@article {pmid40569810,
year = {2025},
author = {Márquez, FJ and Granados, JE and Canet, LM and de Rojas, M and Caruz, AJ and Pérez, JM},
title = {The microbiome of the sucking louse Linognathus stenopsis (Phthiraptera, Anoplura, Linognathiidae).},
journal = {Journal of medical entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jme/tjaf060},
pmid = {40569810},
issn = {1938-2928},
support = {1380336//PAIDI/ ; },
}

@article {pmid40569694,
year = {2025},
author = {Kasmanas, JC and Magnúsdóttir, S and Zhang, J and Smalla, K and Schloter, M and Stadler, PF and de Leon Ferreira de Carvalho, ACP and Rocha, U},
title = {Integrating comparative genomics and risk classification by assessing virulence, antimicrobial resistance, and plasmid spread in microbial communities with gSpreadComp.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf072},
pmid = {40569694},
issn = {2047-217X},
support = {2019/03,396-9//São Paulo Research Foundation/ ; 2022/03,534-5//São Paulo Research Foundation/ ; //Deutsche Forschungsgemeinschaft/ ; //International Development Research Centre/ ; },
mesh = {*Plasmids/genetics ; Humans ; *Genomics/methods ; Virulence/genetics ; *Drug Resistance, Bacterial/genetics ; Gastrointestinal Microbiome/genetics ; Virulence Factors/genetics ; Computational Biology/methods ; Software ; Genome, Bacterial ; *Bacteria/genetics/pathogenicity/drug effects ; },
abstract = {BACKGROUND: Comparative genomics, genetic spread analysis, and context-aware ranking are crucial in understanding microbial dynamics' impact on public health. gSpreadComp streamlines the path from in silico analysis to hypothesis generation. By integrating comparative genomics, genome annotation, normalization, plasmid-mediated gene transfer, and microbial resistance-virulence risk-ranking into a unified workflow, gSpreadComp facilitates hypothesis generation from complex microbial datasets.

FINDINGS: The gSpreadComp workflow works through 6 modular steps: taxonomy assignment, genome quality estimation, antimicrobial resistance (AMR) gene annotation, plasmid/chromosome classification, virulence factor annotation, and downstream analysis. Our workflow calculates gene spread using normalized weighted average prevalence and ranks potential resistance-virulence risk by integrating microbial resistance, virulence, and plasmid transmissibility data and producing an HTML report. As a use case, we analyzed 3,566 metagenome-assembled genomes recovered from human gut microbiomes across diets. Our findings indicated consistent AMR across diets, with diet-specific resistance patterns, such as increased bacitracin in vegans and tetracycline in omnivores. Notably, ketogenic diets showed a slightly higher resistance-virulence rank, while vegan and vegetarian diets encompassed more plasmid-mediated gene transfer.

CONCLUSIONS: The gSpreadComp workflow aims to facilitate hypothesis generation for targeted experimental validations by the identification of concerning resistant hotspots in complex microbial datasets. Our study raises attention to a more thorough study of the critical role of diet in microbial community dynamics and the spread of AMR. This research underscores the importance of integrating genomic data into public health strategies to combat AMR. The gSpreadComp workflow is available at https://github.com/mdsufz/gSpreadComp/.},
}

*Plasmids/genetics
Humans
*Genomics/methods
Virulence/genetics
*Drug Resistance, Bacterial/genetics
Gastrointestinal Microbiome/genetics
Virulence Factors/genetics
Computational Biology/methods
Software
Genome, Bacterial
*Bacteria/genetics/pathogenicity/drug effects

@article {pmid40569658,
year = {2025},
author = {Yan, H and Wang, E and Wei, GS and Xu, X and Hurst, MRH and Zhang, B},
title = {Microbial dynamics across tri-trophic systems: insights from plant-herbivore-predator interactions.},
journal = {FEMS microbiology ecology},
volume = {101},
number = {7},
pages = {},
doi = {10.1093/femsec/fiaf065},
pmid = {40569658},
issn = {1574-6941},
support = {6222052//Beijing Natural Science Foundation/ ; 32070402//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Microbiota ; *Tetranychidae/microbiology/physiology ; *Food Chain ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Herbivory ; Predatory Behavior ; *Mites/microbiology/physiology ; *Plants/microbiology ; },
abstract = {Microbes play a critical role in regulating tri-trophic interactions among plants, herbivores, and their natural enemies, influencing key ecological and evolutionary processes. To fully understand these interactions through the food chain, a well-defined tri-trophic system is required. We investigated microbial dynamics involving plants (beans, cucumbers, and eggplants), spider mites (Tetranychus urticae), and predatory mites (Phytoseiulus persimilis) through 16S rRNA gene sequencing. The results revealed significant variations in microbiota across different trophic levels. Source tracking analysis indicated that microbiota at each trophic level were rarely inherited from the previous one, and deterministic processes played a key role in shaping the endosphere communities of these levels. Most shared zero-radius operational taxonomic units across each trophic level belonged to Pseudomonas, Bacillus, and Staphylococcus. Leaf microbiota differed among plants, while spider mites harbored similar microbiota. Notably, the microbiota of predatory mites on eggplants differed significantly from those on the other two plants. Biomarker selection and correlation analyses revealed that the abundance of Methylobacterium and Stenotrophomonas was strongly correlated with the improved fitness of predatory mites across different plants. Our study highlights the complex and dynamic nature of microbial communities across different trophic levels in a well-defined plant-herbivore-predator system.},
}

Animals
*Microbiota
*Tetranychidae/microbiology/physiology
*Food Chain
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
*Herbivory
Predatory Behavior
*Mites/microbiology/physiology
*Plants/microbiology

@article {pmid40569514,
year = {2025},
author = {Villanueva-Millan, MJ and Leite, G and Mathur, R and Rezaie, A and Fajardo, CM and de Freitas Germano, J and Morales, W and Sanchez, M and Rivera, I and Parodi, G and Weitsman, S and Rashid, M and Hosseini, A and Brimberry, D and Barlow, GM and Pimentel, M},
title = {Hydrogen Sulfide and Methane on Breath Test Correlate with Human Small Intestinal Hydrogen Sulfide Producers and Methanogens.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {40569514},
issn = {1573-2568},
abstract = {BACKGROUND: Evidence indicates that 3 gas breath testing (BT) correlates with stool microbial populations. Breath methane (CH4) levels correlate with stool Methanobrevibacter smithii levels and constipation, while hydrogen sulfide (H2S) levels correlate with stool H2S producers and diarrhea. However, their relationships to small bowel microbes are unknown.

AIMS: To assess relationships between small bowel microbes and breath gases.

METHODS: REIMAGINE study subjects completed a fasting single-sample BT for CH4 and H2S. During esophagogastroduodenoscopy without colon preparation, duodenal aspirates were obtained using double-lumen sterile aspiration catheters. Microbial DNAs underwent shotgun sequencing (NovaSeq6000).

RESULTS: Duodenal bacterial profiles differed significantly in subjects with breath H2S ≥ 1.5 ppm vs. those with < 1.5 ppm, with 2.08-log2fold greater prevalence of phylum Thermodesulfobacteriota. Higher breath H2S levels correlated with greater duodenal prevalences of H2S producers, including Proteus mirabilis (P = 0.002), Desulfosarcina widdelii (P = 0.027), and Desulfobulbus oligotrophicus (P = 0.041); co-occurrence of all 3 species correlated with ~ 50% higher breath H2S levels (P = 0.0001). Duodenal archaeal profiles differed significantly in subjects with intestinal methanogen overgrowth (IMO, CH4 ≥ 10 ppm), with 2.94-log2fold greater prevalence of family Methanobacteriaceae vs. non-IMO subjects. Higher breath CH4 correlated with greater prevalences of methanogens including M. smithii (P = 0.02), Halarchaeum sp. CBA1220 (P = 0.003), Desulfurococcus mucosus (P = 0.046), and Halobaculum rubrum (P = 0.049). IMO was more common in subjects with co-occurrence of all 4 species (P = 0.04). In IMO-positive subjects, CH4 levels correlated with greater constipation severity (P = 0.019); P. mirabilis (P = 0.021) and D. oligotrophicus (P = 0.003) correlated with looser stool in IMO-negative subjects. M. smithii prevalence correlated with known hydrogen-producing syntrophs, e.g., Christensenella minuta (P < 0.001).

CONCLUSION: This study demonstrates that duodenal prevalences of H2S-producing bacteria and methanogenic archaea contribute to H2S and CH4 levels, respectively, on BT.},
}

@article {pmid40569502,
year = {2025},
author = {Mortezaee, K},
title = {Microbiota interaction with Tregs: a target for colitis.},
journal = {Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico},
volume = {},
number = {},
pages = {},
pmid = {40569502},
issn = {1699-3055},
abstract = {Gut-resident microbiota associate with host immune system to promote homeostasis, and regulatory T cells (Tregs) are critical in the maintenance of immune balance. Tregs have immunosuppressive activity, and their presence hampers the development of inflammatory diseases. This review aims to unravel microbiome impact on Tregs in bowel inflammation and harnessing such interaction to combat colitis as a separate disease or a consequence of immune checkpoint inhibitor (ICI) therapy of cancer. Short-chain fatty acids (SCFAs) are microbial-derived metabolites associated positively with Treg generation and maintenance and being effective for hampering bowel inflammation. Treg induction shapes gut microbiota profile and support microorganism colonization in their niche and protect the host from inflammation, while suppression of Treg differentiation and activity directs microbiota-induced Th17 expansion and inducing inflammation. Thus, balancing Treg representation with Th17 cells and Treg reprogramming through manipulation of gut microbiota can offer therapy. Microbiota epithelial attachment/detachment and interaction with antigen-presenting cells (APCs) are important for the final fate of T cell signature. Fecal microbial transplantation (FMT) is a strategy for promoting normobiosis and represents a navel approach to targeting colitis. FMT with appropriate microbiota from healthy donors can reinforce microbial diversity, density and persistence to enrich their environment with transforming growth factor (TGF)-β, induce IL-10 producing APCs and reinforce gut barrier, with all these being effective for recovering Tregs, restoring intestinal homeostasis and hampering colitis. ICI therapy of cancer may predispose subjects to colitis due to the impact on microbiome and reducing Treg population. FMT promotes local Treg reorchestration, being advantageous in cancer patients.},
}

@article {pmid40569263,
year = {2025},
author = {Darlington, DN and Berger, RB and Keesee, JD and Nicholson, SE and Wu, X},
title = {Trauma and Hemorrhage Lead to an Elevation in Fecal Short-Chain Fatty Acids.},
journal = {Shock (Augusta, Ga.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/SHK.0000000000002645},
pmid = {40569263},
issn = {1540-0514},
abstract = {INTRODUCTION: Severe trauma and hemorrhage in rats lead to changes in the beta diversity of the commensal bacteria found in the gut. Because Short-Chain Fatty Acids (SCFA) are produced by these bacteria, SCFA concentration may also change following trauma and hemorrhage and reflect these alterations in the microbiome.

OBJECTIVE: To determine whether changes in SCFA occur after trauma and hemorrhage in the feces and plasma of rodents.

MATERIALS AND METHODS: Polytrauma was induced in isoflurane-anesthetized Sprague-Dawley rats by damage to the small intestine, liver, right leg skeletal muscle, and femur, followed by 20% hemorrhage. Whole blood resuscitation was performed at 1 hour (20%). Rats were euthanized at 2 hours and feces and plasma were analyzed for short-chain fatty acids (SCFA) by liquid chromatography tandem mass spectroscopy.

RESULTS: Of twenty-one SCFA analyzed in the feces and plasma, 11 were measurable. In feces, five demonstrated a significant elevation after 2 hours of severe trauma and hemorrhage (n-8) including propionic (37775 ± 8919 vs. 146591 ± 46734 nM/mg protein: mean ± SEM), pentanoic (10975 ± 2981 vs. 41828 ± 10645), 2-methyl propionic (2621 ± 523 vs. 13798 vs. 2083), 4-methyl pentanoic (1134 ± 302 vs. 4320 ± 1029) and 3-phenyl propionic acid (42194 ± 4863 vs. 153024 ± 38473). The addition of whole blood resuscitation did not change these responses, but led to an additional significant elevation in butyric (68551 ± 10786 vs. 369951 ± 79515) and hexanoic acid (24548 ± 6791 vs. 102002 ± 32069). There was no change in SCFA after trauma, hemorrhage or resuscitation in the plasma (n = 6).

CONCLUSION: Two hours of severe trauma and hemorrhage lead an elevation in many SCFAs in rat feces. No change in SCFA was found in plasma. Because SCFA are primarily derived from commensal bacteria in the gut, these data suggest that the measurement of SCFA could be used as an index of changes in the gut microbiome in pathological condition including trauma and hemorrhage.},
}

@article {pmid40569166,
year = {2025},
author = {Agudelo, FAG and Leblanc, N and Bourdeau-Julien, I and St-Arnaud, G and Dahhani, F and Flamand, N and Veilleux, A and Di Marzo, V and Raymond, F},
title = {Dietary Manganese Modulates Microbiota and Intestinal N-Acylethanolamines in a Sex-Specific Manner in Mice With Diet-Induced Obesity.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {13},
pages = {e70763},
pmid = {40569166},
issn = {1530-6860},
support = {//Canada Excellence Research Chairs, Government of Canada (CERC)/ ; RGPIN 03922//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; //Canadian Government | Canadian Institutes of Health Research (CIHR)/ ; //UL | Sentinelle Nord, Universit Laval (Sentinel North)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Female ; Male ; Mice ; *Obesity/metabolism/etiology/microbiology ; *Manganese/pharmacology/administration & dosage ; Mice, Inbred C57BL ; *Ethanolamines/metabolism ; Diet, High-Fat/adverse effects ; Endocannabinoids/metabolism ; Sex Factors ; Intestines/microbiology ; Diet ; },
abstract = {Obesity is characterized by low-grade inflammation, changes in gut microbiota, and increased tone of the expanded endocannabinoid system (eCBome). The gut is a complex ecosystem that serves as an interface between the diet and its ultimate conversion to nutrients and energy for all cells of the organism. Manganese (Mn) is an essential micronutrient from the diet required for normal cell function and physiological processes. Moreover, it is an indispensable trace mineral for some microbial species since it is a cofactor in several metabolic enzymes. Therefore, we aimed to identify possible interactions between gut microbiota composition and the eCBome during dietary variations of Mn in the context of diet-induced obesity. Female and male mice were fed Mn-depleted and Mn-enriched diets in combination with Low Fat-Low Sucrose (LFLS) or High Fat-High Sucrose (HFHS) diets for 28 days to assess intestinal microbiota and eCBome levels. Mn-enriched diets enhanced the circulating levels of N-docosapentaenoyl-ethanolamine (DPEA) and anandamide (AEA), while they reduced the intestinal concentrations of other N-acylethanolamines, particularly in the caecum. Besides, we found a strong sex effect of Mn on the intestinal levels of 2-monoacylglycerols (2-MAGs), which were lower in females. Other endocannabinoid-like molecules involved in the immune response were impacted by dietary Mn enrichment, such as N-palmitoyl-glycine and N-oleoyl-L-serine. Concomitantly, Mn enrichment promoted segment-specific changes in the relative abundance of several taxa in intestinal microbiota following the HFHS diet. Microbial families such as Peptostreptococcaceae, Muribaculaceae, and Erysipelotrichaceae responded differentially to dietary variations in Mn. This study hints at potential interactions between Mn levels and diet composition with the eCBome and intestinal bacteria during dietary Mn variations within HFHS-induced dysmetabolic processes in a sex-dependent manner. These results will eventually contribute to identifying members of the gut microbiome and mediators of the eCBome useful for improving metabolic health.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Female
Male
Mice
*Obesity/metabolism/etiology/microbiology
*Manganese/pharmacology/administration & dosage
Mice, Inbred C57BL
*Ethanolamines/metabolism
Diet, High-Fat/adverse effects
Endocannabinoids/metabolism
Sex Factors
Intestines/microbiology
Diet

@article {pmid40569073,
year = {2025},
author = {Kobiałka, M and Świerczewski, D and Walczak, M and Urbańczyk, W},
title = {Extremely distinct microbial communities in closely related leafhopper subfamilies: Typhlocybinae and Eurymelinae (Cicadellidae, Hemiptera).},
journal = {mSystems},
volume = {},
number = {},
pages = {e0060325},
doi = {10.1128/msystems.00603-25},
pmid = {40569073},
issn = {2379-5077},
abstract = {UNLABELLED: Among the Hemiptera insects, a widespread way of feeding is sucking sap from host plants. Due to their nutrient-poor diet, these insects enter into obligate symbiosis with their microorganisms involved in the synthesis of components essential for host survival. However, within the Cicadellidae family, there is a relatively large group of mesophyll feeders-Typhlocybinae-that is considered to be devoid of obligate symbiotic companions. In this work, we examine the composition of microorganisms in this subfamily and compare the results with their close relatives-the Eurymelinae subfamily. To study the microbiome, we used high-throughput next-generation sequencing (NGS, Illumina) and advanced microscopic techniques, such as transmission electron microscopy (TEM) and fluorescence in situ hybridization (FISH), in a confocal microscope. In the bodies of Typhlocybinae insects, we did not detect the presence of microorganisms deemed to be obligate symbionts. Their microbial communities consist of facultative symbionts, mainly alphaproteobacteria such as Wolbachia or Rickettsia as well as others that can be considered as facultative, including Spiroplasma, Acidocella, Arsenophonus, Sodalis, Lariskella, Serratia, Cardinium, and Asaia. On the other hand, the Eurymelinae group is characterized by a high diversity of microbial communities, both obligate and facultative, similar to other Cicadomorpha. We find co-symbionts involved in the synthesis of essential amino acids such as Karelsulcia, betaproteobacteria Nasuia, or gammaproteobacteria Sodalis. In other representatives, we observed symbiotic yeast-like fungi from the family Ophiocordycipitaceae or Arsenophonus bacteria inhabiting the interior of Karelsulcia bacteria. Additionally, we investigated some aspects of symbiont transmission and the phylogeny of symbiotic organisms and their hosts.

IMPORTANCE: The Typhlocybinae and Eurymelinae leafhoppers differ significantly in their symbiotic communities. They have different diets, as Typhlocybinae insects feed on parenchyma, which is richer in nutrients, while Eurymelinae, like most representatives of Auchenorrhyncha, consume sap from the phloem fibers of plants. Our work presents comprehensive studies of 42 species belonging to the two above-mentioned, and so far poorly known, Cicadomorpha subfamilies. Phylogenetic studies indicate that the insects from the studied groups have a common ancestor. The diet shift in the Typhlocybinae leafhoppers contributed to major changes in the composition of microorganisms inhabiting the body of these insects. Research on the impact of diet on the microbiome and the subsequent consequences on the evolution and adaptation of organisms plays an important role in the era of climate change.},
}

@article {pmid40569063,
year = {2025},
author = {Bolino, M and Duman, H and Avcı, İ and Kayili, HM and Petereit, J and Zundel, C and Salih, B and Karav, S and Frese, SA},
title = {Proteomic and N-glycomic comparison of synthetic and bovine whey proteins and their effect on human gut microbiomes in vitro.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0020025},
doi = {10.1128/spectrum.00200-25},
pmid = {40569063},
issn = {2165-0497},
abstract = {UNLABELLED: Advances in food production systems and customer acceptance have led to the commercial launch of dietary proteins produced via modern biotechnological approaches as alternatives to traditional agricultural sources. At the same time, a deeper understanding of how dietary components interact with the gut microbiome has highlighted the importance of understanding the nuances underpinning diet-microbiome interactions. Novel food proteins with distinct post-translational modifications resulting from their respective production systems have not been characterized, nor how they may differ from their traditionally produced counterparts. Here, we have characterized the protein composition and N-glycome of a yeast-synthesized and commercially available whey protein ingredient and compared this novel ingredient to whey protein isolate powder derived from bovine milk. Despite strong similarities in protein composition, we found that the N-glycome significantly differs between the two protein sources, reflecting the biosynthetic machinery of the production systems. Furthermore, the diversity of proteins found in yeast-synthesized whey protein were lower relative to bovine whey protein, despite both being predominantly β-lactoglobulin. Finally, to understand whether these differences in N-glycome profiles may affect the human gut microbiome, we compared these proteins in an in vitro fecal fermentation model. The two whey protein sources generated significant differences among three representative gut microbiomes in vitro, most likely due to differences in N-glycan composition and degradation by these representative microbial communities. This work highlights the need to understand how differences in novel biotechnological systems affect the bioactivity of synthesized proteins and how these differences impact the human gut microbiome.

IMPORTANCE: Recent advances in food technology have led to the production of animal-free products from yeast that are traditionally derived from animals, such as milk proteins. These new processes raise important questions about the use of synthetic proteins as a replacement for traditionally sourced protein, especially in the context of the gut microbiome. Importantly, yeast produce N-glycans comprised primarily of mannose, while animals synthesize structurally and compositionally complex N-glycan structures. Given these differences, we characterized a new, yeast-derived whey protein ingredient and compared it to bovine whey protein. We found that yeast-derived whey protein differs in its impact on human gut microbiomes because of differences in N-glycan structures, despite similarity in protein composition. These findings raise important questions as to whether these differences in synthetic proteins lead to significant changes to the gut microbiome in vivo, and whether this may impact the utility of these novel ingredients.},
}

@article {pmid40569025,
year = {2025},
author = {Celik, E and Ozcan, G and Vatansever, C and Paerhati, E and Uygur, L and Unal, C and Guler Cekic, S and Ozten, MA and Gürsoy, A and Keskin, Ö and Turgal, M and Gursoy, T and Can, F},
title = {Alterations in vaginal microbiome in women with short cervix: longitudinal study of microbial diversity and impact of vaginal progesterone treatment.},
journal = {Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1002/uog.29269},
pmid = {40569025},
issn = {1469-0705},
support = {119S463//Türkiye Bilimsel ve Teknolojik Araştırma Kurumu/ ; },
abstract = {OBJECTIVES: A short cervix is a known risk factor for preterm birth, and imbalances in the vaginal microbiome, such as low relative abundance of Lactobacillus, may be associated with an increased risk of preterm birth. The aim of this study was to evaluate differences in the vaginal microbiome between women with a short cervix and those with normal cervical length in the second trimester. Additionally, we aimed to assess longitudinal changes in microbial diversity during pregnancy, as well as the impact of vaginal progesterone treatment on vaginal microenvironment in women with a short cervix.

METHODS: This was a prospective, longitudinal study conducted at Koc University Hospital between January 2020 and May 2023, in women with a singleton pregnancy with a short cervical length (≤ 25 mm) in the second trimester (20 + 0 to 24 + 6 weeks' gestation). After diagnosis of short cervix, administration of 200 mg vaginal progesterone daily was initiated. The control group comprised women with a normal cervical length (> 25 mm) in the second trimester, matched for age and body mass index (BMI). Cervicovaginal swabs were collected from the posterior fornix at three gestational-age ranges: in the first trimester (11 + 0 to 13 + 6 weeks), the second trimester (20 + 0 to 24 + 6 weeks) and the third trimester (28 + 0 to 34 + 6 weeks), and cervical length was measured following sample collection. DNA was extracted and the 16S rRNA bacterial gene was sequenced to analyze and compare the vaginal microbiome between women with a short cervix and controls. We also assessed the microbiome longitudinally in each group, across the first, second and third trimesters. In the short-cervix group, we also compared the microbiome before initiation of progesterone treatment in the second trimester and 4 weeks after its initiation.

RESULTS: Among 490 pregnant women who underwent first-trimester screening during the study period and had vaginal swabs collected, short cervical length was detected in 31 at the second-trimester scan. These women formed the study group. A further 27 women, with a normal cervical length, were matched for BMI and age and assigned to the control group. During the second trimester, women with a short cervix exhibited greater species diversity compared with the control group; this was suggested by the higher Shannon index (0.45 vs 0.33; P = 0.135), which reflects species richness and evenness, and further demonstrated by the higher Chao index (20.2 vs 13.8; P = 0.018), which estimates species richness. In the second trimester, Lactobacillus was less abundant in women with a short cervix than in the control group, although the difference did not reach significance (86.8% vs 95.5%; P = 0.091). At the phylum level, in women with a short cervix compared to those with normal cervical length, the relative abundance of Firmicutes, to which the genus Lactobacillus belongs, was significantly lower (90.7% vs 97.6%; P = 0.041), while the relative abundances of both Bacteroidota (1.73% vs 0.4%; P = 0.004) and Proteobacteria (0.2% vs 0.01%; P = 0.007) were higher. In the second trimester, the relative abundance of Lactobacillus gasseri was significantly lower in women with a short cervix compared to controls (4.7% vs 13.8%; P = 0.023). In the longitudinal analysis of the vaginal microbiome, there were no significant differences among the trimesters in the control group. In contrast, in those with a short cervix, there was a notable decrease in the amount of Lactobacillus crispatus, from 55.0% in the first trimester to 36.1% in the second trimester (P = 0.052). In women with a short cervix, there was no significant difference in bacterial diversity after vs before progesterone treatment (Chao index, 22.6 vs 20.5; P = 0.609).

CONCLUSION: These findings highlight the significant alterations in the vaginal microbiome of pregnant women with a short cervix in comparison to those with normal cervical length, particularly in terms of higher species diversity and distinct community composition. The study also shows that vaginal progesterone treatment in women with a short cervix does not alter the vaginal microbiome, suggesting that it is a safe and effective intervention without disrupting the vaginal microbial balance. Understanding the relationship between cervical length and the vaginal microbiome is essential for developing strategies to reduce the risk of preterm birth in high-risk populations. © 2025 The Author(s). Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.},
}

@article {pmid40568872,
year = {2025},
author = {Han, J and Fan, DJ and Jiang, LC and Lu, Z and Ye, T and Wei, Z and Feng, YQ},
title = {In Situ Dynamic Molecular Monitoring of Single Seed Exudates by Induced Electrospray Ionization Mass Spectrometry.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c01437},
pmid = {40568872},
issn = {1520-6882},
abstract = {Seed exudates are essential for seed germination and shaping the microbiome. However, analyzing single seed exudates in situ is challenging due to their low volume and complexity. This study utilized tapered glass capillary emitters as miniature Petri dishes as well as induced electrospray ionization mass spectrometry (iESI-MS) for in situ collection and real-time analysis of single seed exudates. Through this innovative platform, we observed dynamic changes in amino acids (AAs) and organic acids (OAs) in the central carbon metabolism pathway of single Arabidopsis seed exudates during the imbibition process. Quantitative results revealed that the levels of AAs and OAs exhibited a pattern of an initial increase followed by a decrease. Furthermore, the onset and peak levels of AAs occurred earlier than those of OAs, suggesting that the seeds may adopt a two-step defense mechanism to regulate the composition of the microbiome. This study provides a valuable tool for gaining insight into seed exudates and microbiome interactions.},
}

@article {pmid40568744,
year = {2025},
author = {Sabu Kattuman, EE and Teegala, LR and Darzi, S and Thodeti, CK and Paruchuri, S},
title = {Leukotrienes: Bridging the Inflammatory Gap in Asthma and Inflammatory Bowel Diseases (IBD).},
journal = {Comprehensive Physiology},
volume = {15},
number = {3},
pages = {e70022},
pmid = {40568744},
issn = {2040-4603},
support = {R01AI144115/NH/NIH HHS/United States ; R01HL148585/NH/NIH HHS/United States ; 25PRE1373953//American Heart Association/ ; 971237//American Heart Association/ ; },
mesh = {Humans ; *Inflammatory Bowel Diseases/metabolism/immunology ; *Asthma/metabolism/immunology ; *Leukotrienes/metabolism ; Animals ; Inflammation/metabolism ; Gastrointestinal Microbiome ; },
abstract = {Leukotrienes are potent inflammatory lipid mediators produced primarily by immune cells. Inflammation, being the center stone of two major disease conditions, namely, asthma and inflammatory bowel disease (IBD), has led researchers to study the role of leukotrienes (LTs) in both these disease settings extensively. Several studies indicate a crucial role for LTs in the development and progression of IBD, whereas LTs, especially cysteinyl leukotrienes (cys-LTs), have been identified as the major contributors to asthma initiation and progression for over three decades. Additionally, the lungs and the gut share several common characteristics, including their exposure to the external environment, similar microbiome composition, and inflammatory responses. These similarities suggest a bidirectional relationship, supported by the increased risk of IBD in asthma patients and vice versa. However, the specific role of LTs in this lung-gut connection remains unclear. This review will examine how several common factors, such as physiology, microbiome, environment, and inflammatory mediators, especially LTs, modulate this crosstalk. The review also highlights in detail how altered leukotriene biosynthesis and signaling contribute to the pathogenesis of both asthma and IBD. Furthermore, we will consider the therapeutic implications of targeting leukotriene pathways for patients with concurrent asthma and IBD in the hope of developing more efficient treatment outcomes for these interconnected conditions. Finally, this review will very briefly explore the involvement of neuronal connections in mediating the lung-gut crosstalk.},
}

Humans
*Inflammatory Bowel Diseases/metabolism/immunology
*Asthma/metabolism/immunology
*Leukotrienes/metabolism
Animals
Inflammation/metabolism
Gastrointestinal Microbiome

@article {pmid40568741,
year = {2025},
author = {Pinder, LF and Bertrand, P and Fertitta, V and Cahais, V and Mwanahamuntu, M and Nyambe, N and Chisele, S and Shibemba, AL and McKay-Chopin, S and Cuenin, C and Lucas, E and Korenjak, M and Muwonge, R and Ghantous, A and Herceg, Z and Parham, GP and Zavadil, J and Basu, P and Gheit, T},
title = {Vaginal microbiome composition in women with HIV undergoing treatment of cervical transformation zone in a screen and treat program in Zambia.},
journal = {AIDS (London, England)},
volume = {39},
number = {9},
pages = {1303-1306},
doi = {10.1097/QAD.0000000000004187},
pmid = {40568741},
issn = {1473-5571},
mesh = {Humans ; Female ; Zambia ; *Vagina/microbiology ; *HIV Infections/complications/drug therapy ; *Microbiota ; Adult ; RNA, Ribosomal, 16S/genetics ; Treatment Outcome ; Sequence Analysis, DNA ; Lactobacillus/isolation & purification/genetics/classification ; DNA, Ribosomal/chemistry/genetics ; DNA, Bacterial/genetics/chemistry ; Young Adult ; Middle Aged ; },
abstract = {This study assessed the vaginal microbiome in women with HIV undergoing cervical transformation zone treatment in Zambia. 16S rRNA sequencing showed lower microbial diversity in successful outcomes (N = 18) than those with treatment failure (N = 17) treatment outcome, with Lactobacillus abundance correlated with success. Moreover, HPV-negative women (N = 12) had higher Lactobacillus levels and less pathogens than HPV-positive women (N = 12). These findings suggest a Lactobacillus-dominated microbiome may be associated with positive treatment outcomes.},
}

Humans
Female
Zambia
*Vagina/microbiology
*HIV Infections/complications/drug therapy
*Microbiota
Adult
RNA, Ribosomal, 16S/genetics
Treatment Outcome
Sequence Analysis, DNA
Lactobacillus/isolation & purification/genetics/classification
DNA, Ribosomal/chemistry/genetics
DNA, Bacterial/genetics/chemistry
Young Adult
Middle Aged

@article {pmid40568698,
year = {2025},
author = {Hernández-Luna, MA},
title = {Editorial: Bacteria-host interactions: from infection to carcinogenesis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1634299},
doi = {10.3389/fcimb.2025.1634299},
pmid = {40568698},
issn = {2235-2988},
}

@article {pmid40568683,
year = {2025},
author = {Wang, C and Fan, Y and Zhang, L and Zhao, Z and Luo, F and Sun, K and Zeng, M and Tian, H and Peng, M and Luo, Y and Zhao, H and He, S and Sun, H},
title = {Deciphering the contributions of fecal microbiota from patients with high-grade glioma to tumor development in a humanized microbiome mouse model of glioma.},
journal = {Neuro-oncology advances},
volume = {7},
number = {1},
pages = {vdaf085},
pmid = {40568683},
issn = {2632-2498},
abstract = {BACKGROUND: Recent studies have revealed associations between gut microbiota and glioma. However, the underlying mechanisms remain poorly understood. This study primarily aims to elucidate the impact of altered gut microbiota on tumor progression in glioma-bearing mice.

METHODS: Fecal samples were collected from glioma patients and healthy controls to compare the effects of human-derived gut microbiota on glioma development in mice. We also analyzed the associations between these microbiota profiles and plasma metabolites.

RESULTS: Significant differences were observed in both the composition and diversity of the gut microbiota between glioma patients and healthy controls. Mice transplanted with gut microbiota from high-grade glioma patients (HGG-FMT) exhibited accelerated glioma progression compared to those transplanted with microbiota from healthy individuals (HC-FMT). Specifically, Eisenbergiella, Mailhella, and Merdimonas were significantly enriched in HGG-FMT mice, while Limosilactobacillus and Anaerospora increased in HC-FMT mice. Furthermore, Merdimonas showed a positive correlation with sphingosine, sphingosine 1-phosphate, and D-sphingosine in HGG-FMT mice. Conversely, Limosilactobacillus was positively correlated with stearidonic acid and eicosapentaenoic acid in HC-FMT mice.

CONCLUSIONS: Our findings demonstrate that gut microbiota from high-grade glioma patients can promote glioma progression in mice, potentially through mechanisms involving sphingosine 1-phosphate. This metabolite may enter the bloodstream and accelerate glioma growth, offering novel insights into glioma pathogenesis and potential treatment options.},
}

@article {pmid40568577,
year = {2025},
author = {Qiu, X and Li, D},
title = {Multi-omics analysis untangles the crosstalk between intratumor microbiome, lactic acid metabolism and immune status in lung squamous cell carcinoma.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1603822},
pmid = {40568577},
issn = {1664-3224},
mesh = {Humans ; *Lung Neoplasms/immunology/metabolism/genetics/microbiology/pathology ; *Carcinoma, Squamous Cell/immunology/metabolism/genetics/microbiology ; *Lactic Acid/metabolism ; *Microbiota/immunology ; Transcriptome ; Biomarkers, Tumor/genetics ; Tumor Microenvironment/immunology ; Multiomics ; },
abstract = {INTRODUCTION: Cancer development is intricately linked with metabolic dysregulation, including lactic acid metabolism (LM), which plays a pivotal role in tumor progression and immune evasion. However, its specific implications in lung squamous cell carcinoma (LUSC) remain unclear.

METHODS: We used numerous datasets encompassing bulk and single-cell transcriptome, genome, intratumor microbiome, and digital pathome to systematically investigate the LM patterns in LUSC. Multiple machine learning algorithms were used to generate the LUSC classification. Histopathology image-based deep learning model was used to predict the classification. Casual mediation analysis was conducted to uncover the association among intratumor microbiota, LM, and immunity.

RESULTS: Two LM-based subtypes were discovered endowed with distinct clinical outcomes and biological peculiarities, such as overall survival, somatic mutations, and intratumor microbiota structure. Moreover, the histopathology image-based deep learning model accurately predicted our LM-based LUSC taxonomy, significantly improving its clinical utility. Machine learning models based on seven LM-related genes (CHEK2, LIPT1, TUFM, NDUFA10, AGK, PNPLA2, and GFM1) accurately predicted immunotherapy outcomes for multiple cancer types, including LUSC, and outperformed other currently known biomarkers. Furthermore, mediation analysis identified potential association pathways involving tumor-resident microbes, LM-related gene signatures, and antitumor immune cells.

DISCUSSION: Overall, this study advanced the understanding of the relationship between LM patterns and LUSC tumor biology, as well as its potential clinical implications, which might advance the tailored management of LUSC.},
}

Humans
*Lung Neoplasms/immunology/metabolism/genetics/microbiology/pathology
*Carcinoma, Squamous Cell/immunology/metabolism/genetics/microbiology
*Lactic Acid/metabolism
*Microbiota/immunology
Transcriptome
Biomarkers, Tumor/genetics
Tumor Microenvironment/immunology
Multiomics

@article {pmid40568547,
year = {2025},
author = {Tatarko, AR and Vannette, RL and Frese, S and Leonard, A},
title = {A wild bumble bee shows intraspecific differences in sensitivity to multiple pesticides.},
journal = {Royal Society open science},
volume = {12},
number = {6},
pages = {250281},
pmid = {40568547},
issn = {2054-5703},
abstract = {Wild pollinator declines are increasingly linked to pesticide exposure, yet it is unclear how intraspecific differences contribute to observed variation in sensitivity, and the role gut microbes play in the sensitivity of wild bees is largely unexplored. Here, we investigate site-level differences in survival and microbiome structure of a wild bumble bee exposed to multiple pesticides, both individually and in combination. We collected wild Bombus vosnesenskii foragers (N = 175) from an alpine meadow, a valley lake shoreline and a suburban park and maintained them on a diet containing a herbicide (glyphosate), a fungicide (tebuconazole), an insecticide (imidacloprid) or a combination of these chemicals. Alpine bees had the highest overall survival, followed by shoreline bees then suburban bees. This was in part explained by body size differences across sites and the presence of conopid parasitoids at two of the sites. Notably, site of origin impacted bee survival on the herbicide, fungicide and combination treatment. We did not find evidence of gut microbiome differences across pesticide treatment, nor a site-by-treatment interaction. Regardless, the survival differences we observed emphasize the importance of considering population of origin when studying pesticide toxicity of wild bees.},
}

@article {pmid40568349,
year = {2025},
author = {Aghara, H and Patel, M and Chadha, P and Parwani, K and Chaturvedi, R and Mandal, P},
title = {Unraveling the Gut-Liver-Brain Axis: Microbiome, Inflammation, and Emerging Therapeutic Approaches.},
journal = {Mediators of inflammation},
volume = {2025},
number = {},
pages = {6733477},
pmid = {40568349},
issn = {1466-1861},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Brain/metabolism ; *Inflammation/metabolism ; *Liver/metabolism ; Animals ; Dysbiosis/metabolism ; Probiotics/therapeutic use ; },
abstract = {The gut-liver-brain axis (GLB axis) plays a crucial role in maintaining metabolic, immune, and neurological homeostasis. The gut microbiota influences systemic health through its metabolites, including short-chain fatty acids (SCFAs), bile acids (BAs), and tryptophan (Trp) derivatives, which regulate immune function, lipid metabolism, and neurotransmitter balance. Dysbiosis is an imbalance in gut microbiota that has been implicated in metabolic dysfuntion associated fatty liver disease (MAFLD), alcohol-associated liver disease (AALD), and neuroinflammatory conditions such as schizophrenia. Increased gut permeability allows microbial byproducts like lipopolysaccharides (LPSs) to enter the liver and brain, activating inflammatory pathways that contribute to disease progression. Moreover, hepatic dysfunction can lead to neuroinflammation and cognitive impairments. Understanding the interplay between microbial metabolites and host physiology provides insight into novel therapeutic interventions. Strategies such as probiotics, prebiotics, synbiotics, fecal microbiota transfer (FMT), and postbiotics offer potential treatments to restore gut eubiosis and mitigate disease severity. This review highlights the mechanistic role of the GLB axis in health and disease, emphasizing microbiome-targeted therapies as a promising avenue for managing metabolic and neuropsychiatric disorders. Trial Registration: ClinicalTrials.gov identifier: NCT04823676, NCT02496390, NCT06024681, NCT02721264.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Brain/metabolism
*Inflammation/metabolism
*Liver/metabolism
Animals
Dysbiosis/metabolism
Probiotics/therapeutic use

@article {pmid40568303,
year = {2025},
author = {Wiederkehr, F and Engelhardt, KE and Vetter, J and Ruscheweyh, HJ and Salazar, G and O'Brien, J and Priest, T and Ziegler, M and Sunagawa, S},
title = {Host-level biodiversity shapes the dynamics and networks within the coral reef microbiome.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf097},
pmid = {40568303},
issn = {2730-6151},
abstract = {Coral reefs face severe threats from human activity, resulting in drastic biodiversity loss. Despite the urgency of safeguarding these ecosystems, we know little about the ecological impacts of losing coral reef host-associated microbial communities (microbiomes). Here, we experimentally studied the microbiomes attached to or released from seven benthic reef hosts belonging to the functional groups of stony corals, soft corals, macroalgae, and sponges while manipulating the coral reef metacommunity to mimic biodiverse or degraded reef habitats. Developing an ecological framework, we found host species and functional groups to show distinct patterns of interacting with the environment (i.e. by exuding, maintaining, acquiring, or exchanging microbiome members), with habitat biodiversity primarily influencing microbial acquisition. In a degraded compared to a biodiverse habitat, the microbiomes of stony corals were less connected to soft corals and sponges, while those of soft corals, macroalgae, and sponges became more tightly linked. Our study demonstrates that a decline in metacommunity biodiversity is not merely associated with a proportional loss in microbial diversity; rather, it triggers complex changes in the microbial interactions among the persisting hosts with each other and the environment. These results emphasize the importance of conserving coral reef host biodiversity to preserve the intricately linked microbiomes-and with them the ecosystem functions and services coral reefs provide.},
}

@article {pmid40568126,
year = {2025},
author = {Kumar, R and Sykes, DJ and Band, VI and Schaller, ML and Patel, R and Vitvitsky, V and Sajjakulnukit, P and Singhal, R and Wong, HKA and Hourigan, SK and Ichinose, F and Lyssiotis, CA and Shah, YM and Banerjee, R},
title = {Gut sulfide metabolism modulates behavior and brain bioenergetics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.04.09.647962},
pmid = {40568126},
issn = {2692-8205},
abstract = {UNLABELLED: The host-microbiome interface is rich in metabolite exchanges and exquisitely sensitive to diet. Hydrogen sulfide (H 2 S) is present at high concentrations at this interface, and is a product of both microbial and host metabolism. The mitochondrial enzyme, sulfide quinone oxidoreductase (SQOR), couples H 2 S detoxification to oxidative phosphorylation; its inherited deficiency presents as Leigh disease. Since an estimated two thirds of systemic H 2 S metabolism originates in gut, it raises questions as to whether impaired sulfide clearance in this compartment contributes to disease, and whether it can be modulated by dietary sulfur content. In this study, we report that SQOR deficiency confined to murine intestinal epithelial cells, perturbs colon bioenergetics that is reversed by antibiotics, establishing a significant local contribution of microbial H 2 S to host physiology. We also find that a 2.5-fold higher methionine intake, mimicking the difference between animal and plant proteins, synergized with intestinal SQOR deficiency to adversely impact colon architecture and alter microbiome composition. In serum, increased thiosulfate, a biomarker of H 2 S oxidation, revealed that intestinal SQOR deficiency combined with high dietary methionine, affects sulfide metabolism globally and perturbs energy metabolism as indicated by higher ketone bodies. The mice exhibited lower exploratory locomotor activity while brain MRI revealed an atypical reduction in ventricular volume, which was associated with lower aquaporin 1 that is important for cerebrospinal fluid secretion. Our study reveals the dynamic interaction between dietary sulfur intake and sulfide metabolism at the host-microbe interface, impacting gut health, and the potential for lower dietary methionine intake to modulate pathology.

SIGNIFICANCE STATEMENT: The host-microbiome interface is rich in metabolite-based communications that are modulated by diet. Hydrogen sulfide (H 2 S), which is a respiratory poison at high concentrations, is enriched at this interface, and is detoxified by the host enzyme, sulfide quinone oxidoreductase (SQOR). Given the quantitatively significant contribution of gut to systemic H 2 S metabolism, we examined how SQOR deficiency restricted to murine intestinal epithelial cells, interacts with high dietary methionine, designed to approximate the difference between plant versus animal protein levels, to affect local and global bioenergetics. Our study revealed profound short- and long-range impacts resulting from the synergy between decreased H 2 S clearance capacity in gut and high dietary methionine on global energy metabolism, brain pathology, and behavior.},
}

@article {pmid40567942,
year = {2025},
author = {Zheng, W and Su, M and Hong, N and Ye, P},
title = {Gut-eye axis.},
journal = {Advances in ophthalmology practice and research},
volume = {5},
number = {3},
pages = {165-174},
pmid = {40567942},
issn = {2667-3762},
abstract = {BACKGROUND: The gut microbiome, colonizing the human gastrointestinal tract, is increasingly recognized for its symbiotic relationship with the immune system in maintaining overall host health. This emerging understanding raises intriguing questions about potential connections between the gut microbiome and anatomically distant organs, such as the eye, possibly mediated through immune pathways.

MAIN TEXT: This review synthesizes contemporary research on ocular diseases with the framework of the burgeoning "gut-eye axis" concept. Investigations spanning from the ocular surface to the fundus suggest correlations between the gut microbiome and various ocular disorders. By elucidating the putative pathogenic mechanisms underlying these ocular conditions, we offer novel perspectives to inform future diagnostic and therapeutic interventions in ophthalmology.

CONCLUSIONS: By presenting a critical analysis of current knowledge regarding the role of gastrointestinal microbiota in ocular health, this review shed light on the complex interplay between gut dysbiosis and eye disorders. Our work endeavors to catalyze interdisciplinary research and foster innovative clinical applications, thereby bridging the gap between the gut microbiota and the ocular well-being.},
}

@article {pmid40567545,
year = {2025},
author = {Tang, J and Wang, Y and Zhou, Q and Fang, Z and Lin, Y and Xu, S and Feng, B and Zhuo, Y and Jiang, X and Zhao, H and Wu, D and Che, L},
title = {Effects of maternal and post-weaning supplementation with microbe-derived antioxidants on sow and piglet performance, oxidative status, and gut microbiota.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1574259},
pmid = {40567545},
issn = {2297-1769},
abstract = {The antioxidants were found to improve inflammatory responses and redox status. This study investigated the effects of maternal and post-weaning supplementation with microbe-derived antioxidants (MA) on sow performance, redox status, and fecal microorganisms, as well as the growth performance, inflammatory responses and intestinal microbiota of weaned piglets. Sixty multiparous sows were randomly allocated to the control group (CON, basal diet) and the MA group (basal diet supplemented with 2.0 g MA/kg) from d 90 of gestation to d 24 of lactation, according to the parity and body condition. At weaning, a total of 80 piglets per group were selected and randomly assigned to either the basal diet or the MA-supplemented diet, with 10 pens per group and 4 piglets per pen, for a period of 21-day trial. Results showed that maternal MA supplementation increased litter size at weaning (p < 0.05) and the milk contents of dry matter (p = 0.08) and fat (p = 0.09), while decreasing the plasma activities of alanine aminotransferase and aspartate aminotransferase in sows on d 24 of lactation (p < 0.05). Moreover, maternal MA supplementation reduced plasma malondialdehyde concentration (p ≤ 0.01) in sows at farrowing and weaning, as well as catalase activity at weaning (p = 0.01), and tended to increase total antioxidant capacity at farrowing (p = 0.08). Additionally, the fecal contents of butyrate (p = 0.04) and propionate (p = 0.09) were higher in sows receiving the MA diet at d 24 of lactation. In post-weaning piglets, maternal MA supplementation increased average daily gain (p = 0.07) and average daily feed intake (p < 0.05) throughout the period, and increased plasma immunoglobulin G and interleukin-10 concentrations (p < 0.05). Additionally, either maternal or post-weaning MA supplementation positively influenced the gut microbiome of both sows and weaned piglets. In conclusion, maternal MA supplementation during late gestation and lactation increased litter size at weaning, which may be associated with the improved milk quality and redox status. Furthermore, maternal MA supplementation may enhance the growth performance of post-weaning piglets, potentially linking to the improvements in immunological parameters and gut microbiome.},
}

@article {pmid40567024,
year = {2025},
author = {Ueta, R and Imai, H and Saijo, K and Kawamura, Y and Kodera, S and Ishioka, C},
title = {Influence of Citrobacter freundii on NINJ2 Expression and Oxaliplatin Resistance in Colorectal Cancer.},
journal = {Cancer medicine},
volume = {14},
number = {13},
pages = {e70940},
doi = {10.1002/cam4.70940},
pmid = {40567024},
issn = {2045-7634},
support = {JP22K07293//Japan Society for the Promotion of Science/ ; },
mesh = {*Oxaliplatin/pharmacology/therapeutic use ; Humans ; *Colorectal Neoplasms/drug therapy/genetics/pathology/microbiology/metabolism ; *Citrobacter freundii ; Animals ; *Drug Resistance, Neoplasm/genetics ; Mice ; Cell Line, Tumor ; Xenograft Model Antitumor Assays ; Apoptosis/drug effects ; Gene Expression Regulation, Neoplastic/drug effects ; *Antineoplastic Agents/pharmacology ; Reactive Oxygen Species/metabolism ; Mice, Nude ; Female ; Mice, Inbred BALB C ; },
abstract = {BACKGROUND: Oxaliplatin, a third-generation platinum-based chemotherapeutic agent, is widely used in the treatment of colorectal cancer (CRC). However, some patients do not respond effectively to oxaliplatin, and intrinsic resistance to the drug poses a significant challenge. Recent studies have revealed an association between the gut microbiome and the progression of CRC. We hypothesized that Citrobacter freundii, a component of the gut microbiome, contributes to oxaliplatin resistance by regulating specific gene expression in CRC cells.

METHODS: A bacterial culture filtrate from Citrobacter freundii was employed in the experiments. The CRC cell line RKO, following exposure to this filtrate, was analyzed using high-throughput RNA sequencing. Candidate genes were identified through MTT assays, siRNA knockdown, and overexpression experiments. Apoptosis and reactive oxygen species (ROS) assays were performed to investigate the underlying mechanisms. Finally, a xenograft mouse model was used to evaluate oxaliplatin resistance in vivo.

RESULTS: Exposure to bacterial culture filtrate from Citrobacter freundii induced oxaliplatin resistance in RKO cells with downregulation of the NINJ2 gene as a possible molecular mechanism. ReducedNINJ2 gene expression suppressed oxaliplatin-induced apoptosis and ROS generation. A tendency toward reduced oxaliplatin efficacy was observed in vivo when NINJ2 gene expression was suppressed.

CONCLUSION: This study demonstrates that Citrobacter freundii promotes oxaliplatin resistance in CRC through downregulation of NINJ2 gene. NINJ2 gene may serve as a predictive biomarker and therapeutic target to overcome oxaliplatin resistance in CRC.},
}

*Oxaliplatin/pharmacology/therapeutic use
Humans
*Colorectal Neoplasms/drug therapy/genetics/pathology/microbiology/metabolism
*Citrobacter freundii
Animals
*Drug Resistance, Neoplasm/genetics
Mice
Cell Line, Tumor
Xenograft Model Antitumor Assays
Apoptosis/drug effects
Gene Expression Regulation, Neoplastic/drug effects
*Antineoplastic Agents/pharmacology
Reactive Oxygen Species/metabolism
Mice, Nude
Female
Mice, Inbred BALB C

@article {pmid40566930,
year = {2025},
author = {Liu, Q and Wu, Y and Fan, Q and Liu, J and Chen, Y and He, Y and Wei, W and Zhang, H and Zhao, Y and He, Y and Du, X and Guo, J},
title = {Oral Nanoarmored Live Bacterial Biotherapeutics Bearing Polyphenol-Based Supraparticles Enhance Chemotherapy via Reestablishing Immuno-Oncology-Microbiome Axis.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.5c01158},
pmid = {40566930},
issn = {1936-086X},
abstract = {The immuno-oncology-microbiome (IOM) axis, referring to the gut microbiota-regulated immune interactions on the tumor microenvironment and systemic immunity, is essential for cancer therapies. However, the cytotoxicity of chemotherapeutic agents (Chemos) disrupts the gut microbiota- and gut microbiota-manipulated IOM axis, further diminishing the therapeutic efficacy. Here, we developed oral nanoarmored live bacterial biotherapeutics (supraLBT), to reshape the tumor microenvironment and enhance chemotherapy via reestablishing the IOM axis. The cyto-adhesive polyphenol-based supraparticles, made from green tea polyphenol and food-grade milk protein, attached on microbes (Escherichia coli Nissle1917, EcN) resisted a range of clinically relevant Chemos via phenolic-mediated noncovalent interactions, enhancing supraLBT survival by 27-fold compared with bare EcN. SupraLBT restored the intestinal microbiota and the disrupted IOM axis, thereby reducing the infiltration of regulatory T cells, increasing the recruitment of cytotoxic CD8[+] T cells to the tumor bed, and further inhibiting tumor proliferation and demonstrating enhanced systemic immune responses. Notably, oral supraLBT combined with chemotherapy (doxorubicin) exhibited 2.35-fold greater tumor regression than that of doxorubicin alone, indicating that oral supraLBT can enhance the chemotherapeutic effect. Further investigations revealed that supraLBT reprogrammed the immune tumor microenvironment by upregulating antitumor cytokines and altering the gut microbial composition. Given the intricate interplay between gut microbiota, host immune system, and tumor microenvironment, this work presents a facile and biomaterial-engineered microorganism-based strategy to enhance the synergistic immuno-chemotherapy effects.},
}

@article {pmid40566601,
year = {2025},
author = {Bednarek, K and Wszołek, K and Szewc, M and Gałęcka, M and Mruczyński, A and Bruszewski, A and Wierzchowski, M and Wilczak, M and Chmaj-Wierzchowska, K},
title = {Microbiota of Cervical Canal in Nine Patients Diagnosed with Ectopic Pregnancy: Case Series.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/life15060949},
pmid = {40566601},
issn = {2075-1729},
abstract = {Dysbiosis, or an altered microbiota composition, has been implicated in chronic endometrial inflammation and recurrent implantation failure. Despite growing research on the relationship between the genital microbiome and reproductive health, few studies have examined its role in ectopic pregnancy. Therefore, our study focuses on the microbiota of the cervical canal in women diagnosed with an ectopic pregnancy. Material and methods: The study group consisted of nine women of a reproductive age who were hospitalized at the Department of Maternal and Child Health, Gynecology and Obstetrics, Clinical Hospital of the University of Poznań, between February and September 2023. In nine patients, an ectopic pregnancy was diagnosed based on a transvaginal ultrasound examination. The swabs were collected for quantitative microbiological culture (using Amies transport medium). The microbiological analyses involved quantitative culture on selected selective and differential media, following the Standard Operating Procedure developed by the Institute of Microecology. Results: A reduced Lactobacillus spp. count (≤5 × 10[7] CFU/mL) was observed in 78% of the patients participating in the study, including those that produce H2O2, i.e., with strong protective properties for the environment of the female reproductive tract. The molecular analyses revealed Ureaplasma spp. (U. parvum and U. urealyticum) in 33% of the samples (three patients). However, Chlamydia trachomatis and Mycoplasma genitalium were not detected in any of the analyzed samples. Conclusions: The ease of obtaining material and the minimally invasive nature of lower reproductive tract examinations may allow for the evaluation of microbiota imbalances, helping to identify individuals at an increased risk of reproductive complications.},
}

@article {pmid40566568,
year = {2025},
author = {Papakonstantinou, A and Moustakli, E and Potiris, A and Zikopoulos, A and Tsarna, E and Christodoulaki, C and Tsakiridis, I and Dagklis, T and Panagopoulos, P and Drakakis, P and Stavros, S},
title = {Behind-the-Scenes Actors in Fertility: A Comprehensive Review of the Female Reproductive Tract Microbiome and Its Clinical Relevance.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/life15060916},
pmid = {40566568},
issn = {2075-1729},
abstract = {The study of the microbiome has rapidly progressed over the past few decades, capturing the interest of both scientists and the general public. Nevertheless, there is still no widely agreed-upon definition for the term "microbiome" despite tremendous advances in our knowledge. The international scientific literature consistently underscores the difference between the human microbiome and human microbiota. Recent research has emphasized the importance of the female reproductive tract microbiome in fertility, impacting natural conception and assisted reproductive technologies (ARTs). This review explores the relationship between infertility and the microbiota of the female reproductive tract through a thorough evaluation of research papers and large-scale studies published up to 2024. The objective of this review is to critically assess current evidence on the role of the reproductive tract microbiome in female infertility and ART outcomes. Relevant papers were identified and analyzed through the electronic medical databases PubMed/MEDLINE and Scopus. A comprehensive synthesis of data from 36 original studies was performed, including observational, case-control, cohort, and randomized trials. By focusing on the vagina, cervix, and endometrium, this study offers a comprehensive overview of the microbiome throughout the female reproductive tract. RIF and poor reproductive outcomes are strongly linked to dysbiosis, which is characterized by a reduction in Lactobacillus species. Lactobacillus crispatus, in particular, plays a significant role in protecting against bacterial vaginosis and infertility. A thorough understanding of how the microbiome impacts fertility and the development of clinical strategies to improve reproductive outcomes requires standardized microbiome investigation techniques and larger, randomized trials that account for diverse patient characteristics.},
}

@article {pmid40566488,
year = {2025},
author = {Borrego-Ruiz, A and Borrego, JJ},
title = {The Bidirectional Interplay Between Substances of Abuse and Gut Microbiome Homeostasis.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/life15060834},
pmid = {40566488},
issn = {2075-1729},
abstract = {Specific gut microorganisms and their metabolic by-products have been identified as key regulators of host physiology, contributing to the modulation of the immune system, inflammatory processes, brain function, and behavior, which highlights the gut microbiome as a potential modulator of the neurobiological mechanisms involved in substance use disorders. This narrative review provides an updated overview of how drugs of abuse influence the composition and dynamics of the human gut microbiome and how bacterial dysbiosis may be a contributing factor to substance use disorders by modulating the communication between the gut and the brain. Thus, by examining commonly abused substances such as alcohol, psychostimulants, opioids, cannabinoids, and nicotine, this review aimed to deepen the understanding of the bidirectional relationship between the gut microbiome and substance use. There is evidence indicating that gut microbiome alterations may influence addiction through changes in gut-brain signaling. Furthermore, changes in the gut microbiome and its metabolites may not only result from substance use disorders, but could also modulate behavioral responses to drugs of abuse. Although the exact mechanisms by which the gut microbiome modulates behavioral responses to drugs of abuse are not fully understood, microbial products such as short-chain fatty acids, tryptophan metabolites, bile acids, and neurotransmitters have been suggested to play a role in this process by influencing the blood-brain barrier permeability, host immune activation, neural signaling, and gene expression. Therefore, manipulating the gut microbiome or its by-products may represent a promising approach for enhancing substance use disorder treatments, identifying individuals at increased risk of pathological drug use, and elucidating its role in substance-related behaviors.},
}

@article {pmid40565936,
year = {2025},
author = {Grafanaki, K and Maniatis, A and Anastogianni, A and Bania, A and Pasmatzi, E and Stathopoulos, C},
title = {Nutrition and Diet Patterns as Key Modulators of Metabolic Reprogramming in Melanoma Immunotherapy.},
journal = {Journal of clinical medicine},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/jcm14124193},
pmid = {40565936},
issn = {2077-0383},
abstract = {Background: Melanoma, one of the most aggressive forms of skin cancer, has seen significant therapeutic advances with immune checkpoint inhibitors (ICIs). However, many patients fail to respond or develop resistance, creating the need for adjunct strategies. Objective: The objective of this study is to critically evaluate how specific dietary patterns and nutrient-derived metabolites modulate melanoma metabolism and immunotherapy outcomes, emphasizing translational implications. Methods: We performed an integrative review of preclinical and clinical studies investigating dietary interventions in melanoma models and ICI-treated patients. Mechanistic insights were extracted from studies on nutrient transport, immunometabolism, and microbiome-immune interactions, including data from ongoing nutritional clinical trials. Results: Diets rich in fermentable fibers, plant polyphenols, and unsaturated lipids, such as Mediterranean and ketogenic diets, seem to contribute to the reprogramming of tumor metabolism and enhance CD8+ T-cell activity. Fasting-mimicking and methionine-restricted diets modulate T-cell fitness and tumor vulnerability via nutrient stress sensors (e.g., UPR, mTOR). High fiber intake correlates with favorable gut microbiota and improved ICI efficacy, while excess protein, methionine, or refined carbohydrates impair immune surveillance via lactate accumulation and immunosuppressive myeloid recruitment. Several dietary molecules act as network-level modulators of host and microbial proteins, with parallels to known drug scaffolds. Conclusions: Integrating dietary interventions into melanoma immunotherapy can significantly influence metabolic reprogramming by targeting metabolic vulnerabilities and reshaping the tumor-immune-microbiome axis. When combined with AI-driven nutrient-protein interaction mapping, this approach offers a precision nutrition paradigm that supports both physicians and patients, emerging as a novel layer to enhance and consolidate existing therapeutic strategies.},
}

@article {pmid40565688,
year = {2025},
author = {Yang, X and Kang, X and Li, L and Zhang, S},
title = {Highland Barley Tartary Buckwheat Coarse Grain Biscuits Ameliorated High-Fat Diet-Induced Hyperlipidaemia in Mice Through Gut Microbiota Modulation and Enhanced Short-Chain Fatty Acid Secretion Mice.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/foods14122079},
pmid = {40565688},
issn = {2304-8158},
abstract = {Dietary modification plays a crucial role in managing and preventing hyperlipidemia. This study examined the combination of highland barley, tartary buckwheat, mung beans, Ormosia hosiei, black rice, and corn germ oil in multi-grain biscuit form. This formulation leverages the synergistic interactions among bioactive compounds, which exert preventive and therapeutic effects against lipid disorders. C57BL/6N mice were fed a high-fat diet for 12 weeks to establish a hyperlipidemia model, followed by feeding with highland barley tartary buckwheat coarse-grain biscuits for 4 weeks. The experimental outcomes revealed that the highland barley tartary buckwheat coarse-grain biscuits effectively controlled body weight and reduced fasting blood sugar levels: body weight was restored to approximately 29 g, and the fasting blood sugar level returned to the normal range of 6 mmol/L. We also observed improved organ indices and regulated blood lipids in hyperlipidemic mice. The total cholesterol of high-fat mice was reduced to 5 mmol/L and the triglyceride level to 1 mmol/L. A significant reduction in inflammatory markers and histopathological improvement in hepatic and adipose tissues were also observed. The intervention enhanced leptin and adiponectin secretion while elevating concentrations of acetic, propionic, butyric, valeric, and caproic acids. Microbiome analysis demonstrated favorable shifts in bacterial populations, characterized by increased Bacteroidetes and Verrucomicrobia abundance and a decreased Firmicutes-to-Proteobacteria ratio, promoting beneficial genera while suppressing potentially pathogenic taxa. These findings suggest that the developed highland barley tartary buckwheat coarse-grain biscuits are a promising dietary intervention for hyperlipidemia management. The effects were potentially mediated through gut microbiota modulation and enhanced short-chain fatty acid production. This research provides novel insights into functional food development for hyperlipidemia.},
}

@article {pmid40565559,
year = {2025},
author = {Vohra, J and Barbosa, G and Pascoal, LB and Reis, LO},
title = {Advances in Genitourinary Tumor Genomics and Immunotherapy.},
journal = {Genes},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/genes16060667},
pmid = {40565559},
issn = {2073-4425},
support = {304747/2018-1//National Council for Scientific and Technological Development/ ; 310135/2022-2//National Council for Scientific and Technological Development/ ; },
mesh = {Humans ; *Immunotherapy/methods ; *Genomics/methods ; *Urogenital Neoplasms/genetics/therapy/immunology ; Precision Medicine ; },
abstract = {Advancements in immune monitoring and modulation technologies are driving transformative changes in cancer immunotherapy. These innovations are crucial for assessing patient-specific immune responses, enabling more accurate predictions of therapeutic efficacy and enhancing treatment outcomes. This review provides a comprehensive overview of current technologies used in immune monitoring, such as flow cytometry, single-cell RNA sequencing, and multiplex cytokine profiling. It also explores cutting-edge immune modulation methods, such as biomaterials that activate immune cells and genetically engineered cell-based therapies. We examine the strengths and limitations of these techniques and identify areas where further progress is needed. In particular, we explore how personalized therapies, real-time monitoring systems, and artificial intelligence shape the future of immune-based treatments. Through a comparative analysis of existing platforms and emerging solutions, this paper underscores the importance of integrating diverse scientific approaches-from immunology and bioengineering to data science-in advancing safer, more effective cancer treatments. This interdisciplinary approach promises to enhance the precision and accessibility of immune-based therapies, offering new hope for improved cancer care.},
}

Humans
*Immunotherapy/methods
*Genomics/methods
*Urogenital Neoplasms/genetics/therapy/immunology
Precision Medicine

@article {pmid40565444,
year = {2025},
author = {Wang, X and Sun, Z and Xue, H and An, R},
title = {Artificial Intelligence Applications to Personalized Dietary Recommendations: A Systematic Review.},
journal = {Healthcare (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/healthcare13121417},
pmid = {40565444},
issn = {2227-9032},
abstract = {Background/Objectives: Personalized dietary recommendations are essential for managing chronic conditions such as diabetes and irritable bowel syndrome (IBS). However, traditional approaches often fall short in accounting for individual metabolic variability. This systematic review evaluates the effectiveness of artificial intelligence (AI)-generated dietary interventions in improving clinical outcomes among adults. Methods: Following PRISMA guidelines, we searched six electronic databases for peer-reviewed studies published between 19 November 2015 to 6 September 2024. Eligible studies included adults aged 18 to 91 who received AI-generated dietary recommendations based on biomarkers such as blood glucose, gut microbiome composition, and self-reported data. Study designs included randomized controlled trials (RCTs), pre-post studies, and cross-sectional analyses. The GRADE system was used to assess the quality of evidence. Results: Eleven studies met inclusion criteria (five RCTs, five pre-post designs, one cross-sectional). Most AI methods used in the included studies were based on machine learning (ML), including conventional ML algorithms, deep learning (DL), and hybrid approaches integrating ML with IoT-based systems. Interventions led to improved glycemic control, metabolic health, and psychological well-being. Notable outcomes included a 39% reduction in IBS symptom severity and a 72.7% diabetes remission rate. Among nine studies with comparison groups, six reported statistically significant improvements in AI groups, two found comparable or better outcomes, and one found no difference. Mild side effects such as fatigue and constipation were observed. Conclusions: AI-generated dietary interventions show promise in surpassing traditional approaches by providing personalized, data-driven recommendations. Further research is needed to validate long-term effects, refine intervention protocols, and enhance user adherence in both clinical and public health settings.},
}

@article {pmid40565331,
year = {2025},
author = {Karasalih, B and Duman, H and Bechelany, M and Karav, S},
title = {Osteopontin: Its Properties, Recent Studies, and Potential Applications.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125868},
pmid = {40565331},
issn = {1422-0067},
mesh = {*Osteopontin/metabolism/chemistry/genetics ; Humans ; Animals ; Gastrointestinal Microbiome ; Neoplasms/metabolism ; },
abstract = {OPN is a phosphorylated glycoprotein found in all vertebrate organisms and expressed in many tissues and secretions. It is a pleiotropic protein that plays diverse roles in various pathological and physiological processes. OPN is involved in many tissue transformation events such as intestinal and brain development, the regulation of immune system activity, immune cell activation, and inflammatory responses. This protein increases the functionality of the digestive system by regulating the intestinal microbiome and may help strengthen the intestinal barrier. OPN can also influence cognitive development and behavior. In addition, its recent association with cancer has gained critical importance. The increased expression of OPN has been observed in many cancer types, which may promote tumor cell metastasis. OPN is also effective in bacterial interaction and infections; it can prevent bacterial adhesion, supporting the development of new therapeutic approaches for oral care. Furthermore, the supplementation of OPN in infant formula has positively influenced the immune and intestinal health of infants. Many recent studies have focused on these aspects. This article provides a review and comparison of the existing knowledge on the structure and functions of OPN. It emphasizes how milk-derived OPN impacts human and infant health and disease.},
}

*Osteopontin/metabolism/chemistry/genetics
Humans
Animals
Gastrointestinal Microbiome
Neoplasms/metabolism

@article {pmid40565291,
year = {2025},
author = {Uceda, S and Reiriz, M and Echeverry-Alzate, V and Beltrán-Velasco, AI},
title = {The Interplay Between Exosomes and Gut Microbiota in Neuroinflammation: A New Frontier in Alzheimer's Disease.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125828},
pmid = {40565291},
issn = {1422-0067},
mesh = {Humans ; *Alzheimer Disease/metabolism/microbiology/pathology/etiology ; *Exosomes/metabolism ; *Gastrointestinal Microbiome ; Animals ; *Neuroinflammatory Diseases/metabolism/microbiology ; Dysbiosis ; Biomarkers/metabolism ; },
abstract = {Alzheimer's disease (AD) is a complex neurodegenerative condition that is characterized by the accumulation of amyloid-β, the hyperphosphorylation of tau, and persistent neuroinflammation. However, these hallmarks alone do not fully capture the intricacies of AD pathology, thus necessitating the investigation of emerging mechanisms and innovative tools. Exosomes (nanoscale vesicles involved in cell communication and immune modulation) have emerged as pivotal cellular vehicles due to their dual role-both in the propagation of pathological proteins and the regulation of inflammatory responses. Furthermore, these vesicles have been demonstrated to play a crucial role in the mediation of the effects of microbiota-derived metabolites and the reflection of systemic influences such as dysbiosis, thereby establishing a link between the gut-brain axis and the progression of AD. A comprehensive narrative literature review was conducted using the following databases: ScienceDirect, Scopus, Wiley, Web of Science, Medline, and PubMed, covering studies published between 2015 and 2025. Inclusion and exclusion criteria were established to select research addressing exosomal biogenesis, their functional and diagnosis role, their therapeutic potential, and the emerging evidence on microbiota-exosome interplay in Alzheimer's disease. Exosomes have been identified as integral mediators of intercellular communication, reflecting the molecular state of the central nervous system. These particles have been shown to promote the propagation of pathological proteins, modulate neuroinflammatory responses, and serve as non-invasive biomarkers due to their detectability in peripheral fluids. Advances in exosomal engineering and microbiome-based interventions underscore the potential for targeting systemic and CNS-specific mechanisms to develop integrative therapies for AD. Exosomes present a promising approach for the early diagnosis and personalized treatment of Alzheimer's disease. However, methodological challenges and ongoing controversies, including those related to the influence of systemic factors such as dysbiosis, necessitate multidisciplinary research to optimize and standardize these strategies.},
}

Humans
*Alzheimer Disease/metabolism/microbiology/pathology/etiology
*Exosomes/metabolism
*Gastrointestinal Microbiome
Animals
*Neuroinflammatory Diseases/metabolism/microbiology
Dysbiosis
Biomarkers/metabolism

@article {pmid40565274,
year = {2025},
author = {Zhang, M and Dong, C},
title = {Molecular Mechanisms of Cadmium Stress Resistance in Vegetable Crops.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125812},
pmid = {40565274},
issn = {1422-0067},
support = {2023YFD2300704//the National Key R&D Program of China/ ; 32372795//the National Natural Science Foundation of China/ ; CAAS-ASTIP-IVFCAAS//the Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences/ ; CAAS-ZDRW202302//the Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences/ ; },
mesh = {*Cadmium/toxicity ; *Stress, Physiological/drug effects ; *Crops, Agricultural/genetics/drug effects/metabolism ; *Vegetables/drug effects/genetics/metabolism/growth & development ; Gene Expression Regulation, Plant/drug effects ; Plant Growth Regulators/metabolism ; Oxidative Stress/drug effects ; Plant Proteins/genetics/metabolism ; },
abstract = {Cadmium (Cd) stress poses significant threats to vegetable crops, impacting their growth, physiological processes, and safety as part of the human food chain. This review systematically summarizes the latest advances in the molecular mechanisms of vegetable crops' resistance to Cd stress. First, physiological and biochemical responses are outlined, including growth inhibition, impaired photosynthesis, oxidative stress, disrupted nutrient absorption, altered phytohormone levels, and gene expression changes. Next, key molecular mechanisms are discussed, focusing on the roles of transporter-related genes (e.g., NRAMP, HIPP, ABCG), transcription factors (e.g., HsfA1a, WRKY, ERF), enzyme-related genes (e.g., E3 ubiquitin ligase, P-type ATPase), microRNAs (e.g., miR398), and potential functional genes in Cd uptake, translocation, and detoxification. Additionally, the regulatory roles of phytohormones and their analogues (e.g., brassinosteroids, gibberellin, salicylic acid) in mitigating Cd toxicity are analyzed, highlighting their involvement in antioxidant defense, gene regulation, and stress signaling pathways. Finally, future research directions are proposed, emphasizing species-specific defense mechanisms, root hair-specific Cd exclusion mechanisms, and interdisciplinary approaches integrating AI and microbiome manipulation. This review provides a comprehensive reference for enhancing Cd stress resistance in vegetable crops and promoting safe crop production.},
}

*Cadmium/toxicity
*Stress, Physiological/drug effects
*Crops, Agricultural/genetics/drug effects/metabolism
*Vegetables/drug effects/genetics/metabolism/growth & development
Gene Expression Regulation, Plant/drug effects
Plant Growth Regulators/metabolism
Oxidative Stress/drug effects
Plant Proteins/genetics/metabolism

@article {pmid40565268,
year = {2025},
author = {Dragomanova, S and Kalfin, R and Tancheva, L and Mehan, S and Stanciu, D and Panaiotov, S},
title = {Pathological Alterations in Human Blood Microbiome-An Updated Review.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125807},
pmid = {40565268},
issn = {1422-0067},
support = {KΠ-06-H73/5-05.12.2023//National Science Fund, Sofia, Bulgaria./ ; },
mesh = {Humans ; *Microbiota ; Cardiovascular Diseases/microbiology/blood ; Metabolic Diseases/microbiology/blood ; },
abstract = {The main source of microorganisms in the blood is the intestinal and oral microflora through the route of atopobiosis. It is clear that the blood microbiome undergoes significant changes in response to various pathological conditions within the human body. In this review, we summarized data from studies of the human blood microbiome in diseases of the nervous system and cardiovascular, respiratory, liver, kidney, and metabolite disorders. Links between the blood microbiome and the above mentioned diseases are demonstrated. In support of this understanding, it is evident that analogous alterations in microbiome composition occur across various disease categories; however, the microbial signatures associated with the blood microbiome exhibit specificity. For instance, an elevated abundancy of Proteobacteria has been identified in cardiovascular, renal, and metabolic disorders. Conversely, while Firmicutes are found to be abundant in renal and metabolic conditions, their levels are diminished in cardiovascular diseases. Additionally, patients suffering from respiratory and liver ailments typically show a heightened presence of Bacteroidetes; notably, Flavobacterium is prevalent in respiratory diseases, whereas Enterobacteriaceae is associated with liver diseases. Hence, the human blood microbiome could be considered as a potential biomarker in certain diseases.},
}

Humans
*Microbiota
Cardiovascular Diseases/microbiology/blood
Metabolic Diseases/microbiology/blood

@article {pmid40565258,
year = {2025},
author = {Duda-Madej, A and Viscardi, S and Stecko, J and Szymańska, N and Topola, E and Pacyga, K and Szandruk-Bender, M},
title = {Can Nature Overcome Invasive Gastrointestinal Infections?.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125795},
pmid = {40565258},
issn = {1422-0067},
mesh = {Humans ; Gastrointestinal Microbiome/drug effects ; Animals ; *Gastrointestinal Diseases/drug therapy/microbiology ; *Alkaloids/therapeutic use/pharmacology ; *Bacterial Infections/drug therapy/microbiology ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Intestinal Mucosa/microbiology/drug effects ; },
abstract = {Invasive bacterial gastrointestinal infections represent a substantial clinical burden worldwide, contributing to significant morbidity and, in severe cases, mortality. The causative bacterial agents of these infections include Shigella spp., enteroinvasive Escherichia coli, Salmonella spp., Campylobacter jejuni, Yersinia enterocolitica, and Listeria monocytogenes. Given the growing challenges of therapy failures and rising antibiotic resistance, there is still an unmet need to identify novel, effective, and safe compounds exhibiting antimicrobial, anti-inflammatory, and immunomodulatory activities. In the present review, we aimed to compile current data regarding three alkaloids-berberine, sanguinarine, and cheleritrin-which hold significant promise in treating bacterial invasive gastrointestinal diseases. Our review extended beyond the direct antimicrobial properties of these compounds against pathogens capable of breaching the intestinal epithelial barrier. We also presented their modulatory effects on intestinal barrier integrity and their influence on the composition and function of the resident gut microbiota, thereby highlighting their potential indirect role in attenuating pathogen invasion and disease progression. Thus, our review presents alkaloids as potential preparations that potentiate the activity of classic anti-infective drugs, as well as substances that, by affecting the microbiome and intestinal mucosa, could be used for inflammatory bowel diseases.},
}

Humans
Gastrointestinal Microbiome/drug effects
Animals
*Gastrointestinal Diseases/drug therapy/microbiology
*Alkaloids/therapeutic use/pharmacology
*Bacterial Infections/drug therapy/microbiology
*Anti-Bacterial Agents/therapeutic use/pharmacology
Intestinal Mucosa/microbiology/drug effects

@article {pmid40565108,
year = {2025},
author = {Tkaczyk, M and Mertas, A and Kuśka-Kiełbratowska, A and Fiegler-Rudol, J and Bobela, E and Cisowska, M and Morawiec, T and Skaba, D and Wiench, R},
title = {In Vitro Evaluation of Candida spp. and Staphylococcus aureus Sensitivity to 450 nm Diode Laser-Mediated Antimicrobial Photodynamic Therapy with Curcumin and Riboflavin.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125645},
pmid = {40565108},
issn = {1422-0067},
mesh = {*Curcumin/pharmacology ; *Photochemotherapy/methods ; *Staphylococcus aureus/drug effects/radiation effects ; *Candida/drug effects/radiation effects ; *Riboflavin/pharmacology ; *Lasers, Semiconductor ; *Photosensitizing Agents/pharmacology ; Microbial Sensitivity Tests ; Microbial Viability/drug effects/radiation effects ; },
abstract = {Oral candidiasis, commonly caused by Candida (C.) albicans and other non-albicans Candida species, increases resistance to conventional antifungal therapies. This study aimed to evaluate the in vitro efficacy of antimicrobial photodynamic therapy (aPDT) using a 450 nm diode laser in combination with curcumin and riboflavin against Candida spp. and Staphylococcus (S.) aureus. Reference strains of C. albicans, C. glabrata, C. krusei, and S. aureus were exposed to aPDT under varying incubation times and laser parameters, then viable microorganism cells (CFU) counts were assessed the microbial reduction, and statistical analyses were performed to evaluate significance. aPDT significantly reduced microbial viability in a time- and dose-dependent manner. Optimal incubation times were 20 min for Candida spp. and 10 min for S. aureus, with the highest efficacy observed at 400 mW and 120 s irradiation. The photosensitizer or laser alone had no significant antimicrobial effect. Curcumin/riboflavin-mediated aPDT is a promising alternative or adjunctive approach to conventional antimicrobial therapy, particularly for resistant oral infections.},
}

*Curcumin/pharmacology
*Photochemotherapy/methods
*Staphylococcus aureus/drug effects/radiation effects
*Candida/drug effects/radiation effects
*Riboflavin/pharmacology
*Lasers, Semiconductor
*Photosensitizing Agents/pharmacology
Microbial Sensitivity Tests
Microbial Viability/drug effects/radiation effects

@article {pmid40565024,
year = {2025},
author = {Mitrović, M and Stanković Popović, V and Erceg, S and Perišić Mitrović, M and Dobrosavljević, A and Stupar, A and Vuković, P and Zlatković, D and Svorcan, P},
title = {Exploring the Potential of Oral Butyrate Supplementation in Metabolic Dysfunction-Associated Steatotic Liver Disease: Subgroup Insights from an Interventional Study.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125561},
pmid = {40565024},
issn = {1422-0067},
mesh = {Humans ; Male ; Female ; Middle Aged ; *Butyric Acid/administration & dosage/therapeutic use ; *Dietary Supplements ; Gastrointestinal Microbiome/drug effects ; *Fatty Liver/drug therapy/metabolism ; Aged ; Adult ; *Butyrates/administration & dosage ; Administration, Oral ; Liver/drug effects/metabolism ; Fatty Acids, Volatile/metabolism ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a common cause of chronic liver disease and is closely associated with metabolic abnormalities and cardiovascular risks. Butyrate, a short-chain fatty acid produced by gut microbiota, has the potential to enhance liver health by modulating inflammation and supporting gut barrier integrity. This study aimed to investigate and compare the effects of sodium butyrate and calcium butyrate in patients with MASLD. In this single-center, randomized clinical trial, 181 patients with MASLD were enrolled and assigned to receive either sodium butyrate (n = 121) or calcium butyrate (n = 60) supplementation at a daily dose of 1000 mg. The primary endpoint was the change in liver steatosis, measured using the Controlled Attenuation Parameter (CAP) via FibroScan[®]. Secondary endpoints included liver stiffness, biochemical parameters, hepatic steatosis and fatty liver indices, fecal calprotectin levels, stool short-chain fatty acid levels, and microbiome composition. A subgroup analysis compared responders (a ≥ 5% reduction in CAP) to non-responders. There were no significant changes in CAP values for either group (ΔCAP: sodium butyrate, 0.84; calcium butyrate, -0.23; p = 0.70). Sodium butyrate significantly reduced serum trimethylamine N-oxide and fatty liver index, while calcium butyrate led to a decrease in fecal calprotectin levels. Responders demonstrated a lower body mass index, higher levels of high-sensitivity C-reactive protein and HbA1c, and distinct microbiome profiles, characterized by lower abundance of Subdoligranulum and higher abundance of Catenibacterium. Although butyrate supplementation did not significantly improve liver steatosis as measured by CAP, the differing effects on metabolic and inflammatory markers suggest that there may be potential benefits for specific subgroups of patients with MASLD.},
}

Humans
Male
Female
Middle Aged
*Butyric Acid/administration & dosage/therapeutic use
*Dietary Supplements
Gastrointestinal Microbiome/drug effects
*Fatty Liver/drug therapy/metabolism
Aged
Adult
*Butyrates/administration & dosage
Administration, Oral
Liver/drug effects/metabolism
Fatty Acids, Volatile/metabolism

@article {pmid40564985,
year = {2025},
author = {Jannati, S and Patel, A and Patnaik, R and Banerjee, Y},
title = {Oleocanthal as a Multifunctional Anti-Cancer Agent: Mechanistic Insights, Advanced Delivery Strategies, and Synergies for Precision Oncology.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125521},
pmid = {40564985},
issn = {1422-0067},
mesh = {Humans ; *Antineoplastic Agents/pharmacology/therapeutic use/chemistry ; *Neoplasms/drug therapy/metabolism ; Precision Medicine/methods ; Animals ; *Cyclopentane Monoterpenes/pharmacology/therapeutic use/chemistry ; *Aldehydes/pharmacology/chemistry/therapeutic use ; Drug Delivery Systems ; Phenols ; },
abstract = {Oleocanthal (OC), a secoiridoid phenolic compound exclusive to extra virgin olive oil (EVOO), has emerged as a promising nutraceutical with multifaceted anti-cancer properties. Despite its well-characterized anti-inflammatory and antioxidant effects, the mechanistic breadth and translational potential of OC in oncology remain underexplored and fragmented across the literature. This comprehensive review synthesizes and critically analyzes recent advances in the molecular, pharmacological, and translational landscape of OC's anti-cancer activities, providing an integrative framework to bridge preclinical evidence with future clinical application. We delineate the pleiotropic mechanisms by which OC modulates cancer hallmarks, including lysosomal membrane permeabilization (LMP)-mediated apoptosis, the inhibition of key oncogenic signaling pathways (c-MET/STAT3, PAR-2/TNF-α, COX-2/mPGES-1), the suppression of epithelial-to-mesenchymal transition (EMT), angiogenesis, and metabolic reprogramming. Furthermore, this review uniquely highlights the emerging role of OC in modulating drug resistance mechanisms by downregulating efflux transporters and sensitizing tumors to chemotherapy, targeted therapies, and immunotherapies. We also examine OC's bidirectional interaction with gut microbiota, underscoring its systemic immunometabolic effects. A major unmet need addressed by this review is the lack of consolidated knowledge regarding OC's pharmacokinetic limitations and drug-drug interaction potential in the context of polypharmacy in oncology. We provide an in-depth analysis of OC's poor bioavailability, extensive first-pass metabolism, and pharmacogenomic interactions, and systematically compile preclinical evidence on advanced delivery platforms-including nanocarriers, microneedle systems, and peptide-drug conjugates-designed to overcome these barriers. By critically evaluating the mechanistic, pharmacological, and translational dimensions of OC, this review advances the field beyond isolated mechanistic studies and offers a strategic blueprint for its integration into precision oncology. It also identifies key research gaps and outlines the future directions necessary to transition OC from a nutraceutical of dietary interest to a viable adjunctive therapeutic agent in cancer treatment.},
}

Humans
*Antineoplastic Agents/pharmacology/therapeutic use/chemistry
*Neoplasms/drug therapy/metabolism
Precision Medicine/methods
Animals
*Cyclopentane Monoterpenes/pharmacology/therapeutic use/chemistry
*Aldehydes/pharmacology/chemistry/therapeutic use
Drug Delivery Systems
Phenols

@article {pmid40564914,
year = {2025},
author = {Wong, JKC and Patel, BK and Tai, YK and Tan, TZ and Khine, WWT and Chen, WC and Kukumberg, M and Ching, J and Lee, LS and Chua, KV and Tan, TY and Wu, KY and Bai, X and Iversen, JN and Purnamawati, K and Abdul Jalil, R and Kumar, AP and Lee, YK and Moochhala, SM and Franco-Obregón, A},
title = {Fecal Microbiota Transplantation from Mice Receiving Magnetic Mitohormesis Treatment Reverses High-Fat Diet-Induced Metabolic and Osteogenic Dysfunction.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125450},
pmid = {40564914},
issn = {1422-0067},
support = {A-0001177-01-00//iHealthtech Microbiome in Health, Disease and Aging 2018 Joint Research Grant/ ; MOE-T2EP30120-0016//Ministry of Education/ ; NUHSRO/2023/039/RO5+6/Seed-Mar/04//National University Health System/ ; },
mesh = {Animals ; *Diet, High-Fat/adverse effects ; Mice ; *Fecal Microbiota Transplantation/methods ; Male ; *Osteogenesis ; Mice, Inbred C57BL ; Ceramides/metabolism ; Gastrointestinal Microbiome ; *Magnetic Field Therapy/methods ; Liver/metabolism ; *Metabolic Diseases/therapy/etiology/metabolism ; Bone Density ; },
abstract = {This study compared the metabolic consequences of fecal microbiota transplantation (FMT) from donor mice that had been either administered pulsed electromagnetic field (PEMF) therapy or exercised to recipient mice fed a high-fat diet (HFD). Eight weeks of PEMF treatment (10 min/week) enhanced PGC-1α-associated mitochondrial and metabolic gene expression in white and brown adipose to a greater degree than eight weeks of exercise (30-40 min/week). FMT from PEMF-treated donor mice recapitulated these adipogenic adaptations in HFD-fed recipient mice more faithfully than FMT from exercised donors. Direct PEMF treatment altered hepatic phospholipid composition, reducing long-chain ceramides (C16:0) and increasing very long-chain ceramides (C24:0), which could be transferred to PEMF-FMT recipient mice. FMT from PEMF-treated mice was also more effective at recovering glucose tolerance than FMT from exercised mice. PEMF treatment also enhanced bone density in both donor and HFD recipient mice. The gut Firmicutes/Bacteroidetes (F/B) ratio was lowest in both the directly PEMF-exposed and PEMF-FMT recipient mouse groups, consistent with a leaner phenotype. PEMF treatment, either directly applied or via FMT, enhanced adipose thermogenesis, ceramide levels, bone density, hepatic lipids, F/B ratio, and inflammatory blood biomarkers more than exercise. PEMF therapy may represent a non-invasive and non-strenuous method to ameliorate metabolic disorders.},
}

Animals
*Diet, High-Fat/adverse effects
Mice
*Fecal Microbiota Transplantation/methods
Male
*Osteogenesis
Mice, Inbred C57BL
Ceramides/metabolism
Gastrointestinal Microbiome
*Magnetic Field Therapy/methods
Liver/metabolism
*Metabolic Diseases/therapy/etiology/metabolism
Bone Density

@article {pmid40564903,
year = {2025},
author = {Chung, BS and Yang, K and Park, C and Ryu, T},
title = {Prolonged Intestinal Ethanol Absorption and Oxidative Stress: Revisiting the Gut-Liver Axis in Alcohol-Associated Disease.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125442},
pmid = {40564903},
issn = {1422-0067},
support = {RS-2023-00238039//National Research Foundation of Korea/ ; },
mesh = {Humans ; *Oxidative Stress/drug effects ; *Ethanol/pharmacokinetics/metabolism ; *Intestinal Absorption ; Animals ; *Liver/metabolism/drug effects ; Gastrointestinal Microbiome ; *Liver Diseases, Alcoholic/metabolism ; Intestinal Mucosa/metabolism ; *Alcoholism/metabolism ; Dysbiosis ; },
abstract = {Chronic alcohol consumption induces oxidative stress not only in the liver but also in the gastrointestinal tract, where prolonged intestinal ethanol absorption plays a pivotal and underrecognized role. This review reframes ethanol pharmacokinetics to emphasize sustained jejunal and ileal uptake, which maintains elevated blood alcohol levels and perpetuates redox imbalance across the gut-liver axis. We integrate recent findings on ethanol-induced barrier dysfunction, CYP2E1-mediated ROS production, microbial dysbiosis, and mitochondrial disruption, proposing that the intestine is an active site of injury and a driver of systemic inflammation. Key mechanistic insights reveal that gut-derived endotoxins, compromised epithelial integrity, and microbiome-mitochondria interactions converge to exacerbate hepatic and extrahepatic damage. We further explore emerging therapeutic strategies-ranging from NAD[+] repletion and probiotics to fecal microbiota transplantation-that target this upstream pathology. Recognizing prolonged intestinal ethanol absorption as a clinically meaningful phase offers new directions for early intervention and redox-based treatment in alcohol-associated disease.},
}

Humans
*Oxidative Stress/drug effects
*Ethanol/pharmacokinetics/metabolism
*Intestinal Absorption
Animals
*Liver/metabolism/drug effects
Gastrointestinal Microbiome
*Liver Diseases, Alcoholic/metabolism
Intestinal Mucosa/metabolism
*Alcoholism/metabolism
Dysbiosis

@article {pmid40564803,
year = {2025},
author = {Kunnathodi, F and Arafat, AA and Alhazzani, W and Mustafa, M and Azmi, S and Ahmad, I and Selan, JS and Anvarbatcha, R and Alotaibi, HF},
title = {Unraveling the Genetic Architecture of Obesity: A Path to Personalized Medicine.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/diagnostics15121482},
pmid = {40564803},
issn = {2075-4418},
abstract = {Obesity is a global health challenge characterized by significant heterogeneity in causes and treatment responses, complicating sustainable management. This narrative review explores the genomic architecture of obesity and its implications for personalized interventions, focusing on how genetic variations influence key biological pathways and treatment outcomes. A comprehensive literature search, guided by the authors' expertise, was conducted to identify key publications on the genomics of obesity and personalized approaches. The selection of articles prioritized those that provided direct insights into the genomic basis of obesity and its potential for informing tailored strategies. Genomic studies reveal both monogenic and polygenic influences on obesity, identifying numerous susceptibility loci. Genome-wide association studies (GWASs) have linked common variants in genes like FTO and MC4R to increased BMI and appetite dysregulation, respectively. Epigenetic research highlights the role of DNA methylation and other modifications in gene-environment interactions. Genetic and polygenic risk scores (GRSs and PRSs) show potential for refining risk stratification and predicting treatment response. The gut microbiome and metabolome also contribute to obesity pathogenesis, offering novel targets for intervention. Personalized medicine offers significant potential for improving obesity management through tailored interventions based on an individual's genetic and 'omics' profile. Future research should focus on elucidating the functional consequences of identified variants, exploring gene-environment interactions, and developing strategies to overcome current limitations in clinical translation. With continued advancements, precision medicine can enhance treatment efficacy, increase sustainability, and help reduce the global burden of obesity-related diseases.},
}

@article {pmid40564683,
year = {2025},
author = {Mania, L and Nanobashvili, K and Manjavidze, T and Benashvili, M and Bzishvili, N and Astamadze, I},
title = {Impact of Symptomatic COVID-19 on the Oral Health of Pediatric Patients in Tbilisi City.},
journal = {Children (Basel, Switzerland)},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/children12060725},
pmid = {40564683},
issn = {2227-9067},
support = {PHDF - 22 - 2374//Shota Rustaveli National Science Foundation/ ; },
abstract = {BACKGROUND/PURPOSE: Coronavirus disease 2019 (COVID-19) has become the cause of a global health crisis during the pandemic. This research aimed to study the impact of symptomatic COVID-19 on children's oral health indices and salivary microbiome composition during the post-COVID-19 period.

METHODS: An observational, cross-sectional study was conducted in Tbilisi (Georgia) among children aged 7-12 years. A total of 421 children included in the study had a history of laboratory-confirmed COVID-19 within one year of exposure. No participants met the criteria for comorbid conditions or for PCC. A stratified simple random selection of schools and among selected clusters was used. The selected children were divided into two groups: the exposed group, who were patients with a history of symptomatic COVID-19, and the control group, who were patients with a history of asymptomatic COVID-19. The data were collected from August 2022 to December 2023. Oral screening, microbiological examination of saliva, and administration of questionnaires were also performed. Logistic regression was used to calculate ORs with 95% confidence intervals. The statistical processing of the data was performed with SPSS 23.0. This study was approved by the Biomedical Research Ethical Council of the University of Georgia (UGREC-04-22/9 March 2022).

RESULTS: Statistically significant differences in the means of the oral health indicators between the studied groups were detected (exposed: DMFT + deft = 5.9; MGI = 0.92; S-OHI = 1.9; control: DMFT + deft = 3.8; MGI = 0.56; S-OHI = 1.4). According to the logistic regression, symptomatic COVID-19 had a significant effect on the following oral health indicators: DMFT + deft (OR = 1.26; 95% CI = 1.14-1.39), MGI (OR = 2.31; 95% CI = 1.50-3.55), and S-OHI (OR = 3.43; 95% CI = 2.03-5.76). The effect of symptomatic COVID-19 on the frequency of eradication of the studied microbiome was also significant (OR = 2.12; 95% CI = 1.23-3.63).

CONCLUSIONS: A close association was established between symptomatic COVID-19 and microbiome changes in the oral saliva of children, as well as between oral health indicators and symptomatic COVID-19. Considering the research results, it is assumed that a symptomatic course of COVID-19 may be an additional risk factor associated with poor oral health in the pediatric population in the post-COVID-19 period.},
}

@article {pmid40564364,
year = {2025},
author = {Li, M and Ma, C and Li, Y and An, Z and Yang, Y and Gao, F and Li, C and Liu, Y},
title = {Effect of Adding Alkaline Metal Ions Complexes Rumen Microbiota and Metabolome of Hu Lambs.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/ani15121816},
pmid = {40564364},
issn = {2076-2615},
support = {CARS-38;2021ZD0024//Changqin Li/ ; },
abstract = {This study aimed to evaluate the effects of studying the effects of the alkali metal ion complexes (AMIC) on the rumen of lambs. Eighteen 3-month-old male Hu lambs (30 ± 2.5 kg) were randomly assigned to three groups (n = 6). Dietary treatments were: control group (CG, base diet), group C1 (base diet + 0.15% AMIC), and group C2 (base diet + 0.30% AMIC). After 60 days of feeding, samples were collected for analysis. Compared with CG, rumen weight significantly increased in both C1 and C2 (p < 0.05). In C2, average daily gain (ADG), bacterial crude protein (BCP), propionic acid concentration, and rumen papillary length were significantly higher than in CG (p < 0.05). Rumen microbiota analysis showed that AMIC supplementation changed the microbial community composition, increasing the relative abundance of fiber-degrading bacteria (e.g., Prevotellaceae_UCG-001) and decreasing pathogenic Proteobacteria. In particular, rumen papillary length positively correlated with Unclassified Oscillospiraceae, Candidatus Saccharimonas, and Unclassified Clostridia vadinBB60 group. Metabolomic analysis revealed that quercetin 3-O-glucuronide levels increased in a dose-dependent manner with higher AMIC. This metabolite positively correlated with Prevotellaceae_UCG-001 abundance and ADG. At 0.30% AMIC, phospholipids PC(18:0/18:4(6Z,9Z,12Z,15Z)) and PE(18:0/16:1(9Z)) were significantly upregulated, and both positively correlated with Candidatus Saccharimonas, Unclassified Clostridia vadinBB60 group, and papillary morphology. In summary, AMIC supplementation affected metabolism by modulating the rumen microbiota, thereby promoting energy absorption and growth. The 0.30% AMIC inclusion significantly enhanced rumen papilla growth, increased the absorption area, promoted propionic acid production, reduced the acetic acid to propionic acid ratio, and ultimately improved the growth rate of Hu lambs. Thus, adding 0.30% AMIC was associated with improved growth performance.},
}

@article {pmid40564325,
year = {2025},
author = {Jiang, K and Ma, J and Xu, J and Zhang, Y and Niu, H},
title = {Multi-Omics Revealed the Effects of Different Feeding Systems on Rumen Microorganisms, Cellulose Degradation, and Metabolites in Mongolian Cattle.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/ani15121774},
pmid = {40564325},
issn = {2076-2615},
support = {This research was funded by the National Natural Science Foundation of China (32460813), the Inner Mongolia Natural Science Foundation Project (2022MS03074), and the Program for Young Talents of Science (NJYT22054) and Technology in Universities (GXKY2204//Xinhua Niu,Ying Zhang/ ; },
abstract = {Rumen microbiota is crucial for cellulose degradation and nutrient metabolism in ruminants. Different feeding systems like grazing and housed feeding can significantly impact it. Mongolian cattle show unique cellulose degradation ability, but functional changes under different feeding conditions are unclear. This study aims to investigate the effects of grazing and housed feeding on rumen microbiota, cellulose degradation, and metabolism in Mongolian cattle. In a 90-day trial, 12 female Mongolian cattle were divided into grazing (F group) and housed feeding (S group). Rumen samples were collected to analyze fermentation parameters, enzyme activities, microbiomes, and metabolomes. The F group had higher acetate, cellulase, xylanase, and β-glucosidase activities (p < 0.05). Bacteroidota and Prevotella were more abundant (p < 0.05), while Firmicutes and Ruminococcus were less abundant (p < 0.05) in the F group. Carbohydrate metabolic pathways and CAZymes (GH2, GH10) were upregulated in the F group, while the S group had enriched purine metabolic pathways and CAZyme (GH31). A total of 64 differential metabolites were found, with subaphylline upregulated in the F group and L-arogenate in the S group (p < 0.05). Grazing increased cellulose degradation and subaphylline production in Mongolian cattle, while housed feeding improved starch utilization efficiency and fat synthesis. These findings provide a basis for optimizing feeding strategies and improving fibrous feed resource utilization in Mongolian cattle.},
}

@article {pmid40564310,
year = {2025},
author = {Zeng, S and Shao, L and Zhao, M and Wang, L and Cheng, J and Zhang, T and Lu, H},
title = {Effects of Different Rearing Methods on the Intestinal Morphology, Intestinal Metabolites, and Gut Microbiota of Lueyang Black-Bone Chickens.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/ani15121758},
pmid = {40564310},
issn = {2076-2615},
abstract = {The Lueyang black-bone chicken represents a distinct indigenous avian breed native to China and it is a slow-growing broiler breed. The gut, whose primary function is to digest food and absorb nutrients, is also home to a large and diverse microbial community. The intestinal morphology, intestinal metabolites, and gut microbiota are critical determinants of nutrient utilization efficiency and immune health in poultry. This study investigates the impact of two distinct rearing modalities-cage-raised (CR) and cage-free (CF)-on the intestinal morphology, intestinal metabolites, and gut microbiota of the duodenum and cecum in Lueyang black-bone chickens. Additionally, we have integrated metabolomics and microbiome analyses. Morphological assessments revealed that, in comparison to the CR group, the CF group exhibited a significant increase in duodenal villi height (VH) and crypt depth (CD) (p < 0.01). Furthermore, there was a notable increase in the number of intestinal inflammatory cells within the CF group. Non-targeted metabolomics indicated an upregulation of omega-3 series polyunsaturated fatty acids and bile acid metabolites in the CR group. Conversely, the CF group demonstrated significantly elevated levels of lysophosphatidylcholine (LPC) and phosphatidylcholine (PE) in the intestine. Microbiome analysis revealed that in the duodenum, beneficial bacteria (e.g., Lactobacillus) were the dominant genera in the CF group, while the Bacteroides predominate in the CR group. Correlation analyses indicated a positive association between LPC levels and the presence of eight bacterial genera, including Ureaplasma. The omega-3 series polyunsaturated fatty acids were positively correlated with three bacterial genera, such as Flavobacterium. Notably, bile acid metabolites exhibited a significant positive correlation with Rikenellaceae_RC9_gut_group. In conclusion, this study provides novel insights into how rearing methods influence intestinal morphology, intestinal metabolites, and gut microbiota, offering a new perspective for the scientific management of poultry with the premise of ensuring animal health and welfare.},
}

@article {pmid40564300,
year = {2025},
author = {Boughey, I and Samsing, F and Hall, E and Rodney, R and Bush, R},
title = {Characterisation of the Faecal Microbiome of Alpacas Raised in South Eastern Australia.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/ani15121748},
pmid = {40564300},
issn = {2076-2615},
abstract = {There is limited investigation of the alpaca microbiome on a global scale, with no previous research conducted in Australia characterising the faecal microbiome. The microbiome composition in other ruminants has been shown to impact feed efficiency, average daily gain and methane production. This study aimed to characterise the faecal microbiome of alpacas raised in south-eastern Australia and identify variation across geographic regions. Faecal samples were collected from 59 healthy adult female alpacas, aged between 15 months and 17 years in NSW, Australia. Firmicutes were identified as the dominant phyla, accounting for 57.78% of the cumulative abundance, followed by Bacteroidota (29.12%). These two phyla accounted for 90% of the taxa, with the cumulative abundance of Firmicutes and Bacteriodota significantly differing (p < 0.05) across locations. There was no effect of age on the frequency of microbes identified at either phyla or class levels. The alpaca's production status only significantly affected the abundance of Firmicutes Clostridia Oscillospirales (p = 0.0026). The breakdown of the alpaca faecal microbiome identified here is consistent with previous ruminant and camelid studies. This study provides a valuable baseline for the microbiome characterisation of alpacas in south-eastern Australia and can be used as a baseline for further microbiome studies.},
}

@article {pmid40564287,
year = {2025},
author = {Steinberger, AJ and de Campos, JL and Kates, AE and Goldberg, TL and Ruegg, PL and Safdar, N and Sethi, AK and Shutske, JM and Suen, G},
title = {Assessing the Impacts of Dairy Farm Antimicrobial Use on the Bovine Fecal Microbiome.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/ani15121735},
pmid = {40564287},
issn = {2076-2615},
support = {20017-68003-26500//United States Department of Agriculture/ ; WIS04039//United States Department of Agriculture/ ; },
abstract = {Rising rates of antimicrobial-resistant infections have prompted increased scrutiny on antimicrobial use (AMU) in livestock agriculture. Dairy farms primarily use antimicrobials to maintain animal health and welfare by treating and preventing infectious diseases. However, the impact of dairy farm AMU practices on the cattle fecal microbiome remains largely unclear, partly due to difficulties in quantifying AMU. This study leveraged quantitative AMU data from 40 large commercial dairy farms to identify farms with low (n = 4) and high (n = 4) AMU. Using 16S rRNA gene amplicon sequencing, we compared the fecal bacterial communities of dairy calves and cows (healthy, cull, sick) by both AMU designation (high/low) and by individual farm AMU, summarized by animal defined daily dose (DDD) and mg/kg. We found significant differences in beta-diversity between cattle from high- and low-AMU groups using either method and found that Corynebacterium and Clostridium abundances increased with farm AMU. Additionally, we found fecal bacterial communities differed across farms within high- and low-AMU groupings, highlighting the need to account for farm-to-farm variation when assessing AMU impacts. These findings suggest that dairy farm AMU influences the fecal microbiome and identifies specific taxa that warrant further investigation as potential reservoirs for antimicrobial resistance genes.},
}

@article {pmid40564277,
year = {2025},
author = {Nistelberger, R and Gibler, P and Barones, L and Absenger, A and Kral-Pointner, JB and Salzmann, M and Hartmann, B and Podesser, BK and Hohensinner, PJ and Plasenzotti, R},
title = {Non-Invasive Analyses of Altered Schaedler Flora in C57Bl/6J and Balb/c Mice to Monitor Hygiene Status of a Housing Facility.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/ani15121725},
pmid = {40564277},
issn = {2076-2615},
abstract = {The composition of the gut microbiome, defined by environmental factors, significantly affects research outcomes, with variations observed across animal facilities. Efforts to standardize led to the definition of the 'Altered Schaedler flora' (ASF), comprising eight bacterial groups. Our data highlights the variability of ASF under pathogen contact. Feces from two wild-type strains (C57Bl/6J and Balb/c mice) with and without proven infection was collected in two different animal facilities and analyzed. The data show a significant difference in the quantity (either reduction or increase) of the eight ASF bacterial groups when comparing infected and non-infected mice across different housing areas (SPF-specific pathogen-free, quarantine, and conventional-experimental areas) within a facility, as well as in comparison to another facility. Furthermore, strain-specific differences are also evident, with certain ASF groups showing a reduction in quantity at one facility but an increase at the other, comparing the same housing area. Comparative studies across facilities confirmed the necessity of baseline determination for accurate ASF analysis. Performing ASF analysis, facilitated by in-house qPCR (quantitative polymerase chain reaction) kits, offers prompt and precise microbiome profiling, enhancing experimental accuracy and health monitoring in animal research settings.},
}

@article {pmid40564234,
year = {2025},
author = {Jia, J and Bao, P and Li, N and Kong, S and Chu, M and Chen, Q and Yan, P},
title = {Lactobacillus Supplementation Modulates Rumen Microbiota and Metabolism in Yaks Under Fattening Feeding Conditions: A Comprehensive Multi-Omics Analysis.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/ani15121681},
pmid = {40564234},
issn = {2076-2615},
support = {TCYC-TP2023//Xinjiang Tianchi Talent Research Program/ ; KCXFZ20201221173205015//Shenzhen Science and Technology Program/ ; CARS-37//National Beef Cattle Industry Technology and System/ ; 2022KJ137//Shandong Natural Science Foundation/ ; },
abstract = {The rumen is a critical organ that facilitates nutrient digestion in ruminant animals. However, the biological mechanisms by which rumen microbiota and its metabolites enable Lactobacillus to modulate rumen structure and maintain functional homeostasis under fattening feeding conditions remain poorly understood. In this study, 80 male Pamir yaks were selected, and a 170-day data collection phase was implemented. Correlation phenotypic data and multi-omics analyses (rumen microbial sequencing and rumen epithelial metabolomics) were conducted to investigate the regulatory effects of Lactobacillus supplementation on rumen microbiota and metabolic processes in a concentrate-based rearing yak model. The results demonstrated that feeding a high-energy diet may impair yak ruminal histomorphology, microbiota composition, and function while negatively modulating rumen microbiota-metabolic profiles associated with specific ruminal microbial communities and functions. Lactobacillus intervention treatment optimized the yak ruminal microbiome composition (mucous layer maturation was promoted, Prevotella and Ruminococcus abundance were reduced, and Fibrobacter and Muribaculaceae abundance were increased), thereby altering metabolite concentrations involved in various metabolic pathways under a high-energy feeding pattern (fatty acid metabolism pathways were upregulated). These alterations elucidated the beneficial impacts of the Lactobacillus supplementation strategy on yak ruminal health without compromising the high-energy intensive rearing pattern. Furthermore, the regulated ruminal microbiome metabolites may serve as potential biomarkers for future investigations into the functional impacts of Lactobacillus intervention treatment on healthy feeding strategies for yaks.},
}

@article {pmid40564230,
year = {2025},
author = {Dahadha, R and Hundam, S and Al-Zghoul, MB and Alanagreh, L and Ababneh, M and Mayyas, M and Alghizzawi, D and Mustafa, MA and Gerrard, DE and Dalloul, RA},
title = {Embryonic Thermal Manipulation Affects Body Performance Parameters and Cecum Microbiome in Broiler Chickens in Response to Post-Hatch Chronic Heat Stress Challenge.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/ani15121677},
pmid = {40564230},
issn = {2076-2615},
support = {grant numbers 552/2023 and 400/2024//Deanship of Research at Jordan University of Science and Technology/ ; },
abstract = {Rising global temperatures challenge poultry production by disrupting the cecal microbiota, which is essential for chicken health. Thermal manipulation (TM) during embryogenesis is a potential strategy to enhance thermotolerance in broilers. This study examined TM's effects on the cecal microbiome, body weight (BW), and body temperature (BT) under chronic heat stress (CHS). Fertile Indian River eggs (n = 800) were incubated under control (37.8 °C, 56% RH) or TM conditions (39 °C, 65% RH for 18 h per day from embryonic day 10 to 18). On post-hatch day 18, male chicks were assigned to either CHS (35 ± 0.5 °C for five days) or thermoneutral conditions (24 ± 0.5 °C). The CHS-TM group showed a significantly higher BW than the CHS-CON group (p < 0.05). Under thermoneutral conditions, TM chicks had a lower BT on day 1 (p < 0.05), while the CHS-TM group exhibited a non-significant BT reduction compared to the CHS-CON group under heat stress (p > 0.05). An analysis of the gut microbiome showed that the beta diversity analysis (PERMANOVA, p < 0.05) indicated distinct microbial shifts. Firmicutes and Bacteroidota dominated the phylum level, with CHS increased Bacilli and Lactobacillus while reducing Lachnospirales in the CHS-TM group. These findings suggest that TM modulates gut microbiota and mitigates BW loss, offering a potential strategy to enhance broilers' resilience to heat stress.},
}

@article {pmid40564214,
year = {2025},
author = {Popa, EC and Maghiar, L and Maghiar, TA and Brihan, I and Georgescu, LM and Toderaș, BA and Sachelarie, L and Huniadi, A},
title = {Hashimoto's Thyroiditis and Female Fertility: Endocrine, Immune, and Microbiota Perspectives in Assisted Reproduction-A Narrative Review.},
journal = {Biomedicines},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/biomedicines13061495},
pmid = {40564214},
issn = {2227-9059},
abstract = {Hashimoto's thyroiditis is the most prevalent autoimmune thyroid disorder, and it disproportionately affects women of reproductive age. Its impact on fertility and assisted reproductive technologies [ART] has become an area of growing clinical interest. Thyroid autoimmunity can influence female reproductive health through multiple interconnected mechanisms, including subtle thyroid hormone imbalances, reduced ovarian reserve, altered endometrial receptivity, and dysregulated immune responses. Subclinical hypothyroidism and the presence of anti-thyroid antibodies have been linked to increased miscarriage risk and reduced success rates in ART, particularly in intracytoplasmic sperm injection (ICSI) cycles. Although levothyroxine supplementation is widely used, its benefits in euthyroid women remain uncertain. Recent studies suggest that gut microbiota may modulate immune function and affect fertility outcomes among women with autoimmune thyroid conditions. This narrative review synthesizes findings from a broad literature base of over 40 peer-reviewed publications published between 2010 and 2025, with 30 of the most relevant and methodologically robust studies selected for detailed analysis. The review integrates clinical, endocrine, immunological, and microbiome-related perspectives. The evidence supports the need for personalized fertility management in women with Hashimoto's thyroiditis and highlights directions for future research into immune and microbiota-targeted therapies.},
}

@article {pmid40564196,
year = {2025},
author = {Schoppmeier, CM and Classen, GL and Contini, S and Rebmann, P and Brendlen, D and Wicht, MJ and Barbe, AG},
title = {Introducing a Novel Paper Point Method for Isolated Apical Sampling-The Controlled Apical Sampling Device: A Methodological Study.},
journal = {Biomedicines},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/biomedicines13061477},
pmid = {40564196},
issn = {2227-9059},
abstract = {Objectives: To introduce a novel method for apical lesion sampling using a protected paper point device and to evaluate its effectiveness and robustness during the sampling process in vitro. Methods: A prototype for apical sample collection was developed as an adaptation of the Micro-Apical Placement System-the device features a highly tapered screw head with a thin, hollow, stainless-steel tube and an internal wire piston. Standardized 5 mm paper points (ISO 10; PD Dental, Switzerland) served as carrier material. The prototype was tested using 30 × 3D-printed, single-rooted tooth models inoculated using two bacterial strains (Staphylococcus epidermidis and Escherichia coli) to simulate apical and intraradicular bacterial infections, respectively. The sampling process involved collecting and analyzing samples at specific timepoints, focusing on the presence or absence of E. coli contamination. Following sample collection, cultural detection of bacterial presence was performed by incubating the samples on agar plates to confirm the presence of E. coli. Samples were collected as follows: S0 (sterility control of the prototype), P0 (sterility control of the tooth model), P1 (apical sample collected with the CAPS (controlled apical sampling) device, and P2 (contamination control sample to check for the presence of E. coli inside the root canal). Results: Handling of the CAPS prototype was straightforward and reproducible. No loss of paper points or complications were observed during sample collection. All sterility samples (P0, S0) were negative for tested microorganisms, confirming the sterility of the setup. P2 samples confirmed the presence of E. coli in the root canal in all trials. The P1 samples were free from contamination in 86.67% of trials. Conclusions: The CAPS method for apical sampling demonstrated advances in the successful and precise sample collection of apically located S. epidermidis and will be a useful tool for endodontic microbiological analysis. Its user-friendly design and consistent performance highlight its potential for clinical application, contributing to more accurate microbial diagnostics and later patient-specific therapeutic approaches in endodontic treatments.},
}

@article {pmid40564149,
year = {2025},
author = {Fei, Q and Huang, J and He, Y and Zhang, Y and Zhang, X and Wang, J and Fu, Q},
title = {Immunometabolic Interactions in Obesity: Implications for Therapeutic Strategies.},
journal = {Biomedicines},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/biomedicines13061429},
pmid = {40564149},
issn = {2227-9059},
abstract = {Obesity is characterized by excessive fat accumulation that triggers chronic low-grade inflammation and systemic immune dysregulation, significantly increasing the risk of metabolic disorders including insulin resistance, type 2 diabetes, and cardiovascular disease. This review examines the bidirectional relationship between obesity and immune dysfunction, focusing on how immune cell infiltration in adipose tissue drives inflammatory processes. We highlight the phenotypic shifts in key immune populations-macrophages polarized toward proinflammatory M1 phenotypes, T cell exhaustion occurrs, and alterations appear in B cells, natural killer (NK) cells, and dendritic cells-that collectively contribute to metabolic deterioration. The gut microbiome emerged as a critical mediator in this relationship, influencing both immune responses and metabolic regulation through gut-liver and gut-brain axes. We explore emerging immunomodulatory therapeutic strategies, including anti-inflammatory agents, microbiota interventions, and targeted immune therapies such as innovative nanomedicine approaches. The review also addresses the challenges of immunotherapy in obesity, particularly the paradoxical effects observed in cancer immunotherapy outcomes and the need for personalized treatment approaches. Artificial intelligence is highlighted as a potential tool to enhance patient stratification and treatment optimization in future immunomodulatory interventions. Understanding these immunometabolic interactions provides a foundation for developing more effective therapeutic strategies that could transform obesity management and reduce the burden of obesity-related metabolic diseases.},
}

@article {pmid40564116,
year = {2025},
author = {Lin, W and Liang, Z and Fang, J and Liu, Y and Lei, L and Lin, J and Xia, B and Zheng, Z and Yuan, J and Tang, C},
title = {Association Between Gut Microbiota and Chronic Kidney Disease: A Two-Sample Mendelian Randomization Study in a Chinese Population.},
journal = {Biomedicines},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/biomedicines13061397},
pmid = {40564116},
issn = {2227-9059},
support = {A2402020//Shenzhen Medical Research Fund/ ; JCYJ20210324123414040 and JCYJ20230807110715030//Shenzhen Municipal Science and Technology Innovation Commission/ ; No. A2403069, C2401002//Shenzhen Medical Research Fund/ ; Gastrointestinal Surgery, No.LCYSSQ20220823091203008//the Funding of Shenzhen Clinical Research Center for Gastroenterology/ ; No. 82473707//the Natural Science Foundation of China/ ; No. ZSQYRSSFAR0004//the Research Supporting Start-up Fund for Associate researcher, of SAHSYSU/ ; No. 392012//the Startup Fund for the 100 Top Talents Program, SYSU/ ; },
abstract = {Background: Population differences in gut microbiota composition and related metabolites may influence their potential causal relationship with chronic kidney disease (CKD); however, this relationship remains poorly understood in the Chinese population. Materials and Methods: We conducted a two-sample Mendelian randomization (MR) study using summary statistics of 500 gut microbial features (9 phyla, 3 classes, 14 orders, 32 families, 95 genera, 248 species, and 99 gut metabolic modules (GMMs)) from the 4D-SZ (from Shenzhen, China) discovery cohort (n = 1539). CKD summary statistics were obtained from the China Kadoorie Biobank (CKB) (489 cases and 75,531 controls). Associations between gut microbiota and CKD were evaluated via inverse variance weighted, MR-Egger, weighted median, and MR-PRESSO. To validate our findings, we replicated the analyses in two independent East Asian CKD GWAS datasets: the Biobank of Japan (BBJ) dataset (2117 cases and 174,345 controls) and the J-Kidney-Biobank (JKB) dataset (382 cases and 3471 controls). We further validated the results via a meta-GWAS of BUN and eGFR in Biobank Japan (BBJ) and the Taiwan Biobank (TWB). Additionally, we analyzed 304 serum proteins from the Guangzhou Nutrition and Health Study (GNHS) and conducted mediation MR analyses to explore potential mediators. Result: At the locus-wide significance threshold, we identified 18 gut microbiome features associated with CKD onset in the China Kadoorie Biobank (CKB). Genus Alistipes (OR 1.02, 95% CI 1.00-1.03, p = 0.03) was associated with incident CKD risk in the JKB cohort. Species Bifidobacterium catenulatum-Bifidobacterium pseudocatenulatum complex (OR 1.0074, 95% CI 1.0070-1.0142, p = 0.01) was associated with incident CKD risk in a meta-GWAS of BUN. Sensitivity analyses, including Cochran's Q test, MR-Egger intercept analysis, leave-one-out analysis, and funnel plots, yielded consistent results. Mediation analysis revealed that 26.7% (95% CI: 0.006-0.6700, p = 0.04) of the effect of Alistipes on CKD risk was mediated through the serum protein FBLN1. Conclusions: Our study provides Mendelian randomization-based evidence supporting a potential causal relationship between gut microbiota and CKD, highlighting the potential mediating role of FBLN1 in the association between genus Alistipes and CKD. Further studies are needed to explore whether and how genus Alistipes and FBLN1 contribute to CKD development.},
}

@article {pmid40564111,
year = {2025},
author = {Bieganska, EA and Kosinski, P and Wolski, M},
title = {Possible Applications of Fecal Microbiota Transplantation in the Pediatric Population: A Systematic Review.},
journal = {Biomedicines},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/biomedicines13061393},
pmid = {40564111},
issn = {2227-9059},
abstract = {Background: The potential therapeutic role of fecal microbiota transplantation (FMT) in various diseases has been thoroughly studied over the last few decades. However, the majority of studies focus on the adult population, therefore, conclusions regarding the application of FMT in the pediatric population are much less clear. This systematic review aims to summarize the research conducted so far on the efficacy and safety of FMT in the pediatric population, assess the quality of the evidence of its effectiveness, and outline the most promising areas for future research. Methods: We performed a systematic literature search from the index date to 8 June 2024 on the Embase, PubMed, and Web of Science databases. One author screened the resulting 121 articles. Eventually, 35 eligible studies that reported FMT use in seven different diseases were identified. Results: All of the studies assessed FMT as a safe procedure without many serious adverse effects. The best-documented application, which is the only one recommended in official guidelines, is recurrent Clostridioides difficile infection. Other disease entities in which the use of FMT has been studied with good clinical effects are inflammatory bowel disease, allergic colitis, autism, Tourette syndrome, and colonization with multi-drug-resistant organisms. However, it should be noted that the majority of studies are cohort and case-control studies, without randomization, which translates into low evidence quality. In one randomized, controlled trial focusing on the effect of FMT on weight loss in obese individuals, a lack of effect was found. Conclusions: While FMT and subsequent iterations of gut microbiota-targeted interventions hold promising therapeutic potential for various disease entities in the pediatric population, the current evidence behind this conclusion is of low quality. Based on current studies, these methods appear to be both effective and safe. However, further randomized clinical trials are necessary, especially within the pediatric population, for which such studies remain scarce.},
}

@article {pmid40564077,
year = {2025},
author = {Theis, BF and Park, JS and Kim, JSA and Zeydabadinejad, S and Vijay-Kumar, M and Yeoh, BS and Saha, P},
title = {Gut Feelings: How Microbes, Diet, and Host Immunity Shape Disease.},
journal = {Biomedicines},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/biomedicines13061357},
pmid = {40564077},
issn = {2227-9059},
abstract = {The human gut microbiome is intricately linked to systemic and organ-specific immune responses and is highly responsive to dietary modulation. As metagenomic techniques enable in-depth study of an ever-growing number of gut microbial species, it has become increasingly feasible to decipher the specific functions of the gut microbiome and how they may be modulated by diet. Diet exerts both supportive and selective pressures on the gut microbiome by regulating a multitude of factors, including energy density, macronutrient and micronutrient content, and circadian rhythm. The microbiome, in turn, contributes to local and systemic immune responses by providing colonization resistance against pathogens, shaping immune cell activity and differentiation, and facilitating the production of bioactive metabolites. Emerging research has strengthened the connections between the gut microbiome and cardiometabolic disorders (e.g., cardiovascular disease, obesity, type-2 diabetes), autoimmune conditions (e.g., type-1 diabetes, rheumatoid arthritis, celiac disease), respiratory disease, chronic kidney and liver disease, inflammatory bowel disease, and neurological disorders (e.g., Alzheimer's, Parkinson's disease, depressive disorders). Here, we outline ways in which dietary factors impact host response in diseases through alterations of gut microbiome functionality and composition. Consideration of diet-mediated microbial effects within the context of the diseases discussed highlights the potential of microbiome-targeted treatment strategies as alternative or adjunct therapies to improve patient outcomes.},
}

@article {pmid40564016,
year = {2025},
author = {Paraskevaidis, I and Tsougos, E and Kourek, C},
title = {The Microbiome Connection: A Common Pathway Linking Cancer and Heart Failure.},
journal = {Biomedicines},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/biomedicines13061297},
pmid = {40564016},
issn = {2227-9059},
abstract = {In humans, heart failure (HF) and cancer are among the leading causes of morbidity and mortality. A growing body of evidence highlights a bidirectional relationship between these conditions, underpinned by shared risk factors and overlapping pathophysiological pathways. This review aims to explore the emerging role of the intestinal microbiome as a common mechanistic link between HF and cancer. Specifically, we examine how microbial dysbiosis and its metabolic products-such as trimethylamine N-oxide (TMAO), short-chain fatty acids (SCFAs), bile acids, lipopolysaccharides (LPS), and branched-chain amino acids (BCAAs)-contribute to inflammation, immune dysregulation, oxidative stress, and metabolic dysfunction. These mechanisms promote multiorgan impairment and establish a vicious cycle that fuels both tumorigenesis and cardiac deterioration. HF, cancer, and the gut microbiome are not isolated entities but are deeply interconnected through shared biological mechanisms-including chronic inflammation, microbial dysbiosis, immune and neurohumoral modulation, and metabolic derangement. These findings support the concept of a microbiome-centered axis involving the gut, heart, and tumors, which may underlie many chronic disease processes. Understanding these interactions may provide novel insights into disease pathogenesis and uncover promising therapeutic targets that leverage microbiome modulation to prevent or treat HF, cancer, and other systemic diseases.},
}

@article {pmid40563985,
year = {2025},
author = {Klinsoda, J and Thurakit, T and Tongkhao, K and Treesuwan, K and Yodin, K and Kantrong, H},
title = {Exploring the Bacterial Microbiome of High-Moisture Plant-Based Meat Substituted Soybean Flour with Mung Bean Protein and Duckweed Powder.},
journal = {Biology},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biology14060735},
pmid = {40563985},
issn = {2079-7737},
support = {grant number FF(KU)11.67//Kasetsart University Research and Development Institute (KURDI), Thailand/ ; },
abstract = {(1) Background: This study aimed to investigate the bacterial microbiomes in the ingredients and final PBM products during a storage period of 28 days at 2-4 °C for food safety and quality. (2) Methods: DNA from raw ingredients (i.e., defatted soy flour, potato starch, wheat gluten, mung bean protein, and duckweed) and three PBM formulations were extracted and sequenced using 16S rRNA gene sequencing. (3) Results: Alpha diversity (Simpson and Shannon) was high in the raw ingredients (p ≤ 0.05). Beta diversity showed dissimilarities between the samples. Firmicutes and Proteobacteria were the core microflora in these ingredients. The heat-stable microbes in PBM (e.g., Nostocaceae in SF and Cyanobacteriale in MB and DW) survived after extrusion. After the ingredients were stored at room temperature, the bacterial communities shifted, with Paucibacter being the majority population in raw ingredients and PBM in the 2nd batch. The predictions of Potential_Pathogens related to the abundance of Aeromonadaceae and Enterobacteriaceae need to be monitored during storage. (4) Conclusions: Our results showed that the bacterial community in PBM containing 30% MB and 3% DW did not drastically change during 28 days of storage at cold temperatures. Uncovering bacterial microbiomes in the ingredients should be emphasized for quality and safety, as ingredients influence the microbiome in the final products.},
}

@article {pmid40563973,
year = {2025},
author = {Qumsani, AT},
title = {Gut Microbiome Engineering for Diabetic Kidney Disease Prevention: A Lactobacillus rhamnosus GG Intervention Study.},
journal = {Biology},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biology14060723},
pmid = {40563973},
issn = {2079-7737},
abstract = {The gut microbiota has emerged as a critical modulator in metabolic diseases, with substantial evidence supporting its role in attenuating diabetes-related nephropathy. Recent investigations demonstrate that strategic manipulation of intestinal microflora offers novel therapeutic avenues for safeguarding renal function against diabetic complications. This investigation sought to determine the nephroprotective potential of Lactobacillus rhamnosus GG (LGG) administration in diabetic nephropathy models. Six experimental cohorts were evaluated: control, probiotic-supplemented control, diabetic, diabetic receiving probiotic therapy, diabetic with antibiotics, and diabetic treated with both antibiotics and probiotics. Diabetic conditions were established via intraperitoneal administration of streptozotocin (50 mg/kg) following overnight fasting, according to validated protocols for experimental diabetes induction. Probiotic therapy (3 × 10[9] CFU/kg, bi-daily) began one month before diabetes induction and continued throughout the study duration. Glycemic indices were monitored at bi-weekly intervals, inflammatory biomarkers, renal function indices, and urinary albumin excretion. The metabolic profile was evaluated through the determination of HOMA-IR and the computation of metabolic syndrome scores. Microbiome characterization employed 16S rRNA gene sequencing alongside metagenomic shotgun sequencing for comprehensive microbial community mapping. L. rhamnosus GG supplementation substantially augmented microbiome richness and evenness metrics. Principal component analysis revealed distinct clustering of microbial populations between treatment groups. The Prevotella/Bacteroides ratio, an emerging marker of metabolic dysfunction, normalized following probiotic intervention in diabetic subjects. Results: L. rhamnosus GG administration markedly attenuated diabetic progression, achieving glycated hemoglobin reduction of 32% compared to untreated controls. Pro-inflammatory cytokine levels (IL-6, TNF-α) decreased significantly, while anti-inflammatory mediators (IL-10, TGF-β) exhibited enhanced expression. The renal morphometric analysis demonstrated preservation of glomerular architecture and reduced interstitial fibrosis. Additionally, transmission electron microscopy confirmed the maintenance of podocyte foot process integrity in probiotic-treated groups. Conclusions: The administration of Lactobacillus rhamnosus GG demonstrated profound renoprotective efficacy through multifaceted mechanisms, including microbiome reconstitution, metabolic amelioration, and inflammation modulation. Therapeutic effects suggest the potential of a combined probiotic and pharmacological approach to attenuate diabetic-induced renal pathology with enhanced efficacy.},
}

@article {pmid40563920,
year = {2025},
author = {Zambuzzi, WF and Ferreira, MR and Wang, Z and Peppelenbosch, MP},
title = {A Biochemical View on Intermittent Fasting's Effects on Human Physiology-Not Always a Beneficial Strategy.},
journal = {Biology},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biology14060669},
pmid = {40563920},
issn = {2079-7737},
support = {KICH2.V4P.22.015/NWO_/Dutch Research Council/Netherlands ; },
abstract = {Intermittent fasting (IF) has emerged as a widely practiced dietary regimen, increasingly utilized in both clinical and non-clinical settings for its potential health benefits. Evidence suggests that IF can improve metabolic health by enhancing insulin sensitivity, reducing inflammation, and aiding weight management. Recent studies have also explored its role in mitigating obesity-related diseases, such as type 2 diabetes and non-alcoholic fatty liver disease, and its ability to support cardiovascular health and mental function. The effects of IF, however, vary depending on individual health conditions. Some patients show no clinical improvement, while others experience worsened outcomes. Mechanistically, IF induces metabolic switching and activates adenosine monophosphate-activated protein kinase (AMPK), both of which contribute to its therapeutic potential. These responses are influenced by factors such as underlying pathology, baseline metabolic state, and dietary composition. While preclinical data indicate potential therapeutic effects in diseases like cancer, rheumatoid arthritis, and neurodegenerative conditions, these findings are not yet sufficiently supported by human studies. This review argues that IF holds promise as a disease-modifying intervention. However, its implementation should be personalized according to patient-specific characteristics, and future clinical trials must prioritize identifying optimal fasting protocols to maximize therapeutic outcomes.},
}

@article {pmid40563918,
year = {2025},
author = {Dildar, T and Cui, W and Ikhwanuddin, M and Ma, H},
title = {Aquatic Organisms in Response to Salinity Stress: Ecological Impacts, Adaptive Mechanisms, and Resilience Strategies.},
journal = {Biology},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biology14060667},
pmid = {40563918},
issn = {2079-7737},
support = {32473150//National Natural Science Foundation of China/ ; 2024-SPY-00-013//Agricultural and Rural Department of Guangdong Province/ ; STKJ202209029//Guangdong Provincial Department of Science and Technology/ ; },
abstract = {Salinity stress presents a major ecological challenge for aquatic organisms, particularly in environments where salinity levels fluctuate. These fluctuations are becoming more pronounced due to climate change, further destabilizing aquatic ecosystems. Understanding how organisms adapt to such variability is essential for biodiversity conservation and the sustainable management of aquatic resources. This review examines the physiological, molecular, and behavioral adaptations that enable aquatic organisms to survive and thrive under salinity stress. Specifically, it explores mechanisms of osmotic regulation, ion transport, and oxidative stress responses, highlighting key signaling pathways-such as AMP-activated protein kinase (AMPK), Phosphatidylinositol 3-kinase-protein kinase (PI3K-AKT), Mitogen-activated protein kinase (MAPK), and the Hippo pathway-that facilitate these adaptive processes. The review also emphasizes the genetic and epigenetic modifications that contribute to resilience, underscoring the importance of genetic diversity for species survival in fluctuating salinity conditions. Furthermore, the interactions between host organisms and their microbiomes are discussed as critical factors influencing resilience. The review addresses the impact of salinity fluctuations on species distribution and biodiversity, with a focus on the implications of climate change for aquatic ecosystems. Finally, strategies for mitigating salinity stress, such as nutritional interventions and the development of salinity-resistant varieties, are explored, particularly in aquaculture. Overall, this review consolidates current knowledge on organismal adaptations, molecular mechanisms, and environmental challenges, offering valuable insights for ecological research and aquaculture practices in the face of climate change.},
}

@article {pmid40563880,
year = {2025},
author = {Tayyab, M and Islam, W and Waqas, W and Zhang, Y},
title = {Probiotic-Vaccine Synergy in Fish Aquaculture: Exploring Microbiome-Immune Interactions for Enhanced Vaccine Efficacy.},
journal = {Biology},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biology14060629},
pmid = {40563880},
issn = {2079-7737},
abstract = {The rapid expansion of aquaculture is vital for global food security, yet it faces persistent threats from disease outbreaks, vaccine inefficacy, and antibiotic overuse, all of which undermine sustainability. Conventional vaccines often fail to induce robust mucosal immunity, spurring interest in probiotics as adjuvants to enhance immunogenicity. Probiotics such as Bacillus subtilis and Lactobacillus casei modulate fish microbiomes, fortify mucosal barriers, and activate innate immune responses via mechanisms including Toll-like receptor signaling and cytokine production. These actions prime the host environment for prolonged adaptive immunity, improving antigen uptake and pathogen clearance. Experimental advances-such as Bacillus subtilis-engineered spores increasing survival rates to 86% in Vibrio anguillarum-challenged European seabass-demonstrate the potential of this synergy. Innovations in delivery systems, including chitosan-alginate microcapsules and synbiotic formulations, further address oral vaccine degradation, enhancing practicality. Probiotics also suppress pathogens while enriching beneficial gut taxa, amplifying mucosal IgA and systemic IgM responses. However, challenges such as strain-specific variability, environmental dependencies, and unresolved ecological risks persist. Optimizing host-specific probiotics and advancing multi-omics research is critical to unlocking this synergy fully. Integrating probiotic mechanisms with vaccine design offers a pathway toward antibiotic-free aquaculture, aligning with One Health principles. Realizing this vision demands interdisciplinary collaboration to standardize protocols, validate field efficacy, and align policies with ecological sustainability. Probiotic-vaccine strategies represent not merely a scientific advance but an essential evolution for resilient, ecologically balanced aquaculture systems.},
}

@article {pmid40563845,
year = {2025},
author = {Busayli, AM and Xu, W and Raffah, GA and Chen, G},
title = {Gut Microbiome, Neuroinflammation, and Fetal Alcohol Spectrum Disorders: Insights from Rodent Models.},
journal = {Biology},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biology14060593},
pmid = {40563845},
issn = {2079-7737},
support = {1013179575//University of Kentucky College of Medicine/ ; },
abstract = {Fetal alcohol spectrum disorder (FASD) is a significant public health issue that affects children. It results from ethanol exposure during pregnancy, leading to considerable physical, neurodevelopmental, behavioral, and cognitive deficits. The exact mechanism is not well understood. Recently, considerable attention has been focused on the influence of gut microbiome on brain development through the gut-brain axis. Changes in the gut microbiome resulting from ethanol exposure may contribute to the pathology of FASD, potentially involving neuroinflammation. This literature review summarizes the existing research and primary animal studies on the impact of early ethanol exposure on the gut microbiome, neuroinflammation, brain development, and behavioral consequences. The evidence suggests that early ethanol exposure alters the gut microbiome, which may induce neuroinflammation, brain damage, and cognitive impairment. However, a clear causal relationship among these factors remains to be fully elucidated.},
}

@article {pmid40563824,
year = {2025},
author = {Hasan, A and Scuderi, SA and Capra, AP and Giosa, D and Bonomo, A and Ardizzone, A and Esposito, E},
title = {An Updated and Comprehensive Review Exploring the Gut-Brain Axis in Neurodegenerative Disorders and Neurotraumas: Implications for Therapeutic Strategies.},
journal = {Brain sciences},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/brainsci15060654},
pmid = {40563824},
issn = {2076-3425},
abstract = {The gut-brain axis (GBA) refers to the biochemical bidirectional communication between the central nervous system (CNS) and the gastrointestinal tract, linking brain and gut functions. It comprises a complex network of interactions involving the endocrine, immune, autonomic, and enteric nervous systems. The balance of this bidirectional pathway depends on the composition of the gut microbiome and its metabolites. While the causes of neurodegenerative diseases (NDDs) vary, the gut microbiome plays a crucial role in their development and prognosis. NDDs are often associated with an inflammation-related gut microbiome. However, restoring balance to the gut microbiome and reducing inflammation may have therapeutic benefits. In particular, introducing short-chain fatty acid-producing bacteria, key metabolites that support gut homeostasis, can help counteract the inflammatory microbiome. This strong pathological link between the gut and NDDs underscores the gut-brain axis (GBA) as a promising target for therapeutic intervention. This review, by scrutinizing the more recent original research articles published in PubMed (MEDLINE) database, emphasizes the emerging notion that GBA is an equally important pathological marker for neurological movement disorders, particularly in Alzheimer's disease, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis, Huntington's disease and neurotraumatic disorders such as traumatic brain injury and spinal cord injury. Additionally, the GBA presents a promising therapeutic target for managing these diseases.},
}

@article {pmid40563782,
year = {2025},
author = {Hong, SH and Roh, HW and Nam, YJ and Kim, TW and Cho, YH and Son, SJ and Hong, CH},
title = {Age- and Sex-Specific Gut Microbiota Signatures Associated with Dementia-Related Brain Pathologies: An LEfSe-Based Metagenomic Study.},
journal = {Brain sciences},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/brainsci15060611},
pmid = {40563782},
issn = {2076-3425},
support = {2024-ER0505-00//Korea National Institute of Health (KNIH)/ ; GRRCAjou2023-B02//Gyeonggi-do Regional Research Center program of Gyeonggi province/ ; RS-2022-KH130309//Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea/ ; RS-2021-KH113821//Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea/ ; },
abstract = {BACKGROUND/OBJECTIVES: Emerging evidence suggests that gut microbiota composition is influenced by both age and sex and may contribute to dementia-related brain pathologies. However, comprehensive microbiome-based biomarker discovery stratified by these factors remains limited.

METHODS: We performed a metagenomic analysis of the gut microbiota of participants stratified by sex (female vs. male) and age (<75 vs. ≥75 years). Alpha diversity (observed operational taxonomic unit, Chao1, Shannon, and Simpson) and linear discriminant analysis effect size analyses were conducted to identify dominant taxa associated with Alzheimer's pathology, vascular pathology, and dementia-related structural brain changes.

RESULTS: Females and non-elderly participants (aged < 75 years) exhibited higher gut microbial diversity, characterized by an increased abundance of Bifidobacterium spp. and Blautia spp., whereas males and elderly participants (aged ≥ 75 years) exhibited increased levels of Bacteroides spp. and Bacteroidia, which have been associated with inflammation and dysbiosis. Several taxa, including Bifidobacterium spp. were consistently identified as potential protective biomarkers, while Bacteroides spp. was linked to a higher risk of dementia-related brain pathologies.

CONCLUSIONS: Our findings demonstrate distinct age- and sex-specific differences in gut microbiota composition that may be closely associated with the pathophysiology of dementia-related brain pathologies. These results demonstrate that gut microbiota may serve as potential biomarkers for monitoring cerebrovascular conditions, potentially contributing to the development of personalized therapeutic strategies.},
}

@article {pmid40563710,
year = {2025},
author = {Kazen, AB and Umfleet, LG and Aboulalazm, FA and Cohen, AD and Terhune, S and Mason, L and Obarski, S and Franczak, M and Kindel, TL and Wang, Y and Kirby, JR},
title = {Gut Microbiota and Neurovascular Patterns in Amnestic Mild Cognitive Impairment.},
journal = {Brain sciences},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/brainsci15060538},
pmid = {40563710},
issn = {2076-3425},
support = {1R21AG075501-24A1/NH/NIH HHS/United States ; },
abstract = {Background/Objectives: The interplay between the gut microbiome (GMB) and neurovascular function in neurodegeneration is unclear. The goal of this proof-of-concept, cross-sectional study is to identify relationships between the GMB, neurovascular functioning, and cognition in amnestic mild cognitive impairment (aMCI), the prototypical prodromal symptomatic stage of Alzheimer's disease (AD). Methods: Participants (n = 14 aMCI and 10 controls) provided fecal samples for GMB sequencing (16S and shotgun metagenomics), underwent MRI, and completed cognitive testing. Cerebral vascular reactivity (CVR), cerebral blood flow (CBF), and arterial transit time (ATT) were assessed. Statistical analyses evaluated the relationships between discriminatory taxa, cerebrovascular metrics, and cognition. Results: Sequencing revealed differentially abundant bacterial and viral taxa distinguishing aMCI from controls. Spearman correlations revealed that bacteria known to induce inflammation were negatively associated with CVR, CBF, and cognition, and positively associated with ATT. A reciprocal pattern emerged for the association of taxa with gut health. Conclusions: Our results provide preliminary evidence that pro-inflammatory gut bacterial and viral taxa are associated with neurovascular dysfunction and cognitive impairment in prodromal AD, highlighting their potential as candidate microbial biomarkers and targets for early intervention.},
}

@article {pmid40563519,
year = {2025},
author = {Ahmad, MF and Ahmad, FA and Alsayegh, AA and Zeyaullah, M and Babalghith, AO and Faidah, H and Ahmed, F and Khanam, A and Mozaffar, B and Kambal, N and Bantun, F},
title = {Probiotics and Cancer: Mechanistic Insights and Organ-Specific Impact.},
journal = {Biomolecules},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/biom15060879},
pmid = {40563519},
issn = {2218-273X},
mesh = {*Probiotics/therapeutic use/pharmacology ; Humans ; *Neoplasms/microbiology/prevention & control/drug therapy ; Gastrointestinal Microbiome/drug effects ; Animals ; },
abstract = {Probiotics have been revealed in various studies to modulate the gut microbiome and have a substantial impact on cancers, comprising oesophageal, lung, liver, and colorectal cancer. These properties are endorsed by a diverse mechanism, including the modulation of the gut microbiome; preventing the metabolism of carcinogenic substances; exertion of anti-inflammatory action, immunopotentiator properties, and antioxidant activities; prevention of tumour growth; and decreasing the adverse effects of chemotherapy. There are promising perspectives regarding the new and developing field of probiotic research in relation to cancer treatment. This review demonstrates the recent findings of probiotics efficacy in cancer prevention and treatment and organ-specific impact along with protection from chemotherapy-induced side effects. The present evidence specifies that strategic probiotics application may be an effective complementary approach for the management of numerous kinds of cancer; still, additional studies and clinical trials are required to comprehend the relationships between cancer and probiotics.},
}

*Probiotics/therapeutic use/pharmacology
Humans
*Neoplasms/microbiology/prevention & control/drug therapy
Gastrointestinal Microbiome/drug effects
Animals

@article {pmid40563478,
year = {2025},
author = {Lo, Y and Cheng, TT and Huang, CJ and Cheng, YC and Chyuan, IT},
title = {Advancing Therapeutic Strategies in Atopic Dermatitis: Emerging Targets and Personalized Approaches.},
journal = {Biomolecules},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/biom15060838},
pmid = {40563478},
issn = {2218-273X},
mesh = {Humans ; *Dermatitis, Atopic/immunology/drug therapy/therapy/metabolism ; *Precision Medicine/methods ; Cytokines/metabolism ; Thymic Stromal Lymphopoietin ; Animals ; Immunity, Innate ; Adaptive Immunity ; Molecular Targeted Therapy ; },
abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disorder marked by intricate interplay among skin barrier dysfunction, immune dysregulation, and microbial dysbiosis. While therapeutic advancements targeting T helper 2 (Th2) cytokines, such as interleukin (IL)-4 and IL-13, and the Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway have yielded promising outcomes, a significant proportion of patients still experience inadequate relief, particularly from persistent pruritus. Achieving minimal disease activity remains an unmet clinical priority and a cornerstone of effective AD management. This review provides an in-depth analysis of current therapeutic approaches and integrates findings from recent biologic studies, with a particular focus on innovative strategies under active investigation. These approaches include targeting components of the innate immune system, such as thymic stromal lymphopoietin (TSLP) and IL-1 family cytokines; the adaptive immune system, including OX40-OX40L interactions and Th17- and Th22-related cytokines; and mechanisms associated with pruritus, such as IL-31, histamine receptors, and neurokinin 1 receptor. Emerging insights underscore the transformative potential of personalized therapeutic regimens tailored to the distinct endotypes and severity of AD. Advances in deciphering the pathogenesis of AD are unlocking unprecedented opportunities for precision medicine, offering renewed hope for improved outcomes in this multifaceted and heterogeneous condition.},
}

Humans
*Dermatitis, Atopic/immunology/drug therapy/therapy/metabolism
*Precision Medicine/methods
Cytokines/metabolism
Thymic Stromal Lymphopoietin
Animals
Immunity, Innate
Adaptive Immunity
Molecular Targeted Therapy

@article {pmid40563474,
year = {2025},
author = {Kushawaha, B and Rem, TT and Pelosi, E},
title = {Harnessing Microbiome, Bacterial Extracellular Vesicle, and Artificial Intelligence for Polycystic Ovary Syndrome Diagnosis and Management.},
journal = {Biomolecules},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/biom15060834},
pmid = {40563474},
issn = {2218-273X},
mesh = {*Polycystic Ovary Syndrome/diagnosis/microbiology/therapy ; Humans ; Female ; *Artificial Intelligence ; *Extracellular Vesicles/metabolism ; *Microbiota ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Bacteria/metabolism ; },
abstract = {Polycystic ovary syndrome (PCOS) affects 6-19% of reproductive-age women worldwide, yet diagnosis remains challenging due to heterogeneous presentations and symptoms overlapping with other endocrine disorders. Recent studies have shown that gut dysbiosis plays a significant role in PCOS pathophysiology, with bacterial extracellular vesicles (BEVs) functioning as critical mediators of the gut-ovary axis. BEVs carry distinct cargos in PCOS patients-including specific miRNAs and inflammatory proteins-and show promise for both diagnostic and therapeutic applications. Artificial intelligence (AI) is emerging as a promising significant tool in PCOS research due to improved diagnostic accuracy and the capability to analyze complex datasets combining microbiome, BEV, and clinical parameters. These integrated approaches have the potential to better address PCOS multifactorial nature, enabling improved phenotypic classification and personalized treatment strategies. This review examines recent advances in the last 25 years in microbiome, BEV, and AI applications in PCOS research using PubMed, Web of Science, and Scopus databases. We explore the diagnostic potential of the AI-driven analysis of microbiome and BEV profiles, and address ethical considerations including data privacy and algorithmic bias. As these technologies continue to evolve, they hold increasing potential for the improvement of PCOS diagnosis and management, including the development of safer, more precise, and effective interventions.},
}

*Polycystic Ovary Syndrome/diagnosis/microbiology/therapy
Humans
Female
*Artificial Intelligence
*Extracellular Vesicles/metabolism
*Microbiota
*Gastrointestinal Microbiome
Dysbiosis/microbiology
Bacteria/metabolism

@article {pmid40563468,
year = {2025},
author = {Pagliaro, R and Scialò, F and Schiattarella, A and Cianci, R and Campbell, SFM and Perrotta, F and Bianco, A and Castaldo, G},
title = {Mechanisms of Lung Cancer Development in Cystic Fibrosis Patients: The Role of Inflammation, Oxidative Stress, and Lung Microbiome Dysbiosis.},
journal = {Biomolecules},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/biom15060828},
pmid = {40563468},
issn = {2218-273X},
mesh = {Humans ; *Cystic Fibrosis/complications/microbiology/pathology/metabolism ; *Dysbiosis/microbiology/complications ; *Oxidative Stress ; *Inflammation/pathology/metabolism ; *Lung Neoplasms/pathology/etiology/microbiology/metabolism ; *Microbiota ; *Lung/microbiology/pathology ; Animals ; },
abstract = {Cystic fibrosis (CF) is a genetic disorder caused by mutations in the CFTR gene, leading to defective ion transport and impaired function of various organs. Chronic inflammation, oxidative stress, and microbial dysbiosis are key pathological features of CF patients, contributing to disease progression, lung damage, and an increased susceptibility to infections. Emerging evidence suggests that in CF patients these factors can promote cancer development, especially lung cancer. Chronic inflammation in CF, driven by immune cell dysfunction, results in the release of pro-inflammatory cytokines and reactive oxygen species (ROSs), fostering an environment conducive to cancer initiation. Oxidative stress can amplify cellular damage and hinder airway remodeling. ROSs not only damage cellular components such as lipids, proteins, and DNA but also disrupt lung homeostasis, creating a favorable environment for cancer development. Furthermore, the lung microbiome in CF patients is often dysbiotic, with a reduced diversity and the predominance of pathogenic bacteria such as Pseudomonas aeruginosa, which exacerbate inflammation and may contribute to carcinogenesis. This review explores the mechanisms linking CF to lung cancer, examining the potential clinical implications of these mechanisms for early detection, monitoring, and targeted therapies for lung cancer prevention in CF patients.},
}

Humans
*Cystic Fibrosis/complications/microbiology/pathology/metabolism
*Dysbiosis/microbiology/complications
*Oxidative Stress
*Inflammation/pathology/metabolism
*Lung Neoplasms/pathology/etiology/microbiology/metabolism
*Microbiota
*Lung/microbiology/pathology
Animals

@article {pmid40563386,
year = {2025},
author = {Zeng, M and Li, Y and Cheng, J and Wang, J and Liu, Q},
title = {Prebiotic Oligosaccharides in Skin Health: Benefits, Mechanisms, and Cosmetic Applications.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antiox14060754},
pmid = {40563386},
issn = {2076-3921},
support = {MZGC20240028//Sichuan Science and Technology Innovation Seedling Project/ ; 22208111//National Natural Science Foundation of China/ ; 22378077//National Natural Science Foundation of China/ ; 2023A1515010064//Guangdong Basic and Applied Basic Research Foundation/ ; 2023QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; },
abstract = {Prebiotic oligosaccharides have attracted significant interest in dermatology and skin health due to their ability to modulate the skin microbiome and microbiota-host interactions. This review offers a novel dual perspective, systematically examining the benefits of both oral intake and topical application of prebiotic oligosaccharides, including well-established prebiotics (e.g., human milk oligosaccharides, galacto- and fructo-oligosaccharides) and emerging prebiotic candidates (e.g., gluco-oligosaccharides, chitosan-oligosaccharides, agaro-oligosaccharides). First, cutting-edge synthetic processes for producing diverse oligosaccharides and their structural chemistry are introduced. Then, we discuss in vitro studies demonstrating their efficacy in promoting skin commensals, inhibiting pathogens, and conferring protective effects, such as antioxidant, anti-inflammatory, anti-melanogenic, and wound-healing properties. Furthermore, we emphasize in vivo animal studies and clinical trials revealing that prebiotic oligosaccharides, administered orally or topically, alleviate atopic dermatitis, enhance skin hydration, attenuate acne, and protect against photo-aging by modulating skin-gut microbiota and immune responses. Mechanistically, we integrate genetic and molecular insights to elucidate how oligosaccharides mediate these benefits, including gut-skin axis crosstalk, immune regulation, and microbial metabolite signaling. Finally, we highlight current commercial applications of oligosaccharides in cosmetic formulations while addressing scientific and practical challenges, such as structure-function relationships, clinical scalability, and regulatory considerations. This review bridges mechanistic understanding with practical applications, offering a comprehensive resource for advancing prebiotic oligosaccharides-based skincare therapies.},
}

@article {pmid40563357,
year = {2025},
author = {Clemente-Suárez, VJ and Martín-Rodríguez, A and Beltrán-Velasco, AI and Rubio-Zarapuz, A and Martínez-Guardado, I and Valcárcel-Martín, R and Tornero-Aguilera, JF},
title = {Functional and Therapeutic Roles of Plant-Derived Antioxidants in Type 2 Diabetes Mellitus: Mechanisms, Challenges, and Considerations for Special Populations.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antiox14060725},
pmid = {40563357},
issn = {2076-3921},
abstract = {BACKGROUND: Type 2 diabetes mellitus (T2DM) is a chronic metabolic disorder characterized by persistent hyperglycemia, oxidative stress, and inflammation, contributing to insulin resistance and long-term complications. Dietary antioxidants from plant sources, such as polyphenols, flavonoids, carotenoids, and phenolic acids, have been increasingly studied for their potential to modulate these pathophysiological mechanisms.

OBJECTIVE: This review aims to summarize and critically analyze the current evidence on the biological effects, therapeutic potential, and translational challenges of plant-derived antioxidants in the prevention and management of T2DM.

METHODS: This narrative review was conducted using peer-reviewed literature from PubMed, Scopus, and Web of Science. Emphasis was placed on mechanistic studies, clinical trials, bioavailability data, and advances in formulation technologies related to antioxidant compounds in the context of T2DM.

RESULTS: Plant antioxidants exert beneficial effects by modulating oxidative stress, reducing systemic inflammation, and improving insulin signaling pathways. However, their clinical application is limited by low bioavailability, chemical instability, and high interindividual variability. Recent developments, such as nanoencapsulation, synergistic functional food formulations, and microbiome-targeted strategies, have shown promise in enhancing efficacy. Additionally, personalized nutrition approaches and regulatory advances are emerging to support the integration of antioxidant-based interventions into diabetes care.

CONCLUSIONS: Plant-derived antioxidants represent a promising complementary tool for T2DM management. Nonetheless, their effective clinical use depends on overcoming pharmacokinetic limitations and validating their long-term efficacy in well-designed trials. Integrating food technology, microbiome science, and precision nutrition will be crucial to translate these compounds into safe, scalable, and personalized therapeutic options for individuals with or at risk of T2DM.},
}

@article {pmid40563352,
year = {2025},
author = {He, J and Tang, Q and Liu, YC and Wang, LJ and Chai, YF},
title = {Impact of Diquat on the Intestinal Health and the Composition and Function of the Gut Microbiome.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antiox14060721},
pmid = {40563352},
issn = {2076-3921},
support = {TJYXZDXK-007A//Tianjin Municipal Medical Key Construction Project/ ; PUMF01010010-2024-18//Beijing Union Medical Foundation-Rui E Emergency Medicine Research/ ; },
abstract = {Diquat (DQ) is extensively utilized as a herbicide in farming, and its intake can result in serious systemic toxicity due to its induction of oxidative stress (OS) and disruption of intestinal homeostasis. The gastrointestinal tract is one of the first systems exposed to DQ, and damage to this system can influence the general health of the host. Our review summarizes the toxic effects of DQ on the intestinal barrier integrity, gut microbiome, and microbial metabolites (e.g., short-chain fatty acids [SCFAs], bile acids). By elucidating the mechanisms linking DQ-induced OS to gut dysbiosis, mitochondrial dysfunction, and inflammation, our work provides critical insights into novel therapeutic strategies, including probiotics, antioxidants (e.g., hydroxytyrosol, curcumin), and selenium nanoparticles. These findings address a pressing gap in understanding environmental toxin-related gut pathology and offer potential interventions to mitigate systemic oxidative damage.},
}

@article {pmid40563329,
year = {2025},
author = {Shoham, S and Pintel, N and Avni, D},
title = {Oxidative Stress, Gut Bacteria, and Microalgae: A Holistic Approach to Manage Inflammatory Bowel Diseases.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antiox14060697},
pmid = {40563329},
issn = {2076-3921},
support = {101000501//European Commission/ ; },
abstract = {Oxidative stress is a recognized contributor to the pathophysiology of inflammatory bowel disease (IBD), exacerbating chronic inflammation and tissue damage. While traditional IBD therapies primarily focus on immune modulation, alternative approaches that address oxidative stress and promote gut microbial health present new opportunities for symptom relief and disease management. Microalgae, known for their potent antioxidant, anti-inflammatory, and prebiotic properties, show promise in alleviating oxidative damage and supporting beneficial gut bacteria. This review explores the multifaceted role of oxidative stress in IBD and highlights the therapeutic potential of microalgae-derived compounds. In addition, it examines the synergistic benefits of combining microalgal antioxidants with probiotics to promote gut homeostasis. Advances in delivery systems, including nanotechnology and symbiotic bacteria-microalgae interactions, are also discussed as emerging approaches for targeted treatment. The review concludes by identifying future research priorities focused on clinical translation and microalgae-based bioengineering innovations to enhance the efficacy and accessibility of therapeutics for IBD patients.},
}

@article {pmid40563316,
year = {2025},
author = {Martins-Green, M and Kim, J and Aziz, K},
title = {The Impact of the Skin Microbiome and Oxidative Stress on the Initiation and Development of Cutaneous Chronic Wounds.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antiox14060682},
pmid = {40563316},
issn = {2076-3921},
abstract = {Wound healing is a very complex process composed of several phases in which precise events occur, both temporally and specially. However, when these processes go awry, biofilm-forming bacteria become installed in the healing tissue, and the patient has comorbidities, so the wounds do not heal and become chronic. In this review, we describe the importance of high levels of oxidative stress (OS) and bacteria from the skin microbiome in the initiation and development of chronic wounds. The skin microbiome is diverse in humans, and its composition is dependent on the environment in the specific areas of the body. OS is critical for wound healing as it stimulates the immune system to destroy pathogens and secrete cytokines and growth factors that stimulate healing. When OS levels become high in the wound and the bacteria of the skin install themselves in the wound, chronicity ensues. However, neither OS nor the bacteria of the skin alone can initiate chronicity. However, when present together, chronic wounds develop. Given the complexity of chronic wound initiation, developing treatment for these wounds has been difficult. Here, we also discuss the challenges of treating chronic wounds and offer a potential sequence of approaches to treating these wounds after debridement.},
}

@article {pmid40563121,
year = {2025},
author = {Wang, X and Liu, J and Huoshen, W and Liu, J and Qiao, X and Zhang, H and Zhou, XJ},
title = {Causal relationships between gut microbiota and IgA nephropathy: evidence from Mendelian randomization and microbiome validation.},
journal = {Renal failure},
volume = {47},
number = {1},
pages = {2522979},
doi = {10.1080/0886022X.2025.2522979},
pmid = {40563121},
issn = {1525-6049},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Glomerulonephritis, IGA/microbiology/genetics ; Mendelian Randomization Analysis ; RNA, Ribosomal, 16S/genetics ; Genome-Wide Association Study ; },
abstract = {BACKGROUND: Emerging evidence links gut microbiota strongly with IgA Nephropathy (IgAN). However, the causal role of specific gut microbiota in IgAN remains unclear. This study used a two-sample Mendelian randomization (MR) approach, validated with 16S rRNA datasets, to identify these causal relationships.

METHODS: We performed MR analysis using genetic instruments for 412 gut microbiota taxa from genome-wide association studies (GWAS) as exposures and IgAN GWAS data as outcomes. The inverse-variance weighted method was used as the primary analysis, supplemented by MR-Egger regression, weighted median methods, and Cochran's Q test to assess pleiotropy and heterogeneity. Significant findings were validated using reverse, multivariable, and mediation MR analyses. Results were validated using genus-level 16S rRNA datasets with batch correction (ConQuR), and microbial function was inferred via PICRUSt2.

RESULTS: Three gut microbiota species were protective against IgAN: s_Alistipes_senegalensis (OR = 0.64, p = .002), s_Ruminococcus_bromii (OR = 0.75, p = .040), and s_Bilophila_unclassified (OR = 0.68, p = .040). Six species were associated with increased IgAN risk, including g_Barnesiella (OR = 1.32, p = .030) and s_Rothia_mucilaginosa (OR = 1.52, p = .040). After multiple-testing correction, significant associations persisted for s_Alistipes_senegalensis (p = .043), s_Bacteroides_clarus (p = .035), and s_Bilophila_unclassified (p = .002). Sensitivity analyses confirmed robust results without pleiotropy or heterogeneity. Genus-level validation confirmed consistent microbial shifts. Functional predictions showed upregulation of carbohydrate/fatty acid metabolism and downregulation of the urea cycle.

CONCLUSIONS: This study reveals specific gut microbes and metabolic pathways potentially driving IgAN, offering novel biomarkers and therapeutic targets for microbiome-based interventions.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Glomerulonephritis, IGA/microbiology/genetics
Mendelian Randomization Analysis
RNA, Ribosomal, 16S/genetics
Genome-Wide Association Study

@article {pmid40563092,
year = {2025},
author = {Amimo, JO and Kunyanga, CN and Raev, SA and Kick, M and Micheal, H and Saif, LJ and Vlasova, AN},
title = {Stunting is associated with persistent and transferable alterations in the gut microbiome.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {49},
pmid = {40563092},
issn = {1757-4749},
support = {OPP1117467//Bill and Melinda Gates Foundation/ ; R01A1099451//National Institute of Allergy and Infectious Diseases/ ; },
abstract = {As robust animal models to study the pathophysiology of stunting are absent, we have comparatively characterized the gut microbiota of malnourished/stunted vs. clinically healthy/normal Kenyan toddlers (12-24 months old) and established a gnotobiotic (Gn) pig fecal transplant model to gain understanding of microbial community structure associated with stunting. As expected, the bacterial composition between the two toddler groups was distinct: Actinobacteria was most prevalent in healthy toddlers, whereas Proteobacteria dominated in stunted toddlers. Although the diversity indices showed no significant differences, unique bacterial genera were found in each toddler group: three genera unique to stunted toddlers and ten unique to healthy toddlers, with eight genera shared between the groups. We observed a higher number of enriched bacterial virulence genes in healthy vs. stunted toddlers suggesting that the microbiome plasticity and functional characteristics of the healthy toddlers allow for the pathogen/pathobiont control. In contrast, we noted the presence of more genes associated with antimicrobial-resistance (AMR) bacteria in stunted toddlers, possibly due to early-life antibiotic treatments. Of interest, functional analysis showed that CAZymes associated with carbohydrate biosynthesis, and a few metabolic pathways related to protein/amino acid, carbohydrate and fat catabolism were enriched in stunted toddlers. In contrast carbohydrate degradation CAZymes and numerous anabolic pathways were prevalent in healthy toddlers. These patterns were also evident in the Gn pigs transplanted with stunted/healthy human fecal microbiota (HFM). Overall, our findings suggest that the microbiota transplanted Gn pigs represent a valuable model for studying the infant microbial community structure and the impacts of stunting on the child gut microbiota. Additionally, this is the first study to demonstrate that the healthy vs. stunted microbiota composition and function remained different in the Gn pigs throughout the study. This information and the Gn pig model are vital for developing and testing targeted interventions for malnourished/stunted populations, consequently advancing microbiome-based diagnosis and personalized medicine.},
}

@article {pmid40562845,
year = {2025},
author = {Shiner, YA and Caplan, S and Doweck, I},
title = {Actinomyces findings in tonsillectomy specimens- comparison between adults and pediatrics populations.},
journal = {European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery},
volume = {},
number = {},
pages = {},
pmid = {40562845},
issn = {1434-4726},
abstract = {BACKGROUND: Tonsillectomy is a common surgical procedure primarily performed for obstructive sleep apnea (OSA) and recurrent acute tonsillitis. Actinomyces are gram-positive, anaerobic bacteria commonly found in the oral cavity and known to form part of the human microbiome, occasionally associated with localized infections. While Actinomyces bacterial colonization in tonsils has been previously studied, its correlation with surgical indications and outcomes remains unclear.

OBJECTIVES: The study aimed to investigate the relationship between Actinomyces colonization in tonsillar specimens and surgical indications, and to examine whether Actinomyces presence influences tonsillectomy outcomes, specifically post-operative hemorrhage and hospital stay.

METHODS: This retrospective cohort study analyzed electronic medical records from Lady Davis Carmel Medical Centre between 2011 and 2021. The study included 1,333 patients who underwent extra-capsular tonsillectomies. Patient demographics, surgical indications, length of hospital stay, post-surgical complications, and pathological reports were collected and analyzed using IBM SPSS Statistics 28.0.

RESULTS: The study population consisted of 760 (57%) males and 573 (43%) females, with an age range of 0.98 to 67.5 years (mean 9.1 years). Actinomyces was present in 13.2% of specimens from patients with infectious indications compared to 4.5% in patients with obstructive indications (p < 0.001). A statistically significant age difference was observed between patients with (17.78 years) and without (8.55 years) Actinomyces. Multivariate analysis revealed that age was the most significant predictor of Actinomyces presence (OR 1.047, p < 0.0001).

CONCLUSIONS: The study found a significant correlation between Actinomyces presence, older age, and infectious surgical indications. While Actinomyces colonization did not demonstrate a direct influence on surgical complications, the findings suggest potential clinical relevance that merits further research to elucidate the bacterium's role in tonsillar pathology.},
}

@article {pmid40562776,
year = {2025},
author = {Davidson, S and So, Y and Oscarsson, E and Håkansson, Å and Sjöberg, K},
title = {Presence of viable gram-positive bacteria in blood of patients with inflammatory bowel disease is not affected by treatment.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20283},
pmid = {40562776},
issn = {2045-2322},
mesh = {Humans ; Female ; Male ; Adult ; Middle Aged ; *Gram-Positive Bacteria/isolation & purification/genetics ; *Colitis, Ulcerative/microbiology/blood/drug therapy ; *Inflammatory Bowel Diseases/microbiology/blood/drug therapy ; *Crohn Disease/microbiology/blood/drug therapy ; C-Reactive Protein/metabolism ; Young Adult ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {In inflammatory bowel disease (IBD) the pathogenetic process is characterized by dysbiosis, increased permeability, translocation, and immune activation. The aim of the present study was to assess the presence of viable bacteria in the blood of patients with IBD and to correlate the findings with clinical characteristics. The study included 28 patients with Crohn's disease (CD) (median age 38 years, 50% female, biological treatment in 71%) and 19 patients with ulcerative colitis (UC) (median age 45 years, 33% female, biological treatment in 84%). Identification of viable bacteria in the blood was evaluated by optimized cultivation and Sanger sequencing and for quantification real-time PCR was performed. Viable Gram-positive bacteria were detected in 34 IBD patients (72.3%). There were no associations between the presence of bacteria and gender, antibiotic treatment, intake of alcohol, use of PPI, steroids, or biological treatment. The number of bacterial copies was correlated with higher C-reactive protein (CRP) (p = 0.013). In ¾ of the patients, viable bacteria were identified in the blood despite treatment with biologicals, which indicates a vast barrier defect. This observation also indicates that the disease is still active. To obtain a true deep mucosal healing an intact barrier function is required.},
}

Humans
Female
Male
Adult
Middle Aged
*Gram-Positive Bacteria/isolation & purification/genetics
*Colitis, Ulcerative/microbiology/blood/drug therapy
*Inflammatory Bowel Diseases/microbiology/blood/drug therapy
*Crohn Disease/microbiology/blood/drug therapy
C-Reactive Protein/metabolism
Young Adult
Anti-Bacterial Agents/therapeutic use

@article {pmid40562421,
year = {2025},
author = {Supasitdikul, T and Mazariegos, JRR and Nhat, NN and Tung, YT and Yang, DF and Lee, LJ and Gunawan, SP and Chen, YC},
title = {Sleep Deprivation Alters Gut Microbiome Diversity and Taxonomy: A Systematic Review and Meta-Analysis of Human and Rodent Studies.},
journal = {Journal of sleep research},
volume = {},
number = {},
pages = {e70125},
doi = {10.1111/jsr.70125},
pmid = {40562421},
issn = {1365-2869},
support = {NSTC 112-2314-B-038-051-MY3//National Science and Technology Council/ ; },
abstract = {Sleep deprivation (SD) affects the gut microbiome, but findings across studies vary in terms of microbiota changes, SD induction methods and gut measurements. The effects of SD on the gut microbiome in humans and rodents have not been comprehensively reviewed. This meta-analysis investigated SD-related factors and their effects on the gut microbiome in human and rodent models. We analysed data from studies published before February 28, 2024, and calculated standardised mean differences (SMDs). Subgroup analyses were conducted for rodents and humans. A total of 20 studies (4 human, 5 rat, 8 mouse and 3 combined human and rodent) were included. SD significantly reduced alpha diversity (Shannon and Simpson indices) and increased the Firmicutes-to-Bacteroidetes ratio. In rodents, the Shannon index was lower (SMD = -1.27, 95% CI: -2.20 to -0.34), and the Firmicutes/Bacteroidetes ratio was higher (SMD = 2.60, 95% CI: 1.61-3.59). Human studies showed nonsignificant trends, limited by small sample sizes. Analysis at the phylum, family and genus levels showed a modest decrease in Actinobacteria and Tenericutes and a minor increase in Bacteroidetes, Firmicutes and Proteobacteria. Reductions in Lactobacillaceae and Erysipelotrichaceae and increases in Ruminococcaceae and Lachnospiraceae were observed. A2, Lactobacillus and Ruminococcus_1 were less abundant in the SD group. Overall, SD alters gut microbiome composition. Standardised human studies are needed to clarify translational relevance.},
}

@article {pmid40562254,
year = {2025},
author = {Martelli, A and Mohamed, Y and Gallego-Ferrer, G and Gentile, P and Girón-Hernández, J},
title = {Revolutionizing gut health: Advances in encapsulation strategies for probiotics and bioactive molecules.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108630},
doi = {10.1016/j.biotechadv.2025.108630},
pmid = {40562254},
issn = {1873-1899},
abstract = {Advancements in biotechnology underscore the critical role of gastrointestinal microbiome in health and disease. Probiotic supplementation offers therapeutic potential, particularly for functional gastrointestinal disorders, which affect over 40 % of the global population and impair quality of life. Despite a rapidly growing probiotics market, many formulations suffer from poor efficacy due to challenges such as gastric survival, temperature sensitivity and poor colonization of the gut lining. Encapsulation technologies have emerged as potential solutions, offering protection for probiotics but introducing complexities related to biopolymer coatings and adhesion efficiency. Moreover, reactive oxygen species (ROS) significantly influence gut health, with excess ROS contributing to dysbiosis, intestinal barrier disruption and inflammation. While dietary antioxidants offer some benefits, their rapid clearance and nonspecific biodistribution limit therapeutic efficacy. Encapsulation strategies integrating probiotics with phenolic antioxidants have demonstrated enhanced survival, adhesion, and antioxidant activity, presenting a promising avenue for gut health interventions. This review primarily aims to explore innovative approaches to encapsulated probiotic formulations, emphasizing their potential to address current limitations and improve gut health. Specifically, the review examines key areas of focus including the design and manufacturing of systems incorporating live microorganisms and bioactive molecules; evaluation of their digestion, release and bioactivity; and their in vitro and in vivo efficacy. Finally, regulatory considerations and future research directions, focused on advancing smart encapsulation strategies and novel delivery systems to enhance therapeutic efficacy and address current challenges in gut health interventions are also explored.},
}

@article {pmid40562244,
year = {2025},
author = {Costa, BF and Sawaya, C and Buren, JV and Smith, AL},
title = {Investigating anaerobic digestion microbiome resilience to high PFOA and PFOS mixtures during cometabolism.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132877},
doi = {10.1016/j.biortech.2025.132877},
pmid = {40562244},
issn = {1873-2976},
abstract = {Anaerobic digestion (AD) is a reducing environment with high microbial diversity and potential for biotransformation of PFAS. Yet, their fate and impact on the microbial community remains poorly understood. This study evaluated the long-term impact (100 d) of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) spiked at10 mg/L (low) and 100 mg/L (high), respectively. Although resilient to complete system failure, high PFAS concentrations disrupted AD, evidenced by 25-50 % reduction in methane content, 45 %-48 % reduction in cumulative biogas production, and accumulation of butyric acid. No significant decrease in PFAS concentration was observed in the liquid fraction after 100 d relative to the kill controls, indicating PFAS adsorption behavior. However, PFAS concentrations were temporally variable. Microbial community analysis revealed enrichment of notable AD groups, such as Firmicutes, Synergistetes, and Methanomassillicoccus phyla in high PFAS reactors, which underscores the potential for the microbiome adaptation and informs future strategies for PFAS-contaminated sludge treatment.},
}

@article {pmid40562242,
year = {2025},
author = {Jiang, F and Ye, C and Wang, F and Dong, T and Wei, J and Kapelan, Z and Hofman, J and Xu, Z and Chu, W},
title = {Enhanced thioether formation in stormwater pipes induced by nitrogen-containing pollutants: The role of the sediment microbiome.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132878},
doi = {10.1016/j.biortech.2025.132878},
pmid = {40562242},
issn = {1873-2976},
abstract = {The illicit connections between sewage and stormwater pipes result in the discharge of untreated sewage into receiving rivers, posing significant odor and health hazards. While thioethers are recognized as key odorants in sewage systems, their distribution in stormwater systems remain poorly characterized. This study analyzed 12 types of thioethers in stormwater pipes sampled at 21 sites in China. Advanced analytical techniques, including Mantel analysis and Structural Equation Modeling, were employed to examine the relationships between overlying water properties, sediment microbial characteristics, and thioether concentrations. Results showed that sediment thioether loads (36.77 ± 50.14 μg S/m; range: 7.24-99.96 μg S/m) were substantially higher than those in the overlying water (12.02 ± 42.52 μg S/m; range: 0.03-92.76 μg S/m), highlighting sediment as a critical pollution reservoir. Dissolved oxygen, NH3-N, and terrestrial-derived dissolved organic nitrogen were identified as key factors shaping sediment microbiome composition, particularly fermentative, sulfate-reducing, and denitrifying bacteria, which in turn drives thioether formation. Specifically, dominant compounds like dimethyl disulfide and dimethyl trisulfide were found to be produced through the anaerobic fermentation of methionine and redox conversion of methanethiol, as well as the anaerobic fermentation of cysteine and methylation of polysulfides. Humic substances could facilitate methanethiol redox conversion and polysulfide methylation by serving as methyl donors and enhancing electron transfer efficiency. Additionally, NH3-N may promote microbial metabolism by providing amino groups essential for the synthesis of metabolic precursors. Therefore, effective mitigation of odorous thioethers in stormwater systems necessitates integrated strategies targeting both sulfur-containing organic precursors and nitrogen-rich pollutants.},
}

@article {pmid40562170,
year = {2025},
author = {Gallagher, K and Halperin-Goldstein, S and Paller, AS},
title = {New Treatments in Atopic Dermatitis Update.},
journal = {Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.anai.2025.06.020},
pmid = {40562170},
issn = {1534-4436},
abstract = {This review evaluates the efficacy and safety of novel and emerging topical and systemic therapies for atopic dermatitis (AD) across pediatric and adult populations with an emphasis on recent advancements and future directions. Data were sourced from peer-reviewed publications (PubMed), scientific meeting abstracts, ClinicalTrials.gov, and industry press releases. Several new agents have received Food and Drug Administration approval, expanding therapeutic options for patients. Non-steroidal topical treatments, such as roflumilast and tapinarof creams, are approved for adults and children down to 6 and 2 years, respectively. Topical Janus kinase (JAK) inhibitors, including ruxolitinib, leverage inhibition of the JAK1 pathway with low concern for toxicity. The use of biologics targeting the interleukin (IL)-4/IL-13 pathway has expanded; dupilumab is approved for patients 6 months and older and tralokinumab and lebrikizumab are approved for 12 years and above. Most recently, nemolizumab, targeting the IL-31 receptor, which mediates nonhistaminergic itch, has been approved for those 12 years and above. Although baricitinib is approved in Europe and Japan, upadacitinib and abrocitinib remain the only oral JAK inhibitors approved for U.S. patients 12 years and older. Promising investigational therapies, particularly through topically altering the microbiome (bacteriotherapy) and systemic agents targeting the OX40/OX40L pathway and multispecific antibodies, are in development. These innovations represent a shift toward personalized AD management. As the treatment landscape evolves, ongoing research is essential to assess long-term safety and efficacy, as well as to develop predictive models that optimize treatment strategies, ultimately improving patient outcomes and quality of life.},
}

@article {pmid40561434,
year = {2025},
author = {Cultrera, G and Franco, S and Spoto, G and Libra, M and Falzone, L},
title = {Review Article: Disrupted Oral Microbiota and Its Implications in Cancer Onset and Progression: A Narrative Review.},
journal = {Critical reviews in oncogenesis},
volume = {30},
number = {2},
pages = {83-106},
doi = {10.1615/CritRevOncog.2025059551},
pmid = {40561434},
issn = {0893-9675},
mesh = {Humans ; *Microbiota ; *Neoplasms/microbiology/pathology/etiology ; *Dysbiosis/microbiology/complications ; *Mouth/microbiology ; Disease Progression ; Carcinogenesis ; },
abstract = {The oral microbiota plays a pivotal role in maintaining oral health, but its dysbiosis has been increasingly implicated in the development of systemic diseases, including cancer. Emerging evidence highlights the potential contribution of oral microorganisms to carcinogenesis in the oral cavity and distant organs, such as the lungs, pancreas, and genitourinary tract. This review explores the mechanisms through which the oral microbiota influences cancer development and treatment response, mainly driven by microbial translocation, systemic inflammation, immune modulation, and the release of carcinogenic metabolites. Additionally, the review discusses how oral microbiota perturbations interact with host factors, such as diet, systemic diseases, genetics, and cancer therapies, to influence tumor initiation, progression, and response to treatment. A critical analysis of past and emerging literature shows that specific microbial taxa potentially influence tumor progression and immune responses, including Fusobacterium, Porphyromonas, Aggregatibacter and Treponema. The detection of these microorganisms and the study of oral microbiome profiling in cancer care may offer new diagnostic and therapeutic strategies; however, further studies with homogeneous patient populations are needed to fully understand the contributions of oral dysbiosis in cancer development and treatment responses.},
}

Humans
*Microbiota
*Neoplasms/microbiology/pathology/etiology
*Dysbiosis/microbiology/complications
*Mouth/microbiology
Disease Progression
Carcinogenesis

@article {pmid40561433,
year = {2025},
author = {Vivarelli, S and Marconi, A and Matera, S and Falzone, L and Fenga, C},
title = {Review Article: Night Shift Work, Circadian Disruption, and the Gut Microbiome: Implications for Human Health.},
journal = {Critical reviews in oncogenesis},
volume = {30},
number = {2},
pages = {67-81},
doi = {10.1615/CritRevOncog.2025059579},
pmid = {40561433},
issn = {0893-9675},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Shift Work Schedule/adverse effects ; *Circadian Rhythm/physiology ; *Work Schedule Tolerance/physiology ; Dysbiosis ; },
abstract = {The gut microbiome (GM) plays a critical role in regulating a number of physiological processes within the human host, including metabolism, immune function, and protection from pathogens. Emerging evidence suggests that occupational exposures, particularly working night shifts or during irregular hours, significantly influence the GM composition and functionality. These disruptions are closely tied to the misalignment between the host's circadian rhythms and the GM's internal clocks, leading to dysbiosis and increased systemic inflammation. This misalignment has been linked to the development of several health conditions, including dysmetabolism, type 2 diabetes, obesity, cardiovascular diseases, and gastrointestinal disorders. This review provides a thorough analysis of the current research on workers who are exposed to night shifts, highlighting the profound impact of circadian misalignment on both the GM wellbeing and the overall human health. Innovative interventions, such as dietary supplementation with probiotics, prebiotics, circadian-aligned nutrition, and time-restricted eating, offer promising strategies for restoring the GM balance and synchronizing the microbiome with the host's circadian rhythms affected by occupational stressors. Precision-based interventions tailored to specific occupational exposures and circadian patterns may provide effective solutions for improving worker's health and preventing long-term chronic diseases associated with detrimental exposures. In light of these findings, integrating microbiome-targeted approaches into occupational health policies could lead to better health outcomes, reduce the risk of chronic diseases, and enhance the overall well-being of at-risk workers. Occupational research should continue to explore these personalized approaches, together with novel assessment strategies, to optimize health interventions and mitigate the long-term effects of night shift work.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Shift Work Schedule/adverse effects
*Circadian Rhythm/physiology
*Work Schedule Tolerance/physiology
Dysbiosis

@article {pmid40561432,
year = {2025},
author = {Leyva, BK and Bonavida, B},
title = {Review Article: Probiotics and Oncogenesis: Clinical Implications.},
journal = {Critical reviews in oncogenesis},
volume = {30},
number = {2},
pages = {49-66},
doi = {10.1615/CritRevOncog.2025058336},
pmid = {40561432},
issn = {0893-9675},
mesh = {*Probiotics/therapeutic use/administration & dosage ; Humans ; *Neoplasms/therapy/etiology/prevention & control/microbiology ; Gastrointestinal Microbiome ; *Carcinogenesis/drug effects ; Tumor Microenvironment/immunology ; Animals ; Immunotherapy/methods ; },
abstract = {The interplay between probiotics and cancer development has emerged as a complex but important field in oncology research. While probiotics are known gut microbiome modulators and have the ability to modulate an immune response, their role in the prevention and treatment of cancer are inadequately understood. Evidence from peer-reviewed literature suggests that probiotics-mediated effects contribute to cancer prevention and treatment. Such effects include the enhancement of barrier function, production of anti-inflammatory agents, modulation of immune responses, and regulation of the tumor microenvironment. Clinical studies offer promising results in terms of therapeutic applications in certain cancers where probiotic bacteria may help reduce risk factors while enhancing treatment efficacy. Emerging evidence indicates potential benefits in the combination of probiotics with immunotherapy, including improved response rates and reduced side effects. Significant challenges remain, however, including the standardization of probiotic bacterial constituents, the route of administration, optimal delivery methods and safety concerns. Future research should focus on personalized treatment plans with emphasis on strain-specific effects and the development of next-generation probiotics specifically targeted for cancer applications, in combination with current treatment therapeutics.},
}

*Probiotics/therapeutic use/administration & dosage
Humans
*Neoplasms/therapy/etiology/prevention & control/microbiology
Gastrointestinal Microbiome
*Carcinogenesis/drug effects
Tumor Microenvironment/immunology
Animals
Immunotherapy/methods

@article {pmid40561431,
year = {2025},
author = {Ho, M and Bonavida, B},
title = {Review Article: Probiotics-Mediated Enhancement of Checkpoint Inhibitor Blockade for HER2+ Breast Cancer.},
journal = {Critical reviews in oncogenesis},
volume = {30},
number = {2},
pages = {37-47},
doi = {10.1615/CritRevOncog.2025058633},
pmid = {40561431},
issn = {0893-9675},
mesh = {Humans ; *Breast Neoplasms/drug therapy/metabolism/pathology/immunology ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Probiotics/therapeutic use/administration & dosage ; *Receptor, ErbB-2/metabolism/antagonists & inhibitors ; Female ; Gastrointestinal Microbiome/drug effects/immunology ; Animals ; Immunotherapy/methods ; },
abstract = {Immune checkpoint inhibitors (ICIs) have significantly improved survival rates for many types of cancer, giving patients survival prognoses that had been previously unattainable. Unfortunately, in many advanced cancers, including breast cancer (BC), objective response rates (ORRs) have been reported to be between 5% and 25% and immune-related adverse events (irAEs) can be severe, emphasizing the need to improve the effectiveness of ICIs while minimizing irAEs. In recent years, probiotics and various bacteria consortia have gained growing recognition for their application in immunotherapies for various cancers. Many preclinical models have demonstrated that probiotics significantly influence the gut microbiome, enhancing the production of beneficial metabolites and promoting interactions with cytotoxic T cells to amplify the antitumor effects of ICIs. For the treatment of HER2+ BC, current clinical trials have administered ICIs in combination with anti-HER2 agents (e.g., trastuzumab) to enhance treatment efficacy. Thus far, this combination has shown promising results, especially in patients with advanced PDL1-positive disease. However, as these trials are still ongoing, the efficacy of immune checkpoint blockade (ICB) therapy for HER2+ BCs remains inconclusive and requires further investigation. Thus, this review discusses the use of probiotics in ICB therapy, focusing on the potential role of probiotics in HER2+ BC response to ICIs, their underlying mechanisms and challenges.},
}

Humans
*Breast Neoplasms/drug therapy/metabolism/pathology/immunology
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Probiotics/therapeutic use/administration & dosage
*Receptor, ErbB-2/metabolism/antagonists & inhibitors
Female
Gastrointestinal Microbiome/drug effects/immunology
Animals
Immunotherapy/methods

@article {pmid40561430,
year = {2025},
author = {Ung, W and Bonavida, B},
title = {Review Article: Fecal Microbiota Transplantation in Melanoma: Mechanisms-Mediated Enhancement of Anti-Tumor Immunotherapy.},
journal = {Critical reviews in oncogenesis},
volume = {30},
number = {2},
pages = {23-35},
doi = {10.1615/CritRevOncog.2025058249},
pmid = {40561430},
issn = {0893-9675},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Melanoma/therapy/immunology/microbiology/etiology ; *Immunotherapy/methods ; *Gastrointestinal Microbiome/immunology ; Immune Checkpoint Inhibitors/therapeutic use ; Animals ; *Skin Neoplasms/therapy/immunology/microbiology ; },
abstract = {The gut microbiota is integral to human health, influencing nutrition, metabolism, and immunity. Dysbiosis has been implicated in cancer development and resistance to therapies, highlighting the potential of microbiota modulation as a therapeutic strategy. Melanoma, while comprising only 1% of skin cancer diagnoses, accounts for over 80% of skin cancer related deaths, emphasizing the need for innovative approaches to enhance treatment efficacy. Although immune checkpoint inhibitors (ICIs) such as anti-programmed cell death protein (PD-1) and cytotoxic T-lymphocyte associated protein 4 (CTLA-4) blockade therapies have significantly improved survival for some melanoma patients, the majority fails to achieve durable responses and often develops long-term resistance to these treatments. Fecal microbiota transplantation (FMT) is emerging as a promising intervention to restore microbial balance and enhance treatment efficacy. This review explores the historical evolution and current applications of FMT in oncology, with a focus on its ability to modulate the gut microbiome, augment antitumor immunity, and overcome resistance to checkpoint blockade therapy in melanoma. Despite its promise, significant challenges remain, including ensuring the safety of the procedure, selecting suitable donors, and addressing regulatory hurdles. Future research aimed at optimizing FMT protocols, identifying key microbial strains, and understanding the mechanisms underlying microbiota-immune interactions will be essential to fully harness the potential of FMT as a transformative adjunct in cancer treatment.},
}

Humans
*Fecal Microbiota Transplantation/methods
*Melanoma/therapy/immunology/microbiology/etiology
*Immunotherapy/methods
*Gastrointestinal Microbiome/immunology
Immune Checkpoint Inhibitors/therapeutic use
Animals
*Skin Neoplasms/therapy/immunology/microbiology

@article {pmid40561429,
year = {2025},
author = {Navasardyan, I},
title = {Review Article: Involvement of the Gut Microbiome and Probiotic Interventions in Pediatric Acute Lymphoblastic Leukemia.},
journal = {Critical reviews in oncogenesis},
volume = {30},
number = {2},
pages = {13-21},
doi = {10.1615/CritRevOncog.2025058176},
pmid = {40561429},
issn = {0893-9675},
mesh = {Humans ; *Probiotics/therapeutic use ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology/therapy ; *Gastrointestinal Microbiome/drug effects/immunology ; Child ; Child, Preschool ; },
abstract = {Acute lymphoblastic leukemia (ALL) is a common pediatric cancer marked by uncontrolled proliferation of lymphoblasts, primarily affecting children aged two to five years. While treatment success rates have reached 90% in children, challenges such as therapy toxicity and relapse persist. The gut microbiome, known to impact immune function, is often disrupted in ALL patients, potentially worsening with treatments like chemotherapy and antibiotics. Research suggests probiotics may help restore microbial balance and mitigate side effects, with certain strains showing promise in reducing gastrointestinal symptoms; however, their use requires caution in immunocompromised patients due to infection risks. Probiotics could improve treatment outcomes in ALL, but further research is needed to establish safe, standardized protocols for use in this sensitive population.},
}

Humans
*Probiotics/therapeutic use
*Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology/therapy
*Gastrointestinal Microbiome/drug effects/immunology
Child
Child, Preschool

@article {pmid40561428,
year = {2025},
author = {Kumari, S and Srilatha, M and Nagaraju, GP},
title = {Review Article: Understanding the Role of the Microbiome in Breast Cancer Progression.},
journal = {Critical reviews in oncogenesis},
volume = {30},
number = {2},
pages = {1-11},
doi = {10.1615/CritRevOncog.2024056468},
pmid = {40561428},
issn = {0893-9675},
mesh = {Humans ; *Breast Neoplasms/pathology/microbiology/therapy/etiology/metabolism ; Female ; *Dysbiosis/microbiology ; Disease Progression ; *Gastrointestinal Microbiome ; *Microbiota ; Animals ; },
abstract = {The breast cancer fatality rate poses a global health concern. Dysbiosis of the gut and breast microbiome plays a crucial role in both the onset and metastasis of breast cancer by influencing immune response and hormone metabolism. Probiotics, antibiotics, and KEY WORDS: breast cancer, immunotherapy, microbiome, exosomes, gut microbiota are used in microbiome-targeted drugs as therapy alternatives. Metabolic alterations accelerate the development of cancer. For instance, 27-hydroxycholesterol promotes tamoxifen resistance and estrogen receptor-positive (ER+) breast cancer. Malignant breast tissues differ from healthy breast tissues by their unique microbial profiles. The microbiome influences metabolic pathways such as lipid and glucose metabolism and microbial compounds like β-glucuronidases and short-chain fatty acids (SCFAs) influence metabolism, drug resistance, and progression of cancer. New approaches to treating breast cancer include immunotherapies, nanoparticle drug delivery systems, and emerging therapeutics based on interactions among the microbiome, the immune system, and exosomes. These approaches may improve immune responses, decrease chemotherapy resistance, and stop the spread of cancer. Here, we discuss dysbiosis in breast cancer and therapeutic approaches.},
}

Humans
*Breast Neoplasms/pathology/microbiology/therapy/etiology/metabolism
Female
*Dysbiosis/microbiology
Disease Progression
*Gastrointestinal Microbiome
*Microbiota
Animals

@article {pmid40560629,
year = {2025},
author = {Zhou, Y and Chai, L and Wang, Y and Zhang, H},
title = {Multi-dimensional characterization of the tumor microenvironment profiles in lung squamous cell carcinoma.},
journal = {Physiological genomics},
volume = {},
number = {},
pages = {},
doi = {10.1152/physiolgenomics.00042.2025},
pmid = {40560629},
issn = {1531-2267},
abstract = {Tumor microenvironment (TME) plays an important role in tumorigenesis, development, metastasis and drug sensitivity, but little is known about it in lung squamous cell carcinoma (LUSC). Here, the RNA-sequencing data, clinical and survival data of patients with LUSC in The Cancer Genome Atlas and six independent datasets were collected. Based on the unsupervised clustering of knowledge-based functional gene expression signatures, LUSC was classified into four subtypes. Cluster1 and cluster3 exhibited substantial tumor immune infiltration, suggesting a better response to immunotherapy. Relatively worse survival was observed in cluster4, probably due to higher angiogenesis. Besides, differentially expressed genes in cluster1, cluster2 and cluster3 were prominently enriched in immune-related pathways, while extracellular matrix-related pathways were enriched for cluster4. Genomic data analyses showed significant variations in tumor mutational burden and mutational frequency of several genes, such as TP53, among the four subtypes. Additionally, the four subtypes exhibited heterogeneity in the sensitivity of commonly used chemotherapy drugs for lung cancer and the intratumor microbiome profile. Finally, a prognostic model was developed and its performance and generalization ability were independently validated in multiple datasets. Overall, our study advances the understanding of the TME in LUSC and proposes a prognostic model that facilitates clinical decision-making.},
}

@article {pmid40560537,
year = {2025},
author = {Stummer, BE and Moghaddam, MJ and Roohani-Dezfouli, M and Nidumolu, B and Zhang, X and Harvey, PR},
title = {Wheat rhizosphere persistence of Trichoderma gamsii A5MH during suppression of a Fusarium-Pythium root disease complex differentially impacts the soil fungal and oomycete microbiome.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf158},
pmid = {40560537},
issn = {1365-2672},
abstract = {AIMS: Determine the impacts of inoculant strain Trichoderma gamsii A5MH and crop phenology on the structure of fungal and oomycete communities in wheat rhizosphere soil.

METHODS AND RESULTS: Over two consecutive wheat crops, A5MH inoculation suppressed an oomycete (Globisporangium)-fungal (Fusarium) root disease complex. Amplicon sequencing determined the impacts of A5MH-treatment and crop phenology on the structure of rhizosphere soil fungal and oomycete communities. Culture-dependent (C-D) techniques quantified inoculant impacts on non-target root endophytic fungi, previously co-isolated with strain A5MH and the fungal and oomycete pathogens. Inoculant treatment differentiated the structure of the fungal microbiome in both years, primarily due to increased Trichoderma abundance and decreases in cereal pathogenic, root endophytic and saprophytic taxa. Strain A5MH did not impact the structure of the oomycete microbiome. Crop phenology altered fungal and oomycete community structure, these impacts greater at tillering and grain harvest, respectively. A5MH-induced decreases in rhizosphere abundance (C-D) of root endophytic fungi were associated with increased crop biomass at tillering.

CONCLUSIONS: Whilst the structure of rhizosphere soil fungal and oomycete communities altered as the wheat crop matured, only fungal communities were impacted by A5MH-treatment due to increased Trichoderma and decreased abundance of recognized and emerging plant pathogenic fungi.},
}

@article {pmid40560509,
year = {2025},
author = {Andersen, C and Ebsen, TS and Thorup, CA and Reinholdt, KB and Kjaerulff, AMG and Udholm, N and Khalid, V and Madzak, A and Duez, C and Münch, H and Pauli, S and Danstrup, CS and Petersen, NK and Greve, T and Klug, TE},
title = {Next-generation sequencing of the tonsillar microbiome in severe acute tonsillitis: comparison with healthy controls and culture-based findings.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40560509},
issn = {1435-4373},
abstract = {PURPOSE: Previous culture-based studies suggest three significant pathogens in acute tonsillitis (AT): Streptococcus pyogenes, Fusobacterium necrophorum, and Streptococcus dysgalactiae. Next-generation sequencing (NGS) provides further insights into the human microbiome and may pinpoint additional pathogens in bacterial infections. We aimed to investigate the tonsillar microbiome and identify pathogens associated with AT by applying NGS to tonsillar swabs from patients with severe AT, comparing the findings with both healthy controls and culture-based results.

METHODS: Full-length sequencing of the 16S rRNA gene (16S tNGS) was performed on tonsillar swabs from 64 AT patients and 55 controls, who were prospectively enrolled at two Danish Ear-Nose-Throat Departments between June 2016 and December 2019.

RESULTS: The mean number of detected bacteria was significantly higher in patients analysed with 16S tNGS (36) than with culture methods (6.5, p < 0.001). The alpha diversity was lower in patients compared to controls (p < 0.001) and beta diversity showed separation of the two groups (p = 0.001). S. pyogenes (p = 0.001) and Bifidobacteriaceae (p = 0.002) were significantly more abundant in patients compared to controls. The three suggested pathogens were detected more frequently using 16S tNGS compared to culture: S. pyogenes (38% vs. 27%, p = 0.26), F. necrophorum (19% vs. 11%, p = 0.32), and S. dysgalactiae (14% vs. 11%, p = 0.79).

CONCLUSION: The tonsillar microbiome differed significantly between AT patients and healthy controls. Our findings confirm the role of S. pyogenes in AT, but did not identify additional likely pathogens. The addition of 16S tNGS to cultures increased the collective detection rate of three previously suggested pathogens from 48 to 70%.},
}

@article {pmid40560314,
year = {2025},
author = {Rojas-Chacón, JA and Echeverría-Beirute, F and Jiménez-Madrigal, JP and Varela-Benavides, I and Faggioli, V and Berkelmann, D and Gatica-Arias, A},
title = {Deciphering soil nematode-bacteria-fungi community composition and functional dynamics in coffee agroecosystems under conventional and sustainable management practices in Costa Rica.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {7},
pages = {220},
pmid = {40560314},
issn = {1573-0972},
support = {801-C3-501//UKRI-BBSRC Capacity Building for Bioinformatics in Latin America Network (CABANA-net) grant, between the Chan Zuckerberg Initiative (CZI) and the University of Costa Rica/ ; 801-C3-501//UKRI-BBSRC Capacity Building for Bioinformatics in Latin America Network (CABANA-net) grant, between the Chan Zuckerberg Initiative (CZI) and the University of Costa Rica/ ; 801-C3-501//UKRI-BBSRC Capacity Building for Bioinformatics in Latin America Network (CABANA-net) grant, between the Chan Zuckerberg Initiative (CZI) and the University of Costa Rica/ ; 2022-316296//The Chan Zuckerberg Initiative DAF/ ; 2022-316296//The Chan Zuckerberg Initiative DAF/ ; 2022-316296//The Chan Zuckerberg Initiative DAF/ ; },
mesh = {Costa Rica ; *Soil Microbiology ; Animals ; *Nematoda/classification/genetics/physiology ; Soil/chemistry/parasitology ; *Fungi/classification/genetics/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; Agriculture/methods ; *Coffee/growth & development ; Coffea/growth & development ; High-Throughput Nucleotide Sequencing ; },
abstract = {Understanding the interactions between soil bacteria, fungi, and nematodes in coffee agroecosystems is crucial for optimizing sustainable agriculture. This study investigated the composition and functional dynamics of these communities under conventional and sustainable management systems. Soil samples were collected from three major coffee-growing regions in Costa Rica, representing different agricultural regimes. Nematode community was analyzed using optical microscopy, while microbial communities were analyzed using high-throughput sequencing. In both cases, bioinformatic tools were used for functional prediction based on taxonomy.. Herbivorous nematodes dominated both systems, while bacterivores (Rhabditidae, Cephalobidae) and fungivores (Aphelenchoidae) were significantly more abundant in soils subject to sustainable practice (p < 0.05). Nematode maturity indices and food web diagnostics showed no significant differences between systems, even though metabolic footprints related to organic matter decomposition varied (p < 0.05). Bacterial communities were dominated by the phyla Proteobacteria, Acidobacteria, and Chloroflexi, while the fungal community was largely composed of Ascomycota (53.21% in both systems). The fungal genus Mortierella was particularly prevalent. Soil pH, along with Ca, Mg, K, and extractable acidity, influenced community composition. Functional profiles revealed higher gene abundances linked to nutrient and energy cycling in sustainable systems, particularly phosphorus and sulfur metabolism. Saprotroph-symbiotroph fungi were more common in sustainable soils, while pathotrophic fungi dominated conventional systems. This is the first comprehensive analysis of bacteria, fungi, and nematodes across different agricultural practices in coffee agroecosystems in Costa Rica.},
}

Costa Rica
*Soil Microbiology
Animals
*Nematoda/classification/genetics/physiology
Soil/chemistry/parasitology
*Fungi/classification/genetics/isolation & purification
*Bacteria/classification/genetics/isolation & purification
Agriculture/methods
*Coffee/growth & development
Coffea/growth & development
High-Throughput Nucleotide Sequencing

@article {pmid40560287,
year = {2025},
author = {Zhuang, Y and Lyu, T and Chen, Y and Li, W and Tang, L and Xian, SP and Yang, PF and Wang, L and Zhang, QQ and Mei, C and Lin, YJ and Yan, Z and Li, Z and He, JZ and Zeng, FM},
title = {Mechanistic insights into endometriosis: roles of Streptococcus agalactiae and L-carnitine in lesion development and angiogenesis.},
journal = {Angiogenesis},
volume = {28},
number = {3},
pages = {38},
pmid = {40560287},
issn = {1573-7209},
support = {202401AY070001-120//Yunnan Province Applied Basic Research Program Kunming Medical University Joint Project/ ; WYYXQN-2021016//the Excellent Young Researchers Program of the Fifth Affiliated Hospital of Sun Yat-sen University/ ; 2023080017//the Excellent Young Researchers Program of the Fifth Affiliated Hospital of Sun Yat-sen University/ ; 82102689//National Natural Science Foundation of China/ ; 2022A1515220187//The Guangdong Basic and Applied Basic Research Foundation/ ; 22qntd3502//Fundamental Research Funds for the Central Universities, Sun Yat-sen University/ ; 2018-016//Project of Guiyang Health and Family Planning Commission/ ; },
mesh = {Female ; Humans ; *Streptococcus agalactiae/metabolism ; Animals ; *Carnitine/metabolism/pharmacology ; *Neovascularization, Pathologic/microbiology/pathology/metabolism ; Mice ; *Endometriosis/microbiology/pathology/metabolism ; Adult ; *Streptococcal Infections/microbiology/pathology ; Cell Movement ; Angiogenesis ; },
abstract = {Retrograde menstruation is a widely recognized etiological factor for endometriosis (EMs); however, it is not the sole cause, as not all affected women develop EMs. Emerging evidence suggests a significant association between the vaginal microbiota and EMs. Nonetheless, the precise mechanisms by which microbial communities influence the pathophysiology and progression of EMs remain unclear. In this study, the cervical mucus from patients with EMs showed significantly greater microbial abundance compared with that of controls, with Streptococcus agalactiae (S. agalactiae) exhibiting the most substantial increase as determined by 16S rRNA gene sequencing. In a murine model, elevated S. agalactiae levels significantly increased the lesion number and colonization, whereas antibiotic treatment reduced lesion formation. Metabolomic analyses showed elevated L-carnitine levels in the cervical secretions and serum of patients with EMs, a finding corroborated in murine tissues. Exogenous L-carnitine administration similarly increased the number and weight of endometriotic lesions. Meanwhile, the inhibition of L-carnitine synthesis suppressed lesion formation induced by S. agalactiae. In vitro, both S. agalactiae and L-carnitine promoted EMs cell proliferation, migration, and invasion. L-carnitine synthesis inhibition attenuated cell motility stimulated by S. agalactiae. Mechanistically, S. agalactiae enhanced angiogenesis through L-carnitine by upregulating vascular endothelial growth factor expression and increasing human umbilical vein endothelial cell motility. These findings identify S. agalactiae as a key cervical microbiome component in EMs development and reveal a microbiota-metabolite-angiogenesis axis that may offer novel therapeutic targets.},
}

Female
Humans
*Streptococcus agalactiae/metabolism
Animals
*Carnitine/metabolism/pharmacology
*Neovascularization, Pathologic/microbiology/pathology/metabolism
Mice
*Endometriosis/microbiology/pathology/metabolism
Adult
*Streptococcal Infections/microbiology/pathology
Cell Movement
Angiogenesis

@article {pmid40560276,
year = {2025},
author = {Sharma, A and Bora, P},
title = {Engineering synthetic microbial communities to restructure the phytobiome for plant health and productivity.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {7},
pages = {228},
pmid = {40560276},
issn = {1573-0972},
mesh = {*Plants/microbiology ; *Microbiota ; Soil Microbiology ; Agriculture/methods ; Bacteria/genetics/metabolism ; *Synthetic Biology/methods ; *Microbial Consortia ; },
abstract = {Global agriculture stands at a critical juncture, facing the dual challenge of sustaining food production for a rapidly growing population while mitigating the environmental consequences of intensive farming. The overuse of chemical fertilizers and pesticides has accelerated soil degradation, biodiversity loss, and ecological imbalances, threatening long-term viability. Synthetic microbial communities (SynComs) have emerged as a promising approach to reshape plant-microbe interactions, offering a precise, scalable, and ecologically sustainable alternative to conventional agrochemicals. Unlike native microbial communities, which form naturally and vary with environmental conditions, SynComs are deliberately assembled consortium of multiple microbial strains selected for their complementary functions, ecological compatibility, and ability to perform targeted roles within a host or environment. By engineering microbes with targeted functional traits, SynComs enhance nutrient assimilation, bolster plant defence, and fortify resilience against biotic and abiotic stresses. The understanding of SynCom design, exploring their composition, functional dynamics, and mechanisms for optimizing plant health is crucial for effective synthesis and application, alongside cutting-edge computational tools and genomic databases that enable precision engineering of microbial communities. Despite their transformative potential, large-scale application of SynComs remains constrained by challenges related to field efficacy, regulatory frameworks, and long-term microbial persistence. Addressing these barriers through interdisciplinary research and policy innovation is imperative. As environmental microbiome moves towards sustainability-driven solutions, SynComs hold the key to revolutionizing farming practices, reducing chemical dependence, and ensuring global food security in an era of mounting environmental stressors.},
}

*Plants/microbiology
*Microbiota
Soil Microbiology
Agriculture/methods
Bacteria/genetics/metabolism
*Synthetic Biology/methods
*Microbial Consortia

@article {pmid40560225,
year = {2025},
author = {Li, T and Tian, Y and Wang, Y and Yang, J and Chen, Z and Li, Y},
title = {Elucidation of novel diagnostic biomarkers and therapeutic targets in colorectal carcinoma: an integrative approach leveraging multi-omics, computational biology, and single-cell sequencing technologies.},
journal = {Mammalian genome : official journal of the International Mammalian Genome Society},
volume = {},
number = {},
pages = {},
pmid = {40560225},
issn = {1432-1777},
support = {82104012, 82202950, 82303681//The National Natural Science Foundation of China/ ; 2021-I2M-1-042//the Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences/ ; 3332022063//the Fundamental Research Funds for the Central Universities/ ; },
abstract = {This study employs a comprehensive, multi-layered analytical approach to comprehensively investigate the pathogenesis, diagnostic methodologies, and potential therapeutic targets of colorectal cancer. Integrating data from the Global Burden of Disease (GBD) database, transcriptomics, proteomics, and single-cell sequencing technologies, this study elucidates both the epidemiological characteristics and molecular mechanisms of colorectal cancer. Our findings indicate that VEGFA, ICAM1, and IL6R play prominent roles in cancer progression. Proteomics analysis has identified multiple potential drug targets, and molecular docking and dynamic simulations have provided a theoretical foundation for developing drugs targeting VEGFA. Multi-omics studies have revealed that colorectal cancer progression involves intricate microbiome-host interactions, metabolic regulation, and immune response mechanisms, with factors such as Clostridia, 4E-BP1, AIFM1, and CXCL5 exhibiting dual roles. These discoveries not only deepen our understanding of colorectal cancer pathogenesis but also offer novel insights for optimizing diagnostic and therapeutic strategies, thereby laying the groundwork for developing personalized treatment regimens. Future research should focus on further validating these findings and exploring their potential clinical applications.},
}

@article {pmid40560060,
year = {2025},
author = {Dinakis, E and Xu, C and Muralitharan, R and Jama, H and Xie, L and Leung, C and Mirabito Colafella, K and McArdle, Z and Salimova, E and Camargo Tavares, L and Snelson, M and Johnson, C and Gaspari, T and Mackay, C and O'Donnell, J and Marques, F},
title = {pH-sensor GPR68 plays a role in how dietary fibre lowers blood pressure in a preclinical model of hypertension.},
journal = {Clinical science (London, England : 1979)},
volume = {},
number = {},
pages = {},
doi = {10.1042/CS20243009},
pmid = {40560060},
issn = {1470-8736},
support = {102927, 105663, 106698//National Heart Foundation of Australia/ ; GTN2017382, GNT2017382, GNT1124288//National Health and Medical Research Council/ ; Not applicable//Sylvia and Charles Viertel Charitable Foundation/ ; },
abstract = {Dietary fibre lowers blood pressure (BP) via short-chain fatty acids, acidic metabolites released from fibre fermentation by bacteria in the large intestine. This acidic microenvironment may activate the pH-sensing receptor GPR68, primarily expressed in immune cells. Here, we aimed to investigate whether GPR68 confers the BP-lowering effects of a high-fibre diet in hypertension by regulating inflammatory responses. Baseline BP parameters were measured using telemetry in C57BL/6J wildtype (WT) and GPR68-deficient (Gpr68-/-) male and female mice. Moreover, male mice were fed a control or high-fibre diet following minipump implantation with saline or Angiotensin II (Ang II), where BP was measured weekly by tail-cuff. Cardiac ultrasounds, histological, flow cytometric and gut microbiome (16S) analyses were performed. No BP differences were detected in untreated male and female mice, irrespective of genotype. Similarly to WT mice, Gpr68-/- male mice were susceptible to Ang II-induced hypertension. High-fibre-fed WT mice exhibited blunted elevations in BP and improved cardiac collagen deposition and aortic elastin content compared to control-fed WT mice. These were not observed in high-fibre-fed Gpr68-/- mice. A high-fibre diet decreased pro-inflammatory renal and aortic immune cell counts independently of GPR68. Dietary fibre, rather than GPR68 or Ang II, was the primary factor influencing differences in the gut microbiota. This study provides novel insight into how the pH-sensing receptor GPR68 may be implicated in the protective effects of a high-fibre diet. However, these effects are likely immune-independent.},
}