@article {pmid40368038,
year = {2025},
author = {Silvester, R and Perry, WB and Webster, G and Rushton, L and Baldwin, A and Pass, DA and Byrnes, NA and Farkas, K and Heginbothom, M and Craine, N and Cross, G and Kille, P and Kasprzyk-Hordern, B and Weightman, AJ and Jones, DL},
title = {Metagenomic profiling of hospital wastewater: A comprehensive national scale analysis of antimicrobial resistance genes and opportunistic pathogens.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106503},
doi = {10.1016/j.jinf.2025.106503},
pmid = {40368038},
issn = {1532-2742},
abstract = {BACKGROUND: Healthcare settings are recognised as potential hotspots for the emergence and spread of antimicrobial resistance (AMR).

METHOD: Metagenomic sequencing was conducted on a national scale using wastewater from hospitals across Wales to screen for antimicrobial resistance genes (ARGs) and opportunistic pathogens.

RESULTS: The total abundance and diversity of ARGs varied significantly across the hospitals. Genes conferring resistance to aminoglycosides, beta-lactams, and Macrolide-Lincosamide-Streptogramin-class antibiotics were predominant, with distinct resistome patterns emerging spatially. OXA-type beta-lactamases were the dominant ARG types. Spatial variability was observed in the distribution of the "big five" carbapenemases (KPC, IMP, VIM, NDM, OXA-48-like) and mcr genes, as well as WHO-listed fungal priority pathogens and Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli (ESKAPEE) pathogens. Furthermore, antibiotic concentrations in the effluents often exceeded risk quotients, posing a substantial risk for AMR emergence.

CONCLUSIONS: Overall, the study highlights the effectiveness of combining wastewater-based epidemiology with metagenomics to gain critical insights into the distinct resistome and microbiome profiles in hospital settings. Tailored strategies are essential to mitigate the spread of antibiotics, clinically relevant ARGs and pathogens in these settings. This study underscores the necessity of implementing pre-treatment processes for hospital effluents before release into community sewers and environmental waters to curb the spread of these micro-pollutants.

AVAILABILITY OF DATA: The data will be made available upon request.},
}

@article {pmid40368024,
year = {2025},
author = {Lammert, C and Vuppalanchi, S and Green, K and Blessing, N and Desai, A and Stump, T and Miller, NG and Spence, L and Wright, A},
title = {Effect of Mediterranean and Western diets on fatigue in patients with autoimmune hepatitis: Protocol for a randomized crossover diet intervention trial.},
journal = {Contemporary clinical trials},
volume = {},
number = {},
pages = {107951},
doi = {10.1016/j.cct.2025.107951},
pmid = {40368024},
issn = {1559-2030},
abstract = {BACKGROUND: Fatigue is a debilitating symptom in patients with autoimmune hepatitis (AIH), and no effective treatment interventions are currently available. The anti-inflammatory properties of a Mediterranean diet (MD) may offer a potential non-pharmacological approach to reducing fatigue. This paper outlines the rationale, design, and protocol for a randomized crossover diet intervention trial to assess the effects of Mediterranean diet (MD) compared to a Western diet (WD) on fatigue levels in patients with AIH.

METHODS: In this crossover study, 48 subjects will be randomized to start either a MD or WD arm. After completing the initial arm, participants will switch to the opposite diet. The study team (including the PI and coordinator) and patients will remain blinded to the dietary intervention. The primary outcome will be the change in the fatigue component score of the PROMIS®-29 Profile v.2.0 survey during each dietary intervention. Secondary outcomes include changes in individual PROMIS-29 domain scores, mental and physical summary scores, circulating markers of inflammation (C-reactive protein and others), key liver serum biomarker levels (alanine aminotransferase, immunoglobulin G, total protein), stool microbiome (16S) and short-chain fatty acids, liver stiffness and steatosis, serum iron studies (ferritin, total iron binding capacity, transferrin saturation, hemoglobin), and nutritional markers such as serum vitamin D and magnesium levels.

CONCLUSION: If the Mediterranean diet (MD) is associated with a statistically significant decrease in the fatigue component score of the PROMIS®-29 survey, it could serve as a promising non-pharmacological intervention to reduce fatigue in AIH patients, offering a novel approach to improve quality of life in this population.

CLINICALTRIALS: gov ID: NCT06250309.},
}

@article {pmid40367854,
year = {2025},
author = {Ahmad, W and Coffman, L and Ray, R and Woldesenbet, S and Singh, G and Khan, AL},
title = {Flooding episodes and seed treatment influence the microbiome diversity and function in the soybean root and rhizosphere.},
journal = {The Science of the total environment},
volume = {982},
number = {},
pages = {179554},
doi = {10.1016/j.scitotenv.2025.179554},
pmid = {40367854},
issn = {1879-1026},
abstract = {Climate change-related events such as flooding have threatened crop productivity, agricultural sustainability, and global food security by causing hypoxic conditions. Such conditions impaire root development and nutrient acquisition, and alter root rhizospheric microbial communities that are vital for plant health and productivity. Seed treatment with pathogen protection have been key to maintaining early seed germination and plant productivity in field conditions. Still, their role in flooding stress and microbiome diversity and functionality in soybeans is poorly understood. Here, we performed field-based investigations to understand the impact of flooding episodes (0, 3, and 7 days after floodings; DAF) and seed treatment (Cruiser MAXX) on soybean plant growth and rhizosphere microbiome diversity and functionality. Flooding episodes significantly reduced seed yield (746 kg ha[-1]) compared to untreated control. However, the seed treatment increased plant height and pods per plant (3-DAF) and reduced flood injury by 33 % (7-DAF). The shotgun metagenomic analysis showed that seed treatment significantly enhanced the microbial community in rhizospheric soil. Flooding episodes impacted the microbial communities with higher abundance at 3-DAF than at 7-DAF. Flooding stress reduced the microbial diversity, although Proteobacteria increased as root endophytes. Seed treatment and flooding combinations decreased microbiome functionality and reduced gene counts for phytohormone biosynthesis, fermentation, nitrogen, symbiosis, and degradation pathways. Similarly, flooding stress shifted the carbohydrate synthesis to a more specialized substrate. These findings enhance understanding of soybean root and rhizosphere microbiome diversity and functionality dynamics during flooding stress and provide a platform to develop sustainable agricultural practices for enhancing soybean stress tolerance to flooding.},
}

@article {pmid40367778,
year = {2025},
author = {Wang, D and Lu, Q and Liu, X and Li, Y and Du, M and Zhao, M and Tong, Y and Ni, BJ},
title = {[P(CH2OH)4]Cl induced natural shift of methanogenic pathway through disrupting bacterial disulfide bonds and reshaping microbial community structure.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138609},
doi = {10.1016/j.jhazmat.2025.138609},
pmid = {40367778},
issn = {1873-3336},
abstract = {Ionic liquids (ILs), which are expanding produced and applied as alternatives to volatile organic solvents, have shown the ability to deteriorate the anaerobic biotransformation of organics. It is unclear, nevertheless, how ILs affect different functional anaerobes during anaerobic digestion, leaving a knowledge gap in the environmental risks of ILs. Here, we revealed that the differences of Gram-staining bacteria probably were the part drivers of a shift in methanogenic pathway from acetoclastic to hydrogenotrophic methanogenesis in anaerobic microcosms exposed to a typical IL (Tetrakis (hydroxymethyl) phosphonium chloride, [P(CH2OH)4]Cl). The results showed that 0.1-4 mg/L [P(CH2OH)4]Cl respectively decreased methane production rate and carbon-use efficiency by 4.43-43.90 % and 0.52-57.23 % during anaerobic digestion. Microbial community and microscopic examination analysis indicated that most Gram-positive bacteria were more likely to survive in the [P(CH2OH)4]Cl-present environment than Gram-negative bacteria. Mechanistically, [P(CH2OH)4]Cl distorted cell walls of anaerobes, and then perturbed protein homeostasis in the periplasm by breaking disulfide bonds and disrupting disulfide-bond-forming pathways. Moreover, Gram-positive bacteria exhibited a higher tolerance than Gram-negative bacteria, potentially due to their thicker peptidoglycan structures and reliance less on disulfide bonds to stabilize proteins, leading to the remodeling of microbiome function and carbon-transport pathway. This study is the first to reveal the differential impact of [P(CH2OH)4]Cl on Gram-positive vs. Gram-negative anaerobes during methanogenesis, providing new insights into the ecological risks of ILs and contributing to their optimal design.},
}

@article {pmid40367291,
year = {2025},
author = {Meister, M and He, X and Noël, A and Park, JA and Crotty Alexander, L and Zelikoff, J and Christiani, D and Hess, J and Shannahan, J and Wright, C},
title = {Beyond the puff: health consequences of vaping.},
journal = {Inhalation toxicology},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/08958378.2025.2500646},
pmid = {40367291},
issn = {1091-7691},
abstract = {Electronic nicotine delivery systems (ENDS) arrived on the U.S. market in 2007 and rapidly grew in popularity as a harm reduction tool for traditional cigarette users. While initially marketed as a healthier alternative to combustible cigarettes, the unique mixture of chemical constituents in ENDS products and their emissions have led to rising concern about their safety and the long-term health implications. Given the lack of long-term, epidemiological research on the health effects of these products, recent research has sought to understand the impacts on cellular components and gain understanding of acute effects to inform potential chronic health implications. Studies have demonstrated the deleterious effects the use of ENDS has on the oral cavity, respiratory, and cardiovascular systems. ENDS use has been linked to gingival inflammation and alterations in the oral microbiome contributing to periodontal disease. Further, the presence of heavy metals and other constituents in ENDS emissions contribute to aberrant oxidative stress and inflammation within the lung, contributing to alterations in functional lung capacity and respiratory symptoms in ENDS users. In addition, harmful components of ENDS emissions make their way to the circulatory system, leading to detrimental impacts in cardiovascular functioning such as a rise in blood pressure, impaired vascular functioning, and increased heart rate, all of which are known to underscore long-term cardiovascular ailments. This review will provide an in-depth discussion of the current literature available on the consequences of ENDS use on the oral cavity, respiratory, and cardiovascular systems as well as provide insight into long-term implications that may result.},
}

@article {pmid40366861,
year = {2025},
author = {Li, Y and Li, H and Chen, W and O'Riordan, K and Mani, N and Qi, Y and Liu, T and Mani, S and Ozcan, A},
title = {Deep learning-based detection of bacterial swarm motion using a single image.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2505115},
doi = {10.1080/19490976.2025.2505115},
pmid = {40366861},
issn = {1949-0984},
abstract = {Motility is a fundamental characteristic of bacteria. Distinguishing between swarming and swimming, the two principal forms of bacterial movement, holds significant conceptual and clinical relevance. Conventionally, the detection of bacterial swarming involves inoculating samples on an agar surface and observing colony expansion, which is qualitative, time-intensive, and requires additional testing to rule out other motility forms. A recent methodology that differentiates swarming and swimming motility in bacteria using circular confinement offers a rapid approach to detecting swarming. However, it still heavily depends on the observer's expertise, making the process labor-intensive, costly, slow, and susceptible to inevitable human bias. To address these limitations, we developed a deep learning-based swarming classifier that rapidly and autonomously predicts swarming probability using a single blurry image. Compared with traditional video-based, manually processed approaches, our method is particularly suited for high-throughput environments and provides objective, quantitative assessments of swarming probability. The swarming classifier demonstrated in our work was trained on Enterobacter sp. SM3 and showed good performance when blindly tested on new swarming (positive) and swimming (negative) test images of SM3, achieving a sensitivity of 97.44% and a specificity of 100%. Furthermore, this classifier demonstrated robust external generalization capabilities when applied to unseen bacterial species, such as Serratia marcescens DB10 and Citrobacter koseri H6. This competitive performance indicates the potential to adapt our approach for diagnostic applications through portable devices, which would facilitate rapid, objective, on-site screening for bacterial swarming motility, potentially enhancing the early detection and treatment assessment of various diseases, including inflammatory bowel diseases (IBD) and urinary tract infections (UTI).},
}

@article {pmid40366801,
year = {2025},
author = {Oyama, S and Arslanian, KJ and Savo Sardaro, ML and Duckham, RL and Kershaw, EE and Wood, AN and Fidow, UT and Naseri, T and Reupena, MS and Amato, KR and Hawley, NL},
title = {Gut microbial composition and diversity varies by CREBRF genotype among Samoan infants.},
journal = {Physiological genomics},
volume = {},
number = {},
pages = {},
doi = {10.1152/physiolgenomics.00014.2024},
pmid = {40366801},
issn = {1531-2267},
support = {Downs Fellowship//Yale | Yale School of Public Health, Yale University (YSPH)/ ; R01HL093093//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; International Dissertation Research Fellowship//Yale | Whitney and Betty MacMillan Center for International and Area Studies (MacMillan Center)/ ; Faculty Research Grant//Yale | Whitney and Betty MacMillan Center for International and Area Studies (MacMillan Center)/ ; DDRIG1749911//National Science Foundation (NSF)/ ; T32GM136651//HHS | National Institutes of Health (NIH)/ ; D43TW010540//HHS | NIH | Fogarty International Center (FIC)/ ; //HHS | NIH | Office of Research on Women's Health (ORWH)/ ; F30HD111263//HHS | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; },
abstract = {Introduction: Over 40% of Samoans have at least one copy of the minor A allele at rs373863828 in CREB3 regulatory factor (CREBRF), which is associated with increased BMI but decreased odds of type 2 diabetes mellitus. The mechanisms underlying this paradoxical effect remain unknown. We hypothesized that gut microbiota may play a role and examined associations between CREBRF genotype and gut microbial diversity and composition among Samoan infants. Methods: Fecal samples were collected from Samoan infants aged 0 (n=23), 4 (n=20), and 21 (n=27) months. Microbiota community structure was analyzed using 16S rRNA bacterial gene sequencing. Results: Both cross-sectional and longitudinal analyses revealed no associations between CREBRF genotype and overall microbiome composition or diversity at 0 or 4 months. Cross-sectional analysis at 21 months revealed a significant association between genotype and unweighted UniFrac distances (F1,24=1.855, R2=0.072, p=0.015). Longitudinal differential abundance analysis also revealed several differentially abundant taxa at 21 months. Notably, the AG genotype was associated with lower relative abundance of Escherichia Shigella (β=-6.741, SE=2.243, p=.004, q=.042). Discussion: Significant genotype differences in gut microbiome composition and diversity at 21 months suggest that gut microbiota may be involved in relationships between CREBRF genotype and metabolic health. No genotype differences were observed at 0 or 4 months, suggesting that environmental and/or maternal variables have greater influence on the gut microbiome in early infancy and genotype effects emerge later. Further research should examine whether genotype differences in gut microbiota are associated with functional differences in metabolic or immune signaling pathways or energy extraction.},
}

@article {pmid40366770,
year = {2025},
author = {Baba, Y and Tsuge, D and Aoki, R},
title = {Enhancement of carbohydrate metabolism by probiotic and prebiotic intake promotes short-chain fatty acid production in the gut microbiome: A randomized, double-blind, placebo-controlled crossover trial.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/bbb/zbaf071},
pmid = {40366770},
issn = {1347-6947},
abstract = {Short-chain fatty acids (SCFAs) are thought to be a key factor in the health benefits of prebiotics and probiotics. This study investigated the effect of Bifidobacterium animalis subsp. lactis GCL2505 and inulin (BL+IN) on fecal SCFAs and gut microbial composition and function. A placebo-controlled, randomized, double-blind, crossover study was conducted with 120 participants. Two weeks of BL+IN intake significantly increased acetate, propionate, and butyrate concentrations and Bifidobacterium abundance compared to placebo. Functional analysis of the gut metagenome showed enrichment of genes associated with carbohydrate and amino acid metabolism, suggesting an enhanced capacity for SCFA production. A responder was defined as a participant with increased fecal SCFAs after BL+IN consumption. Responder metagenomes exhibited greater enrichment of genes involved in SCFA production and carbohydrate metabolism. In conclusion, short-term BL+IN ingestion may benefit healthy adults by increasing fecal SCFAs through influencing the composition and functional activation of SCFA-associated pathways in the gut microbiome.},
}

@article {pmid40366727,
year = {2025},
author = {Wang, R and Li, J and Li, X and Guo, Y and Chen, P and Peng, T},
title = {Exercise-induced modulation of miRNAs and gut microbiome: a holistic approach to neuroprotection in Alzheimer's disease.},
journal = {Reviews in the neurosciences},
volume = {},
number = {},
pages = {},
pmid = {40366727},
issn = {2191-0200},
abstract = {Alzheimer's disease (AD), a progressive neurodegenerative disorder, is marked by cognitive decline, neuroinflammation, and neuronal loss. MicroRNAs (miRNAs) have emerged as critical regulators of gene expression, influencing key pathways involved in neuroinflammation and neurodegeneration in AD. This review delves into the multifaceted role of exercise in modulating miRNA expression and its interplay with the gut microbiome, proposing a comprehensive framework for neuroprotection in AD. By synthesizing current research, we elucidate how exercise-induced changes in miRNA profiles can mitigate inflammatory responses, promote neurogenesis, and reduce amyloid-beta and tau pathologies. Additionally, we explore the gut-brain axis, highlighting how exercise-driven alterations in gut microbiota composition can further influence miRNA expression, thereby enhancing cognitive function and reducing neuroinflammatory markers. This holistic approach underscores the potential of targeting exercise-regulated miRNAs and gut microbiome interactions as a novel, noninvasive therapeutic strategy to decelerate AD progression and improve quality of life for patients. This approach aims to decelerate disease progression and improve patient outcomes, offering a promising avenue for enhancing the effectiveness of AD management.},
}

@article {pmid40366158,
year = {2025},
author = {Geonczy, SE and Hillary, LS and Santos-Medellín, C and Sorensen, JW and Emerson, JB},
title = {Patchy burn severity explains heterogeneous soil viral and prokaryotic responses to fire in a mixed conifer forest.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0174924},
doi = {10.1128/msystems.01749-24},
pmid = {40366158},
issn = {2379-5077},
abstract = {UNLABELLED: Effects of fire on soil viruses and virus-host dynamics are largely unexplored, despite known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we assessed how viral and prokaryotic communities responded to a prescribed burn in a mixed conifer forest. We sequenced 91 viral-size fraction metagenomes (viromes) and 115 16S rRNA gene amplicon libraries from 120 samples: four samples at five timepoints (two before fire and three after fire) at six sites (four treatment, two control). We hypothesized that compositional differences would be most significant between burned and unburned soils, but instead, plot location best distinguished viral communities, more than treatment (burned or not), depth (0-3 or 3-6 cm), or timepoint. For both viruses and prokaryotes, some burned communities resembled unburned controls, while others were significantly different, revealing heterogeneous responses to fire. These patterns were explained by burn severity, here defined by soil chemistry. Viral but not prokaryotic richness decreased significantly with burn severity, and low viromic DNA yields indicated substantial loss of viral biomass at higher severity. The relative abundances of Firmicutes, Actinobacteriota, and the viruses predicted to infect them increased significantly with burn severity, suggesting survival and viral infection of these fire-responsive and potentially spore-forming taxa. The degree of burn severity experienced by each patch of soil, rather than burn status alone, differed over mere meters in the same fire. Therefore, our analyses highlight the importance of high-resolution, paired biogeochemical data to explain soil community responses to fire.

IMPORTANCE: The impact of fire on the soil microbiome, particularly on understudied soil viral communities, warrants investigation, given known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we collected 120 soil samples before and after a prescribed burn in a mixed conifer forest to assess the impacts of this disturbance on soil viral and prokaryotic communities. We show that simple categorical comparisons of burned and unburned areas were insufficient to reveal the underlying community response patterns. The patchy nature of the fire (indicated by soil chemistry data) led to significant changes in viral and prokaryotic community composition in areas of high burn severity, while communities that experienced lower burn severity were indistinguishable from those in unburned controls. Our results highlight the importance of considering highly resolved burn severity and biogeochemical measurements, even in nearby soils after the same fire, in order to understand soil microbial responses to prescribed burns.},
}

@article {pmid40366139,
year = {2025},
author = {Crouch, AL and Severance, BM and Creary, S and Hood, D and Bailey, M and Mejias, A and Ramilo, O and Gillespie, M and Ebelt, S and Sheehan, V and Kopp, BT and Anderson, MZ},
title = {Altered nasal and oral microbiomes define pediatric sickle cell disease.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0013725},
doi = {10.1128/msphere.00137-25},
pmid = {40366139},
issn = {2379-5042},
abstract = {UNLABELLED: Sickle cell disease (SCD) is a chronic blood disorder that disrupts multiple organ systems and can lead to severe morbidity. Persistent and acute symptoms caused by immune system dysregulation in individuals with SCD could contribute to disease either directly or indirectly via dysbiosis of commensal microbes and increased susceptibility to infection. Here, we explored the nasal and oral microbiomes of children with SCD (cwSCD) to uncover potential dysbiotic associations with the blood disorder. Microbiota collected from nasal and oral swabs of 40 cwSCD were compared to eight healthy siblings using shotgun metagenomic sequencing. Commensal taxa were present at similar levels in the nasal and oral microbiome of both groups. However, the nasal microbiomes of cwSCD contained a higher prevalence of Pseudomonadota species, including pathobionts such as Yersinia enterocolitica and Klebsiella pneumoniae. Furthermore, the oral microbiome of cwSCD displayed lower α-diversity and fewer commensal and pathobiont species compared to the healthy siblings. Thus, subtle but notable shifts seem to exist in the nasal and oral microbiomes of cwSCD, suggesting an interaction between SCD and the microbiome that may influence health outcomes.

IMPORTANCE: The oral and nasal cavities are susceptible to environmental exposures including pathogenic microbes. In individuals with systemic disorders, antibiotic exposure, changes to the immune system, or changes to organ function could influence the composition of the microbes at these sites and the overall health of individuals. Children with sickle cell disease (SCD) commonly experience respiratory infections, such as pneumonia or sinusitis, and may have increased susceptibility to infection because of disrupted microbiota at these body sites. We found that children with SCD (cwSCD) had more pathobiont bacteria in the nasal cavity and reduced bacterial diversity in the oral cavity compared to their healthy siblings. Defining when, why, and how these changes occur in cwSCD could help identify specific microbial signatures associated with susceptibility to infection or adverse outcomes, providing insights into personalized treatment strategies and preventive measures.},
}

@article {pmid40366134,
year = {2025},
author = {Gilbert, NE and Kimbrel, JA and Samo, TJ and Siccardi, AJ and Stuart, RK and Mayali, X},
title = {A bloom of a single bacterium shapes the microbiome during outdoor diatom cultivation collapse.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0037525},
doi = {10.1128/msystems.00375-25},
pmid = {40366134},
issn = {2379-5077},
abstract = {Algae-dominated ecosystems are fundamentally influenced by their microbiome. We lack information on the identity and function of bacteria that specialize in consuming algal-derived dissolved organic matter in high algal density ecosystems such as outdoor algal ponds used for biofuel production. Here, we describe the metagenomic and metaproteomic signatures of a single bacterial strain that bloomed during a population-wide crash of the diatom, Phaeodactylum tricornutum, grown in outdoor ponds. 16S rRNA gene data indicated that a single Kordia sp. strain (family Flavobacteriaceae) contributed up to 93% of the bacterial community during P. tricornutum demise. Kordia sp. expressed proteins linked to microbial antagonism and biopolymer breakdown, which likely contributed to its dominance over other microbial taxa during diatom demise. Analysis of accompanying downstream microbiota (primarily of the Rhodobacteraceae family) provided evidence that cross-feeding may be a pathway supporting microbial diversity during diatom demise. In situ and laboratory data with a different strain suggested that Kordia was a primary degrader of biopolymers during algal demise, and co-occurring Rhodobacteraceae exploited degradation molecules for carbon. An analysis of 30 Rhodobacteraceae metagenome assembled genomes suggested that algal pond Rhodobacteraceae commonly harbored pathways to use diverse carbon and energy sources, including carbon monoxide, which may have contributed to the prevalence of this taxonomic group within the ponds. These observations further constrain the roles of functionally distinct heterotrophic bacteria in algal microbiomes, demonstrating how a single dominant bacterium, specialized in processing senescing or dead algal biomass, shapes the microbial community of outdoor algal biofuel ponds.IMPORTANCEAquatic biogeochemical cycles are dictated by the activity of diverse microbes inhabiting the algal microbiome. Outdoor biofuel ponds provide a setting analogous to aquatic algal blooms, where monocultures of fast-growing algae reach high cellular densities. Information on the microbial ecology of this setting is lacking, and so we employed metagenomics and metaproteomics to understand the metabolic roles of bacteria present within four replicated outdoor ponds inoculated with the diatom Phaeodactylum tricornutum. Unexpectedly, after 29 days of cultivation, all four ponds crashed concurrently with a "bloom" of a single taxon assigned to the Kordia bacterial genus. We assessed how this dominant taxon influenced the chemical and microbial fate of the ponds following the crash, with the hypothesis that it was primarily responsible for processing senescent/dead algal biomass and providing the surrounding microbiota with carbon. Overall, these findings provide insight into the roles of microbes specialized in processing algal organic matter and enhance our understanding of biofuel pond microbial ecology.},
}

@article {pmid40366128,
year = {2025},
author = {Skarlupka, JH and Cox, MS and Steinberger, AJ and Sbardellati, DL and Scheftgen, AJ and Zuniga-Chaves, I and Paget, E and Skadron, C and Attipetty, N and McClure, JC and Bickhart, DM and Suen, G},
title = {Correlating the oral swab microbial community with milk production metrics in Holstein dairy cows.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0016725},
doi = {10.1128/msphere.00167-25},
pmid = {40366128},
issn = {2379-5042},
abstract = {Oral swabs of dairy cows have been suggested as a proxy for direct ruminal sampling, and this approach can identify the presence of up to 70% of the rumen microbial community. Here, we further extend the utility of this approach by correlating the bacterial community of swabs collected from 226 dairy cows on a research farm in Wisconsin, USA, with average milk yield and days in milk, two phenotypes previously associated with differences in the ruminal microbiome. We then obtained milk production efficiency data for a subset of these animals (gross feed efficiency [GFE] and residual feed intake [RFI]) and correlated these metrics against their associated microbial data. We found that when using the oral swabs, we could identify correlations between bacterial genera and days in milk (P < 0.05). We further show that the ruminal microbiota was associated with average milk yield and days in milk for animals in their first lactation. Differential abundance testing identified amplicon sequence variants (ASVs) associated with these metrics (P < 0.05). Our comparison of bacterial communities between high and low efficiency groups, as determined by GFE and RFI, identified a significant difference in Shannon's diversity in second lactation cows (P < 0.05). We also found that RFI was significantly correlated with the bacterial community in second lactation animals (P < 0.05). Differential abundance analysis identified multiple oral- and rumen-associated ASVs correlated with GFE and RFI (P < 0.05). This study further establishes the utility of oral swabs as a ruminal proxy.IMPORTANCEImproving milk production efficiency is a key goal in the dairy industry and is traditionally pursued through genetic selection, diet optimization, and herd management practices. The ruminal microbiome, essential for digesting feed, has been linked to milk production efficiency, suggesting that microbiome modulation could improve efficiency. However, the integration of rumen microbiology into current management practices is hampered by the difficulty of large-scale rumen sampling, as proxies like fecal samples do not accurately reflect the ruminal microbiota. Traditional methods, like cannulation and stomach tubing, are labor-intensive and impractical for extensive sampling. Our research demonstrates the potential use of oral swabs as a scalable, effective method for characterizing the microbiome and its associations with milk production metrics, recapitulating established associations obtained through traditional ruminal sampling methods.},
}

@article {pmid40366070,
year = {2025},
author = {Herz, CT and Kulterer, OC and Prager, M and Marculescu, R and Prager, G and Kautzky-Willer, A and Hacker, M and Trajanoski, S and Köfeler, HC and Gallé, B and Haug, AR and Berry, D and Kiefer, FW},
title = {Bariatric surgery promotes recruitment of brown fat linked to alterations in the gut microbiota.},
journal = {European journal of endocrinology},
volume = {192},
number = {5},
pages = {603-611},
doi = {10.1093/ejendo/lvaf081},
pmid = {40366070},
issn = {1479-683X},
support = {P 27391//Austrian Science Fund/ ; 17094//Medical Scientific Fund of the Mayor of the City of Vienna/ ; //Austrian Diabetes Association Research Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Adipose Tissue, Brown/metabolism/diagnostic imaging ; Female ; *Bariatric Surgery ; Male ; Middle Aged ; Adult ; *Obesity, Morbid/surgery/metabolism/microbiology ; Fatty Acids, Volatile/metabolism/blood ; Positron Emission Tomography Computed Tomography ; Energy Metabolism/physiology ; Weight Loss/physiology ; },
abstract = {OBJECTIVE: The mechanisms of bariatric surgery-induced weight loss and metabolic improvements are still incompletely understood and reach beyond malabsorption or calorie restriction. We sought to investigate the effect of bariatric surgery on brown adipose tissue (BAT) activity and a potential connection with changes in energy metabolism, the gut microbiota, and short-chain fatty acid (SCFA) composition.

METHODS: We included 32 subjects (25 females) with morbid obesity and analyzed their metabolic profile, gut microbiota composition, circulating SCFAs, energy expenditure, and cold-induced BAT activity using [18F]Fluorodeoxyglucose-positron emission tomography-computed tomography before and up to 1 year after bariatric surgery.

RESULTS: Twelve months after surgery, the percentage of individuals with active BAT had increased from 28% to 53%. The BAT-negative (BATneg) individuals who had an adverse metabolic profile at baseline compared with subjects with active BAT (BATpos) showed a greater metabolic benefit after surgery. While no changes in overall gut bacterial diversity were observed between BATpos and BATneg, the abundance of 3 specific bacterial families, including Akkermansiaceae, Pasteurellaceae, and Carnobacteriaceae, was distinctly regulated between BAT groups. The bacterial genera most strongly increased in BATpos vs BATneg subjects were all positively correlated with BAT volume and BAT activity. Finally, circulating concentrations of the SCFAs acetate, butyrate, and propionate rose after bariatric surgery and were related to bacterial genera such as Akkermansia, Dialister, and Lachnospiraceae FCS020 group, all known SCFA producers.

CONCLUSIONS: Bariatric surgery helps recruit active BAT in individuals with obesity and is linked to distinct alterations in the gut microbiome and SCFA composition.

TRIAL REGISTRATION NUMBER: ClinicalTrials.gov (NCT03168009).},
}

Humans
*Gastrointestinal Microbiome/physiology
*Adipose Tissue, Brown/metabolism/diagnostic imaging
Female
*Bariatric Surgery
Male
Middle Aged
Adult
*Obesity, Morbid/surgery/metabolism/microbiology
Fatty Acids, Volatile/metabolism/blood
Positron Emission Tomography Computed Tomography
Energy Metabolism/physiology
Weight Loss/physiology

@article {pmid40365358,
year = {2025},
author = {Bruno, JS and Al-Qadami, G and Gopinath, D and Laheij, AMGA},
title = {Editorial: Unravelling the role of the oral microbiome in cancer.},
journal = {Frontiers in oral health},
volume = {6},
number = {},
pages = {1606144},
pmid = {40365358},
issn = {2673-4842},
}

@article {pmid40365077,
year = {2025},
author = {Rodríguez-Lago, I and Marigorta, UM and Mateos, B and Mañosa, M and Márquez-Mosquera, L and Menchén, L and Rodríguez-Moranta, F and Alonso, I and Aguas, M and Alonso-Galán, H and Borràs, P and Castro, B and Domènech, E and Ferreiro-Iglesias, R and de Francisco, R and García-Alonso, FJ and García, N and García-Bosch, O and Gargallo, C and Gisbert, JP and Iglesias, E and Mesonero, F and Ortiz de Zárate, J and Ramos, L and Sáinz, E and Ladrón, P and Suria, C and Ferrer, CS and Tejido, C and Varela, P and Vicente, R and Zabana, Y and Castany, G and Rodríguez, E and Gutiérrez, A and Barreiro-de Acosta, M},
title = {Natural history, immunological and genetic characteristics of preclinical inflammatory bowel disease (EARLY): study protocol for a prospective cohort study.},
journal = {Therapeutic advances in gastroenterology},
volume = {18},
number = {},
pages = {17562848251338647},
pmid = {40365077},
issn = {1756-283X},
abstract = {BACKGROUND: The period prior to the diagnosis of inflammatory bowel disease (IBD), defined as the preclinical phase, has emerged as a potential target for disease modification strategies. Despite the relevance of an early diagnosis to the prognosis of the disease, only a limited number of patients are diagnosed during this window of opportunity.

OBJECTIVES: To determine the risk of developing symptoms after an incidental diagnosis of IBD and to describe the clinical, genetic, and immunological characteristics of IBD during its preclinical phase.

DESIGN: This study protocol describes a prospective, multicenter cohort study in which incidental (i.e., asymptomatic) IBD within the colorectal cancer screening program will be characterized from a clinical and multi-omic perspective and compared with symptomatic patients and healthy non-IBD controls.

METHODS: Samples from blood, urine, stool, and intestinal endoscopic biopsies will be obtained at baseline. A second sample set will be obtained after 52 weeks from those who remain asymptomatic; samples will also be obtained in those with new-onset symptoms. Medical treatment will be prescribed in all patients following current guidelines. Follow-up visits will be performed every 6 months for 10 years, and all new-onset symptoms, changes in disease behavior, extraintestinal manifestations, IBD-related medical therapies, or surgeries will be recorded. Two control cohorts will be included: one including recently diagnosed symptomatic IBD patients (<3 months), and another with healthy non-IBD controls after a normal ileocolonoscopy, in whom samples will be obtained at baseline. Samples from patients and controls will undergo genetic, proteomic, transcriptomic, single-cell RNA sequencing, metabolomic, and microbiome analyses, and integration of data between the different omic perspectives will also be performed. The study has been approved by the Basque Country Ethics Committee (PI2021116).

CONCLUSION: EARLY will generate a unique dataset addressing a previously unexplored area of IBD, with the final aim of describing the prognosis of patients from its earlier phases on the disease and integrating clinical and omic data into useful tools for the long-term prediction of disease outcomes.

TRIAL REGISTRATION: NCT05698745.},
}

@article {pmid40365061,
year = {2025},
author = {Liu, L and Wang, Z and Luo, C and Deng, Y and Wu, W and Jin, Y and Wang, Y and Huang, H and Wei, Z and Zhu, Y and He, X and Guo, L},
title = {Beneficial soil microbiome profiles assembled using tetramycin to alleviate root rot disease in Panax notoginseng.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1571684},
pmid = {40365061},
issn = {1664-302X},
abstract = {BACKGROUND: Root rot disease is a major threat to the sustainable production of Panax notoginseng. Tetramycin has a broad-spectrum fungicidal efficacy, low toxicity, and high efficiency, However, the prevention and control of root rot disease of P. notoginseng and the specific mechanism of action are still unclear.

METHODS: In this paper, a combination of indoor and pot experiments was used to assess the effectiveness of tetramycin at alleviating root rot disease challenges encountered by P. notoginseng. Amplicon sequencing, metagenomic analysis with microbial verification were used to investigate the microecological mechanisms underlying tetramycin's ability to reduce soil biological barriers.

RESULTS: We found that tetramycin significantly inhibited mycelial growth and spore germination of pathogenic fungi. Tetramycin, T2 (1000×) and T3 (500×), applied to continuous cropping soil, increased the seedling survival rates of P. notoginseng. Additionally, tetramycin reduced fungal α-diversity and shifted the fungal community assembly from deterministic to stochastic process. The microbial functions influenced by tetramycin were primarily associated with antibiotic synthesis and siderophore synthesis. Antibiotic efflux and inactivation have also been identified as the main resistance mechanisms. Microbial verification results showed that the artificially assembled tetramycin-regulated microbial community could indeed alleviate the occurrence of diseases. Furthermore, the cross-kingdom synthetic community assembled by the three key strains (Pseudomonas aeruginosa, Variovorax boronicumulans, and Cladosporium cycadicola) significantly improved the control of root rot disease and promoted plant growth.

DISCUSSION: This study provides novel insights into developing efficient biological control strategies and elucidates the role and mechanism of tetramycin in modulating soil microflora assembly to strengthen host disease resistance.},
}

@article {pmid40364844,
year = {2025},
author = {Nazir, A and Hussain, FHN and Nadeem Hussain, TH and Al Dweik, R and Raza, A},
title = {Therapeutic targeting of the host-microbiota-immune axis: implications for precision health.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1570233},
pmid = {40364844},
issn = {1664-3224},
mesh = {Humans ; *Precision Medicine/methods ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Prebiotics/administration & dosage ; *Gastrointestinal Microbiome/immunology ; Animals ; *Host Microbial Interactions/immunology ; *Microbiota/immunology ; Immunomodulation ; },
abstract = {The human body functions as a complex ecosystem, hosting trillions of microbes that collectively form the microbiome, pivotal in immune system regulation. The host-microbe immunological axis maintains homeostasis and influences key physiological processes, including metabolism, epithelial integrity, and neural function. Recent advancements in microbiome-based therapeutics, including probiotics, prebiotics and fecal microbiota transplantation, offer promising strategies for immune modulation. Microbial therapies leveraging microbial metabolites and engineered bacterial consortia are emerging as novel therapeutic strategies. However, significant challenges remain, including individual microbiome variability, the complexity of host-microbe interactions, and the need for precise mechanistic insights. This review comprehensively examines the host microbiota immunological interactions, elucidating its mechanisms, therapeutic potential, and the future directions of microbiome-based immunomodulation in human health. It will also critically evaluate challenges, limitations, and future directions for microbiome-based precision medicine.},
}

Humans
*Precision Medicine/methods
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Prebiotics/administration & dosage
*Gastrointestinal Microbiome/immunology
Animals
*Host Microbial Interactions/immunology
*Microbiota/immunology
Immunomodulation

@article {pmid40364797,
year = {2025},
author = {Briand, A and Bensignor, E and Dropsy, H and Crosaz, O and Humeau, L and Cheval, J and Demontant, V and Debi, MN and Fantini, O and Dal, H and Guillot, J and Faivre, NC},
title = {Effect of a ceruminolytic ear cleaner on clinical, microbiological and ear canal microbiome evolution in canine erythemato-ceruminous otitis externa associated with proliferation of Malassezia yeasts.},
journal = {Veterinary dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/vde.13352},
pmid = {40364797},
issn = {1365-3164},
support = {//VETOQUINOL/ ; },
abstract = {BACKGROUND: Erythemato-ceruminous otitis externa (ECOE) is commonly associated with Malassezia spp. and microbial imbalance.

HYPOTHESIS/OBJECTIVE: To assess the clinical performance of an ear cleaner in dogs suffering from ECOE associated with Malassezia spp. overgrowth and to measure its impact on the microbiota.

ANIMALS: Thirty privately owned dogs suffering from mild-to-moderate ECOE associated with Malassezia spp. overgrowth.

MATERIALS AND METHODS: Pruritus score (PS), clinical score (0-3 Otitis Index Score [OTIS3]: based on secretions, erythema, hyperplasia and ulceration) and cytological score (CS) were assessed on Day (D)0, D7, and D14. Sterile ear swabs were used on D0 and D14 to perform fungal culture DNA extraction, and PCR amplification of the 18 ITS and 16S rRNA gene was carried out to evaluate the composition and changes of the otic microbiome. Ears were cleaned with a cerumenolytic ear cleanser daily, every other day, or twice a week depending on the secretion score.

RESULTS: Fifty-seven ears (30 dogs) completed the study. PS, OTIS-3, and CS were significantly decreased at D7 and D14 (-45%, -43%, -60% and -77%, -66%, -76%, respectively; p < 0.0001 Wilcoxon test). Fungal culture was positive (Malassezia spp.) in only 34 ears at D0 and was negative in all ears at D14. Mycobiota composition was significantly different before and after treatment with an increase of fungal diversity (Shannon index; p < 0.003 Wilcoxon test) at D14 compared to D0. There was no change in bacterial composition.

In case of ECOE associated with Malassezia spp. overgrowth, the use of the tested ear cleaner showed a positive impact on the fungal dysbiosis and Malassezia spp. overgrowth.},
}

@article {pmid40364768,
year = {2025},
author = {Adelfio, M and Callen, GE and He, X and Paster, BJ and Hasturk, H and Ghezzi, CE},
title = {Engineered Tissue Models to Decode Host-Microbiota Interactions.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2417687},
doi = {10.1002/advs.202417687},
pmid = {40364768},
issn = {2198-3844},
support = {2337322//National Science Foundation CAREER Award/ ; R03DE030224/DE/NIDCR NIH HHS/United States ; },
abstract = {A mutualistic co-evolution exists between the host and its associated microbiota in the human body. Bacteria establish ecological niches in various tissues of the body, locally influencing their physiology and functions, but also contributing to the well-being of the whole organism through systemic communication with other distant niches (axis). Emerging evidence indicates that when the composition of the microbiota inhabiting the niche changes toward a pathogenic state (dysbiosis) and interactions with the host become unbalanced, diseases may present. In addition, imbalances within a single niche can cause dysbiosis in distant organs. Current research efforts are focused on elucidating the mechanisms leading to dysbiosis, with the goal of restoring tissue homeostasis. In vitro models can provide critical experimental platforms to address this need, by reproducing the niche cyto-architecture and physiology with high fidelity. This review surveys current in in vitro host-microbiota research strategies and provides a roadmap that can guide the field in further developing physiologically relevant in vitro models of ecological niches, thus enabling investigation of the role of the microbiota in human health and diseases. Lastly, given the Food and Drug Administration Modernization Act 2.0, this review highlights emerging in vitro strategies to support the development and validation of new therapies on the market.},
}

@article {pmid40364743,
year = {2025},
author = {Li, X and Zhao, Y and Liu, M and Zhang, M and Zhu, Z and Liao, A and Pan, L and Lv, X and Liu, F and Huang, J},
title = {Fermented Wheat Germ Ameliorates High-Fat Diet-Induced Maternal Obesity in Rats: Insights from Microbiome and Metabolomics.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c10847},
pmid = {40364743},
issn = {1520-5118},
abstract = {Maternal obesity significantly increases the risk of adverse outcomes for the mother and fetus. Fermented wheat germ (FWG) has demonstrated the potential to improve metabolic disorders, yet its effects have not been explored in maternal obesity models. This study investigated the ameliorating impact of FWG in rats with maternal obesity, focusing on its mechanisms through biochemical, gut microbiome, and serum metabolomics analysis. The results demonstrated that FWG was more effective than wheat germ in reducing body weight gain and fat accumulation, improving glycolipid metabolism disorders, and alleviating inflammation. Specifically, FWG modulated the composition of gut microbiota by fostering the growth of beneficial bacteria (e.g., Corynebacterium) while suppressing genera associated with maternal obesity (e.g., Blautia, Akkermansia, Dorea_A, and Faecousia). Furthermore, FWG modified high-fat diet-induced metabolites, primarily affecting pyrimidine metabolism and amino acid metabolism. These findings suggest that FWG may serve as a promising dietary intervention for mitigating maternal obesity and improving pregnancy outcomes.},
}

@article {pmid40364602,
year = {2025},
author = {Netter, U and Bisht, V and Gaurav, A and Sharma, R and Ghosh, A and Bisht, VS and Ambatipudi, K and Sharma, HP and Mohanty, S and Loat, S and Sarkar, M and Tahlan, K and Navani, NK},
title = {Discovery and mechanistic characterization of a probiotic-origin 3β-OH-Δ[5-6]-cholesterol-5β-reductase directly converting cholesterol to coprostanol.},
journal = {The FEBS journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/febs.70131},
pmid = {40364602},
issn = {1742-4658},
support = {BT/NER/95/SP47965/2022//Department of Biotechnology, Ministry of Science and Technology, India/ ; 09/143(1022)/2020-EMR-I//Council of Scientific and Industrial Research (CSIR), India/ ; },
abstract = {Cholesterol serves as a fundamental molecule in various structural and biochemical pathways; however, high cholesterol levels are linked to cardiovascular diseases. Some selected strains of Lactobacilli are known for modulating cholesterol levels. However, the molecular mechanism underlying cholesterol transformation by lactobacilli has remained elusive. This study describes the discovery and function of a microbial 3β-OH-Δ[5-6]-cholesterol-5β-reductase (5βChR) from Limosilactobacillus fermentum NKN51, which directly converts cholesterol to coprostanol, thereby unraveling this longstanding mystery. Protein engineering of the reductase enzyme identified the cholesterol and NADPH interacting amino acid residues, detailing the catalytic mechanism of 5βChR. Phylogenetic analyses highlight the prevalence of 5βChRs in gut commensal lactobacilli, which share a common evolutionary origin with plant 5β reductases. Meta-analysis of microbiomes from healthy individuals underscores the importance of 5βChR homologs, while a cohort study demonstrates an inverse association between 5βChR abundance and diabetes. The discovery of the 5βChR enzyme and its molecular mechanism in cholesterol metabolism paves the way for a better understanding of the gut-associated microbiome and the design of practical applications to ameliorate dyslipidemia.},
}

@article {pmid40364584,
year = {2025},
author = {Shao, K and Li, J and Shen, X and Li, M and Wei, S and Wu, X and Li, Y and Ge, Z},
title = {Antibiotic-Induced Gut Microbiome Dysbiosis Aggravates Cerebral Injury During Extracorporeal Membrane Oxygenation.},
journal = {Catheterization and cardiovascular interventions : official journal of the Society for Cardiac Angiography & Interventions},
volume = {},
number = {},
pages = {},
doi = {10.1002/ccd.31589},
pmid = {40364584},
issn = {1522-726X},
support = {//This study was supported by the National Key R&D Program of China (NO.2021YFC2701700, NO.2021YFC2701703); the Science and Technology Planning Project of Chengguan District (NO.2022RCCX0023); Joint Scientific Research Project of Gansu (NO.23JRRA1502); the Fundamental Research Funds for the Central Universities of Lanzhou University (NO.lzujbky-2023-stlt01); the Talent Introduction Plan of the Lanzhou University Second Hospital (No.YJRCKYQDJ-2021-02); the National Natural Foundation of China (NO.82460559); Cuiying Scientific and Technological Innovation Program of Lanzhou University Second Hospital (No. CY2022-YB-A04)./ ; },
abstract = {BACKGROUND: Extracorporeal membrane oxygenation (ECMO) is an effective treatment for cardiopulmonary failure. However, it is associated with severe complications, including cerebral injury, which contribute to elevated mortality and disability rates. The administration of antibiotics may lead to gut microbiome dysbiosis among critically ill patients.

AIMS: This study aims to investigate the association between antibiotic-induced gut microbiome dysbiosis and cerebral injury during ECMO treatment.

METHODS: The compositional changes in the gut microbiome induced by antibiotic (ABX) treatment were analyzed using microbiome analysis techniques. ECMO treatment models were established by using rat. Brain tissue pathology was assessed using H&E and Nissl staining. Serum concentrations of S100β and NSE were quantified using ELISA. Pro-inflammatory factors in the brain and serum were analyzed, and microglial activation was evaluated via immunofluorescence.

RESULTS: Gut microbiome dysbiosis induced by ABX treatment. Compared to the sham group, significant cerebral injury was observed in both the ECMO and ECMO-ABX groups. The expression levels of S100β and NSE were significantly elevated in the ECMO-ABX group. Additionally, parameters of microglial activation, such as cell body area, total branch length, mean length of branches, and number of branch points, were significantly increased in the ECMO-ABX group compared to the ECMO group.

CONCLUSIONS: This study demonstrates that cerebral injury occurs during ECMO treatment, and antibiotic-induced gut microbiome dysbiosis may exacerbate this cerebral injury.},
}

@article {pmid40364490,
year = {2025},
author = {Kong, C and Huang, L and Yang, M and Yue, N and Zhang, Y and Tian, C and Wei, D and Shi, R and Liang, Y and Yao, J and Wang, L and Li, D},
title = {Engineering the microbiome: A novel frontier in inflammatory bowel disease treatment.},
journal = {Chinese medical journal},
volume = {},
number = {},
pages = {},
pmid = {40364490},
issn = {2542-5641},
}

@article {pmid40364449,
year = {2025},
author = {Chen, TL and Zhang, TL and Lu, HJ and Yue, AX and Wang, YE and Zhou, YJ and Hou, J},
title = {Comment on "Oral Microbiome and Serological Analyses on Association of Alzheimer's Disease and Periodontitis".},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.15379},
pmid = {40364449},
issn = {1601-0825},
support = {2023SHZDZX02-030702//Shanghai Science and Technology Major Special Project "International Human Phenome Project"/ ; //2023 Basic Medical Research Special Project of the First Affiliated Hospital of Naval Medical University (2023PY09)/ ; //234 Discipline Peak Climbing Project of the First Affiliated Hospital of Naval Medical University (2020YXK028)/ ; },
}

@article {pmid40364216,
year = {2025},
author = {Levy, RL and Murphy, TB and Heitkemper, MM and van Tilburg, MAL and McMeans, AR and Chang, J and Boutte, C and Lamparyk, K and Chumpitazi, BP and Shulman, RJ},
title = {Protocol for a Randomized Controlled Trial to Determine if Biomarkers Predict Response to a Pediatric Chronic Pain Symptom Management Program.},
journal = {Journal of clinical medicine},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/jcm14093185},
pmid = {40364216},
issn = {2077-0383},
support = {1R01NR016786-05S5/NH/NIH HHS/United States ; },
abstract = {Background/Objectives: Disorders of gut-brain interaction (DGBI), characterized by chronic abdominal pain and significant disability, affect 15-20% of children and adults and continue into adulthood in ~60% of cases. Costs for adults reach USD 30 billion per year, yet effective management strategies are elusive. Studies support using cognitive behavioral therapy (CBT), but abdominal pain only improves in ~40% of patients. Dietary management (low FODMAP diet; LFD) has also shown promise but it is effective in only a similar percentage of patients. Studies suggest that biologic factors (biomarkers) contribute to CBT response. Similarly, gut microbiome composition appears to influence abdominal pain response to the LFD. However, no previous CBT trials in children or adults have measured these biomarkers, and it is unclear which patients respond best to CBT vs. LFD. Methods: Children aged 7-12 years with DGBIs (n = 200) will be categorized as having/not having Autonomic Nervous System imbalance and/or abnormalities in gut physiology. We will randomize these children to either CBT or a LFD to compare the effectiveness of these treatments in those with/without abnormal physiologic biomarkers. We hypothesize that CBT will be more effective in those without abnormal physiology and LFD will be more effective in children with abnormal physiology. Primary outcome measures include the following: (1) Symptom improvement (abdominal pain frequency/severity) and (2) improvement in health-related quality of life. Conclusions: This innovative multidisciplinary study is the first to identify physiological characteristics that may moderate the response to two different management strategies. Identification of these characteristics may reduce the burden of these disorders through timely application of the intervention most likely to benefit an individual patient.},
}

@article {pmid40364140,
year = {2025},
author = {Piłot, M and Dzięgielewska-Gęsiak, S and Walkiewicz, KW and Bednarczyk, M and Waniczek, D and Muc-Wierzgoń, M},
title = {Gut Microbiota and Metabolic Dysregulation in Elderly Diabetic Patients: Is There a Gender-Specific Effect.},
journal = {Journal of clinical medicine},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/jcm14093103},
pmid = {40364140},
issn = {2077-0383},
support = {BNW-1-056/K/3/Z//Medical University of Silesia in Katowice, Poland/ ; },
abstract = {Background/Objectives: The aim of this study was to qualitatively and quantitatively assess the bacterial domain of the gut microbiome in elderly patients with type 2 diabetes (T2D), with a focus on sex differences, glycemic control, and lipid disorders. Methods: This study included 60 older adults with T2D (38 women and 22 men) treated with metformin or a combination of metformin and insulin. The gut microbiota was profiled using 16S rRNA gene sequencing. Statistical analyses, including correlation analysis and multiple regression, were performed to identify the associations between microbial taxa, sex, and metabolic parameters. Results: No statistically significant differences in alpha or beta diversity were observed between the sexes. Multiple regression analysis indicated a positive relationship between Tenericutes and HbA1c in male participants (β = 2.22931, CI [0.75, 3.70], R = 0.67; R[2] = 0.36; unadjusted p = 0.0052; adjusted p = 0.0496). In female participants, G0' (β = -2.24107, CI [-3.19, -1.30], R = 0.78; R[2] = 0.58; unadjusted p = 0.00003; adjusted p = 0.0005) and HbA1c (β = -1.86670, CI [-2.61, -1.12], R = 0.78; R[2] = 0.58; unadjusted p = 0.00001; adjusted p = 0.0003) correlated negatively with Verrucomicrobia as well G0' (β = -1.90427, CI [-2.95, -0.85], R = 0.46; R[2] = 0.17; unadjusted p = 0.0008; adjusted p = 0.007) and HbA1c (β = -1.69561, CI [-2.52, -0.87], R = 0.46; R[2] = 0.17; unadjusted p = 0.0002; adjusted p = 0.002) correlated negatively with OD1 bacteria, known as Parcubacteria. Conclusions: In this elderly population with type 2 diabetes, biological sex did not significantly affect the gut microbiota diversity. However, several exploratory associations between microbial taxa and metabolic parameters differed between men and women, suggesting that sex may influence specific aspects of microbiota-metabolism interactions. These preliminary findings underscore the importance of considering both age- and sex-related factors when investigating the gut microbiome in the context of type 2 diabetes.},
}

@article {pmid40364013,
year = {2025},
author = {Dumitru, IG and Todor, SB and Ichim, C and Helgiu, C and Helgiu, A},
title = {A Literature Review on the Impact of the Gut Microbiome on Cancer Treatment Efficacy, Disease Evolution and Toxicity: The Implications for Hematological Malignancies.},
journal = {Journal of clinical medicine},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/jcm14092982},
pmid = {40364013},
issn = {2077-0383},
abstract = {The gut microbiome plays a crucial role in modulating the efficacy and toxicity of cancer therapies, particularly in hematological malignancies. This review examines the dynamic interplay between gut microbiota and cancer treatments, such as chemotherapy, immunotherapy, and hematopoietic stem cell transplantation (HSCT). Disruptions in the gut microbiome, known as dysbiosis, are associated with adverse effects like gastrointestinal toxicity, neutropenia and cardiotoxicity during chemotherapy. Conversely, the supplementation of probiotics has shown potential in mitigating these side effects by enhancing gut barrier function and regulating immune responses. In HSCT, a higher diversity of gut microbiota is linked to better patient outcomes, including reduced graft-versus-host disease (GVHD) and improved survival rates. The microbiome also influences the efficacy of immunotherapies, such as immune checkpoint inhibitors and CAR-T cell therapy, by modulating immune pathways. Research suggests that certain bacteria, including Bifidobacterium and Akkermansia muciniphila, enhance therapeutic responses by promoting immune activation. Given these findings, modulating the gut microbiome could represent a novel strategy for improving cancer treatment outcomes. The growing understanding of the microbiome's impact on cancer therapy underscores its potential as a target for personalized medicine and offers new opportunities to optimize treatment efficacy while minimizing toxic side effects.},
}

@article {pmid40363959,
year = {2025},
author = {Gullo, G and Satullo, M and Billone, V and De Paola, L and Petousis, S and Kotlik, Y and Margioula-Siarkou, C and Perino, A and Cucinella, G},
title = {The Role of the Genital Tract Microbiome in Human Fertility: A Literature Review.},
journal = {Journal of clinical medicine},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/jcm14092923},
pmid = {40363959},
issn = {2077-0383},
abstract = {Background/Objectives: Infertility is a multifactorial condition influenced by various factors, including dysbiosis and alterations in the genital tract microbiome. Recent studies emphasize the microbiome's significant role in influencing a woman's fertility potential, thereby affecting the chances of spontaneous conception and the outcomes of assisted reproductive treatments. Understanding the microbial characteristics and unique features of a healthy genital microbiome, as well as how changes in its composition can impact fertility, would allow for a more comprehensive and personalized approach to managing assisted reproductive treatments. The microbiome also influences pregnancy outcomes, and restoring its balance has been shown to improve fertility in infertile couples. The human microbiome plays a key role in maintaining the body's overall health. Disruptions in microbiome balance among women of reproductive age can contribute to a range of pregnancy-related complications, with notable consequences for both maternal and fetal well-being. Emerging research has highlighted a connection between the reproductive tract microbiome and outcomes of assisted reproductive technologies (ART), suggesting that re-establishing a healthy microbial environment may enhance fertility in couples facing infertility. Methods: We conducted a search on PubMed using the keywords "microbiome", "infertility", and "ART" over the past 10 years. This article aims to provide an updated overview of the role of the microbiome in female reproductive health, with a focus on its implications for fertility treatment. Results: The microbiome has a significant role in influencing women's fertility. Conclusions: Understanding the microbiome's impact on fertility and pregnancy outcomes may lead to more effective and personalized approaches in fertility treatments, improving the chances of successful conception and pregnancy.},
}

@article {pmid40362907,
year = {2025},
author = {Christopher, CJ and Morgan, KH and Tolleson, CM and Trudell, R and Fernandez-Romero, R and Rice, L and Abiodun, BA and Vickery, Z and Jones, KA and Woodall, BM and Nagy, C and Mieczkowski, PA and Bowen, G and Campagna, SR and Ellis, JC},
title = {Specific Bacterial Taxa and Their Metabolite, DHPS, May Be Linked to Gut Dyshomeostasis in Patients with Alzheimer's Disease, Parkinson's Disease, and Amyotrophic Lateral Sclerosis.},
journal = {Nutrients},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/nu17091597},
pmid = {40362907},
issn = {2072-6643},
support = {N/A//The Cole Family who support Parkinson's care and research at the Cole Center for Parkinson's Disease and Movement Disorders/ ; N/A//University of Tennessee at Knoxville's Human Health & Wellness Program/ ; N/A//Laboratory Directed Research and Development Program at Oak Ridge National Laboratory, managed by UT-Battelle, LLC, for the U.S. Department of Energy/ ; N/A//A philanthropic donor to ALS research at the University of Tennessee Medical Center/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Parkinson Disease/microbiology/metabolism ; *Alzheimer Disease/microbiology/metabolism ; *Dysbiosis/microbiology ; Male ; Female ; *Amyotrophic Lateral Sclerosis/microbiology/metabolism ; Aged ; Middle Aged ; Feces/microbiology ; *Bacteria/metabolism/classification ; Homeostasis ; Metabolomics ; Case-Control Studies ; },
abstract = {Background: Neurodegenerative diseases (NDDs) are multifactorial disorders frequently associated with gut dysbiosis, oxidative stress, and inflammation; however, the pathophysiological mechanisms remain poorly understood. Methods: Using untargeted mass spectrometry-based metabolomics and 16S sequencing of human stool, we investigated bacterial and metabolic dyshomeostasis in the gut microbiome associated with early disease stages across three NDDs-amyotrophic lateral sclerosis (ALS), Alzheimer's disease (AD), Parkinson's disease (PD)-and healthy controls (HC). Results: We discovered a previously unrecognized link between a microbial-derived metabolite with an unknown role in human physiology, 2,3-dihydroxypropane-1-sulfonate (DHPS), and gut dysbiosis in NDDs. DHPS was downregulated in AD, ALS, and PD, while bacteria involved in DHPS metabolism, Eubacterium and Desulfovibrio, were increased in all disease cohorts. Additionally, select taxa within the Clostridia class had strong negative correlations to DHPS, suggesting a potential role in DHPS metabolism. A catabolic product of DHPS is hydrogen sulfide, and when in excess, it is known to promote inflammation, oxidative stress, mitochondrial damage, and gut dysbiosis, known hallmarks of NDDs. Conclusions: These findings suggest that cryptic sulfur metabolism via DHPS is a potential missing link in our current understanding of gut dysbiosis associated with NDD onset and progression. As this was a hypothesis generating study, more work is needed to elucidate the role of DHPS in gut dysbiosis and neurodegenerative diseases.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Parkinson Disease/microbiology/metabolism
*Alzheimer Disease/microbiology/metabolism
*Dysbiosis/microbiology
Male
Female
*Amyotrophic Lateral Sclerosis/microbiology/metabolism
Aged
Middle Aged
Feces/microbiology
*Bacteria/metabolism/classification
Homeostasis
Metabolomics
Case-Control Studies

@article {pmid40362889,
year = {2025},
author = {Jiménez-González, C and Alonso-Peña, M and Argos Vélez, P and Crespo, J and Iruzubieta, P},
title = {Unraveling MASLD: The Role of Gut Microbiota, Dietary Modulation, and AI-Driven Lifestyle Interventions.},
journal = {Nutrients},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/nu17091580},
pmid = {40362889},
issn = {2072-6643},
support = {101095679//European Commission/ ; PI18/01304//Instituto de Salud Carlos III/ ; PMP21/00112//European Union-NextGenerationEU/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Artificial Intelligence ; *Life Style ; *Diet ; *Non-alcoholic Fatty Liver Disease/microbiology/diet therapy ; Precision Medicine ; *Fatty Liver/microbiology ; },
abstract = {Gut microbiota has a crucial role in the pathophysiology of metabolic-associated steatotic liver disease (MASLD), influencing various metabolic mechanisms and contributing to the development of the disease. Dietary interventions targeting gut microbiota have shown potential in modulating microbial composition and mitigating MASLD progression. In this context, the integration of multi-omics analysis and artificial intelligence (AI) in personalized nutrition offers new opportunities for tailoring dietary strategies based on individual microbiome profiles and metabolic responses. The use of chatbots and other AI-based health solutions offers a unique opportunity to democratize access to health interventions due to their low cost, accessibility, and scalability. Future research should focus on the clinical validation of AI-powered dietary strategies, integrating microbiome-based therapies and precision nutrition approaches. Establishing standardized protocols and ethical guidelines will be crucial for implementing AI in MASLD management, paving the way for a more personalized, data-driven approach to disease prevention and treatment.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Artificial Intelligence
*Life Style
*Diet
*Non-alcoholic Fatty Liver Disease/microbiology/diet therapy
Precision Medicine
*Fatty Liver/microbiology

@article {pmid40362873,
year = {2025},
author = {Nohesara, S and Mostafavi Abdolmaleky, H and Pirani, A and Pettinato, G and Thiagalingam, S},
title = {The Obesity-Epigenetics-Microbiome Axis: Strategies for Therapeutic Intervention.},
journal = {Nutrients},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/nu17091564},
pmid = {40362873},
issn = {2072-6643},
mesh = {Humans ; *Obesity/microbiology/genetics/therapy ; *Epigenesis, Genetic ; *Gastrointestinal Microbiome/genetics/physiology ; Probiotics ; Animals ; Prebiotics/administration & dosage ; Diet ; },
abstract = {Obesity (OB) has become a serious health issue owing to its ever-increasing prevalence over the past few decades due to its contribution to severe metabolic and inflammatory disorders such as cardiovascular disease, type 2 diabetes, and cancer. The unbalanced energy metabolism in OB is associated with substantial epigenetic changes mediated by the gut microbiome (GM) structure and composition alterations. Remarkably, experimental evidence also indicates that OB-induced epigenetic modifications in adipocytes can lead to cellular "memory" alterations, predisposing individuals to weight regain after caloric restriction and subsequently inducing inflammatory pathways in the liver. Various environmental factors, especially diet, play key roles in the progression or prevention of OB and OB-related disorders by modulating the GM structure and composition and affecting epigenetic mechanisms. Here, we will first focus on the key role of epigenetic aberrations in the development of OB. Then, we discuss the association between abnormal alterations in the composition of the microbiome and OB and the interplays between the microbiome and the epigenome in the development of OB. Finally, we review promising strategies, including prebiotics, probiotics, a methyl-rich diet, polyphenols, and herbal foods for the prevention and/or treatment of OB via modulating the GM and their metabolites influencing the epigenome.},
}

Humans
*Obesity/microbiology/genetics/therapy
*Epigenesis, Genetic
*Gastrointestinal Microbiome/genetics/physiology
Probiotics
Animals
Prebiotics/administration & dosage
Diet

@article {pmid40362863,
year = {2025},
author = {Liu, L and Qi, W and Zhang, N and Zhang, J and Liu, S and Wang, H and Jiang, L and Sun, Y},
title = {Nutraceuticals for Gut-Brain Axis Health: A Novel Approach to Combat Malnutrition and Future Personalised Nutraceutical Interventions.},
journal = {Nutrients},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/nu17091551},
pmid = {40362863},
issn = {2072-6643},
support = {32372386//National Natural Science Foundation of China/ ; LH 2022C048//Natural Science Foundation of Heilongjiang Province/ ; },
mesh = {Humans ; *Dietary Supplements ; *Gastrointestinal Microbiome/physiology ; *Malnutrition/therapy/microbiology ; *Brain ; Probiotics/administration & dosage ; Dysbiosis ; Prebiotics/administration & dosage ; *Brain-Gut Axis/physiology ; Precision Medicine ; Biomarkers ; },
abstract = {The gut-brain axis (GBA) is a bidirectional communication network between the gastrointestinal tract and the brain, modulated by gut microbiota and related biomarkers. Malnutrition disrupts GBA homeostasis, exacerbating GBA dysfunction through gut dysbiosis, impaired neuroactive metabolite production, and systemic inflammation. Nutraceuticals, including probiotics, prebiotics, synbiotics, postbiotics, and paraprobiotics, offer a promising approach to improving GBA homeostasis by modulating the gut microbiota composition and related neuroactive metabolites. This review aims to elucidate the interplay between gut microbiota-derived biomarkers and GBA dysfunction in malnutrition and evaluate the potential of nutraceuticals in combating malnutrition. Furthermore, it explores the future of personalised nutraceutical interventions tailored to individual genetic and microbiome profiles, providing a targeted approach to optimise health outcomes. The integration of nutraceuticals into GBA health management could transform malnutrition treatment and improve cognitive and metabolic health.},
}

Humans
*Dietary Supplements
*Gastrointestinal Microbiome/physiology
*Malnutrition/therapy/microbiology
*Brain
Probiotics/administration & dosage
Dysbiosis
Prebiotics/administration & dosage
*Brain-Gut Axis/physiology
Precision Medicine
Biomarkers

@article {pmid40362845,
year = {2025},
author = {Varlas, VN and Bohîlțea, LC and Suciu, N},
title = {The Influences of Oral Probiotics on the Immunometabolic Response During Pregnancy and Lactation: A Systematic Review.},
journal = {Nutrients},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/nu17091535},
pmid = {40362845},
issn = {2072-6643},
mesh = {Humans ; *Probiotics/administration & dosage ; Female ; Pregnancy ; *Lactation/immunology/metabolism ; Diabetes, Gestational/prevention & control/immunology ; Administration, Oral ; Pregnancy Complications/immunology/prevention & control ; Pre-Eclampsia/prevention & control ; Adult ; Gastrointestinal Microbiome ; Dysbiosis ; },
abstract = {BACKGROUND/OBJECTIVES: In recent years, due to the emergence of antimicrobial resistance, probiotics have been increasingly used during pregnancy and lactation with real maternal-fetal benefits. Probiotic intervention, especially multi-strain probiotics, due to their anti-inflammatory, metabolic, and immunomodulatory actions, can be performed prophylactically and therapeutically with promising results regarding maternal, fetal, and neonatal health. The administration of probiotics can modulate the maternal microbiome, regulate microflora imbalance in various conditions (overweight/obesity, gestational diabetes mellitus (GDM), preeclampsia, allergic diseases), and influence several reactions such as modulating the non-specific cellular immune system, metabolic processes, and inhibition of pathogens. This study aimed to analyze, based on available data, how the administration of probiotic supplements to women during pregnancy can modify immunometabolic responses to microbial dysbiosis to limit weight gain and the risk of obesity, to improve glucose homeostasis and reduce the risk of GDM, to prevent preeclampsia and its effects on maternal-fetal outcomes, and to reduce rates of atopic eczema and allergic diseases in infants.

METHODS: We performed a systematic search in MEDLINE/PubMed to identify studies that have investigated the effects of probiotic intervention on the immunometabolic response in pregnancy and lactation, especially in women with diabetes, overweight/obesity, preeclampsia, and allergic conditions.

RESULTS: Fifty-six RCT studies, totaling 15,044 women, matched the inclusion criteria, of which eight were for interventions on the immune response, twenty on allergic conditions, seven on obesity and excess weight gain in pregnancy, and twenty-one on GDM.

CONCLUSIONS: Due to the heterogeneous structure and the size of the samples, the methodologies, formulations, moment of initiation, and study durations, future research is needed to establish their effectiveness and safety in pregnancy and lactation regarding maternal-fetal health and outcomes in childhood and adult life.},
}

Humans
*Probiotics/administration & dosage
Female
Pregnancy
*Lactation/immunology/metabolism
Diabetes, Gestational/prevention & control/immunology
Administration, Oral
Pregnancy Complications/immunology/prevention & control
Pre-Eclampsia/prevention & control
Adult
Gastrointestinal Microbiome
Dysbiosis

@article {pmid40362809,
year = {2025},
author = {Koller, AM and Săsăran, MO and Mărginean, CO},
title = {Small Intestinal Bacterial Overgrowth and Pediatric Obesity-A Systematic Review.},
journal = {Nutrients},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/nu17091499},
pmid = {40362809},
issn = {2072-6643},
mesh = {Humans ; *Pediatric Obesity/microbiology/epidemiology/complications ; *Intestine, Small/microbiology ; Child ; Dysbiosis ; *Gastrointestinal Microbiome ; Inflammation/microbiology ; Probiotics/therapeutic use ; *Blind Loop Syndrome/epidemiology/microbiology ; Biomarkers/blood ; *Bacteria/growth & development ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {Background/Objectives: Childhood obesity is a growing global concern linked to metabolic disorders such as nonalcoholic fatty liver disease (NAFLD). Small intestinal bacterial overgrowth (SIBO) may exacerbate these conditions by promoting systemic inflammation and metabolic dysfunction. This review evaluates the prevalence of SIBO in obese children, its association with inflammatory and metabolic markers, and the efficacy of diagnostic and therapeutic strategies. Methods: A systematic search of PubMed, Scopus, and Web of Science (2010-present) was conducted using Boolean operators: ('small intestinal bacterial overgrowth' OR 'SIBO') AND 'prevalence' AND ('low-grade inflammatory markers' OR 'metabolic status') AND 'gut microbiome' AND 'dysbiosis' AND 'obese children'. Results: The data show that SIBO is frequently observed in obese pediatric populations and is associated with gut dysbiosis, impaired nutrient absorption, and reduced production of short-chain fatty acids. These changes contribute to increased intestinal permeability, endotoxemia, and chronic low-grade inflammation. Several microbial taxa have been proposed as biomarkers and therapeutic targets. Diagnostic inconsistencies persist, but treatments such as probiotics, prebiotics, dietary interventions, and selective antibiotics show potential, pending further validation. Conclusions: Early identification and treatment of SIBO with tailored strategies may help reduce metabolic complications and improve outcomes in children with obesity.},
}

Humans
*Pediatric Obesity/microbiology/epidemiology/complications
*Intestine, Small/microbiology
Child
Dysbiosis
*Gastrointestinal Microbiome
Inflammation/microbiology
Probiotics/therapeutic use
*Blind Loop Syndrome/epidemiology/microbiology
Biomarkers/blood
*Bacteria/growth & development
Anti-Bacterial Agents/therapeutic use

@article {pmid40362805,
year = {2025},
author = {Sălcudean, A and Cîmpian, DM and Popovici, RA and Forna, N and Corodan-Comiati, DM and Sasu, AB and Cozma, MM and Bodo, CR and Enache, EC and Păcurar, M and Crăciun, RE and Blidaru, A and Jinga, V and Pașca, MD and Lukacs, EE and Tilinca, MC and Strete, EG and Crișan, AI and Osz, BE and Muntean, DL},
title = {Dietary Habits and Their Influence on the Microbiome and Mental Health in Adolescents.},
journal = {Nutrients},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/nu17091496},
pmid = {40362805},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Adolescent ; *Mental Health ; *Feeding Behavior/psychology/physiology ; *Mental Disorders/microbiology ; Dysbiosis ; *Diet ; },
abstract = {Adolescence represents a critical developmental stage where diet, gut microorganisms, and mental health are strongly interconnected. The current literature evidences the bidirectional role between dietary habits and psychological well-being, which is mediated by the gut-brain axis. The purpose of this review is to highlight the importance of dietary habits in adolescence period and the impact of different food choices on microbiota and secondary on mental health. Gut microbiota plays a vital role in the synthesis of neurotransmitters such as serotonin, dopamine, noradrenaline, and metabolites like short-chain fatty acids (SCFAs). The disruption in the composition of microbiota is called dysbiosis, which has been associated with a systemic inflammation state and chronic stress. They contribute to the onset of psychiatric disorders including MDD, anxiety, ADHD, and autism. Diets with a high quantity of sugar and low fiber contribute to alteration of microbiota and poor mental health. Additionally, early-life stress, antibiotic usage, and chronic inflammation may alter bacterial communities, with long-term implications for adolescents mental health. Dietary interventions, including the intake of prebiotics, probiotics, SCFAs, and micronutrients could restore microbial balance and improve psychiatric symptoms. This literature review highlights the critical role of diet and gut microbiota for adolescent mental health and emphasizes the need for integrative strategies to promote psychological resilience through microbiome regulation.},
}

Humans
*Gastrointestinal Microbiome/physiology
Adolescent
*Mental Health
*Feeding Behavior/psychology/physiology
*Mental Disorders/microbiology
Dysbiosis
*Diet

@article {pmid40362788,
year = {2025},
author = {Carvalho, MCDC and Ribeiro, SA and de Sousa, LS and Lima, AÂM and Maciel, BLL},
title = {Undernutrition and Intestinal Infections in Children: A Narrative Review.},
journal = {Nutrients},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/nu17091479},
pmid = {40362788},
issn = {2072-6643},
mesh = {Humans ; *Malnutrition/complications/microbiology ; Child, Preschool ; Infant ; *Intestinal Diseases/microbiology ; *Child Nutrition Disorders/microbiology ; Gastrointestinal Microbiome ; Diarrhea/microbiology ; Female ; Male ; Child Development ; Feces/microbiology ; },
abstract = {Undernutrition affects thousands of children under five years old worldwide, and various factors are related to its onset, among which we highlight enteric infections and gastrointestinal barrier dysfunction. The cycle of intestinal infections and undernutrition has long-term consequences, such as cognitive deficits, poor growth, and metabolic diseases in adulthood. This review explores factors linked to childhood undernutrition, focusing on intestinal infections and markers of intestinal permeability that affect child development. This narrative review was conducted using Medline/PubMed, Web of Science, and Scopus, from July 2024 to March 2025. Studies involving children under five years old and addressing undernutrition, intestinal infections, or intestinal permeability markers were included. Exclusion criteria comprised studies without therapeutic focus, and books, case reports, or academic theses. No language restrictions were applied, and registration on global platforms was not required. Overall, the studies reported a close relationship between enteric pathogens, diarrheal and non-diarrheal stools, and undernutrition. Among the pathogens most frequently found in the feces of malnourished children were Shigella, enterotoxigenic Escherichia coli, enteroaggregative E. coli (EAEC), and Cryptosporidium. The studies also showed the relationship between gastrointestinal barrier function and undernutrition, with the deterioration of nutrient absorption and, consequently, repercussions on development, linear growth, and weight in children. Although the studies analyzed had different designs and heterogeneity in the age range of the studied children, it was possible to observe the relationship between the infection/undernutrition cycle. Future studies should optimize personalized nutrient-based therapies, assess long-term effects on gut health and growth, and explore the gut microbiome's role in enteric infection susceptibility and undernutrition.},
}

Humans
*Malnutrition/complications/microbiology
Child, Preschool
Infant
*Intestinal Diseases/microbiology
*Child Nutrition Disorders/microbiology
Gastrointestinal Microbiome
Diarrhea/microbiology
Female
Male
Child Development
Feces/microbiology

@article {pmid40362753,
year = {2025},
author = {Shen, CL and Santos, JM and Elmassry, MM and Chen, F and Ji, G and Presto, P and Kiritoshi, T and Liu, X and Neugebauer, V},
title = {Crosstalk Among Gut Microbiota, Fecal Metabolites, and Amygdala Neuropathology Genes After Ginger Polyphenol Administration in Female Rats with Neuropathic Pain: Evidence for Microbiota-Gut-Brain Connection.},
journal = {Nutrients},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/nu17091444},
pmid = {40362753},
issn = {2072-6643},
support = {2021-67017-34026//United States Department of Agriculture/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Female ; *Neuralgia/drug therapy/microbiology ; *Zingiber officinale/chemistry ; Rats ; *Amygdala/drug effects/metabolism/pathology ; *Feces/microbiology/chemistry ; *Polyphenols/pharmacology/administration & dosage ; Rats, Sprague-Dawley ; *Catechols/pharmacology/administration & dosage ; Disease Models, Animal ; Behavior, Animal/drug effects ; Anxiety ; *Brain-Gut Axis/drug effects ; Fatty Alcohols ; },
abstract = {Objectives. The relationships among neuropathic pain, gut microbiota, microbiome-derived metabolites, and neuropathology have received increasing attention. This study examined the effects of two dosages of gingerol-enriched ginger (GEG) on mechanical hypersensitivity, anxiety-like behavior, gut microbiome composition and its metabolites, and neuropathology markers in female rats in the spinal nerve ligation (SNL) model of neuropathic pain. Methods. Forty female rats were assigned to 4 groups: sham-vehicle, SNL-vehicle, SNL+GEG at 200 mg/kg BW, and SNL+GEG at 600 mg/kg BW via oral gavage. All animals were given an AIN-93G diet for 5 weeks. Mechanical hypersensitivity was assessed by the von Frey test. Anxiety-like behavior was assessed by the open field test. Fecal microbiota composition and metabolites were determined using 16S rRNA gene sequencing and GC-MS, respectively. Neuropathology gene expression profiling of the amygdala was assessed by an nCounter[®] Neuropathology pathway panel. Results. Both GEG-treated groups showed decreased mechanical hypersensitivity and anxiety-like behavior in the SNL model. Gut microbiome diversity in both GEG groups was decreased compared with untreated SNL rats. In the SNL model, phyla such as Bacteroidota, Proteobacteria and Verrucomicrobiota were decreased. Compared with the untreated SNL group, both GEG groups exhibited increased abundance of the phyla Bacteroidota (i.e., Rikenella, Alistipes, Muribaculaceae, Odoribacter), Firmicutes (i.e., UBA1819, Ruminococcaceae, Oscillospiraceae, Roseburia), and Verrucomicrobiota (i.e., Victivallis). GEG groups had higher levels of nine hydrophilic positive metabolites [val-glu, urocanic acid, oxazolidinone, L-threonine, L-norleucine, indole, imino-tryptophan, 2,3-octadiene-5,7-diyn-1-ol, and (2E)-3-(3-hydroxyphenyl) acrylaldehyde] and two hydrophilic negative metabolites [methylmalonic acid and metaphosphoric acid], as well as lower levels of five hydrophilic metabolites [xanthine, N-acetylmuramic acid, doxaprost, adenine, and 1-myristoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine]. Among the 770 neuropathology genes, 1 gene (PLA2G4A) was upregulated and 2 genes (CDK5R1 and SHH) were downregulated in SNL rats. GEG caused the upregulation of nine genes (APC, CCNH, EFNA5, GRN, HEXB, ITPR1, PCSK2, TAF9, and WFS1) and downregulation of three genes (AVP, C4A, and TSPO) in the amygdala. Conclusions. GEG supplementation mitigated pain-associated behaviors in female rats with neuropathic pain, in part by reversing the molecular neuropathology signature of the amygdala. This was associated with changes in the gut microbiome composition and fecal metabolites, which could play a role in mediating the effects of GEG on neuropathic pain.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Female
*Neuralgia/drug therapy/microbiology
*Zingiber officinale/chemistry
Rats
*Amygdala/drug effects/metabolism/pathology
*Feces/microbiology/chemistry
*Polyphenols/pharmacology/administration & dosage
Rats, Sprague-Dawley
*Catechols/pharmacology/administration & dosage
Disease Models, Animal
Behavior, Animal/drug effects
Anxiety
*Brain-Gut Axis/drug effects
Fatty Alcohols

@article {pmid40362711,
year = {2025},
author = {Yi, L and Li, Z and Xu, H and Shi, D and Huang, Y and Pan, H and Zhao, Y and Zhao, H and Yang, M and Wei, H and Zhao, S},
title = {Microbiota-Based Intervention Alleviates High-Fat Diet Consequences Through Host-Microbe Environment Remodeling.},
journal = {Nutrients},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/nu17091402},
pmid = {40362711},
issn = {2072-6643},
support = {202102AA310054 and 202202AE090032//Major Science and Technology Project of Yunnan Province/ ; 32360808, 31760645, 31260592, 31060331//National Natural Science Foundation of China/ ; no//Sci-Tech Service Station of Farmer Academician in Fuyuan County/ ; },
mesh = {*Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome/physiology ; Animals ; Humans ; Bile Acids and Salts/metabolism ; Probiotics ; *Obesity/microbiology/etiology ; *Host Microbial Interactions ; Mice ; Body Weight ; },
abstract = {A high-fat diet leads to metabolic disturbances, which are important factors in the development of obesity. Gut microbial composition and diversity are altered by a high-fat diet. In general, a high-fat diet resulted in increased Firmicutes abundance and decreased alpha diversity. Bile acids (BAs) are involved in the digestion and absorption of fats in the small intestine and are also the metabolic substrates of microorganisms with bile salt hydrolase (BSH) activity. High-fat diets (HFDs) have been shown to alter gut microbiota composition and BA profiles in murine models. Similarly, probiotic supplementation reverses HFD-induced adverse effects. This review focuses on the energy composition characteristics of a high-fat diet and its effects on body weight, plasma lipid-related biochemical markers, changes in gut microbiome characteristics, and the important role of BAs. The regular mechanism by which a high-fat diet affects the intestinal microenvironment was attempted to be found.},
}

*Diet, High-Fat/adverse effects
*Gastrointestinal Microbiome/physiology
Animals
Humans
Bile Acids and Salts/metabolism
Probiotics
*Obesity/microbiology/etiology
*Host Microbial Interactions
Mice
Body Weight

@article {pmid40362641,
year = {2025},
author = {Niechcial, A and Schwarzfischer, M and Wawrzyniak, P and Determann, M and Pöhlmann, D and Wawrzyniak, M and Gueguen, E and Walker, MR and Morsy, Y and Atrott, K and Wilmink, M and Linzmeier, L and Spalinger, MR and Holowacz, S and Leblanc, A and Scharl, M},
title = {Probiotic Administration Modulates Gut Microbiota and Suppresses Tumor Growth in Murine Models of Colorectal Cancer.},
journal = {International journal of molecular sciences},
volume = {26},
number = {9},
pages = {},
doi = {10.3390/ijms26094404},
pmid = {40362641},
issn = {1422-0067},
support = {n.a.//PiLeJe SA, France/ ; },
mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/pathology/microbiology/drug therapy/chemically induced ; Mice ; Disease Models, Animal ; Dextran Sulfate ; Azoxymethane ; Cell Line, Tumor ; Bifidobacterium ; Lactobacillus ; Male ; Mice, Inbred C57BL ; },
abstract = {Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide with limited treatment options for advanced disease stages. Growing evidence implicates the gut microbiota in CRC pathogenesis, prompting interest in probiotics as a potential therapeutic strategy. In this study, we evaluated the effects of two probiotic compositions, CI (a mix of lactobacilli and bifidobacteria) and CII (bifidobacteria alone), in two murine CRC models: the orthotopic MC-38 cecum injection model and the inflammation-driven azoxymethane/dextran sodium sulfate (AOM/DSS) model. CI showed significant anti-tumor effects in the orthotopic model, reducing tumor weight and volume, which was, however, not associated with robust immune activation, suggesting microbiota-driven mechanisms. In contrast, CII was more effective in the AOM/DSS model, reducing colonic inflammation and completely preventing tumor development. Our study demonstrates that probiotics might have great therapeutic potential via modulation of the gut microbiota, and they can exert anti-tumor effects in murine models of CRC with distinct compositions showing differential efficacy depending on the model. CI stabilized the gut microbiome and inhibited pro-tumorigenic taxa in the MC-38 cecum injection model, while CII exhibited anti-inflammatory properties in the AOM/DSS model, highlighting the potential of probiotics as context-specific interventions for CRC. These findings contribute to the growing body of evidence supporting microbiota-targeted strategies in oncology and their relevance for therapeutic applications.},
}

Animals
*Probiotics/pharmacology/administration & dosage
*Gastrointestinal Microbiome/drug effects
*Colorectal Neoplasms/pathology/microbiology/drug therapy/chemically induced
Mice
Disease Models, Animal
Dextran Sulfate
Azoxymethane
Cell Line, Tumor
Bifidobacterium
Lactobacillus
Male
Mice, Inbred C57BL

@article {pmid40362530,
year = {2025},
author = {Wen, H and Zhang, Y and Liu, Y and Long, H and Yao, Y},
title = {The Significance of Circulating Microbial Signatures in the Prognosis and Immune Microenvironment of Patients with Cervical Cancer.},
journal = {International journal of molecular sciences},
volume = {26},
number = {9},
pages = {},
doi = {10.3390/ijms26094293},
pmid = {40362530},
issn = {1422-0067},
support = {grant no. 621QN0887, 122RC653//Hainan Provincial Natural Science Foundation of China/ ; grant no. 62162025//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Female ; *Uterine Cervical Neoplasms/microbiology/immunology/blood/mortality ; *Tumor Microenvironment/immunology ; Prognosis ; *Microbiota ; Biomarkers, Tumor/blood ; Nomograms ; Middle Aged ; },
abstract = {An increasing body of research indicates that the circulating microbiome plays a significant role in cancer initiation and progression and the treatment response. The genomic characteristics of circulating microorganisms may influence the tumor immune microenvironment, thereby affecting cancer progression and therapeutic outcomes. However, whether the circulating microbiome can serve as a prognostic biomarker for cervical cancer patients and its mechanistic role in the tumor immune microenvironment still requires further investigation. Univariate, Lasso, and multivariate Cox regression analyses were utilized to identify the circulating microbial signatures associated with overall survival (OS) in patients with cervical cancer. A circulating Microbial Abundance Prognostic Score (MAPS) model was constructed based on these findings. A nomogram that integrated clinical features and MAPSs was developed to predict the OS rates in patients with cervical cancer. Blood microbiome data were combined with matched tumor RNA-seq data to analyze the differences in the tumor microenvironment between high- and low-MAPS groups, elucidating the impact of the MAPS on the tumor immune microenvironment. Finally, the potential application of the circulating MAPS to predicting the efficacy of immunotherapy and chemotherapy was assessed. The MAPS predictive model, which includes 15 circulating microorganisms, has shown independent prognostic value for patients with cervical cancer. Integrating the MAPS into a nomogram improved the accuracy of the prognostic predictions. Combined microbial and gene analyses revealed potential interactions between prognostic tumor microbiomes and the tumor immune microenvironment. The drug sensitivity analysis indicated the potential of MAPS as a predictor of chemotherapy's efficacy. Our findings suggest that circulating microbial signatures hold promise as novel prognostic biomarkers and may inform personalized treatment strategies in cervical cancer. Further large-scale and multicenter studies are warranted to validate the clinical utility of the MAPS.},
}

Humans
Female
*Uterine Cervical Neoplasms/microbiology/immunology/blood/mortality
*Tumor Microenvironment/immunology
Prognosis
*Microbiota
Biomarkers, Tumor/blood
Nomograms
Middle Aged

@article {pmid40362500,
year = {2025},
author = {Muttiah, B and Hanafiah, A},
title = {Gut Microbiota and Cardiovascular Diseases: Unraveling the Role of Dysbiosis and Microbial Metabolites.},
journal = {International journal of molecular sciences},
volume = {26},
number = {9},
pages = {},
doi = {10.3390/ijms26094264},
pmid = {40362500},
issn = {1422-0067},
support = {DIP-2024-005//National University of Malaysia/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/metabolism/complications ; *Cardiovascular Diseases/microbiology/metabolism/etiology ; Animals ; Methylamines/metabolism ; Fatty Acids, Volatile/metabolism ; },
abstract = {Cardiovascular diseases (CVDs), including heart failure (HF), hypertension, myocardial infarction (MI), and atherosclerosis, are increasingly linked to gut microbiota dysbiosis and its metabolic byproducts. HF, affecting over 64 million individuals globally, is associated with systemic inflammation and gut barrier dysfunction, exacerbating disease progression. Similarly, hypertension and MI correlate with reduced microbial diversity and an abundance of pro-inflammatory bacteria, contributing to vascular inflammation and increased cardiovascular risk. Atherosclerosis is also influenced by gut dysbiosis, with key microbial metabolites such as trimethylamine-N-oxide (TMAO) and short-chain fatty acids (SCFAs) playing crucial roles in disease pathogenesis. Emerging evidence highlights the therapeutic potential of natural compounds, including flavonoids, omega-3 fatty acids, resveratrol, curcumin, and marine-derived bioactives, which modulate the gut microbiota and confer cardioprotective effects. These insights underscore the gut microbiota as a critical regulator of cardiovascular health, suggesting that targeting dysbiosis may offer novel preventive and therapeutic strategies. Further research is needed to elucidate underlying mechanisms and optimize microbiome-based interventions for improved cardiovascular outcomes.},
}

Humans
*Gastrointestinal Microbiome
*Dysbiosis/microbiology/metabolism/complications
*Cardiovascular Diseases/microbiology/metabolism/etiology
Animals
Methylamines/metabolism
Fatty Acids, Volatile/metabolism

@article {pmid40362493,
year = {2025},
author = {Žukienė, G and Narutytė, R and Rudaitis, V},
title = {Association Between Vaginal Microbiota and Cervical Dysplasia Due to Persistent Human Papillomavirus Infection: A Systematic Review of Evidence from Shotgun Metagenomic Sequencing Studies.},
journal = {International journal of molecular sciences},
volume = {26},
number = {9},
pages = {},
doi = {10.3390/ijms26094258},
pmid = {40362493},
issn = {1422-0067},
mesh = {Humans ; Female ; *Papillomavirus Infections/complications/microbiology/virology ; *Vagina/microbiology/virology ; *Microbiota/genetics ; Metagenomics/methods ; *Uterine Cervical Dysplasia/microbiology/virology/etiology ; Papillomaviridae ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The role of vaginal dysbiosis in the progression of human papilloma virus (HPV) associated cervical lesions has gained attention in recent years. While many studies use 16S rRNA gene sequencing for microbiota analysis, shotgun metagenomic sequencing offers higher taxonomic resolution and insights into microbial gene functions and pathways. This systematic review evaluates the relationship between compositional and functional changes in the vaginal microbiome during HPV infection and cervical lesion progression. A literature search was performed according to PRISMA guidelines in PubMed, Web of Science, Scopus, and ScienceDirect databases. Seven studies utilizing metagenomic sequencing in patients with HPV infection or HPV-associated cervical lesions were included. Progression from HPV infection to cervical lesions and cancer was associated with a reduction in Lactobacillus species (particularly Lactobacillus crispatus) and an enrichment of anaerobic and pathogenic species, especially Gardnerella vaginalis. Heterogeneous enriched metabolic pathways were also identified, indicating functional shifts during lesion progression. As most studies were conducted in Asia, further research in diverse regions is needed to improve the generalizability of findings. Future studies employing metagenomic sequencing may help identify biomarkers for early pre-cancerous lesions and clarify the role of vaginal microbiota in persistent HPV infection and cervical dysplasia.},
}

Humans
Female
*Papillomavirus Infections/complications/microbiology/virology
*Vagina/microbiology/virology
*Microbiota/genetics
Metagenomics/methods
*Uterine Cervical Dysplasia/microbiology/virology/etiology
Papillomaviridae
Dysbiosis/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid40362352,
year = {2025},
author = {Valencia, S and Zuluaga, M and Florian Pérez, MC and Montoya-Quintero, KF and Candamil-Cortés, MS and Robledo, S},
title = {Human Gut Microbiome: A Connecting Organ Between Nutrition, Metabolism, and Health.},
journal = {International journal of molecular sciences},
volume = {26},
number = {9},
pages = {},
doi = {10.3390/ijms26094112},
pmid = {40362352},
issn = {1422-0067},
support = {Convocatoria 934//Ministerio de Ciencia Tecnología e Innovación de Colombia/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Probiotics ; Prebiotics ; Dysbiosis/microbiology ; Obesity/microbiology/metabolism ; },
abstract = {The gut microbiome plays a vital role in human health, functioning as a metabolic organ that influences nutrient absorption and overall well-being. With growing evidence that dietary interventions can modulate the microbiome and improve health, this review examines whether healthcare systems should prioritize personalized microbiome-targeted therapies, such as probiotics, prebiotics, and microbiota transplants, over traditional pharmaceutical treatments for chronic diseases like obesity, diabetes, cardiovascular risk, and inflammatory conditions. A systematic review using Web of Science and Scopus databases was conducted, followed by a scientometric analysis. Key metabolic pathways, such as dietary fiber fermentation and short-chain fatty acid production, were explored, focusing on their impact on lipid and glucose metabolism. The interactions between microbial metabolites and the immune system were also investigated. Dietary interventions, including increased fiber and probiotic intake, show potential for addressing dysbiosis linked to conditions, such as type 2 diabetes, obesity, and autoimmune diseases. The review emphasizes the need to incorporate microbiome modulation strategies into clinical practice and research, calling for a multidisciplinary approach that integrates nutrition, microbiology, and biochemistry to better understand the gut microbiome's complex role in health.},
}

Humans
*Gastrointestinal Microbiome/physiology
Probiotics
Prebiotics
Dysbiosis/microbiology
Obesity/microbiology/metabolism

@article {pmid40362199,
year = {2025},
author = {Schellekens, HCJ and Schmidt, LMS and Morré, SA and van Esch, EMG and de Vos van Steenwijk, PJ},
title = {Vaginal Microbiota and Local Immunity in HPV-Induced High-Grade Cervical Dysplasia: A Narrative Review.},
journal = {International journal of molecular sciences},
volume = {26},
number = {9},
pages = {},
doi = {10.3390/ijms26093954},
pmid = {40362199},
issn = {1422-0067},
mesh = {Humans ; Female ; *Microbiota/immunology ; *Papillomavirus Infections/immunology/virology/microbiology/complications ; *Vagina/microbiology/immunology/virology ; *Uterine Cervical Dysplasia/immunology/virology/microbiology/pathology ; *Papillomaviridae/immunology ; *Uterine Cervical Neoplasms/immunology/virology/microbiology/pathology ; },
abstract = {Persistent high-risk Human Papillomavirus infection is the primary factor in cervical carcinogenesis. However, other host-related features are believed to play a role as well. Recent research suggests that the vaginal microbiome and the immune microenvironment play a significant role in the acquisition and persistence of Human Papillomavirus infection, as well as in the regression or progression of cervical intraepithelial lesions. Studies in this emerging field describe factors associated with this interaction, though the precise nature remains incompletely understood. In this narrative review, we aim to summarize the current literature on the topic and propose hypotheses and recommendations for future research and treatment strategies.},
}

Humans
Female
*Microbiota/immunology
*Papillomavirus Infections/immunology/virology/microbiology/complications
*Vagina/microbiology/immunology/virology
*Uterine Cervical Dysplasia/immunology/virology/microbiology/pathology
*Papillomaviridae/immunology
*Uterine Cervical Neoplasms/immunology/virology/microbiology/pathology

@article {pmid40362152,
year = {2025},
author = {Wang, X and Shao, Y and Zhou, X and Li, Z and Liu, J and Tang, M and Yang, Y and Deng, L},
title = {Dynamic Changes in the Gut Microbiota During Peripartum in Jennies.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/ani15091337},
pmid = {40362152},
issn = {2076-2615},
support = {2024YFD1300502//National Key R&D Program of China/ ; 32260844//National Natural Science Foundation of China/ ; LSNFW201904//Department of Education of Liaoning Province, China/ ; },
abstract = {The peripartum period is critical for breeding female donkeys (i.e., jennies) and ensuring the delivery of healthy neonatal foals. The gut microbiota deeply influences the host metabolism. This study aimed to investigate the dynamic changes in the gut microbiome during the peripartum period in jennies. Fresh fecal samples of eight adult jennies were collected at the following seven sampling time points: 21, 7, and 3 days prepartum (G21, G7, and G3) and 1, 3, 7, and 14 days postpartum (L1, L3, L7, and L14). Sequencing of the V4 hypervariable regions of the 16S rRNA genes was carried out using fecal samples to identify the differences in the microbiome across the peripartum period. Bacteroidota and Firmicutes were the most abundant bacterial phyla in the feces. Treponema and Lachnospiraceae XPB1014 group significantly increased in the L3 group compared to the G7 group (q < 0.05), and a decline trend was observed in L1 group around parturition. The genus Clostridium sensu stricto 1, family Clostridiaceae, and order Clostridiales were considered to be biomarkers of the L3 group. Among the 25 functional pathways detected by Kyoto Encyclopedia of Genes and Genomes pathway analysis, beta lactam resistance, insulin resistance, and peptidases were the top three important pathways observed in the gut microbiota during the peripartum period in jennies. The gut microbial structure changed significantly at different time points during the peripartum period in jennies. These results contribute to a better understanding of the gut microbiota to ensure health care during important phases from late pregnancy to early lactation in jennies.},
}

@article {pmid40362078,
year = {2025},
author = {Kongpanna, P and Jamikorn, U and Tripipat, T and Tantituvanont, A and Ngampak, R and Nilubol, D},
title = {Efficacy of Three Doses of Halquinol on Growth Performance, Diarrhea Incidence, Nutrient Digestibility, and Fecal Microbiome of Weaned Pigs.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/ani15091258},
pmid = {40362078},
issn = {2076-2615},
support = {0001//Thailand Science Research and Innovation Fund, Chulalongkorn University./ ; },
abstract = {The weaning period is a critical phase for nursery pigs that is characterized by rapid growth and alterations in the intestinal microbiome associated with nutrient utilization. The present study aimed to investigate the efficacy of halquinol, when used as an antibiotic (ABO), on the growth performance, diarrhea incidence, coefficient of apparent total tract digestibility (CATTD), fecal volatile fatty acids (VFAs), and microbiota in pigs. A total of 210 healthy weaned pigs with an average initial weight of 6.9 kg and aged 28 ± 2 days were assigned to five treatments (six pens/treatment) in a complete randomized design, including a control group (T1, CON; feed with no ABO), a colistin group (T2, CLT; feed containing 120 ppm colistin), and three halquinol groups (T3 to T5, HAL; feed containing 180, 240, and 360 ppm halquinol, respectively). The experiment period lasted for 10 days. Field recordings, observation, and feces collection were performed on D1, D5, and D10. CATTD and VFA assessments were conducted on D10. The composition of the fecal microbiota was analyzed via 16S rRNA gene sequencing using the Illumina Miseq platform. The results demonstrated that the in-feed ABO groups exhibited a significantly lower ADFI (p < 0.01). Pigs fed the T3 and T4 diets had the lowest FCR (p < 0.01) on D5 and D10 and, thus, had reduced ADFI (p < 0.01). A quadratic contrast was found in ADFI and FCR on D5 and D10, indicating a negative correlation with HAL concentration (p < 0.01). Pigs fed CLT and HAL had significantly reduced levels of coliform (p < 0.01) and E. coli (p < 0.01). Moreover, pigs receiving ABO also had a lower fecal score compared to those on the CON diet (p < 0.01). Dietary in-feed ABO had no effect on all the parameters of the CATTD on D10 (p > 0.05), except for fat digestibility in pigs that received T4 (p < 0.01). Pigs fed the T4 and T5 diets had higher propionate concentrations and lower A/P ratios than pigs fed T1, T2, and T3 (p < 0.01). The microbial diversity shifted quickly through the early weaning period. The relative abundance of beneficial Enterococcus microbes increased in pigs fed in-feed ABO, whereas the relative prevalence of pathogenic bacteria, such as Escherichia and Klebsiella, decreased. Escherichia and Bacteroides were negatively correlated with carbohydrate digestibility and butyric and valeric acid production (p < 0.05). Overall, the appropriate HAL dosage was 240 ppm (T4), and this antimicrobial can potentially be characterized as an in-feed colistin replacer that improves feed efficiency and fat digestion, enhancing VFA production, alleviating post-weaning diarrhea, and protecting ABO-resistant piglets.},
}

@article {pmid40362059,
year = {2025},
author = {Wang, Z and Cui, L and Wang, X and Shen, C and Wang, Y and Jiang, W and Gu, Y},
title = {Comparative Transcriptomics and Intestinal Microbiome Analysis Provide Insights into the Semi-Terrestrial Adaptation of Helice tientsinensis.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/ani15091244},
pmid = {40362059},
issn = {2076-2615},
support = {No. 31702014//National Natural Science Foundation of China/ ; JKLBS2019006//Jiangsu Provincial Key Laboratory for Bioresources of Saline Soils Open Foundation/ ; none//Doctoral Scientific Research Foundation of Yancheng Teachers University/ ; },
abstract = {Helice tientsinensis, a Grapsidae family member, can adapt to terrestrial and semi-terrestrial environments. This study used transcriptomic and microbiome analyses to explore its adaptation mechanisms. Transcriptome analysis showed gene changes related to cytoskeleton-motor, water-osmotic pressure, and energy metabolism. For example, DST was upregulated in the aquatic environment compared to the semi-terrestrial one, and SPAST was downregulated in some groups. ATP2A and SLC6A3 were upregulated with osmotic regulation, and IDH3 was upregulated when comparing the aquatic and semi-terrestrial habitats; at the same time, many energy-related genes were downregulated between the terrestrial and semi-terrestrial habitats. Regarding the gut microbiota, no significant differences in alpha diversity were found between habitats, but there were differences at the genus level. Pseudomonas and Malaciobacter were more abundant in the aquatic habitat, and Dietzia in the semi-terrestrial one. These results provide insights into H. tientsinensis' terrestrial adaptation, benefiting crustacean evolution study and aquaculture.},
}

@article {pmid40361725,
year = {2025},
author = {Liu, Z and Wang, X and Li, Q and Kang, X and Li, Y and Gong, C and Liu, Y and Chen, H},
title = {Physiological Functions of the By-Products of Passion Fruit: Processing, Characteristics and Their Applications in Food Product Development.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/foods14091643},
pmid = {40361725},
issn = {2304-8158},
abstract = {The by-products of passion fruit are typically discarded during processing, contributing to resource waste and environmental harm. These residues are rich in dietary fiber and polyphenols, compounds linked to health benefits, including blood sugar regulation, improved lipid profiles, gut microbiome balance, and weight management. Beyond their nutritional value, these by-products possess dual functional roles in food systems: their bioactive components act as natural fortifiers and health-promoting agents. Recent studies indicate they can enhance food quality by improving water retention and texture while serving as prebiotics to promote beneficial gut bacteria growth. This dual functionality supports both food innovation and metabolic health, particularly in reducing post-meal blood sugar spikes. To advance research and industry applications, this review synthesizes recent findings on the nutritional properties of passion fruit by-products and their use in food products such as dairy, pasta, and meat. The analysis aims to guide the sustainable utilization of these underrated resources and expand their role in functional food development.},
}

@article {pmid40361643,
year = {2025},
author = {de Oliveira, JMC and Antunes, AEC and Sales, GFC and Costa, CNM and Alves, AMDS and de Lima, KYG and de Oliveira, CJB and do Egito, AS and Dos Santos, KMO and de Souza, EL and Pacheco, MTB and de Oliveira, MEG},
title = {Influence of Autochthonous Lactic Acid Bacteria Cultures on the Microbiota and Biogenic Amine Production in Medium-Ripened Artisan Goat Cheese.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/foods14091561},
pmid = {40361643},
issn = {2304-8158},
support = {001//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; 1010/2021//Fundação de Apoio à Pesquisa do Estado da Paraíba/ ; 308253/2020-5//National Council for Scientific and Technological Development/ ; 946/2021//Fundação de Apoio à Pesquisa do Estado da Paraíba/ ; 2019/23896-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
abstract = {This study evaluated the effects of adding the autochthonous cultures Limosilactobacillus mucosae CNPC007 (LM) and Lactiplantibacillus plantarum CNPC003 (LP), originally isolated from goat milk and goat cheese, respectively, on microbiological safety, microbiota composition (analyzed through 16S rRNA gene metataxonomic sequencing), and biogenic amine (BA) production in artisanal goat (coalho) cheese made from raw or pasteurized milk during 60 days of ripening at 10 °C. Six types of cheese were produced, varying in milk treatment (raw or pasteurized) and the presence or absence of LP or LM cultures. Adding either LP or LM significantly modulated the microbiota, favoring Streptococcus dominance and reducing overall bacterial diversity compared to non-inoculated cheeses. Raw milk cheeses with added autochthonous cultures exhibited a microbial profile like pasteurized cheeses, suggesting a homogenizing effect on the microbiome. Both cultures effectively reduced microbial load in raw milk cheeses after 20 days, reaching levels comparable to pasteurized cheeses by the end of ripening. Although BA concentrations increased over time, all samples remained within safe limits. Cheeses with LP addition exhibited lower BA levels, suggesting a modulating effect on their biosynthesis. Histamine concentrations were higher in raw milk cheeses with added cultures but remained well below hazardous levels. These findings suggest that incorporating either LP or LM strains is a promising strategy for enhancing the microbial safety and standardization of artisanal goat cheese while preserving its traditional characteristics.},
}

@article {pmid40361641,
year = {2025},
author = {Mafe, AN and Büsselberg, D},
title = {Could a Mediterranean Diet Modulate Alzheimer's Disease Progression? The Role of Gut Microbiota and Metabolite Signatures in Neurodegeneration.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/foods14091559},
pmid = {40361641},
issn = {2304-8158},
support = {NPRP 14S0311-210033//Qatar National Research Fund/ ; },
abstract = {Neurodegenerative disorders such as Alzheimer's disease (AD), the most common form of dementia, represent a growing global health crisis, yet current treatment strategies remain primarily palliative. Recent studies have shown that neurodegeneration through complex interactions within the gut-brain axis largely depends on the gut microbiota and its metabolites. This review explores the intricate molecular mechanisms linking gut microbiota dysbiosis to cognitive decline, emphasizing the impact of microbial metabolites, including short-chain fatty acids (SCFAs), bile acids, and tryptophan metabolites, on neuroinflammation, blood-brain barrier (BBB) integrity, and amyloid-β and tau pathology. The paper highlights major microbiome signatures associated with Alzheimer's disease, detailing their metabolic pathways and inflammatory crosstalk. Dietary interventions have shown promise in modulating gut microbiota composition, potentially mitigating neurodegenerative processes. This review critically examines the influence of dietary patterns, such as the Mediterranean and Western diets, on microbiota-mediated neuroprotection. Bioactive compounds like prebiotics, omega-3 fatty acids, and polyphenols exhibit neuroprotective effects by modulating gut microbiota and reducing neuroinflammation. Furthermore, it discusses emerging microbiome-based therapeutic strategies, including probiotics, prebiotics, postbiotics, and fecal microbiota transplantation (FMT), as potential interventions for slowing Alzheimer's progression. Despite these advances, several knowledge gaps remain, including interindividual variability in microbiome responses to dietary interventions and the need for large-scale, longitudinal studies. The study proposes an integrative, precision medicine approach, incorporating microbiome science into Alzheimer's treatment paradigms. Ultimately, cognizance of the gut-brain axis at a mechanistic level could unlock novel therapeutic avenues, offering a non-invasive, diet-based strategy for managing neurodegeneration and improving cognitive health.},
}

@article {pmid40361614,
year = {2025},
author = {Dong, Y and Wu, X and Zhang, Y and Hu, A and Zhou, Q and Yue, X and Liu, Z and Li, M},
title = {The Role of Probiotics in Modulating the Gut Microbiome in Alzheimer's Disease: A Review.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/foods14091531},
pmid = {40361614},
issn = {2304-8158},
abstract = {Alzheimer's disease (AD) has emerged as a global public health priority characterized by escalating prevalence and the limited efficacy of current therapeutic approaches. Although the pathological complexity of AD is well-recognized, its underlying etiology remains incompletely elucidated. Current research highlights a bidirectional gut-brain axis (GBA) interaction, wherein gut microbiome perturbations may impair intestinal barrier stability, influence immune responses, and blood-brain barrier permeability through microbial metabolite-mediated pathways, thereby contributing to AD pathophysiology. Notably, probiotics demonstrate therapeutic potential by restoring gut microbiome homeostasis, reinforcing intestinal barrier integrity, and mitigating neuroinflammatory responses via GBA. This review focuses on investigating the gut microbiome alterations in AD pathogenesis, the interaction of probiotics with GBA, and its significance in AD pathogenesis. By synthesizing current clinical evidence, this review aims to establish a scientific foundation for probiotic-based interventions as a novel therapeutic strategy in AD management.},
}

@article {pmid40361602,
year = {2025},
author = {Kuan, S and Chin, NL and Tee, TP and Hasnan, NZN},
title = {Microbiome Diversity in Seafood Factories via Next-Generation Sequencing for Food Safety Management System (FSMS) Certifications in Malaysia.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/foods14091517},
pmid = {40361602},
issn = {2304-8158},
support = {KKM.600-19/7/5//MINISTRY OF HEALTH MALAYSIA/ ; },
abstract = {Next-Generation Sequencing (NGS) technology was applied to evaluate Food Safety Management System (FSMS) performance in seafood-processing factories by exploring microbiome diversity alongside traditional methods for detecting foodborne pathogens. A total of 210 environmental swabs collected from processing zones in six factories underwent 16S rRNA amplicon sequencing. FSMS-certified factories exhibited significantly higher species richness, with alpha diversity p-values of 0.0036 for observed ASVs, 0.0026 for Faith's PD and 0.032 for Shannon. Beta diversity analysis also revealed significant differences, with p-values of 0.001 for Bray-Curtis, unweighted UniFrac and Jaccard. Pathogens like Listeria monocytogenes, Salmonella spp. and Bacillus cereus were present in "uncertified" factories but absent in the "certified" factories. The "certified" factories had a significantly higher proportion of lactic acid bacteria (LAB) genera (70.22%) compared to "uncertified" factories (29.78%). The LAB genera included Streptococcus, Lactococcus, Lactobacillus and others. NGS has demonstrated superior capability by providing comprehensive microbiome detection, including the unculturable microorganisms and insights into microbial diversity, so it lacks the limitations that come with traditional culturing. These findings highlight the potential for leveraging beneficial microbes in bioremediation and pathogen control to enhance FSMS effectiveness in seafood-processing environments.},
}

@article {pmid40361425,
year = {2025},
author = {Lukac, S and Fink, V and Dayan, D and Rack, B and Janni, W and Lato, K and Veselinovic, K and Heublein, S and Friedl, TWP and Leinert, E},
title = {Negative Effect of Intravenous Antibiotics on Survival in Patients with Triple-Negative Breast Cancer.},
journal = {Cancers},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/cancers17091498},
pmid = {40361425},
issn = {2072-6694},
abstract = {BACKGROUND: The anti-tumor response of the immune system is pivotal for treating triple-negative breast cancer (TNBC), particularly as targeted therapies are limited. However, the impact of immune-modulating factors such as the application of granulocyte-stimulating factors (G-CSFs) or infections, including febrile neutropenia, prophylactic or therapeutical application of oral antibiotics (OABs), and the need for intravenous antibiotics (IABs), on survival outcomes remains unclear.

METHODS: 1583 patients with early-stage TNBC enrolled in the SUCCESS A or C study underwent primary surgery, adjuvant chemotherapy, and radiotherapy if indicated. All patients had Eastern Cooperative Oncology Group (ECOG) status ≤ 2. The effects of G-CSF, OAB, and IAB application on overall survival (OS), invasive disease-free survival (iDFS), breast cancer-specific survival (BCSS), and distant disease-free survival (DDFS) were assessed.

RESULTS: Only IAB treatment was significantly associated with decreased survival in univariable analyses (OS: p = 0.003; iDFS: p = 0.036; BCSS: p = 0.011; DDFS: p = 0.044), while G-CSF and OAB administration were not. Adjusted multivariable Cox regressions including febrile neutropenia and dose reduction/shift, ECOG, age of patients, and other clinicopathological parameters confirmed a significant negative effect of IABs on OS (p = 0.020), BCSS (p = 0.018), and DDFS (p = 0.044).

CONCLUSIONS: In summary, IABs during adjuvant chemotherapy seems to be a risk factor for inferior OS, BCSS, and DDFS in TNBC patients, possibly by affecting microbiome-related immune response modulation. Hence, preventive measures to avoid the need for IABs should be considered in these patients.},
}

@article {pmid40361242,
year = {2025},
author = {Lanou, HB and Somé, JW and Koumbem, MAA and Kouanda, S},
title = {Microbiome-directed food to promote sustained recovery in children with uncomplicated acute malnutrition: protocol for a randomized controlled trial in Burkina Faso.},
journal = {BMC nutrition},
volume = {11},
number = {1},
pages = {92},
pmid = {40361242},
issn = {2055-0928},
abstract = {BACKGROUND: Acute malnutrition still affects millions of children under five years of age globally each year and contributes to approximately half of all annual childhood deaths. A considerable proportion of patients who recover from acute malnutrition experience poor health and nutrition and eventually relapse after they are discharged from community management of acute malnutrition programs. A microbiota-directed complementary food (MDCF) showed a superior effect compared to standard ready-to-use supplementary food (RUSF) in terms of ponderal growth and potential benefit for bacterial taxa that were correlated with weight-for-height z-score (WHZ). This paper describes a protocol for the MDCF phase III trial on a larger African sample for promoting sustained recovery.

METHODS: This study is an individually controlled open-label phase III trial to determine the efficacy of MDCF on programmatic and sustained recovery compared to standards RUTF and RUSF. Eligible MAM children will be randomly assigned to MDCF or RUSF and those with SAM to MDCF or RUTF. Supplementation and follow-up visits will be performed following national guidelines for acute malnutrition management. Primary outcomes are programmatic recovery at 12 weeks after enrollment and sustained recovery at 12 weeks after recovery. The secondary outcomes included the mean WHZ, weight-for-age z score, height-for-age z score change, average length of stay, nonresponse, failure and dropout.

DISCUSSION: The present study is designed to investigate the efficacy of a microbiota-targeted food in treating acute uncomplicated malnutrition and preventing relapses. It will provide evidence as a phase III clinical trial.

TRIAL REGISTRATION: Clinicaltrials.gov Protocol registration and results system (NCT05586139). Registered on 2022-10-14. https://register.

CLINICALTRIALS: gov/ .},
}

@article {pmid40361240,
year = {2025},
author = {Fares, M and Tharwat, EK and Cleenwerck, I and Monsieurs, P and Van Houdt, R and Vandamme, P and El-Hadidi, M and Mysara, M},
title = {The unresolved struggle of 16S rRNA amplicon sequencing: a benchmarking analysis of clustering and denoising methods.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {51},
pmid = {40361240},
issn = {2524-6372},
abstract = {BACKGROUND: Although 16S rRNA gene amplicon sequencing has become an indispensable method for microbiome studies, this analysis is not error-free, and remains prone to several biases and errors. Numerous algorithms have been developed to eliminate these errors and consolidate the output into distance-based Operational Taxonomic Units (OTUs) or denoising-based Amplicon Sequence Variants (ASVs). An objective comparison between them has been obscured by various experimental setups and parameters. In the present study, we conducted a comprehensive benchmarking analysis of the error rates, microbial composition, over-merging/over-splitting of reference sequences, and diversity analyses using the most complex mock community, comprising 227 bacterial strains and the Mockrobiota database. Using unified preprocessing steps, we were able to compare DADA2, Deblur, MED, UNOISE3, UPARSE, DGC (Distance-based Greedy Clustering), AN (Average Neighborhood), and Opticlust objectively.

RESULTS: ASV algorithms-led by DADA2- resulted in having a consistent output, yet suffered from over-splitting, while OTU algorithms-led by UPARSE-achieved clusters with lower errors, yet with more over-merging. Notably, UPARSE and DADA2 showed the closest resemblance to the intended microbial community, especially when considering measures for alpha and beta diversity.

CONCLUSION: Our unbiased comparative evaluation examined the performance of eight algorithms dedicated to the analysis of 16S rRNA amplicon sequences with a wide range of mock datasets. Our analysis shed light on the pros and cons of each algorithm and the accuracy of the produced OTUs or ASVs. The utilization of the most complex mock community and the benchmarking comparison presented here offer a framework for the comparison between OTU/ASV algorithms and an objective method for the assessment of new tools and algorithms.},
}

@article {pmid40361225,
year = {2025},
author = {George, C and Kortheerakul, C and Khunthong, N and Sharma, C and Luo, D and Chan, KG and Daroch, M and Hyde, KD and Lee, PKH and Goh, KM and Waditee-Sirisattha, R and Pointing, SB},
title = {Spatial scale modulates stochastic and deterministic influence on biogeography of photosynthetic biofilms in Southeast Asian hot springs.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {50},
pmid = {40361225},
issn = {2524-6372},
abstract = {Hot springs, with their well-characterized major abiotic variables and island-like habitats, are ideal systems for studying microbial biogeography. Photosynthetic biofilms are a major biological feature of hot springs but despite this large-scale studies are scarce, leaving critical questions about the drivers of spatial turnover unanswered. Here, we analysed 395 photosynthetic biofilms from neutral-alkaline hot springs (39-66 °C, pH 6.4-9.0) across a 2100 km latitudinal gradient in Southeast Asia. The Cyanobacteria-dominated communities were categorized into six biogeographic regions, each characterized by a distinct core microbiome and biotic interactions. We observed a significant decline in the explanatory power of major abiotic variables with increasing spatial scale, from 62.6% locally, 55% regionally, to 26.8% for the inter-regional meta-community. Statistical null models revealed that deterministic environmental filtering predominated at local and regional scales, whereas stochastic ecological drift was more influential at the inter-regional scale. These findings enhance our understanding of the differential contribution of ecological drivers and highlight the importance of spatial scale in shaping biogeographic distributions for microorganisms.},
}

@article {pmid40361215,
year = {2025},
author = {Ma, Y and Jiang, J and Yang, Z and Li, Y and Bai, H and Liu, Z and Zhang, S and Zhi, Z and Yang, Q},
title = {Changes of gastric microflora and metabolites in patients with chronic atrophic gastritis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {537},
pmid = {40361215},
issn = {1479-5876},
support = {No.21377724D//Hebei Provincial Department of Science and Technology/ ; No. 18//National Administration of Traditional Chinese Medicine Science and Technology/ ; 246W7701D//Provincial Science and Technology Plan of Hebei Province/ ; },
mesh = {Humans ; *Gastritis, Atrophic/microbiology/metabolism ; Chronic Disease ; Middle Aged ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Metabolome ; *Stomach/microbiology ; Metabolomics ; *Microbiota ; Bacteria/genetics/metabolism ; Adult ; Aged ; *Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Chronic atrophic gastritis (CAG) is related to the body's microbial and metabolic systems. Combined studies of microbiome and metabolomics can clarify the mechanisms of disease occurrence and progression. We used 16S rRNA sequencing, metagenomics sequencing and metabolomics sequencing to depict the landscapes of bacterium and metabolites, construct correlation networks of different bacterium and metabolites describe potential pathogenic mechanisms of chronic atrophic gastritis.

METHODS: The gastric juices of 30 non-atrophic gastritis (NAG) patients and 30 CAG patients were collected. Gastric microflora was analyzed by 16S rRNA sequencing and metagenomics sequencing. Gastric metabolites were analyzed by LC-MS analysis. Different bioinformatics methods were used to analyze the data of microbiome and metabolome, and to analyze the relationship between them.

RESULTS: In atrophic gastritis, bacteria diversity decreased. The genera with a mean decrease in Gini greater than 1.5 included peptostreptococcus, fusobacterium, prevotella, sphingomonas and bacteroides. KEGG pathway included renal cell carcinoma, proximal tubule bicarbonate reclamation, citrate cycle and aldosterone synthesis and secretion with significant enrichment of differential metabolites. Peptostreptococcus, fusobacterium, prevotella and sphingomonas were in pivot positions of the correlation network of differential metabolites and differential bacterium. Viral carcinogenesis, glycine serine and threonine metabolism, RNA polymerase, galactose metabolism and retinol metabolism were enriched in chronic atrophic gastritis based on the metagenomic sequencing data.

CONCLUSION: Peptostreptococcus, fusobacterium, prevotella, sphingomonas and bacteroides were the essential features that distinguish atrophic gastritis from non-atrophic gastritis, and caused disease by altering various metabolic pathways. Viral carcinogenesis, glycine serine and threonine metabolism, RNA polymerase, galactose metabolism and retinol metabolism may be related to the occurrence and progression of CAG.},
}

Humans
*Gastritis, Atrophic/microbiology/metabolism
Chronic Disease
Middle Aged
Female
Male
RNA, Ribosomal, 16S/genetics
Metabolome
*Stomach/microbiology
Metabolomics
*Microbiota
Bacteria/genetics/metabolism
Adult
Aged
*Gastrointestinal Microbiome

@article {pmid40361187,
year = {2025},
author = {Deng, S and Kim, W and Cheng, K and Yang, Q and Singh, Y and Bae, G and Bézière, N and Mager, L and Kommoss, S and Sprengel, J and Trautwein, C},
title = {Identification and impact of microbiota-derived metabolites in ascites of ovarian and gastrointestinal cancer.},
journal = {Cancer & metabolism},
volume = {13},
number = {1},
pages = {21},
pmid = {40361187},
issn = {2049-3002},
abstract = {BACKGROUND: Malignant ascites is a common complication of advanced ovarian cancer (OC) and gastrointestinal cancer (GI), significantly impacting metastasis, quality of life, and survival. Increased intestinal permeability can lead to blood or lymphatic infiltration and microbial translocation from the gastrointestinal or uterine tract. This study aimed to identify microbiota-derived metabolites in ascites from OC (stages II-III and IV) and GI patients, assessing their roles in tumor progression.

METHODS: Malignant ascites samples from 18 OC and GI patients were analyzed using a four-dimensional (4D) untargeted metabolomics approach combining reversed-phase (RP) and hydrophilic interaction liquid chromatography (HILIC) with trapped ion mobility spectrometry time-of-flight mass spectrometry (timsTOF-MS). Additonally, a targeted flow cytometry-based cytokine panel was used to screen for inflammatory markers. Non-endogenous, microbiota-derived metabolites were identified through the Human Microbial Metabolome Database (MiMeDB).

RESULTS: OC stage IV exhibited metabolic profiles similar to GI cancers, while OC stage II-III differed significantly. Stage IV OC patients exhibited higher levels of 11 typically microbiome-derived metabolites, including 1-methylhistidine, 3-hydroxyanthranilic acid, 4-pyridoxic acid, biliverdin, butyryl-L-carnitine, hydroxypropionic acid, indole, lysophosphatidylinositol 18:1 (LPI 18:1), mevalonic acid, N-acetyl-L-phenylalanine, and nudifloramide, and lower levels of 5 metabolites, including benzyl alcohol, naringenin, o-cresol, octadecanedioic acid, and phenol, compared to stage II-III. Correlation analysis revealed positive associations between IL-10 and metabolites such as glucosamine and LPCs, while MCP-1 positively correlated with benzyl alcohol and phenol.

CONCLUSION: 4D metabolomics revealed distinct metabolic signatures in OC and GI ascites, highlighting microbiota-derived metabolites involved in lipid metabolism and inflammation. Metabolites like 3-hydroxyanthranilic acid, indole, and naringenin may serve as markers of disease progression and underscore the microbiota's role in shaping malignant ascites and tumor biology.},
}

@article {pmid40361148,
year = {2025},
author = {Magwebu, ZE and Khoza, S and Mazinu, M and Jordaan, E and Ghai, M and Chauke, CG},
title = {The impact of dietary salt on the development of hypertension and gut microbiome dysbiosis in captive-bred vervet monkeys (Chlorocebus aethiops).},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {339},
pmid = {40361148},
issn = {1746-6148},
support = {UID 113583//National Research Foundation/ ; UID 113583//National Research Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/veterinary/chemically induced/microbiology ; *Hypertension/veterinary/etiology/chemically induced ; *Sodium Chloride, Dietary/adverse effects/administration & dosage ; Male ; Chlorocebus aethiops ; Blood Pressure/drug effects ; *Monkey Diseases/microbiology/etiology ; Female ; Feces/microbiology ; Diet/veterinary ; },
abstract = {BACKGROUND: The study was designed to establish a hypertensive nonhuman primate model to evaluate the role of dietary salt intake on blood pressure levels and gut microbiome regulation. Sixteen adult vervet monkeys were selected and assigned into two groups (control and experimental). The control group was given a maintenance diet (100 g), whereas the diet of the experimental group was supplemented with 1.5 g/day of dietary salt in the mornings for six months (T0-T6), thereafter, the dose was increased to 2 g/day for additional six months (T9-T12). Blood and stool samples were collected for biochemical and 16 S ribosomal RNA gene sequencing.

RESULTS: The control group was borderline hypertensive (134.7/62.9 mmHg), whereas elevated blood pressure levels (171.3/81.3 mmHg) were observed at T12 indicating the experimental group to be salt sensitive. Furthermore, gut microbiome analysis showed two main phyla, Bacteroidetes and Firmicutes. However, there was no significant difference for alpha and beta diversity for both groups.

CONCLUSION: These findings suggested that dietary salt intake (1.5-2 g/day) caused alterations in systolic blood pressure levels, chloride and alkaline phosphatase (ALP). However, these changes were not associated with gut microbiome dysbiosis even though significant changes were observed over time for the individual groups.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Dysbiosis/veterinary/chemically induced/microbiology
*Hypertension/veterinary/etiology/chemically induced
*Sodium Chloride, Dietary/adverse effects/administration & dosage
Male
Chlorocebus aethiops
Blood Pressure/drug effects
*Monkey Diseases/microbiology/etiology
Female
Feces/microbiology
Diet/veterinary

@article {pmid40360784,
year = {2025},
author = {Voolstra, CR and Schlotheuber, M and Camp, EF and Nitschke, MR and Szereday, S and Bejarano, S},
title = {Spatially restricted coral bleaching as an ecological manifestation of within-colony heterogeneity.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {740},
pmid = {40360784},
issn = {2399-3642},
support = {468583787//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Animals ; *Anthozoa/physiology/microbiology ; Coral Reefs ; *Coral Bleaching ; Symbiosis ; Ecosystem ; Dinoflagellida/physiology ; },
abstract = {Coral bleaching is a widespread stress response of reef-building corals to elevated sea temperatures, resulting in the loss of symbiotic algae and often leading to coral death and reef degradation. Although coral bleaching occurs globally, not all reefs, species, colonies, or polyps bleach equally. Understanding intra-colony bleaching heterogeneity is crucial to anticipate the extent of coral loss at 2°C warming and harness variability to inform restorative interventions. Partially bleached coral colonies are commonly documented yet rarely tracked to determine whether they reflect ecologically distinct heterogeneity (e.g., in thermal tolerance) or eventually bleach completely. Focusing on bleaching that appears restricted to certain areas within a coral colony, we examine its putative basis in the spatial variability of the holobiont. A coral's three-dimensional structure creates mosaics of microenvironments. Adaptations to these microenvironments are underpinned by intra-colony differences in Symbiodiniaceae association, microbiome assemblage, and nutritional status, giving rise to microhabitats. Genetic mosaicism and epigenetic changes further contribue to intra-colony phenotypic heterogeneity. We pinpoint methodologies to align spatially restricted bleaching to different forms of coral surface heterogeneity, examine the common assumption that coral fragments represent entire colonies, and illuminate implications for coral biology and restoration.},
}

Animals
*Anthozoa/physiology/microbiology
Coral Reefs
*Coral Bleaching
Symbiosis
Ecosystem
Dinoflagellida/physiology

@article {pmid40360555,
year = {2025},
author = {Baek, JW and Lim, S and Park, N and Song, B and Kirtipal, N and Nielsen, J and Mardinoglu, A and Shoaie, S and Kim, JI and Son, JW and Koh, A and Lee, S},
title = {Extensively acquired antimicrobial-resistant bacteria restructure the individual microbial community in post-antibiotic conditions.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {78},
pmid = {40360555},
issn = {2055-5008},
support = {2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; },
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/genetics/classification/isolation & purification ; *Gastrointestinal Microbiome/drug effects/genetics ; *Drug Resistance, Bacterial ; Metagenome ; *Microbiota/drug effects ; Microbial Sensitivity Tests ; Metagenomics ; },
abstract = {In recent years, the overuse of antibiotics has led to the emergence of antimicrobial-resistant (AMR) bacteria. To evaluate the spread of AMR bacteria, the reservoir of AMR genes (resistome) has been identified in environmental samples, hospital environments, and human populations, but the functional role of AMR bacteria and their persistence within individuals has not been fully investigated. Here, we performed a strain-resolved in-depth analysis of the resistome changes by reconstructing a large number of metagenome-assembled genomes from the gut microbiome of an antibiotic-treated individual. Interestingly, we identified two bacterial populations with different resistome profiles: extensively acquired antimicrobial-resistant bacteria (EARB) and sporadically acquired antimicrobial-resistant bacteria, and found that EARB showed broader drug resistance and a significant functional role in shaping individual microbiome composition after antibiotic treatment. Our findings of AMR bacteria would provide a new avenue for controlling the spread of AMR bacteria in the human community.},
}

Humans
*Anti-Bacterial Agents/pharmacology
*Bacteria/drug effects/genetics/classification/isolation & purification
*Gastrointestinal Microbiome/drug effects/genetics
*Drug Resistance, Bacterial
Metagenome
*Microbiota/drug effects
Microbial Sensitivity Tests
Metagenomics

@article {pmid40360545,
year = {2025},
author = {Rampelli, S and Pomstra, D and Barone, M and Fabbrini, M and Turroni, S and Candela, M and Henry, AG},
title = {Consumption of only wild foods induces large scale, partially persistent alterations to the gut microbiome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {16593},
pmid = {40360545},
issn = {2045-2322},
support = {677576/ERC_/European Research Council/International ; 818290//Horizon 2020 Framework Programme/ ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Male ; *Diet ; Adult ; Bacteria/genetics/classification ; },
abstract = {The gut microbiome (GM) is implicated in human health and varies among lifestyles. So-called "traditional" diets have been suggested to promote health-associated taxa. However, most studies focused only on diets including domesticated foods. Historically, humans consumed only wild foods, which might uniquely shape GM composition. We explored the impact of a wild-food-only diet on GM, particularly whether it increases the presence of health-associated and/or "old friend" taxa, and if the alterations to GM are persistent or transient. One participant collected daily fecal samples and recorded daily food consumption over an eight-week period, the middle four weeks of which he consumed only wild foods. Samples were profiled by 16S rRNA sequencing, and oligotyping and network analysis were conducted to assess microbial co-occurrence patterns. A wild-food-only diet considerably alters the composition of the GM, and the magnitude of the changes is larger than that observed in other diet interventions. No new taxa, including "old friends" appeared; instead, the proportions of already-present taxa shifted. Network analysis revealed distinct microbial co-abundance groups restructuring across dietary phases. There is a clear successional shift from the pre-, during- and post-wild-food-only diet. This analysis highlighted structural and functional shifts in microbial interactions, underscoring diet's role in shaping the gut ecosystem.},
}

*Gastrointestinal Microbiome
Humans
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Male
*Diet
Adult
Bacteria/genetics/classification

@article {pmid40360544,
year = {2025},
author = {Barroso-Sousa, R and Zanudo, JGT and Li, T and Reddy, SM and Emens, LA and Kuntz, TM and Silva, CAC and AlDubayan, SH and Chu, H and Overmoyer, B and Lange, P and DiLullo, MK and Montesion, M and Kasparian, J and Hughes, ME and Attaya, V and Basta, A and Lin, NU and Tayob, N and Jeselsohn, R and Mittendorf, EA and Tolaney, SM},
title = {Nivolumab plus low-dose ipilimumab in hypermutated HER2-negative metastatic breast cancer: a phase II trial (NIMBUS).},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4430},
pmid = {40360544},
issn = {2041-1723},
mesh = {Humans ; Female ; *Ipilimumab/administration & dosage/adverse effects/therapeutic use ; *Nivolumab/administration & dosage/adverse effects/therapeutic use ; *Breast Neoplasms/drug therapy/genetics/pathology/mortality ; Middle Aged ; Receptor, ErbB-2/genetics/metabolism ; Adult ; Aged ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/adverse effects ; Mutation ; Progression-Free Survival ; Neoplasm Metastasis ; Treatment Outcome ; Biomarkers, Tumor/genetics ; },
abstract = {In the phase II NIMBUS trial, patients with human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer (MBC) and high tumor mutational burden (TMB ≥ 9 mut/Mb) received nivolumab (3 mg/kg biweekly) and low-dose ipilimumab (1 mg/kg every 6 weeks) for 2 years or until progression. The primary endpoint was objective response rate (ORR) per RECIST 1.1 criteria. Among 30 patients enrolled, the median TMB was 10.9 mut/Mb (range: 9-110) and the confirmed objective response rate was 20%. Secondary endpoints included progression-free survival, overall survival, clinical benefit rate, and safety and tolerability, including immune-related adverse events (irAEs). A prespecified correlative outcome was to evaluate the ORR in patients with a TMB ≥ 14 mut/Mb. Patients with TMB ≥ 14 mut/Mb (n = 6) experienced higher response rates (60% vs 12%; p = 0.041) and showed a trend towards improved progression-free survival and overall survival compared to patients with TMB < 14 mut/Mb. Exploratory genomic analyses suggested that ESR1 and PTEN mutations may be associated with poor response, while clinical benefit was associated with a decrease or no change in tumor fraction by serial circulating tumor DNA during treatment. Stool microbiome analysis revealed that baseline blood TMB, PD-L1 positivity, and immune-related diarrhea are associated with distinct taxonomic profiles. In summary, some patients with hypermutated HER2-negative MBC experience extended clinical benefit with a dual immunotherapy regimen; a higher TMB, and additional genomic and microbiome biomarkers may optimize patient selection for therapy with nivolumab plus low-dose ipilimumab. (Funded by Bristol Myers Squibb; ClinicalTrials.gov identifier, NCT03789110).},
}

Humans
Female
*Ipilimumab/administration & dosage/adverse effects/therapeutic use
*Nivolumab/administration & dosage/adverse effects/therapeutic use
*Breast Neoplasms/drug therapy/genetics/pathology/mortality
Middle Aged
Receptor, ErbB-2/genetics/metabolism
Adult
Aged
*Antineoplastic Combined Chemotherapy Protocols/therapeutic use/adverse effects
Mutation
Progression-Free Survival
Neoplasm Metastasis
Treatment Outcome
Biomarkers, Tumor/genetics

@article {pmid40360188,
year = {2025},
author = {Dai, ZM and Xu, ML and Zhang, QQ and Zhu, B and Wu, JZ and Liu, Q and Li, Y and Li, HB},
title = {Alterations of the gut commensal akkermansia muciniphila in patients with COVID-19.},
journal = {Virulence},
volume = {},
number = {},
pages = {2505999},
doi = {10.1080/21505594.2025.2505999},
pmid = {40360188},
issn = {2150-5608},
abstract = {Dysbiosis of gut microbiota is well established in coronavirus disease 2019 (COVID-19). While studies have attempted to establish a link between the gut commensal Akkermansia muciniphila (A. muciniphila) and COVID-19, the findings have been inconsistent and sometimes controversial. The intestinal microbial abundance information of COVID-19 patients was acquired and analysed from GMrepo database. Subsequently, A. muciniphila's metabolites, target-genes, and metabolite-target relationships was extracted from GutMGene database. Lastly, coronascape module in Metascape database is used for gene annotation and enrichment analysis in various host cells and tissues after SARS-CoV-2 infection. The results indicated that, in comparison to the health people, A. muciniphila was significantly elevated in COVID-19 patients. This bacterium was found to be associated with heightened expression of IL-10, TLR2, TLR4, CLGN, CLDN4, TJP2, and TJP3, while concurrently experiencing a reduction in the expression of IL-12A and IL-12B in humans. The regulatory genes of A. muciniphila primarily enhance responses to viruses and cytokines, positively regulate cell migration, and control epithelial cell proliferation. Our study revealed a significant increase in the gut commensal A. muciniphila in COVID-19 patients. This bacterium can modulate host immune responses and may also serve as a probiotic with antiviral properties.},
}

@article {pmid40360052,
year = {2025},
author = {Wolf, M and Lange, J and Benndorf, D and Welz, L and Nikolaus, S and Sievers, L and Tran, F and Schallert, K and Hellwig, P and Schreiber, S and Gunzer, M and Rosenstiel, P and Reichl, U and Adolph, T and Jucic, A and Aden, K and Heyer, R},
title = {Fecal metaproteomics enables functional characterization of remission in patients with inflammatory bowel disease.},
journal = {Journal of proteomics},
volume = {},
number = {},
pages = {105455},
doi = {10.1016/j.jprot.2025.105455},
pmid = {40360052},
issn = {1876-7737},
abstract = {The gut microbiome is an important contributor to the development and the course of inflammatory bowel disease (IBD). While changes in the gut microbiome composition were observed in response to IBD therapy using biologics, studies elucidating human and microbial proteins and pathways in dependence on therapy success are sparse. Fecal samples of a cohort of IBD patients were collected before and after 14 weeks of treatment with three different biologics. Clinical disease activity scores were used to determine the clinical response and remission. Fecal metaproteomes of remitting patients (n = 12) and of non-remitting patients (n = 12) were compared before treatment and changes within both groups were assessed over sampling time to identify functional changes and potential human and microbial biomarkers. The abundance of proteins associated with neutrophilic granulocytes, and immunoglobulins significantly decreased in remitting patients. There were changes in pathways of microbial metabolism in samples from patients with remission after therapy, including an increased butyrate fermentation. Distinct changes of proteins related to gut inflammation and gut microbiome metabolism showed whether IBD remission was achieved or not. This suggests that metaproteomics could be a useful tool for monitoring remission in IBD therapies. SIGNIFICANCE: IBD is rising in incidence, especially in newly industrialized countries, and the microbiome is an important contributor to its pathogenesis. Despite manifold therapeutical options, achieving remission is often ineffective, and choosing new alternative drugs remains often empirical. Therefore, efficient tools for monitoring therapeutic response and assessing the effectiveness of drugs in specific patients are mandatory. In the present study, we show that the use of metaproteomics is a promising avenue to address these challenges. We observed the amelioration of inflammation and restoration of a healthy microbiome in remitting patients in contrast to non-remitting patients. Therefore, metaproteomics is a valuable tool for monitoring the therapy success in IBD.},
}

@article {pmid40360014,
year = {2025},
author = {Dang, S and Zhang, X and Zhang, Y and Zhang, H},
title = {New thoughts on the intestinal microbiome-B cell-IgA axis and therapies in IgA nephropathy.},
journal = {Autoimmunity reviews},
volume = {},
number = {},
pages = {103835},
doi = {10.1016/j.autrev.2025.103835},
pmid = {40360014},
issn = {1873-0183},
abstract = {IgA nephropathy (IgAN), as the most common chronic glomerulonephritis worldwide, is often triggered by mucosal infections and follows a chronic progression, with the majority of patients ultimately progressing to end-stage renal disease (ESRD) during their lifetimes. Since the mystery of its complete pathogenesis has not been fully solved, the resulting lack of effective early diagnosis and treatment greatly affects the prognosis of patients. Given the well-defined pathological feature of IgA deposition in the mesangial region, the source and role of pathogenic IgA has been focused on. Starting from the microbiology and immunity of the gut, we systematically review both the physiological and the pathological process of microbiome-B cell-IgA axis, from microbial-induced IgA production to the role of IgA in the intestinal immune milieu, and ultimately end up with the various aspects of microbiome-B cell-IgA axis in the pathogenesis of IgAN as well as the corresponding therapeutic initiatives available. Our retrospective review helps researchers to systematically understand the complex role between intestinal flora dysbiosis and pathogenic IgA in IgAN. This understanding provides a foundation for in-depth explorations to uncover more detailed pathogenic mechanisms and to develop more precise and effective diagnostic and therapeutic approaches.},
}

@article {pmid40359832,
year = {2025},
author = {Kolathingal-Thodika, N and Elayadeth-Meethal, M and Dunshea, FR and Eckard, R and Flavel, M and Chauhan, SS},
title = {Is early life programming a promising strategy for methane mitigation and sustainable intensification in ruminants?.},
journal = {The Science of the total environment},
volume = {982},
number = {},
pages = {179654},
doi = {10.1016/j.scitotenv.2025.179654},
pmid = {40359832},
issn = {1879-1026},
abstract = {Sustainable animal production requires lowering emissions and adapting to climate change. Numerous nutritional and management interventions that enhance adult ruminants' efficiency and resilience produce only temporary results, reducing the sustainability of the programs. This is because only short-lived changes in the host and rumen microbiome occur, which revert to the original levels when the intervention ceases. Early life programming (ELP) is a promising approach to increase sustainable livestock production, enhance efficiency and reduce greenhouse gas emissions. Early influences using ELP have profound and enduring effects on molecular pathways, physiological adaptations, and long-term phenotypic consequences later in life. These effects occur from the embryonic stage to birth (foetal programming, FP), birth to weaning, and beyond. The underlying mechanisms of ELP include the sequential development of the rumen and microbial colonisation in the rumen, orchestrated through molecular changes, including transcriptomic and epigenetic modifications. This review highlights the key mechanisms behind ELP and explores strategies across different production systems that can improve livestock performance while helping to achieve net-zero emissions. Management strategies like step-down weaning, dietary modifications including increasing solid feed and high-fibre diets and adding anti-methanogenic agents and other feed additives to target the desired rumen microbial community, such as propionate-producing Prevotella, Sharpea, Coprococcus and Megasphaera, are promising strategies for implementing ELP. Creating alternate hydrogen sinks through ELP by favouring metabolic pathways that enhance propionate production can also be targeted. Furthermore, recent innovative strategies, such as using methanotroph-methylotroph consortium as probiotics and oxidising feed additives, are worth researching for ELP.},
}

@article {pmid40359780,
year = {2025},
author = {Gaulke, CA and Yuan, F and Yang, L and Duan, L and Connolly, MG and Hsiao, SH and Antonson, AM and Fang, Y},
title = {Maternal vaccination partially protects piglets against influenza A virus associated alteration of the microbiome and hippocampal gene expression.},
journal = {Veterinary microbiology},
volume = {306},
number = {},
pages = {110544},
doi = {10.1016/j.vetmic.2025.110544},
pmid = {40359780},
issn = {1873-2542},
abstract = {Influenza A virus (IAV) causes respiratory disease with systemic complications in a variety of avian and mammalian hosts, including humans and pigs. Infection with IAV in newborns can be particularly damaging as viral infection is known to disrupt the rapid developmental processes that occur during this period. Maternal IAV vaccination can reduce the risk of IAV infection in infants, but it is unknown whether passive transfer of anti-IAV antibodies protect against the downstream complications of infection. In this study, we evaluated the impact of maternal vaccination on the gut and nasal microbiota development and hippocampal transcriptome in neonatal piglets infected with influenza A virus. Sows were either vaccinated with an experimental influenza A vaccine at 70- and 90-days gestation, or mock-vaccinated with PBS. Neonatal piglets born from vaccinated and unvaccinated sows were challenged with a pathogenic IAV isolate or mock-challenged with PBS at 6 days post-farrowing and euthanized five days post challenge. Vaccination significantly reduced lung lesions and infectious viral load in piglets. Nasal and gut microbial community development was also partially protected from viral disruption as indicated by increased deviation from pre-challenge timepoints compared to animals challenged with the virus from unvaccinated mothers. Bulk RNA sequencing of hippocampal tissue identified 1146 differentially expressed genes (FDR < 0.05) between groups. IAV-infected piglets from vaccinated sows showed increases in genes related to viral immune responses, while IAV-infected piglets from unvaccinated sows showed increases in genes related to neurogenesis and decreases in genes related to vascular development. Many of these differentially regulated genes were strongly correlated with microbial community abundances, indicating that the microbiota may contribute to IAV outcomes. Notably, nasal microbial abundances intricately connected with hippocampal gene expression patterns, suggesting a strong nasal microbiome-brain communication axis in early development. Together, our results indicate that maternal vaccination partially protects neonatal piglets against influenza virus infection and mitigates the potential long-term impacts of IAV infection on the microbiome and cognition.},
}

@article {pmid40359747,
year = {2025},
author = {Lin, T and He, L and Liu, S and Li, Y and Huang, Z and Cai, D and Wang, Y and Mo, Z and Zhu, Y and Chen, Z and Xu, P and Lou, X and Sheng, J and Chen, G and Wang, X},
title = {Per- and polyfluoroalkyl substances mixture impairs intestinal barrier function through microbiota-derived 21-deoxycortisol and cortisol metabolism dysregulation.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138378},
doi = {10.1016/j.jhazmat.2025.138378},
pmid = {40359747},
issn = {1873-3336},
abstract = {Per- and polyfluoroalkyl substances (PFASs) are persistent environmental pollutants linked to various health risks, including intestinal disorders. However, the effect of real-world PFASs mixture on intestinal health remains unclear. Therefore, this study aimed to investigate the effects of a PFASs mixture by mimicking the exposure composition in a population on intestinal homeostasis in rats. Although the colon showed no significant morphological alterations, transcriptomic analysis revealed dose-dependent changes in gene expression levels related to cell-cell and tight junctions. Immunofluorescence and immunohistochemistry further confirmed these findings, demonstrating a dose-dependent decrease in key tight junction proteins, occludin and claudin-1, in the colonic epithelium. Integrative analysis revealed that PFASs mixture exposure disrupted the growth and metabolism of gut bacteria, such as Ruminococcus, leading to increased production of 21-deoxycortisol (21-DF). 21-DF inhibited cortisol to cortisone conversion, elevating cortisol levels in intestinal epithelial cells. Consequently, the increased cortisol levels suppressed the expression of tight junction proteins and disrupted the intestinal barrier function. Our findings provide novel insights into the underlying mechanisms by which real-world PFASs mixture disrupt intestinal barrier function through the gut microbiome-metabolome-epithelial cell axis, highlighting the need to consider the complex interplay between environmental pollutants, gut microbiota, and host health in risk assessment and development of intervention strategies.},
}

@article {pmid40359297,
year = {2025},
author = {Pakuwal, E and Tan, JL and Page, AJ and Stringer, AM and Woodman, RJ and Chinnaratha, MA},
title = {A systematic review and meta-analysis on the efficacy of fecal microbiome transplantation in patients with severe alcohol-associated hepatitis.},
journal = {European journal of gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1097/MEG.0000000000003003},
pmid = {40359297},
issn = {1473-5687},
abstract = {BACKGROUND: Severe alcohol-associated hepatitis (sAH) has a high short-term mortality, with limited treatment options. Fecal microbiota transplantation (FMT) has shown benefits in small, uncontrolled studies.

AIM: Perform a systematic review and meta-analysis to provide updated evidence on the efficacy and safety of FMT in sAH patients.

METHOD: Electronic databases were searched till 4 December 2023 for studies comparing FMT with standard of care (SOC) in sAH patients. Sensitivity analysis (leave-one-out method) and subgroup analyses were performed. Pooled risk ratio (RR) was used to compare the survival outcomes.

RESULTS: Eight studies with 444 patients (FMT: 218; SOC: 226) met the eligibility criteria and were included in this meta-analysis. The 28- and 90-day survival range was higher in the FMT group (75-100% and 53-87%) compared to the SOC group (48-80% and 25-56%). The random-effects model showed a statistically significant increase in survival in the FMT arm at 28 days [RR (95% confidence interval) 2.30 (1.24-4.28), P = 0.01] and 90 days [2.53 (1.34-4.77), P < 0.001]. However, there was no statistically significant change in survival at the 6-month [1.89 (0.89-4.05), P = 0.10] and the 12-month time [1.86 (0.68-5.08), P = 0.23]. Sensitivity analysis showed no major changes in the overall effect sizes, and subgroup analysis showed that the survival benefit was restricted only to the retrospective studies. No serious treatment-related adverse events were reported.

CONCLUSION: FMT is a safe and efficacious treatment option that improves short-term survival in sAH patients, without major adverse events. A multicentre randomized controlled trial with an adequate sample size is required to confirm these findings.},
}

@article {pmid40359154,
year = {2025},
author = {Marquez, IS and Griesbaum, K and Clark, LV and Ainsworth, EA and Christian, N and Heath, KD},
title = {Dominant foliar endophytes influence soybean yield and transcriptome.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf053},
pmid = {40359154},
issn = {1574-6941},
abstract = {Microorganisms associated with plants can affect nutrient and water acquisition, plant defenses, and ecological interactions, with effects on plant growth that range from beneficial to antagonistic. In Glycine max (soybean), many studies have examined the soil microbiome and the legume-rhizobium relationship, but little is known about foliar endophytes, their effects on plant biomass and fitness, and how plants respond to their presence. To address these questions, we inoculated Glycine max with field-collected isolates of previously-isolated, dominant strains of Methylobacterium and Colletotrichum in either sterile or non-sterile soil. We then used RNAseq to compare the transcriptomic responses of plants to single- and co-inoculation of endophytes. We found that all endophyte treatments increased soybean growth compared to control, but only in sterile soil. These results suggest context-dependency, with endophytes serving as facultative mutualists under stress or nutrient-deprivation. Similarly, transcriptomic analyses revealed that soybean defense and stress responses depended on the interaction of endophytes; Methylobacterium elicited the strongest response but was modulated by the presence of Colletotrichum. Our findings highlight the environmentally-dependent effects of co-existing endophytes within soybean leaves.},
}

@article {pmid40359128,
year = {2025},
author = {Kamdougha, H and Taminiau, B and Fall, PA and Ben Amor, S and Trigui, A and Daube, G and Mnif, B},
title = {Alterations of ocular surface microbiome in glaucoma and its association with dry eye.},
journal = {Journal of medical microbiology},
volume = {74},
number = {5},
pages = {},
doi = {10.1099/jmm.0.002013},
pmid = {40359128},
issn = {1473-5644},
mesh = {Humans ; *Microbiota ; Male ; Middle Aged ; Female ; *Dry Eye Syndromes/microbiology/complications ; Aged ; *Glaucoma/microbiology/complications ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Conjunctiva/microbiology ; Adult ; },
abstract = {Introduction. Alterations in ocular surface microbiota (OSM) have been noted in both dry eye disease (DED) and glaucoma. However, the combined effects of these conditions on OSM have not been explored.Hypothesis. We hypothesized that patients with both glaucoma and dry eye would exhibit distinct changes in OSM composition and diversity compared to those with only glaucoma, only dry eye or healthy individuals.Aim. We employed amplicon sequencing to investigate OSM profiles in patients with glaucoma and/or dry eye disease.Methods. Swab samples from the conjunctiva of both eyes were collected from 28 glaucomatous patients [13 without dry eye syndrome (G-only) and 15 with dry eye syndrome (G-DED)], 13 DED patients without glaucoma (DED-only) and 31 age-matched healthy controls (HCs). After V3-V4 16S rRNA sequencing, MOTHUR tools and R language were used to elucidate and compare OSM composition and diversity between groups.Results. Our data revealed very diverse bacterial communities with 28 phyla and 785 genera. All the groups shared the three most abundant phyla, Actinobacteria (67.47%), Firmicutes (17.14%) and Proteobacteria (13.73%). Corynebacterium (54.75%), Staphylococcus (10.71%), Cutibacterium (8.77%) and Streptococcus (3.20%) were the most abundant genera. Only the G-DED group showed higher alpha diversity than the HC group (P<0.05). However, significant differences in beta diversity were observed between all three patient groups and the HC group. The Differential Expression for Sequencing 2 (DESeq2) analysis unveiled an increased presence of opportunistic bacteria across all pathological groups, with the G-DED group demonstrating the most pronounced alterations.Conclusions. Our findings confirm the predominance of Gram-positive bacteria in normal OSM and the rise of opportunistic Gram-negative bacteria in glaucoma and dry eye disease. This is the first study to characterize OSM in glaucoma patients with DED.},
}

Humans
*Microbiota
Male
Middle Aged
Female
*Dry Eye Syndromes/microbiology/complications
Aged
*Glaucoma/microbiology/complications
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
*Conjunctiva/microbiology
Adult

@article {pmid40359034,
year = {2025},
author = {Chandra, S and Popovic, J and Singhal, NK and Watkins, EA and Dodiya, HB and Weigle, IQ and Salvo, MA and Ramakrishnan, A and Chen, Z and Watson, JT and Shetti, A and Piehl, N and Zhang, X and Cuddy, LK and Sadleir, KR and Schwulst, SJ and Prakriya, M and Gate, D and Sisodia, SS and Vassar, R},
title = {The gut microbiome controls reactive astrocytosis during Aβ amyloidosis via propionate-mediated regulation of IL-17.},
journal = {The Journal of clinical investigation},
volume = {},
number = {},
pages = {},
doi = {10.1172/JCI180826},
pmid = {40359034},
issn = {1558-8238},
abstract = {Accumulating evidence implicates the gut microbiome (GMB) in the pathogenesis and progression of Alzheimer's disease (AD). We recently showed that the GMB regulates reactive astrocytosis and Aβ plaque accumulation in male APPPS1-21 AD model mice. Yet, the mechanism(s) by which GMB perturbation alters reactive astrocytosis in a manner that reduces Aβ deposition remain unknown. Here, we performed metabolomics on plasma from mice treated with antibiotics (abx) and identified a significant increase in plasma propionate, a gut-derived short chain fatty acid, only in male mice. Administration of sodium propionate reduced reactive astrocytosis and Aβ plaques in APPPS1-21 mice, phenocopying the abx-induced phenotype. Astrocyte-specific RNA sequencing on abx and propionate treated mice showed reduced expression of pro-inflammatory and increased expression of neurotrophic genes. Next, we performed flow cytometry experiments where we found abx and propionate decreased peripheral RAR-related orphan receptor-γ (Rorγt)+ CD4+ (Th17) cells and IL-17 secretion, which positively correlated with reactive astrocytosis. Lastly, using an IL-17 monoclonal antibody to deplete IL-17, we found that propionate reduces reactive astrocytosis and Aβ plaques in an IL-17-dependent manner. Together, these results suggest that gut-derived propionate regulates reactive astrocytosis and Aβ amyloidosis by decreasing peripheral Th17 cells and IL-17 release. Thus, propionate treatment or strategies boosting propionate production may represent novel therapeutic strategies for AD.},
}

@article {pmid40359032,
year = {2025},
author = {Cabré, N and Fondevila, MF and Wei, W and Yamazaki, T and Raya Tonetti, F and Eguileor, A and Garcia-Carbonell, R and Meijnikman, AS and Miyamoto, Y and Mayo, S and Wang, Y and Zhang, X and Trimbuch, T and Lehnardt, S and Eckmann, L and Fouts, DE and Llorente, C and Tsukamoto, H and Stärkel, P and Schnabl, B},
title = {Activation of intestinal endogenous retroviruses by alcohol exacerbates liver disease.},
journal = {The Journal of clinical investigation},
volume = {},
number = {},
pages = {},
doi = {10.1172/JCI188541},
pmid = {40359032},
issn = {1558-8238},
abstract = {Alcohol-associated liver disease represents a significant global health challenge, with gut microbial dysbiosis and bacterial translocation playing a critical role in its pathogenesis. Patients with alcohol-associated hepatitis had increased fecal abundance of mammalian viruses including retroviruses. This study investigated the role of endogenous retroviruses (ERVs) in the development of alcohol-associated liver disease. Transcriptomic analysis of duodenal and liver biopsies revealed increased expression of several human ERVs, including HERV-K and HERV-H, in patients with alcohol-associated liver disease compared with controls. Chronic-binge ethanol feeding markedly induced ERV abundance in intestinal epithelial cells, but not the liver of mice. Ethanol increased ERV expression and activated the Z-DNA binding protein 1 (Zbp1)-mixed lineage kinase domain-like pseudokinase (Mlkl) signaling pathways to induce necroptosis in intestinal epithelial cells. Antiretroviral treatment reduced ethanol-induced intestinal ERV expression, stabilized the gut barrier, and decreased liver disease in microbiota-humanized mice. Furthermore, mice with an intestine-specific deletion of Zbp1 were protected against bacterial translocation and ethanol-induced steatohepatitis. These findings indicate that ethanol exploits this pathway by inducing ERVs and promoting innate immune responses, which results in the death of intestinal epithelial cells, gut barrier dysfunction and liver disease. Targeting the ERV-Zbp1 pathway may offer new therapies for patients with alcohol-associated liver disease.},
}

@article {pmid40358997,
year = {2025},
author = {Connan, C and Fromentin, S and Benallaoua, M and Alvarez, AS and Pons, N and Quinquis, B and Morabito, C and Nazare, JA and Borezée-Durant, E and , and Haimet, F and Ehrlich, SD and Valeille, K and Cavezza, A and Blottière, H and Veiga, P and Almeida, M and Doré, J and Benamouzig, R},
title = {Associations Among Diet, Health, Lifestyle, and Gut Microbiota Composition in the General French Population: Protocol for the Le French Gut - Le Microbiote Français Study.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e64894},
doi = {10.2196/64894},
pmid = {40358997},
issn = {1929-0748},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; France ; *Life Style ; Feces/microbiology ; *Diet ; Adult ; Prospective Studies ; *Health Status ; Female ; Male ; Metagenomics/methods ; },
abstract = {BACKGROUND: Over the past 2 decades, the gut microbiota has emerged as a key player in human health, being involved in many different clinical contexts. Yet, many aspects of the relationship with its host are poorly documented. One obstacle is the substantial variability in wet-laboratory procedures and data processing implemented during gut microbiota studies, which poses a challenge of comparability and potential meta-analysis.

OBJECTIVE: The study protocol described here aimed to better understand the relationship between health, dietary habits, and the observed heterogeneity of gut microbiota composition in the general population. "Le French Gut - Le microbiote français" aimed to collect, sequence, and analyze 100,000 fecal samples from French residents using a high-quality shotgun metagenomic pipeline, complemented with comprehensive health, lifestyle, and dietary metadata.

METHODS: "Le French Gut - Le microbiote français" is a prospective, noninterventional French national study involving individuals, the creation of a biological collection (feces), and the exploitation of data from questionnaires and the National Health Data System (Système National des Données de Santé). This national study is open to all metropolitan French adult residents, excluding those who have undergone a colectomy or digestive stoma, or who have had a colonoscopy or taken antibiotics in the last 3 months. This is a home-based trial in which volunteers complete a questionnaire with insights about their health and habits, and in which stool samples are self-collected. Data analysis is structured into 6 work packages, each focusing on a specific aspect of the gut microbiome, including its composition and associations with lifestyle, quality of life, and health.

RESULTS: This paper outlines the study protocol, with recruitment having started in September 2022 and expected to continue until the end of December 2025. As of January 2025, a total of 20,000 participants have been enrolled. The first scientific publications based on the data analysis are expected by mid-2025.

CONCLUSIONS: "Le French Gut" aims to provide a reference database and new ecosystem tools for understanding the relationship between the gut microbiota, its host, and diet. We expect to be able to find new signatures or targets and promote the design of innovative preventive strategies, personalized nutrition, and precision medicine.

TRIAL REGISTRATION: ClinicalTrials.gov NCT05758961; https://clinicaltrials.gov/study/NCT05758961.

DERR1-10.2196/64894.},
}

Humans
*Gastrointestinal Microbiome/physiology/genetics
France
*Life Style
Feces/microbiology
*Diet
Adult
Prospective Studies
*Health Status
Female
Male
Metagenomics/methods

@article {pmid40358692,
year = {2025},
author = {Morgan, CJ and Atkins, H and Wolfe, AJ and Brubaker, L and Aslam, S and Putonti, C and Doud, MB and Burnett, LA},
title = {Phage Therapy for Urinary Tract Infections: Progress and Challenges Ahead.},
journal = {International urogynecology journal},
volume = {},
number = {},
pages = {},
pmid = {40358692},
issn = {1433-3023},
support = {Basic Science Grant//International Urogynecological Association/ ; },
abstract = {INTRODUCTION AND HYPOTHESIS: Urinary tract infection (UTI) treatment is a growing public health concern owing to increasing antimicrobial resistance. Phage therapy, an alternative or adjunctive treatment to antibiotics, has the potential to address this challenge. However, clinical use of phage therapy is hindered by knowledge gaps and inconsistent reporting. The objective was to review the current state of phage therapy for UTIs and highlight research priorities that can optimize phage clinical efficacy.

METHODS: Current literature on UTI phage therapy was examined, focusing on the lack of standardized phage susceptibility testing, phage characterization, and microbiological assessments during and after treatment.

RESULTS: Critical areas requiring further investigation include appropriate phage dosing, optimal routes of administration, and the dynamics of phage-host and phage-patient interactions. The influence of the urinary microbiome, including endogenous phages, on treatment outcomes also needs to be better understood. Suggested data collection and reporting standards should be developed and implemented to improve clinical impact of studies examining phage therapy for UTI. Randomized clinical trials are needed to establish efficacy and determine the best practices for clinical use.

CONCLUSION: Phage therapy is a promising alternative to antibiotics for managing UTIs, especially in the face of rising antimicrobial resistance. To fully realize its potential, however, future research must focus on standardized protocols, dosing strategies, and the role of the urinary microbiome, with an emphasis on rigorously conducted clinical trials. These steps are essential for integrating phage therapy into mainstream UTI treatment regimens.},
}

@article {pmid40358678,
year = {2025},
author = {Del Carmen García-Rodríguez, M and Kacew, S},
title = {Green tea catechins: protectors or threats to DNA? A review of their antigenotoxic and genotoxic effects.},
journal = {Archives of toxicology},
volume = {},
number = {},
pages = {},
pmid = {40358678},
issn = {1432-0738},
support = {PAPIIT-IN216122//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; },
abstract = {This review examines the dual behavior of green tea catechins (GTCs), demonstrating the compound's ability to protect against oxidative stress and DNA damage while also potentially inducing genotoxicity under certain conditions. This duality may be attributed to their capacity both to scavenge free radicals and to generate these species via autooxidation. GTCs' antigenotoxic activities are mediated by multiple mechanisms, including reactive oxygen species (ROS) scavenging, regulation of endogenous antioxidant system (EAS), DNA repair, selective apoptosis of genetically compromised cells, epigenetic modulation, and metal ion (Cu, Fe, Zn) chelation-all of which collectively maintain cellular homeostasis and help reduce inflammation. However, at specific concentrations and in certain cellular conditions, GTCs' prooxidant effects-i.e., high ROS levels-might damage DNA and promote pro-apoptotic processes, potentially benefiting elimination of malignant cells. In contrast, lower ROS levels might stimulate antioxidant defenses via Nrf2 activation. Although evidence from both in vitro and in vivo studies indicates that GTCs consumption offers significant protection against diseases linked to oxidative DNA injury, the prooxidant properties of GTCs warrant careful consideration. Future research might focus on (1) optimizing GTC formulations for improved bioavailability, (2) assessing long-term outcomes, (3) evaluating toxicity at higher doses, and (4) investigating gut microbiome interactions. The dual antigenotoxic and genotoxic actions of GTCs indicate the potential role in preventive and complementary medicine, aligning with sustainable beneficial health strategies utilizing natural compounds.},
}

@article {pmid40358410,
year = {2025},
author = {Podgorny, PM and Weiss, S and Bang, C and Rühlemann, M and Wiese, ML and Völzke, H and Franke, A and Zeissig, S and Sendler, M and Aghdassi, AA and Lerch, MM and Weiss, FU and Frost, F},
title = {The fecal mycobiome in chronic pancreatitis is characterized by an increase in Candida species and Nakaseomyces.},
journal = {Clinical and translational gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ctg.0000000000000855},
pmid = {40358410},
issn = {2155-384X},
abstract = {INTRODUCTION: The exocrine pancreas is an important determinant of the intestinal microbiome composition and stability. While chronic pancreatitis (CP) is known to severely affect the bacterial community, its impact on the intestinal mycobiome is currently unknown.

METHODS: A total of 93 patients with clinical and imaging evidence of CP were prospectively recruited and compared with two equally sized matched control cohorts. One control group was matched for age, sex, body mass index, and smoking (Con-1), and the other additionally for exocrine pancreatic function (stool elastase) and diabetes (Con-2). Fecal samples were collected from all 279 individuals to determine the fecal mycobiome via internal transcribed spacer 2 (ITS2) sequencing.

RESULTS: In CP patients, fungal reads were increased (3.7-fold and 2.0-fold) as compared to Con-1 and Con-2. In comparison with Con-1, CP patients demonstrated higher total abundance of Candida (4.5-fold, q=0.009) as well as higher mean relative abundance (11.4% vs. 1.0%, q=0.008) and presence (25.8% vs. 9.7%, q=0.025) of Nakaseomyces. In contrast to Con-2, CP patients showed higher Candida total abundance (1.9-fold, p=0.016) which was, however, not significant after correction for multiple testing (q=0.056).

CONCLUSIONS: Not only the microbiome, but also the mycobiome in CP patients is characterized by distinct changes, with higher abundances of Candida or Nakaseomyces. Exocrine pancreatic dysfunction in CP patients likely contributes to this observation. This may result in increased rates of fungal infections, chronic inflammation and could be contributing to the development of pancreatic cancer.},
}

@article {pmid40358243,
year = {2025},
author = {Robinson-Papp, J and Mehta, M and Mueller, BR and Neupane, N and Zhao, Z and Cedillo, G and Coyle, K and Campbell, M and George, MC and Benn, EKT and Lee, G and Semler, J},
title = {Gastrointestinal Dysmotility, Autonomic Function and Small Intestinal Bacterial Overgrowth among People with Well-Controlled HIV.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf238},
pmid = {40358243},
issn = {1537-6613},
abstract = {INTRODUCTION: Gastrointestinal dysfunction, including microbiome changes and increased bacterial translocation across a compromised gastrointestinal barrier plays a role in the chronic systemic inflammation experienced by people with HIV (PWH). It is unknown whether autonomic neuropathy (AN) may contribute to these mechanisms by altering gastrointestinal motility.

METHODS: This is a cross-sectional study of 100 PWH and 89 controls. All participants underwent assessment of gastrointestinal transit times using a wireless motility capsule (WMC). All PWH and a subset of controls also underwent: a standardized battery of autonomic function tests summarized as the Modified Composite Autonomic Severity Score (MCASS) and its adrenergic, cardiovagal and sudomotor sub-scores, breath testing for small intestinal bacterial overgrowth (SIBO), and the Patient Assessment of Upper Gastrointestinal Disorders Symptoms (PAGI-SYM) and Composite Autonomic Symptom Score 31 (COMPASS-31) questionnaires.

RESULTS: Compared to controls, PWH displayed shorter gastric emptying times (GET) and longer small bowel and colonic transit times (SBTT, CTT). Among PWH, GET was associated with PAGI-SYM score. The MCASS and its sudomotor sub-score (reflecting peripheral sympathetic function) were associated with SBTT but not GET or CTT. PWH with prolonged SBTT (>6h) were more likely to have SIBO.

CONCLUSION: Gastrointestinal motility is altered in PWH. This study provides preliminary evidence that changes in autonomic function may influence SBTT in PWH and that prolonged SBTT may contribute to the development of SIBO. Future studies are needed to more fully elucidate the pathophysiologic links between HIV-associated AN, altered gastrointestinal motility, the gastrointestinal microbiome, chronic inflammation, and resulting morbidity and mortality among PWH.},
}

@article {pmid40358205,
year = {2025},
author = {An, Y and Garcia, SL and Hambäck, PA},
title = {Microbial transfer through fecal strings on eggs affects leaf beetle microbiome dynamics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0172324},
doi = {10.1128/msystems.01723-24},
pmid = {40358205},
issn = {2379-5077},
abstract = {UNLABELLED: Gut microbiomes of holometabolous insects can be strongly affected by metamorphosis. Previous studies suggest that microbiome colonization and community development often rely on specialized transmission routes between host life stages. However, there is a lack of comparative studies of microbial community dynamics from different transmission mechanisms. We compared the gut microbial community dynamics across life stages in five Galerucella species that differ in their potential microbial transfer mechanism by sequencing amplicons of the 16S rRNA gene. Females of three of the studied species place a fecal string on top of the egg, which may enhance the transfer of gut microbes, whereas females of the two other species do not. We found that the α-diversity was more stable between life stages in fecal string-placer species compared with the non-fecal string-placer species. Moreover, there were consistent microbiome differences between species, with multiple taxa in each species consistently appearing in all life stages. Fecal strings placed on eggs seem to play an important role in the diversity and dynamics of gut bacteria in Galerucella species, facilitating the vertical transfer of gut bacteria between host insect generations. Alternative, but less efficient, transmission routes appear to occur in non-fecal string-placer species.

IMPORTANCE: We explore the consequences of having different mechanisms for transferring and establishing the gut microbiome between generations on gut microbial community dynamics. This process is often problematic in holometabolous insects, which have a complete metamorphosis between larval and adult stages. In our previous research, we found that females of some species within the genus Galerucella (Chrysomelidae) place a fecal string on the eggs, which is later consumed by the hatching larvae, whereas other species in the same genus do not have this behavior. In this paper, we therefore quantify the microbial community dynamics across all life stages in five Galerucella beetles (three with and two without fecal strings). Our results also indicate that the dynamics are much more stable in the species with fecal strings, particularly in the early life stages.},
}

@article {pmid40358144,
year = {2025},
author = {Mukherjee, SD and Suryavanshi, M and Knight, J and Lange, D and Miller, AW},
title = {Metagenomic and phylogenetic analyses reveal gene-level selection constrained by bacterial phylogeny, surrounding oxalate metabolism in the gut microbiota.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0091324},
doi = {10.1128/msphere.00913-24},
pmid = {40358144},
issn = {2379-5042},
abstract = {The gut microbiota is critical for neutralizing dietary toxins. Oxalate is a toxin commonly produced by plants to deter herbivory and is widely consumed in the human diet. Excess levels of systemic or urinary oxalate increase risk of multiple urologic and cardiometabolic diseases. The current study employed multiple amplicon-based and shotgun metagenomic methodologies, alongside comparative phylogenetic analyses, to interrogate evolutionary radiation surrounding microbial oxalate degradation within the human gut microbiome. In conservative genome-based estimates, over 30% of gut microbial species harbored at least one oxalate-handling gene, with the specific pathways used dependent on bacterial phylum. Co-occurrence analyses revealed interactions between specialist genes that can metabolize oxalate or its by-products, but not multi-functional genes that can act in more than one oxalate-related pathway. Specialization was rare at the genome level. Amplicon-based metagenomic sequencing of the oxalate-degrading gene, formyl-CoA transferase (frc), coupled with molecular clock phylogenetic analyses are indicative of rapid evolutionary divergence, constrained by phylum. This was corroborated by paired analyses of non-synonymous to synonymous substitutions (dN/dS ratios), which pointed toward neutral to positive selection. Sequence similarity network analyses of frc sequences suggest extensive horizontal gene transferring has occurred with the frc gene, which may have facilitated rapid divergence. The frc gene was primarily allocated to the Pseudomonodota phylum, particularly the Bradyrhizobium genus, which is a species capable of utilizing oxalate as a sole carbon and energy source. Collectively evidence provides strong support that, for oxalate metabolism, evolutionary selection occurs at the gene level, through horizontal gene transfer, rather than at the species level.IMPORTANCEA critical function of the gut microbiota is to neutralize dietary toxins, such as oxalate, which is highly prevalent in plant-based foods and is not degraded by host enzymes. However, little is known about the co-evolutionary patterns of plant toxins and the mammalian gut microbiota, which are expected to exhibit features of an evolutionary arms race. In the current work, we present molecular evidence that microbial genes for oxalate degradation are highly prevalent in humans, potentially driven by extensive horizontal gene transfer events. Phylogenetic analyses reveal that oxalate-degrading genes are under a positive selection pressure and have historically undergone rapid diversification events, which has led to diverse ecological strategies for handling oxalate by gut bacteria. Collectively, data shed light on potential evolutionary relationships between the diet and the gut microbiota that occur relatively independently of the mammalian host.},
}

@article {pmid40357979,
year = {2025},
author = {Ntiri, ES and Chun Nin Wong, A},
title = {Microbial metabolites as engines of behavioral variation across animals.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2501191},
doi = {10.1080/19490976.2025.2501191},
pmid = {40357979},
issn = {1949-0984},
mesh = {Animals ; *Behavior, Animal/physiology ; *Gastrointestinal Microbiome/physiology ; *Bacteria/metabolism/genetics/classification ; Vertebrates/physiology/microbiology ; Invertebrates/physiology/microbiology ; Humans ; Circadian Rhythm ; Signal Transduction ; },
abstract = {The microbiome, especially that present in the gut, has emerged as a key modulator of animal behavior. However, the extent of its influence across species and behavioral repertoires, as well as the underlying mechanisms, remains poorly understood. Increasing evidence suggests that microbial metabolites play an important role in driving behavioral variation. In this review, we synthesize findings from vertebrates to invertebrates, spanning both model and non-model organisms, to define key groups of microbial-derived metabolites involved in modulating seven distinct behaviors: nutrition, olfaction, circadian rhythms, reproduction, locomotion, aggression, and social interactions. We discuss how these microbial metabolites interact with host chemosensory systems, neurotransmitter signaling, and epigenetic modifications to shape behavior. Additionally, we highlight critical gaps in mechanistic understanding, including the need to map additional host receptors and signaling pathways, as well as the untapped potential of microbial biosynthetic gene clusters as sources for novel bioactive compounds. Advancing these areas will enhance understanding of the microbiome's role in behavioral modulation and open new avenues for microbiome-based interventions for behavioral disorders.},
}

Animals
*Behavior, Animal/physiology
*Gastrointestinal Microbiome/physiology
*Bacteria/metabolism/genetics/classification
Vertebrates/physiology/microbiology
Invertebrates/physiology/microbiology
Humans
Circadian Rhythm
Signal Transduction

@article {pmid40357977,
year = {2025},
author = {Pai, VV and Sarath, AP and Kerkar, Z},
title = {Gut microbiome in dermatology - A narrative review.},
journal = {Indian journal of dermatology, venereology and leprology},
volume = {},
number = {},
pages = {1-11},
doi = {10.25259/IJDVL_1094_2024},
pmid = {40357977},
issn = {0973-3922},
abstract = {The gut microbiome and human body have co-evolved in a synergistic host-microbial relationship. The ideal composition of human gut microbiota is an elusive concept, but every individual has a unique gut microbiota profile with regional differences. Newer diagnostic techniques have helped identify different bacteria and their roles in health and disease. The gut microbiome composition is affected by various factors like age, diet, immune system, environmental factors, exercise, and drugs. The microbiome has varied roles in metabolism, immune response, immune tolerance and antimicrobial protection. Diet plays an important role in maintaining the gut microbial diversity. Loss of homoeostasis in the microbiome results in dysbiosis. Dysbiosis plays a role in many dermatological diseases like atopic dermatitis, psoriasis, acne, rosacea, hidradenitis suppurativa, connective tissue disorders and many other systemic conditions like obesity, diabetes, neurological disease and malignancy. Reconstitution of the gut microbiome ecology in the form of bacteriotherapy with the reintegration of certain strains of microbiota has a beneficial role in many of these disorders.},
}

@article {pmid40357939,
year = {2025},
author = {Hemalatha, M and Dev, A and Mahajan, R and De, D and Handa, S},
title = {Non-pharmacological therapies and their efficacy in atopic dermatitis: A narrative review.},
journal = {Indian journal of dermatology, venereology and leprology},
volume = {},
number = {},
pages = {1-9},
doi = {10.25259/IJDVL_1076_2024},
pmid = {40357939},
issn = {0973-3922},
abstract = {Atopic dermatitis (AD) is a complex immune-mediated disease characterised by recurrent eczematous lesions and pruritus, which adversely affects the quality of life (QoL). Genetic factors, environmental factors, immune dysregulation, and skin barrier dysfunction contribute to its pathophysiology. Non-pharmacological management strategies aim to preserve the skin barrier, address immune dysregulation, and minimise triggers. In this review, wediscuss various non-pharmacological interventions, including allergen (aeroallergens, food allergens, and contact allergens) avoidance, bathing-related measures, moisturisers, clothing choices, therapies targeting the skin microbiome, and allergen-specific immunotherapy, in addition to education and psychotherapy. Non-pharmacological therapies are essential for the holistic management of AD, but their effectiveness varies, highlighting the need for further research and tailored approaches to individual patient needs.},
}

@article {pmid40357729,
year = {2025},
author = {Pirolli, NH and Raufman, JP and Jay, SM},
title = {Therapeutic Potential and Translational Challenges for Bacterial Extracellular Vesicles in Inflammatory Bowel Disease.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf107},
pmid = {40357729},
issn = {1536-4844},
abstract = {Despite the availability of numerous new immune-directed therapeutics, the major constituents of inflammatory bowel disease (IBD)-ulcerative colitis (UC) and Crohn's disease (CD)-continue to afflict millions worldwide, resulting in significant morbidity and long-term health risks. IBD results from a triad of immune, environmental (eg, gut microbiome), and genetic (including epigenetic) mechanisms, and therefore has been subject to a wide variety of therapeutic strategies. Among these, the administration of probiotics, particularly Gram-positive lactic acid bacteria (LAB), targeting both immune and environmental factors, has shown promising potential for efficacy in selected populations in early clinical trials. However, knowledge gaps and inconsistent efficacy currently prevent recommendations for the use of probiotics in larger IBD patient populations. The inconsistent efficacy of probiotics is likely due to variable cell viability and potency after administration, further exacerbated by IBD patient heterogeneity. Thus, an alternative to live probiotics for IBD has emerged in the form of bacterial extracellular vesicles (BEVs)-cell-secreted nanovesicles containing abundant bioactive cargo that, like live probiotics, can regulate immune and environmental factors but with fewer viability limitations and safety concerns. In this review, we summarize the work done to date establishing the potential of BEVs to provide the therapeutic benefits in IBD and discuss the hurdles BEVs must overcome to achieve clinical translation. We also consider future directions for BEV therapeutics, especially treatment potential for necrotizing enterocolitis (NEC), which shares similarities in pathophysiology with IBD.},
}

@article {pmid40357706,
year = {2025},
author = {Bhardwaj, S and Badiyal, A and Dhiman, S and Bala, J and Walia, A},
title = {Exploring Halophiles for Reclamation of Saline Soils: Biotechnological Interventions for Sustainable Agriculture.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70048},
doi = {10.1002/jobm.70048},
pmid = {40357706},
issn = {1521-4028},
support = {//This work was supported by Department of Science and Technology, Ministry of Science and Technology, India, Grant/Award Number CRG/2022/003064./ ; },
abstract = {Soil salinization is a major constraint on agricultural productivity, particularly in arid and semi-arid regions where limited rainfall cannot wash salts from plant root zones. This leads to disruptions in water uptake, ion balance, photosynthesis, respiration, nutrient absorption, hormone regulation and rhizosphere microbiome disturbances in plants. Chemical and biological methods can help mitigate soil salinity, but biological approaches, like using halophytes and salt-tolerant microorganisms, are preferred for environmental sustainability. Halophytes, however, represent only about 1% of flora and are habitat specific, so halophilic plant growth-promoting (PGP) microbes have emerged as a key eco-friendly solution. Halophilic PGP bacteria have shown promise in remediating saline soils, enhancing fertility and boosting crop resilience by inducing salinity tolerance (IST) and promoting plant growth traits. In the era of modern agriculture where chemical inputs are at their peak of application rendering the soil infertile, halophilic PGP bacteria represent a promising, sustainable approach to support food security, aligning with Sustainable Development Goals for zero hunger.},
}

@article {pmid40357412,
year = {2024},
author = {King, ML and Bajwa, B and Hanna, N and Xing, X and Low, KE and Neuberger, P and Hall, E and Veltri, M and Weighill, B and Klassen, L and Plain Eagle, N and Big Bull, W and Lynes, LS and Montina, T and Thomas, PJ and Gorzelak, MA and Abbott, DW},
title = {Comparative analysis of the soil microbiome and carbohydrate content of Anthoxanthum nitens (Sweetgrass) and other Poaceae grass tissues and associated soils.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1384204},
doi = {10.3389/fmicb.2024.1384204},
pmid = {40357412},
issn = {1664-302X},
abstract = {Sweetgrass (Anthoxanthum nitens) is a culturally and environmentally significant perennial grass to many Indigenous Peoples; however, little is known about the potential of Sweetgrass as a contributor to soil health, biodiversity, and climate adaptation. Here, a team of transdisciplinary experts from academia, a non-governmental organization, and a First Nation community collaborated to investigate the structural composition of the rhizomes, stems, and leaves of greenhouse-grown Sweetgrass in comparison to other Poaceae grass members found in a nearby field. The data shows that the monosaccharide composition of A. nitens was evenly distributed throughout the three tissues, and that cellulose was the predominant polysaccharide followed by glucuronoararbinoxylans. There were lesser amounts of xyloglucans, mixed-linkage glucans, homogalacturonans, and rhamnogalacturonans as the hemicellulosic and pectic polysaccharides, respectively. The carbohydrate composition seen in A. nitens was consistent with the other Poaceae grasses evaluated in this study, with the exception of Setaria chondrachne, which contained elevated pectin levels in its stems and leaves. Additionally, the analysis of the carbohydrate content within the soil samples revealed a higher abundance of carbohydrates within greenhouse soil when compared to field soil samples, with significantly more mannose, galactose, and galacturonic acid. Further, there were structural differences in the microbial communities across sampling sites, including a significant increase in the abundance of Bacillus spp. in the greenhouse soil. Overall, this study provides the glycome and associated soil microbial community baseline for greenhouse-grown Sweetgrass.},
}

@article {pmid40357400,
year = {2025},
author = {Xie, J and Zhu, N and Xu, W},
title = {Integrative multi-omics analysis of the microbiome and metabolome in bronchoalveolar lavage fluid from patients with early-stage lung cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1513270},
doi = {10.3389/fcimb.2025.1513270},
pmid = {40357400},
issn = {2235-2988},
mesh = {Humans ; *Lung Neoplasms/microbiology/pathology/diagnosis ; *Bronchoalveolar Lavage Fluid/microbiology/chemistry ; *Metabolome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Female ; Male ; Middle Aged ; *Metabolomics/methods ; Aged ; DNA, Ribosomal/genetics/chemistry ; Chromatography, Liquid ; Bacteria/classification/genetics/isolation & purification ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; Mass Spectrometry ; Multiomics ; },
abstract = {Lung cancer is a significant health concern that poses a considerable threat to human health and quality of life. In order to enhance the prognosis of patients with lung cancer, we conducted a combined analysis of 16S rDNA gene sequencing of alveolar lavage fluid and LC-MS metabolomics research, with the objective of identifying biomarkers in patients with early-stage lung cancer presenting as SPN. A comparison of the benign nodule group and the early-stage lung cancer patients revealed that the phylum-level Bacteroidetes and the genus-level Chryseobacterium and Delftia were more abundant in the latter group. Additionally, the Fusobacteriales might serve as a predictive marker for the diagnosis of early-stage lung cancer. In the context of metabolomics, the early-stage lung cancer was found to be characterised by elevated levels of specific metabolites, including Alternariol, dTMP, Oxymatrine, Gedunin, PC 36:4. Conversely, reductions in other metabolites, such as LPC O-24:0, PC 18:2_18:3, PC 19:2_19:2, Cholecalciferol and T-2 Triol, were also observed. Correlation analyses demonstrated that alveolar lavage microorganisms were closely associated with differential metabolites. Specifically, reductions in Cholecalciferol were associated with a variety of high-abundance flora and involved in vitamin digestion and absorption pathways. Furthermore, reductions in cholecalciferol may serve as a robust predictor of early-stage lung cancer. These findings provide new predictive biomarkers for early-stage lung cancer manifested by SPN, which is clinically important and requires further study of the potential mechanisms of action and function of the targets.},
}

Humans
*Lung Neoplasms/microbiology/pathology/diagnosis
*Bronchoalveolar Lavage Fluid/microbiology/chemistry
*Metabolome
*Microbiota
RNA, Ribosomal, 16S/genetics
Female
Male
Middle Aged
*Metabolomics/methods
Aged
DNA, Ribosomal/genetics/chemistry
Chromatography, Liquid
Bacteria/classification/genetics/isolation & purification
DNA, Bacterial/genetics/chemistry
Sequence Analysis, DNA
Mass Spectrometry
Multiomics

@article {pmid40357375,
year = {2025},
author = {Zhao, Z and Xiang, L and Hong, JS and Wang, Y and Feng, J},
title = {Mechanisms of Acetate in Alleviating SETDB1-Linked Neuroinflammation and Cognitive Impairment in a Mouse Model of OSA.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {5931-5950},
doi = {10.2147/JIR.S510690},
pmid = {40357375},
issn = {1178-7031},
abstract = {BACKGROUND: Microglia-mediated neuroinflammation is crucial for obstructive sleep apnea (OSA)-induced cognitive impairment. We aimed to investigate roles of acetate (ACE) and SET domain bifurcated histone lysine methyltransferase 1 (SETDB1) in neuroinflammation of OSA.

METHODS: After C57BL/6J mice were exposed to OSA-associated intermittent hypoxia (IH) or normoxia for four weeks, the composition of the gut microbiota (GM) and the levels of serum short-chain fatty acids (SCFAs) were measured by 16S rRNA and GC-MS methods, respectively. To assess the effect of ACE on IH mice, glyceryl triacetate (GTA) was gavaged in IH-exposed mice and the cognitive function, microglial activation, and hippocampal neuronal death were examined. Moreover, ACE-treated BV2 microglia cells were also utilized for further mechanistic studies.

RESULTS: IH disrupts the gut microbiome, reduces microbiota-SCFAs, and impairs cognitive function. Gavage with GTA significantly mitigated these cognitive deficits. Following IH exposure, we observed substantial increases in SETDB1 both in vivo and in vitro, along with elevated levels of histone H3 lysine 9 trimethylation (H3K9me3). Genetic or pharmacological inhibition of SETDB1 in microglia led to decreased induction of proinflammatory factors, as well as reduced reactive oxygen species (ROS) generation. Mechanistically, SETDB1 was found to upregulate the transcription factors p-signal transducer and activator of transcription 3 (p-STAT3) and p-NF-κB. In vitro, ACE supplementation effectively repressed high SETDB1 and H3K9me3 levels, thereby inhibiting microglial pro-inflammatory responses induced by IH. In vivo, ACE supplementation significantly reduced hippocampal levels of p-STAT3, p-NF-κB, and pro-inflammatory cytokines while also protecting neuronal integrity.

CONCLUSION: This study provides the first evidence that H3K9 methyltransferase SETDB1 promotes microglial pro-inflammatory response distinct from its previously shown role in macrophages. Our findings also identify ACE supplementation as a promising dietary intervention for OSA-related cognitive impairment with SETDB1 serving as both a mechanistic biomarker and potential therapeutic target.},
}

@article {pmid40357032,
year = {2025},
author = {Song, J and Fu, J},
title = {Association between dietary index for gut microbiota and osteoarthritis in the US population: the mediating role of systemic immune-inflammation index.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1543674},
doi = {10.3389/fnut.2025.1543674},
pmid = {40357032},
issn = {2296-861X},
abstract = {OBJECTIVE: Osteoarthritis (OA) is one of the most prevalent chronic conditions among the elderly. The dietary index for gut microbiota (DI-GM) is a novel proposed indicator reflecting gut microbiome diversity. However, the role of DI-GM in OA remains unclear. This study thus aims to explore the association between DI-GM and the risk of OA and analyze the mediating roles of systemic immune-inflammation index (SII).

METHODS: We utilized data from the National Health and Nutrition Examination Survey (NHANES) spanning 2007-2018. OA was assessed through self-reported questionnaires, and dietary recall data were used to calculate the DI-GM. Univariate and weighted multivariate logistic regression analyses were employed to evaluate the association between DI-GM and OA, the weighted linear regression analyses were employed to investigate the association of DI-GM with SII, while restricted cubic splines (RCS) curves were used to assess the non-linear relationship between these variables. Subgroup analyses were subsequently conducted to validate the robustness of the findings. Mediation analysis evaluated the role of SII.

RESULTS: This study included 15,875 participants, revealing a significant inverse association between the DI-GM and OA risk (p < 0.001), higher DI-GM demonstrated a substantially reduced OA risk (adjusted model OR: 0.83; 95% CI: 0.79-0.86) and were negatively associated with the SII [β (95% CI): -9.2 (-13.0, -2.0)]. The RCS curve indicated a non-linear relationship between DI-GM and OA risk. Subgroup analysis showed that various demographic and clinical factors did not significantly alter the association between DI-GM and OA risk (interaction p-value > 0.05). The mediating effect of SII accounted for 12.69% of association between DI-GM and OA.

CONCLUSION: This study found a significant negatively association between DI-GM and OA prevalence in the US population. Mediation analyses demonstrated a significant mediating effect of SII.},
}

@article {pmid40356958,
year = {2025},
author = {Mao, QL and Yu, ZH and Nie, L and Wang, FX and Dong, YH and Qi, XF},
title = {Gastrointestinal injury in cardiopulmonary bypass: current insights and future directions.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1542995},
doi = {10.3389/fphar.2025.1542995},
pmid = {40356958},
issn = {1663-9812},
abstract = {Cardiopulmonary bypass (CPB) is an essential component of cardiac surgery. As CPB technology continues to advance and innovate, it has enabled the expansion of surgical boundaries and the resolution of many previously inoperable challenges. However, the occurrence of various complications during CPB warrants attention, with their prevention and management being paramount. The gastrointestinal tract, directly connected to the external environment, is vulnerable not only to external factors but also to internal changes that may induce damage. Both preclinical and clinical research have demonstrated the incidence of gastrointestinal injuries following CPB, often accompanied by dysbiosis and abnormal metabolic outputs. Currently, interventions addressing gastrointestinal injuries following CPB remain insufficient. Although recent years have not seen notable progress in this field, emerging academic research underscores the essential role of the gut microbiome and its metabolic products in sustaining overall health and internal equilibrium. Notably, their significance as the body's "second genome" is increasingly recognized. Consequently, reevaluating the gastrointestinal damage post-CPB, alongside the associated dysbiosis and metabolic disturbances, is imperative. This reassessment carries substantial theoretical and practical implications for enhancing treatment strategies and bettering patient outcomes after CPB. This review aims to deliver a comprehensive synthesis of the latest preclinical and clinical research on CPB, address current challenges and gaps, and explore potential future research directions.},
}

@article {pmid40356907,
year = {2025},
author = {Pan, Q and Huang, X and Liu, C and Pan, Q and Huang, S},
title = {Systemic lupus erythematosus and atherosclerosis: immune pathways and the uncharted territory of gut microbiota and metabolism.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1492726},
doi = {10.3389/fimmu.2025.1492726},
pmid = {40356907},
issn = {1664-3224},
mesh = {Humans ; *Lupus Erythematosus, Systemic/immunology/metabolism/complications ; *Atherosclerosis/immunology/metabolism/etiology ; *Gastrointestinal Microbiome/immunology ; Animals ; },
abstract = {Patients with Systemic Lupus Erythematosus (SLE) are significantly more susceptible to atherosclerosis, which may elevate their mortality risk. The review explores recent understandings of the origins and remedies for atherosclerosis associated with SLE. Our focus is particularly on the consequences of immune system disparities, interruptions in intestinal bacteria, and metabolic complications. The influence of SLE on atherosclerosis extends past usual risk elements, including processes specific to the disease. The list encompasses excessive immune cell activity, production of autoantibodies, inflammatory responses. A variety of therapies for atherosclerosis linked to SLE encompass cholesterol-lowering medications, anti-inflammatory drugs, immune suppressors, antimalarials, interferon treatments, NET inhibitors, and methods aimed at T and B-cells. However, existing research has its shortcomings, necessitating additional clinical trials to ascertain the efficacy and security of these therapies. The direct interactions among SLE, gut microbiota, metabolism, and atherosclerosis is underexplored, presenting innovation opportunities. Research into specific gut microbial strains and metabolites' effects on immune responses and atherosclerosis progression in SLE patients is needed. Such research could uncover novel therapeutic targets and biomarkers, advancing prevention and treatment strategies for SLE cardiovascular complications.},
}

Humans
*Lupus Erythematosus, Systemic/immunology/metabolism/complications
*Atherosclerosis/immunology/metabolism/etiology
*Gastrointestinal Microbiome/immunology
Animals

@article {pmid40356888,
year = {2025},
author = {Gao, YY and Li, XX and Zuo, H and Zhang, P},
title = {Analysis of the Relationship Between Cervical Cancer Progression and the Microbiome.},
journal = {International journal of general medicine},
volume = {18},
number = {},
pages = {2449-2460},
doi = {10.2147/IJGM.S520936},
pmid = {40356888},
issn = {1178-7074},
abstract = {BACKGROUND: Cervical cancer remains a leading malignancy among women worldwide. Emerging evidence suggests that alterations in the cervical microbiota may influence its development and progression.

OBJECTIVE: To compare the cervical microbiota composition and diversity between cervical cancer patients and healthy women using 16S rRNA gene sequencing.

METHODS: Between January and June 2024, cervical tissue samples were collected from 40 cervical cancer patients and 40 healthy women. Microbial DNA was extracted and the V3-V4 region of the 16S rRNA gene was sequenced using the Illumina Novaseq 6000 platform. QIIME2 and R software were used for microbial classification and diversity analysis. LEfSe was applied to identify differentially abundant taxa between groups.

RESULTS: At the phylum level, Firmicutes dominated the control group (67.91%), while dropped to 31.03% in cervical cancer patients. Actinobacteria (26.22% vs 14.37%) and Proteobacteria (27.61% vs 0.72%) were significantly elevated in the cancer group. At the genus level, Lactobacillus was predominant in controls (46.27%), while reduced in patients, and Rhodococcus and Klebsiella were notably enriched. Alpha diversity (Shannon index) exhibited no significant difference between groups, whereas richness indices (Chao1 and ACE) were significantly higher in the cancer group (p < 0.05). Beta diversity analysis revealed a clear distinction in community structure (t = 10.225, P = 0.001). LEfSe identified Rhodococcus (LDA = 5.24), Klebsiella (LDA = 5.17), and Ralstonia as significantly more abundant in the cancer group, while Firmicutes (LDA = 5.31) was characteristic of the control group.

CONCLUSION: Cervical cancer patients exhibited distinct cervical microbiota profiles, with reduced Firmicutes and elevated Actinobacteria and Proteobacteria. Increased levels of Rhodococcus and Klebsiella suggested a potential association between microbial dysbiosis and cervical cancer. These findings highlight the microbiome's relevance to tumor biology and support further investigation into its diagnostic and therapeutic potential.},
}

@article {pmid40356878,
year = {2025},
author = {Debray, R and Conover, A and Koskella, B},
title = {Phages indirectly maintain tomato plant pathogen defense through regulation of the commensal microbiome.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf065},
doi = {10.1093/ismeco/ycaf065},
pmid = {40356878},
issn = {2730-6151},
abstract = {As parasites of bacteria, phages can regulate microbiome diversity and composition and may therefore affect susceptibility to pathogens and disease. Many infectious diseases are associated with altered bacteriophage communities, but observational studies alone do not allow us to determine when altered phage community composition is a contributor to disease risk, a response to infection, or simply an indicator of dysbiosis. To address this question directly, we used size-selective filtration to deplete plant-associated microbial communities of phages, then challenged plants with the bacterial pathogen Pseudomonas syringae. Plants with phage-depleted microbiomes were more susceptible to infection, an effect that could not be explained by direct effects of the phage communities on either P. syringae or the plant host. Moreover, the presence of phages was most impactful when the phage communities were isolated from neighboring field locations rather than from the same host plant as the bacteria, possibly suggesting that moderate rates of lysis maintain a community structure that is most resistant to pathogen invasion. Overall, our results support the idea that phage communities contribute to plant defenses by modulating the microbiome.},
}

@article {pmid40356777,
year = {2025},
author = {Gong, X and Bai, S and Lei, E and Lu, T and Chen, Y and Cai, J and Liu, J},
title = {A bibliometric analysis of metabolic dysfunction-associated steatotic liver disease in children from 2004 to 2024.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1468788},
doi = {10.3389/fped.2025.1468788},
pmid = {40356777},
issn = {2296-2360},
abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD), once known as Non-alcoholic fatty liver disease, impacts between 3% and 10% of children and adolescents globally, as well as nearly one-third of obsessed boys and one-quarter of obsessed girls, and is the most frequent cause of pediatric liver disease associated with the obesity epidemic. With the growing attention and increasing volume of literature on pediatric MASLD, there is an urgent need for bibliometric analysis and visualization in the area of pediatric MASLD study in terms of dissecting study priorities.

METHODS: Literature was searched in the Web of Science Core Collection database, followed by categorization, bibliometric study as well as visual analysis conducted by applying software including Citespace, VOSviewer, and the R language. The study concentrated on analyzing information related to key authors, spatial and temporal distribution, core keywords, and important citations.

RESULTS: In total, 3,409 publications on pediatric MASLD were collected in the study, including 2,697 articles and 712 review articles. Between 2004 and 2024, the volume of publications had been constantly increasing per year. The country with the most numerous publications was the United States, which had extensive exchanges and collaborations with Italy, China, and England, followed by Italy. The Journal of Pediatric Gastroenterology and Nutrition had the greatest quantity of publications in this domain. The core literature was a clinical guideline. Insulin resistance, metabolic syndrome, steatohepatitis, hepatocellular carcinoma, cardiovascular risk, diabetes risk, diagnostic accuracy, lifestyle intervention, gut microbiome, probiotics, and metabolic dysfunction-associated steatotic liver disease were also hot topics and frontier trends in pediatric MASLD studies.

CONCLUSION: This research represents the inaugural application of bibliometric analysis to examine the developmental trajectory of pediatric MASLD studies over the past two decades, which reveals that the etiology, pathological changes of the liver, relationship with obesity, complications, comorbidities, diagnosis and treatments of pediatric MASLD are the key focuses and provides academic references for pediatric clinicians and scholars to grasp the hotspots, the cutting edge and the evolving trends in the area.},
}

@article {pmid40356669,
year = {2025},
author = {Yang, H and Zhang, X and Wang, R and Wang, Q and Wang, Y and Zhang, G and Sun, P and Lu, B and Wu, M and Yan, Z},
title = {Endophytic fungal community composition and function response to strawberry genotype and disease resistance.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19383},
doi = {10.7717/peerj.19383},
pmid = {40356669},
issn = {2167-8359},
mesh = {*Fragaria/microbiology/genetics ; Colletotrichum/pathogenicity ; *Plant Diseases/microbiology/genetics ; Genotype ; *Disease Resistance/genetics ; Alternaria/pathogenicity ; *Endophytes/genetics ; *Fungi/genetics/classification/isolation & purification ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Mycobiome ; },
abstract = {BACKGROUND: Utilizating the plant endophytic microbiomes to enhance pathogen resistance in crop production is an emerging alternative method to chemical pesticides. However, research on the composition and role of microbial communities related to perennial fruit plants, such as the strawberry, is still limited.

METHODS: We provide a comprehensive description of the composition and diversity of fungal communities in three niches (root, stem, and leaf) of three strawberry cultivars ('White Elves', 'Tokun', and 'Akihime') using internal transcribed spacer (ITS) rRNA amplicon sequencing and isolation culture methods. In addition, we also evaluated the disease tolerance ability of three strawberry cultivars to Colletotrichum gloeosporioides and Alternaria alternata through pathogenicity testing.

RESULTS: 'White Elves' has stronger resistance to Colletotrichum gloeosporioides, and Alternaria alternata, followed by 'Tokun', while 'Akihime' has relatively weaker resistance to these pathogens. A total of 258 fungal strains were isolated from healthy strawberry plants and assigned to 34 fungal genera based on morphological and molecular characteristics analysis. Beneficial fungal genera such as Trichoderma and Talaromyces were more prevalent in 'White Elves', whereas common pathogenic fungi in strawberry, such as Colletotrichum, Alternaria, and Fusarium, were more prevalent in 'Akihime'. The composition and diversity of microbial communities vary among genotypes, and resistance to pathogens may play dominant roles in determining the microbial community structure. This study's results aid the biological control of strawberry fungal diseases and are useful for plant microbiome engineering in strawberry cultivation.},
}

*Fragaria/microbiology/genetics
Colletotrichum/pathogenicity
*Plant Diseases/microbiology/genetics
Genotype
*Disease Resistance/genetics
Alternaria/pathogenicity
*Endophytes/genetics
*Fungi/genetics/classification/isolation & purification
Plant Leaves/microbiology
Plant Roots/microbiology
Mycobiome

@article {pmid40356667,
year = {2025},
author = {Martínez-Mota, R and Vásquez-Aguilar, AA and Hernández-Rodríguez, D and Suárez-Domínguez, EA and Krömer, T},
title = {Close neighbors, not intruders: investigating the role of tank bromeliads in shaping faunal microbiomes.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19376},
doi = {10.7717/peerj.19376},
pmid = {40356667},
issn = {2167-8359},
mesh = {Animals ; *Diptera/microbiology ; Larva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Mexico ; *Bromeliaceae/microbiology ; *Bacteria/genetics/classification ; Ecosystem ; },
abstract = {BACKGROUND: Tropical montane cloud forests contain high levels of epiphyte diversity. Epiphytic tank bromeliads play an important role in the functioning of these ecosystems and provide a microhabitat for many species of invertebrates. Microbial ecology theory suggests that the environment serves as a source of microbes for animals, but the contribution of this factor to the composition of an animal microbiome varies. In this study, we examined the extent to which tank bromeliads (Tillandsia multicaulis) serve as a source of microbes for two species of fly larvae in a cloud forest fragment in central Veracruz, Mexico.

METHODS: We used 16S rRNA sequencing to characterize the bacterial communities in the organic matter within bromeliad tanks and in the whole bodies (surface and gut) of larvae from two fly taxa (Austrophorocera sp., Tachinidae, and Copestylum sp., Syrphidae) that inhabit these bromeliads. To assess the contribution of bromeliads to the microbiome of the fly larvae, we conducted fast expectation-maximization microbial source tracking (FEAST) analysis.

RESULTS: The bacterial communities in bromeliad tanks were primarily composed of Pseudomonadota, Acidobacteriota, Bacteroidota, Verrucomicrobiota, and Spirochaetota. Similarly, communities of the fly larvae contained Pseudomonadota, Bacteroidota, Bacillota, and Actinomycetota. Bromeliad tanks exhibited the highest bacterial richness, followed by Copestylum and Austrophorocera larvae. Beta diversity analyses indicated that bacterial communities clustered by species. We found a modest contribution of bromeliads to the fly microbiome, with nearly 30% of the larvae microbiome traced to the organic matter deposited in the tanks.

CONCLUSIONS: Our data suggest that the microbiome of flies, which inhabit tank bromeliads during their larval stage, is nourished to some extent by the bacterial communities present in the organic matter within the tank.},
}

Animals
*Diptera/microbiology
Larva/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota
Mexico
*Bromeliaceae/microbiology
*Bacteria/genetics/classification
Ecosystem

@article {pmid40356660,
year = {2025},
author = {Wang, K and Zhou, C and Xu, K and Yin, J},
title = {Editorial: Harnessing natural plant extracts and probiotics to enhance host-gut microbiome interactions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1607339},
doi = {10.3389/fmicb.2025.1607339},
pmid = {40356660},
issn = {1664-302X},
}

@article {pmid40356655,
year = {2025},
author = {Hone, H and Li, T and Kaur, J and Wood, JL and Sawbridge, T},
title = {Often in silico, rarely in vivo: characterizing endemic plant-associated microbes for system-appropriate biofertilizers.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1568162},
doi = {10.3389/fmicb.2025.1568162},
pmid = {40356655},
issn = {1664-302X},
abstract = {The potential of phosphate-solubilizing microbes (PSMs) to enhance plant phosphorus uptake and reduce fertilizer dependency remains underutilized. This is partially attributable to frequent biofertilizer-farming system misalignments that reduce efficacy, and an incomplete understanding of underlying mechanisms. This study explored the seed microbiomes of nine Australian lucerne cultivars to identify and characterize high-efficiency PSMs. From a library of 223 isolates, 94 (42%) exhibited phosphate solubilization activity on Pikovskaya agar, with 15 showing high efficiency (PSI > 1.5). Genomic analysis revealed that the "high-efficiency" phosphate-solubilizing microbes belonged to four genera (Curtobacterium, Pseudomonas, Paenibacillus, Pantoea), including novel strains and species. However, key canonical genes, such as pqq operon and gcd, did not reliably predict phenotype, highlighting the limitations of in silico predictions. Mutagenesis of the high-efficiency isolate Pantoea rara Lu_Sq_004 generated mutants with enhanced and null solubilization phenotypes, revealing the potential role of "auxiliary" genes in downstream function of solubilization pathways. Inoculation studies with lucerne seedlings demonstrated a significant increase in shoot length (p < 0.05) following treatment with the enhanced-solubilization mutant, indicating a promising plant growth-promotion effect. These findings highlight the potential of more personalized "system-appropriate" biofertilizers and underscore the importance of integrating genomic, phenotypic, and in planta analyses to validate function. Further research is required to investigate links between genomic markers and functional outcomes to optimize the development of sustainable agricultural inputs.},
}