in tissues orchestrate diverse biological functions by communicating with parenchymal cells[1]. The contribution of the innate immune compartment in the meninges and the central nervous system (CNS) is well-characterized; however, whether cells of the adaptive immune system reside in the brain and are involved in maintaining homeostasis is unclear[2-4]. Here we show that the subfornical organ (SFO) of the brain is a nucleus for parenchymal αβ T cells in the steady-state brain in both mice and humans. Using unbiased transcriptomics, we show that these extravascular T cells in the brain are distinct from meningeal T cells: they secrete IFNγ robustly and express tissue-residence proteins such as CXCR6, which are required for their retention in the brain and for normal adaptive behaviour. These T cells are primed in the periphery by the microbiome, and traffic from the white adipose and gastrointestinal tissues to the brain. Once established, their numbers can be modulated by alterations to either the gut microbiota or the composition of adipose tissue. In summary, we find that CD4 T cells reside in the brain at steady state and are anatomically concentrated in the SFO in mice and humans; that they are transcriptionally and functionally distinct from meningeal T cells; and that they secrete IFNγ to maintain CNS homeostasis through homeostatic fat-brain and gut-brain axes.},
}

@article {pmid40437008,
year = {2025},
author = {Zhu, Y and Wang, J and Zhang, X and Cidan, Y and Wang, H and Pubu, P and Ali, M and Li, K and Basang, W},
title = {Traditional Chinese herbal formulas modulate inflammatory mediators, antioxidant enzyme levels, and ruminal microbiota composition in postpartum female Yaks.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18610},
pmid = {40437008},
issn = {2045-2322},
mesh = {Animals ; Female ; Cattle ; *Rumen/microbiology/drug effects ; Postpartum Period/drug effects ; *Antioxidants/metabolism ; *Drugs, Chinese Herbal/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Inflammation Mediators/metabolism ; Animal Feed ; Bacteria/genetics/classification ; },
abstract = {Traditional Chinese Medicine (TCM) is an emerging area due to increased antimicrobial resistance (AMR). The objective of this research was to explore the antioxidant, and anti-inflammatory potential of three traditional Chinese herbal formulas (TCHFs), along with variations in rumen bacteria. In this study, forty postpartum (80 ± 15) female yaks after the calves had weaned (PWFs) were divided into three experimental groups, which were offered basal feed with 5% (95% basal diet) TCHF1 (DE group), 5% TCHF2 (DF group) and 5% TCHF3 (DG group), and fourth, control group (DH group), fed only a basal diet for 30 days. Following blood and rumen fluid samples on the 15th and 30th day, ELISA testing was performed to check antioxidant enzyme levels and inflammatory mediators. The results indicated that TCHF2 significantly upregulated the interleukin-10 (IL-10) (p < 0.05). Additionally, 16 S rRNA sequencing results showed that TCHF2 significantly enhanced Firmicutes to Bacteroidetes ratio (F/B) at the phylum level. On day 15th, phylum Actinobacteria, SR1, Cyanobacteria, and Armatimonadetes were found to be significantly (p < 0.05) different, while, at the genus level, Butyrivibrio, CF231, YRC22, Moraxella, Clostridium, etc. were significantly different (p < 0.05). On day 30, phylum SR1, Armatimonadetes, Chlorobi, and genus Coprococcus, Oscillospira, Selenomonas, L7A_E11, Clostridium, etc. were found to be significantly different (p < 0.05). This study concluded that TCHF2 is the most effective one among all.},
}

Animals
Female
Cattle
*Rumen/microbiology/drug effects
Postpartum Period/drug effects
*Antioxidants/metabolism
*Drugs, Chinese Herbal/pharmacology
*Gastrointestinal Microbiome/drug effects
*Inflammation Mediators/metabolism
Animal Feed
Bacteria/genetics/classification

@article {pmid40436959,
year = {2025},
author = {Nath, S and Zilm, P and Jamieson, L and Santiago, PHR and Ketagoda, DHK and Weyrich, L},
title = {The influence of diet, saliva, and dental history on the oral microbiome in healthy, caries-free Australian adults.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18755},
pmid = {40436959},
issn = {2045-2322},
support = {2019/GNT1187737//NHMRC Ideas Grant/ ; },
mesh = {Humans ; *Saliva/microbiology ; Adult ; Middle Aged ; Male ; Female ; *Microbiota ; Aged ; *Dental Caries/microbiology ; Young Adult ; Adolescent ; Cross-Sectional Studies ; Australia ; *Diet ; Aged, 80 and over ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; Hydrogen-Ion Concentration ; },
abstract = {Oral microbiome transplantation (OMT) has the potential to serve as a therapeutic approach for managing dental caries; however, it is essential to identify suitable donors. The aim of this study was to analyse the relationship between dietary (i.e., energy, water, carbohydrate and sugar intake), saliva quality (i.e., saliva flow rate and salivary pH), and clinical factors (i.e., past caries experience and fluoride exposure) on the oral microbiome composition of potential OMT donors. For this cross-sectional study, a comprehensive dental examination was conducted for 93 healthy, caries-free adults (aged 18-85 years) without systemic or oral disease. All participants completed questionnaires on food frequency and socio-economic, lifestyle, and behavioural factors. Supragingival plaque samples were collected, and bacterial 16S rRNA genes were amplified, sequenced, and assigned to bacterial taxa. Stimulated saliva samples were collected for salivary flow rate and pH measurements. Constrained partial ordination analysis revealed that dietary factors, such as carbohydrate and sugar intake, had strong directional influences on microbial composition, while salivary factors like flow rate and pH showed opposing effects. Correlation analysis linked high sugar intake and reduced salivary pH to increased Streptococcus abundance. Differential abundance analysis identified significantly higher abundance of Streptococcus species among low water and high carbohydrate and sugar consumers. In mediation analysis, sugar consumption was directly and indirectly linked to reduced salivary pH, with Streptococcus showing a significant negative mediation effect (mean: -0.198; 95% CI: -0.387 to -0.010). High carbohydrate and sugar intake significantly influenced alpha diversity metrics (p < 0.05). Beta diversity permutational multivariate ANOVA revealed that covariates explained 11.45-12.52% of microbial variation (p < 0.05). This study emphasises that OMT donors with diverse oral microbiomes, low sugar and carbohydrate intake, and reduced levels of acidogenic taxa, such as Streptococcus, which significantly mediate salivary pH reduction, may be preferred for caries prevention.},
}

Humans
*Saliva/microbiology
Adult
Middle Aged
Male
Female
*Microbiota
Aged
*Dental Caries/microbiology
Young Adult
Adolescent
Cross-Sectional Studies
Australia
*Diet
Aged, 80 and over
RNA, Ribosomal, 16S/genetics
*Mouth/microbiology
Hydrogen-Ion Concentration

@article {pmid40436954,
year = {2025},
author = {Rahimi-Rizi, M and Norouzi, H and Sohrabi, M and Dashtipoor, S and Omidi Nasab, M and Boustie, J},
title = {Elevational microhabitats influence some endolichenic traits of Umbilicaria aprina, an alpine lichen species.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18602},
pmid = {40436954},
issn = {2045-2322},
mesh = {*Lichens/metabolism/microbiology/physiology ; *Altitude ; Microbiota ; *Ecosystem ; Metabolomics/methods ; Metabolome ; },
abstract = {Understanding the dynamics of lichen-environment interactions, particularly in terms of elemental composition, microbial, and metabolic profiles, is crucial for elucidating the adaptive strategies of lichens. Here we aimed to investigate the impact of elevational microhabitats on the elemental compositions, microbial profiles, and metabolic profiles of different colonies of Umbilicaria aprina along an elevational gradient. Ionomics showed variations in elemental compositions of colonies at different elevations with distinct patterns of accumulation for specific elements. Untargeted metabolomics revealed metabolic alterations in different colonies of U. aprina across elevations, suggesting a potential role of lichen secondary metabolites in responding to environmental changes. Culture-based analysis of microbiome also showed variations in the microbial profiles of colonies with changes in elevation, confirming the influence of elevational microhabitats on lichen-associated microbial communities. We further examined possible correlations between the relative intensity of different metabolites and the other two endolichenic traits (i.e., elemental composition and microbial profile). Although no consistent correlative patterns emerged, some metabolite-specific correlations were observed. Overall, our study shows that certain endolichenic traits undergo variations even within a restricted alpine range, corresponding to minor changes in environmental conditions.},
}

*Lichens/metabolism/microbiology/physiology
*Altitude
Microbiota
*Ecosystem
Metabolomics/methods
Metabolome

@article {pmid40436643,
year = {2025},
author = {Li, J and Wu, Y and Yang, Y and Chen, L and He, C and Zhou, S and Huang, S and Zhang, X and Wang, Y and Gui, Q and Lu, H and Zhang, Q and Yang, Y},
title = {Metagenomics reveals an increased proportion of an Escherichia coli-dominated enterotype in elderly Chinese people.},
journal = {Journal of Zhejiang University. Science. B},
volume = {26},
number = {5},
pages = {477-492},
doi = {10.1631/jzus.B2400341},
pmid = {40436643},
issn = {1862-1783},
support = {82101665, 82271588, 82200665 and 82100795//the National Natural Science Foundation of China/ ; LY22H030009//the Zhejiang Provincial Natural Science Foundation of China/ ; 2023ZL480//the Zhejiang Provincial Science and Technology Program of Traditional Chinese Medicine/ ; 2023RC153//the Medical and Health Research Project of Zhejiang Province/ ; },
mesh = {Aged ; Aged, 80 and over ; Female ; Humans ; Male ; Middle Aged ; Bacteroides ; China ; Diabetes Mellitus, Type 2/microbiology ; *Escherichia coli/genetics/isolation & purification/classification ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; East Asian People ; },
abstract = {Gut microbial communities are likely remodeled in tandem with accumulated physiological decline during aging, yet there is limited understanding of gut microbiome variation in advanced age. Here, we performed a metagenomics-based enterotype analysis in a geographically homogeneous cohort of 367 enrolled Chinese individuals between the ages of 60 and 94 years, with the goal of characterizing the gut microbiome of elderly individuals and identifying factors linked to enterotype variations. In addition to two adult-like enterotypes dominated by Bacteroides (ET-Bacteroides) and Prevotella (ET-Prevotella), we identified a novel enterotype dominated by Escherichia (ET-Escherichia), whose prevalence increased in advanced age. Our data demonstrated that age explained more of the variance in the gut microbiome than previously identified factors such as type 2 diabetes mellitus (T2DM) or diet. We characterized the distinct taxonomic and functional profiles of ET-Escherichia, and found the strongest cohesion and highest robustness of the microbial co-occurrence network in this enterotype, as well as the lowest species diversity. In addition, we carried out a series of correlation analyses and co-abundance network analyses, which showed that several factors were likely linked to the overabundance of Escherichia members, including advanced age, vegetable intake, and fruit intake. Overall, our data revealed an enterotype variation characterized by Escherichia enrichment in the elderly population. Considering the different age distribution of each enterotype, these findings provide new insights into the changes that occur in the gut microbiome with age and highlight the importance of microbiome-based stratification of elderly individuals.},
}

Aged
Aged, 80 and over
Female
Humans
Male
Middle Aged
Bacteroides
China
Diabetes Mellitus, Type 2/microbiology
*Escherichia coli/genetics/isolation & purification/classification
*Gastrointestinal Microbiome/genetics
*Metagenomics
East Asian People

@article {pmid40436366,
year = {2025},
author = {DiK, B and Hatipoglu, D and Kahraman, O and Parlak, TM and Inanc, ZS and Celik, M and Damar, S},
title = {Liraglutide as a Novel Therapeutic for Overweight in Canines: A Clinical Study.},
journal = {Veterinary journal (London, England : 1997)},
volume = {},
number = {},
pages = {106376},
doi = {10.1016/j.tvjl.2025.106376},
pmid = {40436366},
issn = {1532-2971},
abstract = {BACKGROUND: The overweight/obesity in dogs is defined as a condition of abnormal fat accumulation or, beyond that, a multifactorial condition involving excessive fat accumulation along with different factors (insufficient physical activity, genetics (breed), metabolism, the microbiome, etc.). Preclinical obesity conditions increases the risk of progressing to clinical obesity and developing obesity-associated diseases such as type 2 diabetes, cardiovascular disease, certain cancers, and mental disorders.

OBJECTIVES: This study aimed to determine the weight-loss effects of liraglutide in dogs that do not engage in sufficient exercise, are fed table scraps, and develop obesity owing to aging.

ANIMALS: In this study, 21 senior Golden Retriever dogs were divided into three equal groups.

METHODS: Group 1 was considered healthy and consisted of dogs within the range of ideal body live weight and body condition scores, and fed dry commercial dog food at the amount of their daily metabolizable energy requirements. Group 2 included seven senior dogs with obesity fed commercial dry food adjusted for their daily metabolizable energy requirements. Group 3 comprised seven senior dogs with obesity fed commercial dry food adjusted for their daily energy requirements and concurrently treated with subcutaneous liraglutide at a dose of 1.2mg/dog. The trial lasted for 40 days.

RESULTS: Liraglutide treatment resulted in a decrease in body condition score (BCS) and body weight by day 40, although the reduction in body weight (13.27%) did not reach statistical significance. Liraglutide significantly lowered cholesterol and triglyceride levels, and appetite tests revealed a marked suppression of food intake over consecutive days in treated dogs.

Liraglutide treatment may offer a viable option for treating obesity in dogs, and could potentially be used as a new anti-obesity drug in canines. Future long-term and detailed trials of liraglutide in dogs with obesity could facilitate its effective use in the field.},
}

@article {pmid40436194,
year = {2025},
author = {Chang, VC and Purandare, V and Li, S and Andreotti, G and Hua, X and Wan, Y and Dagnall, CL and Jones, K and Hicks, BD and Hutchinson, A and Yano, Y and Dalton, KR and Lee, M and Parks, CG and London, SJ and Sandler, DP and Gail, MH and Shi, J and Hofmann, JN and Sinha, R and Abnet, CC and Vogtmann, E and Beane Freeman, LE},
title = {Animal farming and the oral microbiome in the Agricultural Health Study.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121964},
doi = {10.1016/j.envres.2025.121964},
pmid = {40436194},
issn = {1096-0953},
abstract = {BACKGROUND: Raising farm animals imparts various exposures that may shape the human microbiome. The oral microbiome has been increasingly implicated in disease development. Animal farming has also been associated with certain chronic diseases such as cancer; however, underlying biological mechanisms are unclear. We investigated associations between raising farm animals and the oral microbiome in the Agricultural Health Study.

METHODS: This analysis included 1,245 participants (865 farmers and 380 spouses) who provided oral wash specimens and information on types and numbers of specific animals raised on their farms within 2 years before sample collection. The oral microbiome was measured by sequencing the V4 region of the 16S ribosomal RNA gene. We evaluated associations of farm animal exposures with alpha and beta diversity metrics (within- and between-sample diversity, respectively), as well as presence and relative abundance of specific bacterial genera. All analyses adjusted for potential confounders (e.g., age, sex, smoking, alcohol consumption).

RESULTS: Overall, 63% of participants raised farm animals, most commonly cattle (46%) and hogs (20%). Those who raised a large number of hogs (≥2,000 vs. no hogs) had higher alpha diversity. Conversely, raising sheep/goats and raising larger numbers of poultry were associated with lower alpha diversity. Beta diversity was not significantly different between participants with and without any farm animals. Participants raising any farm animals had higher relative abundance of Porphyromonas and lower relative abundances of Prevotella and Ruminococcaceae UCG-014. Several genera were more likely to be absent with specific animal exposures (e.g., Capnocytophaga for cattle and sheep/goats; Corynebacterium, Dialister, Stomatobaculum, and Solobacterium for sheep/goats and poultry).

CONCLUSIONS: This was the largest study of farm animal exposures and the human microbiome to date. Findings suggest that raising specific farm animals may influence the oral microbiome, supporting the need to further investigate the potential role of animal farming in disease etiology.},
}

@article {pmid40435940,
year = {2025},
author = {Wang, J and Tan, Q and Ni, M and Chen, F and Yang, J and Wang, G and Zhao, X and Zhang, X and Zhang, S},
title = {High-Fat Diet-Induced Gut Microbiota Disruption Promotes Colorectal Cancer Lymphatic Metastasis via Propionate/GPR41 Signaling.},
journal = {Digestion},
volume = {},
number = {},
pages = {1-27},
doi = {10.1159/000545843},
pmid = {40435940},
issn = {1421-9867},
abstract = {OBJECTIVE: High-fat diets (HFD) are known to affect the gut microbiome structure and potentially promote the development and metastasis of colorectal cancer (CRC). This study aims to elucidate the molecular mechanisms through which gut microbiome dysbiosis, mediated by the propionate/GPR41 signaling pathway, promotes lymphangiogenesis and lymph node (LN) metastasis in CRC, providing new insights for CRC treatment.

METHODS: Microbial diversity and composition in rectal cancer were compared between CRC patients and healthy controls using 16s rRNA sequencing. Key genes related to short-chain fatty acid metabolism, HFD, and gut microbiota were identified. In vitro assays assessed CRC cell proliferation, migration, invasion, and lymphangiogenesis. A CRC mouse model on an HFD was used to measure fecal propionate levels and analyze GPR41 expression in tumors. In vivo fluorescence imaging was employed to track cancer cell migration and lymph node metastasis.

RESULTS: HFD-induced microbial dysbiosis led to a significant reduction in SCFA-producing bacteria and an increase in pro-inflammatory species. This dysbiosis contributed to the suppression of propionate's protective effects. Propionate inhibited CRC cell proliferation, migration, and invasion under HFD conditions by activating the GPR41 pathway. Silencing GPR41 reversed these inhibitory effects, highlighting the key role of GPR41 in mediating propionate's anti-tumor effects. In vivo experiments further confirmed that propionate suppressed HFD-enhanced CRC lymphatic metastasis through the GPR41 signaling pathway, linking microbial dysbiosis with the modulation of cancer progression.

CONCLUSION: This study reveals that HFD promotes CRC lymphangiogenesis and LN metastasis through gut microbiota dysbiosis and suppression of the propionate-activated GPR41 signaling pathway. These findings highlight the therapeutic potential of targeting the propionate/GPR41 axis , offering a promising strategy for developing novel anticancer therapies.},
}

@article {pmid40435904,
year = {2025},
author = {Liu, Z and Yan, K and Li, J and Zhang, C and Xu, D and Wang, Y and Xie, X and Li, H and Qie, J and Li, J and Dong, X and Dong, L and Cui, H},
title = {Acute appendicitis in children: Two microbial states associated with clinical indicators and severity.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {2},
pages = {116925},
doi = {10.1016/j.diagmicrobio.2025.116925},
pmid = {40435904},
issn = {1879-0070},
abstract = {BACKGROUND: Acute appendicitis (AA) is one of the most common abdominal emergencies worldwide. It is associated with dysbiosis and is usually classified clinically as either simple appendicitis (SA) or complicated appendicitis (CA) . The etiology and pathogenesis of AA remain incompletely understood.

METHODS: A total of 74 pediatric intra-abdominal pus samples from appendectomy cases (aged 3-15) were collected for AA at Tianjin Children's Hospital (Feb 2022-Sep 2023). The samples were categorised into two groups based on pathological findings: SA (n = 27) and CA (n = 47). Metagenomic profiling was employed to characterized the microbial composition and function in both groups. Additionally, clinical parameters associated with the microbiota were analysed.

RESULTS: The SA group exhibited higher levels of Burkholderia, Mycobacterium, and Klebsiella, while the CA group demonstrated higher levels of Porphyromonas, Bacteroides, Fusobacterium, Prevotella, and Tannerella. Additionaly, there were significant differences in clinical parameters, including C-reactive protein (CRP), procalcitonin (PCT), fibrinogen, sodium, potassium, phosphorus, complement C3, and chloride, between two groups. Furthermore, functional profiling revealed alterations in microbial metabolism and antibiotic resistance, highlighting the complex interplay between microbial communities and host inflammatory responses in appendicitis.

CONCLUSIONS: This study identifies unique microbial and serum biomarkers and their correlates in varying severities of acute appendicitis, highlighting the role of the microbiome in the aetiology of acute appendicitis.},
}

@article {pmid40435837,
year = {2025},
author = {Torre, V and Marchese, E and Willison, E and Monaco, M and Bozzo, M and De Negri Atanasio, G and Taddeucci, A and Trebesova, H and Rispo, F and Rosenwasser, N and Turrini, F and Olivero, G and Candiani, S and Grasselli, E and Marchese, A and Alcaro, S and Boggia, R and Romeo, I and Grilli, M and Di Pilato, V and Costa, G and Pittaluga, A},
title = {Presynaptic release-regulating α2 receptors and Urolithins: A bridge between systemic EA administration and central health properties.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {188},
number = {},
pages = {118187},
doi = {10.1016/j.biopha.2025.118187},
pmid = {40435837},
issn = {1950-6007},
abstract = {Ellagic acid (EA) is a natural compound exerting beneficial effects in mammals, including central neuroprotection. Among the central targets, the noradrenergic pathway has been proposed as a suitable candidate and, in this view, we recently proposed the presynaptic α2 autoreceptors as possible sites of action of this natural polyphenol. Although attractive, our hypothesis is questioned by the unfavourable pharmacokinetic profile of EA, which limits its access to the central nervous system, making impossible its interaction with these receptors. To substantiating the correlation linking EA treatment and the central noradrenergic pathway, we have now extended the study to Urolithins. These are the principal EA metabolites, which are brought in for EA central effects because of their high systemic bioavailability. To address the point, we employed a multidisciplinary approach, which included computational, "in vitro" and "in vivo" studies. The results from "computational" and "in vitro" experiments revealed that Urolithin A (UroA), but not Urolithin B (UroB) or C (UroC), binds to and activates α2 receptor subtypes. Furthermore, the "in vivo" prolonged administration of formulated microdispersion of EA (EAm) in mice led to a marked desensitization of cortical and hippocampal α2 autoreceptors, also reducing their density. Notably, central effects were associated to a significant changes in gut microbiome composition, towards a metabotype that would preferentially produce UroA. Based on these observations, we propose UroA as one of the systemic "effectors" of the EAm-induced central noradrenergic adaptation, confirming the role of noradrenaline in mediating the EA-mediated health effects.},
}

@article {pmid40435624,
year = {2025},
author = {Soufi, L and Kampouris, ID and Lüneberg, K and Heyde, BJ and Pulami, D and Glaeser, SP and Siebe, C and Siemens, J and Smalla, K and Grohmann, E and Gallego, S},
title = {Wastewater-borne pollutants influenced antibiotic resistance genes and mobile genetic elements in the soil without affecting the bacterial community composition in a changing wastewater irrigation system.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138680},
doi = {10.1016/j.jhazmat.2025.138680},
pmid = {40435624},
issn = {1873-3336},
abstract = {Over decades, untreated wastewater from México City was used to irrigate crops in the Mezquital Valley. With the construction of a wastewater treatment plant (WWTP), irrigation was replaced by WWTP effluent. To investigate how this shift affects the abundance, diversity, and dissemination of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in the short term, we conducted a soil microcosm experiment over 4 weeks. Soils from the Mezquital Valley with a long history of irrigation with untreated wastewater were irrigated with WWTP influent or effluent, both spiked with or without antibiotics and disinfectants. The spiking of irrigation water increased water-extractable soil concentrations of sulfamethoxazole. ARG and MGE abundances were affected by the spiking, whereas soil type and water quality had no effect. Contrarily, the soil microbiome was only determined by the soil type and the duration of incubation. Among the most abundant soil amplicon sequence variants (ASVs), one affiliated to Pseudomonas was affected by the spiking. Two ASVs affiliated to Methylotenera detected among the most abundant in wastewater and soil increased in relative abundance in soil after wastewater irrigation, indicating that they were likely introduced with the irrigation water or benefited from it. Most isolates from WWTP influent or effluent belonged to Proteobacterial genera. These findings highlight the importance of water pollution on the dissemination and spread of ARGs.},
}

@article {pmid40435194,
year = {2025},
author = {Ito, A and Shoji, H and Arai, H and Kakiuchi, S and Sato, K and Jinno, S and Takahashi, N and Masumoto, K and Yoda, H and Shimizu, T},
title = {Feeding infant formula with low sn-2 palmitate causes changes in newborn's intestinal environments through an increase in fecal soaped palmitic acid.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0324256},
doi = {10.1371/journal.pone.0324256},
pmid = {40435194},
issn = {1932-6203},
mesh = {Humans ; *Infant Formula/chemistry ; *Feces/chemistry ; *Palmitic Acid/analysis/metabolism ; Infant, Newborn ; Male ; Female ; *Gastrointestinal Microbiome/drug effects ; Infant ; Bifidobacterium/growth & development ; *Palmitates/analysis ; *Intestines/microbiology ; },
abstract = {BACKGROUND/OBJECTIVES: Soaped palmitic acid (PA) has been reported to be excreted in stool after feeding infant formulas containing low sn-2 palmitate levels, which corresponds to high sn-1 or -3 palmitate levels. While an in vitro study showed that soaped PA inhibits the Bifidobacteria growth, few clinical studies have evaluated effects of soaped PA on intestinal environments of infants. In this study, we aimed to evaluate associations between increased fecal soaped PA levels and inhibition of growth of the intestinal microbiome using clinical data, and to evaluate changes in the intestinal environment with formula-feeding.

METHODS: This study was conducted as a secondary analysis to our observational study of Japanese 1-month-old infants (n = 172). Infant formulas were classified into high sn-2 formula (≥ 50%) and low sn-2 formula (< 50%) according to the sn-2 binding ratio of PA. Multiple regression analyses and path analysis were performed as statistical analyses.

RESULTS: In the multiple regression analysis, the occupancy of Bifidobacteria was negatively correlated with the fecal soaped PA levels (β = -0.15, 95% confidence interval = -0.28- - 0.02). A path analysis suggested that low sn-2 formula feeding led to increased fecal soaped PA levels, decreased Bifidobacteria occupancy, and finally increased fecal pH.

CONCLUSIONS: Our clinical data showed significant associations between higher fecal soaped PA levels and lower Bifidobacteria occupancy in the newborn gut, which agreed well with the report of the in vitro study. Our study also suggests that feeding infant formula with low sn-2 palmitate causes changes in the intestinal environment through an increase in fecal soaped palmitic acids.},
}

Humans
*Infant Formula/chemistry
*Feces/chemistry
*Palmitic Acid/analysis/metabolism
Infant, Newborn
Male
Female
*Gastrointestinal Microbiome/drug effects
Infant
Bifidobacterium/growth & development
*Palmitates/analysis
*Intestines/microbiology

@article {pmid40435188,
year = {2025},
author = {Eladham, MW and Sharif-Askari, NS and Sekar, P and Mdkhana, B and Selvakumar, B and Al-Sheakly, BKS and Sharif-Askari, FS and Hachim, I and Halwani, R},
title = {The role of gut leakage and immune cell miss-homing on gut dysbiosis-induced lung inflammation in a DSS mice model.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0324230},
doi = {10.1371/journal.pone.0324230},
pmid = {40435188},
issn = {1932-6203},
mesh = {Animals ; *Dysbiosis/immunology/complications/microbiology/chemically induced ; Mice ; Disease Models, Animal ; *Pneumonia/immunology/pathology/etiology/microbiology ; *Gastrointestinal Microbiome/immunology ; Dextran Sulfate/toxicity ; Mice, Inbred C57BL ; Lung/pathology/immunology ; Colitis/chemically induced/immunology/microbiology/pathology ; Male ; },
abstract = {BACKGROUND: Inflammatory Bowel Disease (IBD), encompassing Crohn's disease and ulcerative colitis, affects millions globally, with extraintestinal manifestations (EIMs) occurring in 25-40% of patients. Among these, respiratory complications are of particular concern, yet the immunologic and physiologic mechanisms underlying gut-lung interactions remain poorly understood. The gut-lung axis (GLA) describes bi-directional communication between the gut and lungs, where microbial dysbiosis in the gut can drive lung inflammation and immune dysregulation.

METHODS: Mice were treated with 4% DSS for 7 days to induce colitis. Gut permeability, tight junction protein expression, lung inflammation, immune cell trafficking, and microbial translocation were assessed through histology, qPCR, flow cytometry, and GFP-tagged fecal microbiome experiments.

RESULTS: DSS treatment led to significant disruption of the gut barrier, with upregulation of gut leakage markers and downregulation of tight junction proteins. Lung inflammation was characterized by elevated IL-17, neutrophil infiltration, and airway hyperresponsiveness. Flow cytometry revealed mis-homing of gut-primed immune cells (α4β7+ and CCR9 + CD4+) to the lungs and tracking bacteria via GFP- tagged fecal microbiome confirmed microbial translocation from the gut to the lungs which may contribute to lung inflammation.

CONCLUSION: Disrupted gut integrity facilitates microbial translocation and immune cell mis-homing, contributing to lung inflammation. These results provide new insights into how gut dysbiosis influences respiratory inflammation.},
}

Animals
*Dysbiosis/immunology/complications/microbiology/chemically induced
Mice
Disease Models, Animal
*Pneumonia/immunology/pathology/etiology/microbiology
*Gastrointestinal Microbiome/immunology
Dextran Sulfate/toxicity
Mice, Inbred C57BL
Lung/pathology/immunology
Colitis/chemically induced/immunology/microbiology/pathology
Male

@article {pmid40434948,
year = {2025},
author = {Brock, MT and Nozue, K and Kliebenstein, DJ and Ewers, BE and Mackay, DS and Maignien, L and Wang, DR and Weinig, C and Maloof, JN},
title = {Characterization of transcriptional and metabolic responses to a complex plant growth-promoting soil inoculum.},
journal = {Plant biology (Stuttgart, Germany)},
volume = {},
number = {},
pages = {},
doi = {10.1111/plb.70034},
pmid = {40434948},
issn = {1438-8677},
support = {CA-D-PLB-2795-H//National Institute of Food and Agriculture/ ; 1444571//National Science Foundation/ ; 1547796//National Science Foundation/ ; },
abstract = {Soil microbes can have large impacts on plant growth and physiology. However, how these impacts manifest at the transcriptional and metabolite level is not well understood, especially responses to complex mixtures of soil microbes. Here we characterize the transcriptional and metabolomic response of Brassica rapa to a complex, naturally occurring soil inoculum that promotes shoot growth. Brassica rapa plants were treated with mock or growth-promoting soil inocula and monitored for growth. Root and shoot tissues were harvested for RNA-seq and metabolite analysis. Gene co-expression analysis and penalized regression were used to test for gene co-expression modules and metabolites that influence growth. We identify gene co-expression modules that both respond to microbial treatment and are associated with leaf growth. Gene ontology and custom category analysis of these modules revealed root modules that are enriched for mineral nutrition (especially nitrogen, phosphorus, and sulfur) and leaf modules enriched for photosynthetic and cellular processes. The metabolite data show an association of leaf length with nucleotide and amino acid levels, consistent with gene ontology terms observed in the leaf and perhaps reflecting the overall impact of growth-promoting microbes on key nitrogen-associated metabolic processes. Overall, this work provides an in-depth characterization of the molecular responses of plants to plant growth-promoting microbes.},
}

@article {pmid40434915,
year = {2025},
author = {Kuntz, TM and Liu, L and Wang, K and Everett, C and Eliassen, AH and Willett, WC and Sinha, R and Chan, AT and Rimm, EB and Garrett, WS and Segata, N and Piccinno, G and Huttenhower, C and Morgan, X and Song, M},
title = {Comparing the metagenomic performance of stools collected from custom cards and 95% ethanol in epidemiologic studies.},
journal = {Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology},
volume = {},
number = {},
pages = {},
doi = {10.1158/1055-9965.EPI-25-0157},
pmid = {40434915},
issn = {1538-7755},
abstract = {Background Stool cards have been used for microbiome assessment in epidemiological studies. Methods We compared shotgun metagenomic sequencing from 32 participants who self-collected stool samples from the same bowel movement using a custom stool card vs. a collection tube with 95% ethanol fixative in the Nurses' Health Study II. We evaluated the agreement between methods at both the whole-community and individual species levels. To contextualize the comparison for disease association studies, we assessed the performance of the two collection methods for differentiating colorectal cancer-associated taxa. Results Overall, metagenomes from cards and 95% ethanol were highly correlated within individuals. No difference was found in alpha diversity and only ~1% of variation in beta diversity was explained by the collection method. At the species level, while the relative abundances were highly correlated between card and ethanol sample pairs (Spearman rho = 0.96), 10 (out of 239) species showed a differential abundance in paired samples, including overrepresentation of Escherichia coli and underrepresentation of three Streptococcus species in cards compared with ethanol. Among a set of 99 colorectal cancer-associated species, 4 showed differential abundances between collection methods; however, this number was consistent with what would be expected by chance. Conclusions Metagenomic sequencing using stool samples self-collected using stool cards or 95% ethanol yielded largely consistent results, although differential abundances were observed for a small number of individual species. Impact Stool cards can be a cost-effective alternative to collect stool samples for metagenomic sequencing in epidemiologic studies but warrant additional considerations for data analysis.},
}

@article {pmid40434833,
year = {2025},
author = {Müller, L and Steiger, S and Körner, M},
title = {Surviving in the fast lane: No increased mortality, but faster growth for pathogen-exposed larvae of a family living beetle.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jeb/voaf068},
pmid = {40434833},
issn = {1420-9101},
abstract = {Animal taxa exhibiting post-hatching care can be found throughout the animal kingdom. During this period, parents aggregate with their offspring and allow them to invest their resources into growth and development as parents take over energy consuming tasks. For instance, studies show that food provisioning and social immunity by parents can alleviate the costs of an offspring's immune response to pathogen exposure. However, this issue has rarely been explored in offspring of species showing plasticity in their dependency on parental care. Here, we raise the question of how offspring are affected by pathogen exposure if they have access to social immunity through a caring parent. Parents of Nicrophorus vespilloides, a species exhibiting facultative post-hatching care, control the carcass microbiome by coating it with their antimicrobial exudates, stopping further decay and protecting their offspring from potential pathogens. We exposed N. vespilloides offspring to a generalist entomopathogenic fungus, Beauveria bassiana, while manipulating presence or absence of post-hatching parental care. We monitored offspring performance parameters throughout their development and found, curiously, larvae showed an increase in mean weight and growth rate after being exposed to the pathogen, while their survival and adult immunity were unaffected. These effects of pathogen exposure occurred regardless of parental care. Simultaneously, our results indicate that females invest fewer resources into their offspring if they have been exposed to the pathogen. Overall, we show that offspring of facultative subsocial species may not respond differently to pathogen exposure depending on their parents' aid. Additionally, our results indicate that offspring of facultatively subsocial species may adjust their growth rate in response to pathogen exposure in the nest.},
}

@article {pmid40434822,
year = {2025},
author = {Berelson, MFG and Heavens, D and Nicholson, P and Clark, MD and Leggett, RM},
title = {From air to insight: the evolution of airborne DNA sequencing technologies.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {5},
pages = {},
doi = {10.1099/mic.0.001564},
pmid = {40434822},
issn = {1465-2080},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Air Microbiology ; *Sequence Analysis, DNA/methods ; *DNA, Environmental/genetics/analysis/isolation & purification ; Humans ; Environmental Monitoring/methods ; Computational Biology/methods ; Biodiversity ; },
abstract = {Historically, the analysis of airborne biological organisms relied on microscopy and culture-based techniques. However, technological advances such as PCR and next-generation sequencing now provide researchers with the ability to gather vast amounts of data on airborne environmental DNA (eDNA). Studies typically involve capturing airborne biological material, followed by nucleic acid extraction, library preparation, sequencing and taxonomic identification to characterize the eDNA at a given location. These methods have diverse applications, including pathogen detection in agriculture and human health, air quality monitoring, bioterrorism detection and biodiversity monitoring. A variety of methods are used for airborne eDNA analysis, as no single pipeline meets all needs. This review outlines current methods for sampling, extraction, sequencing and bioinformatic analysis, highlighting how different approaches can influence the resulting data and their suitability for specific use cases. It also explores current applications of airborne eDNA sampling and identifies research gaps in the field.},
}

*High-Throughput Nucleotide Sequencing/methods
*Air Microbiology
*Sequence Analysis, DNA/methods
*DNA, Environmental/genetics/analysis/isolation & purification
Humans
Environmental Monitoring/methods
Computational Biology/methods
Biodiversity